0s autopkgtest [14:47:12]: starting date and time: 2025-10-18 14:47:12+0000 0s autopkgtest [14:47:12]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:47:12]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7y44snwq/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-10.secgroup --name adt-resolute-arm64-apbs-20251018-144711-juju-7f2275-prod-proposed-migration-environment-20-6327803f-a831-4a2c-9d91-21323807397a --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-apbs-20251018-144711-juju-7f2275-prod-proposed-migration-environment-20-6327803f-a831-4a2c-9d91-21323807397a from image adt/ubuntu-resolute-arm64-server-20251018.img (UUID f7a49384-4e4d-4350-9a26-1f59236f89dd)... 60s autopkgtest [14:48:12]: testbed dpkg architecture: arm64 60s autopkgtest [14:48:12]: testbed apt version: 3.1.6ubuntu2 61s autopkgtest [14:48:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [14:48:13]: testbed release detected to be: None 62s autopkgtest [14:48:14]: updating testbed package index (apt update) 62s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 62s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 62s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 62s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 63s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [81.1 kB] 63s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 63s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [223 kB] 63s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 63s Fetched 831 kB in 1s (883 kB/s) 64s Reading package lists... 65s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade... 69s The following packages will be upgraded: 69s apt flash-kernel gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 69s libpython3-stdlib lto-disabled-list python3 python3-minimal 69s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 2671 kB of archives. 69s After this operation, 66.6 kB of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 69s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 69s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 69s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.8ubuntu1 [1055 kB] 70s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.8ubuntu1 [1373 kB] 70s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgirepository-1.0-1 arm64 1.86.0-6 [84.5 kB] 70s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-girepository-2.0 arm64 1.86.0-6 [25.3 kB] 70s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 flash-kernel arm64 3.109ubuntu7 [58.8 kB] 70s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 lto-disabled-list all 71 [12.5 kB] 70s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 2671 kB in 1s (2785 kB/s) 71s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83359 files and directories currently installed.) 71s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 71s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 71s Setting up python3-minimal (3.13.7-2) ... 71s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83359 files and directories currently installed.) 71s Preparing to unpack .../0-python3_3.13.7-2_arm64.deb ... 72s running python pre-rtupdate hooks for python3.13... 72s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 72s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_arm64.deb ... 72s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 72s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_arm64.deb ... 72s Unpacking libapt-pkg7.0:arm64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 72s Preparing to unpack .../3-apt_3.1.8ubuntu1_arm64.deb ... 72s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 72s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_arm64.deb ... 72s Unpacking libgirepository-1.0-1:arm64 (1.86.0-6) over (1.84.0-1) ... 72s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_arm64.deb ... 72s Unpacking gir1.2-girepository-2.0:arm64 (1.86.0-6) over (1.84.0-1) ... 73s Preparing to unpack .../6-flash-kernel_3.109ubuntu7_arm64.deb ... 73s Unpacking flash-kernel (3.109ubuntu7) over (3.109ubuntu6) ... 73s Preparing to unpack .../7-lto-disabled-list_71_all.deb ... 73s Unpacking lto-disabled-list (71) over (69) ... 73s Setting up lto-disabled-list (71) ... 73s Setting up libgirepository-1.0-1:arm64 (1.86.0-6) ... 73s Setting up libapt-pkg7.0:arm64 (3.1.8ubuntu1) ... 73s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 73s Setting up apt (3.1.8ubuntu1) ... 74s Setting up python3 (3.13.7-2) ... 74s running python rtupdate hooks for python3.13... 74s running python post-rtupdate hooks for python3.13... 74s Setting up gir1.2-girepository-2.0:arm64 (1.86.0-6) ... 74s Setting up flash-kernel (3.109ubuntu7) ... 75s flash-kernel: deferring update (trigger activated) 75s Processing triggers for libc-bin (2.42-0ubuntu3) ... 75s Processing triggers for man-db (2.13.1-1) ... 77s Processing triggers for initramfs-tools (0.150ubuntu3) ... 77s update-initramfs: Generating /boot/initrd.img-6.17.0-5-generic 106s System running in EFI mode, skipping. 106s Processing triggers for flash-kernel (3.109ubuntu7) ... 106s System running in EFI mode, skipping. 107s autopkgtest [14:48:59]: upgrading testbed (apt dist-upgrade and autopurge) 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Solving dependencies... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [14:49:04]: rebooting testbed after setup commands that affected boot 142s autopkgtest [14:49:34]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 144s autopkgtest [14:49:36]: @@@@@@@@@@@@@@@@@@@@ apt-source apbs 155s Get:1 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (dsc) [2694 B] 155s Get:2 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (tar) [85.8 MB] 155s Get:3 http://ftpmaster.internal/ubuntu resolute/universe apbs 3.4.1-6build2 (diff) [20.4 MB] 155s gpgv: Signature made Fri Jan 3 11:01:58 2025 UTC 155s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 155s gpgv: Can't check signature: No public key 155s dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6build2.dsc: no acceptable signature found 157s autopkgtest [14:49:49]: testing package apbs version 3.4.1-6build2 164s autopkgtest [14:49:56]: build not needed 172s autopkgtest [14:50:04]: test test-apbs: preparing testbed 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Solving dependencies... 173s The following NEW packages will be installed: 173s apbs apbs-data apbs-doc fonts-font-awesome fonts-lato fonts-mathjax 173s libamd-comgr2 libamd3 libamdhip64-5 libapbs-dev libapbs3t64 libarpack2t64 173s libblas3 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdrm-amdgpu1 173s libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfetk-dev 173s libfetk1.9t64 libgfortran5 libgomp1 libhsa-runtime64-1 libhsakmt1 173s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjs-jquery libjs-mathjax 173s libjs-sphinxdoc libjs-underscore liblapack3 libllvm17t64 libmaloc-dev 173s libmaloc1 libopenmpi40 libpciaccess0 librdmacm1t64 libspqr4 173s libsuitesparseconfig7 libsuperlu7 libucx0 libumfpack6 libxnvctrl0 173s ocl-icd-libopencl1 python3-apbslib sphinx-rtd-theme-common 173s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 81.8 MB of archives. 173s After this operation, 341 MB of additional disk space will be used. 173s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1 [2781 kB] 174s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 apbs-data all 3.4.1-6build2 [1769 kB] 174s Get:3 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmaloc1 arm64 1.5-2 [88.6 kB] 174s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 174s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsuperlu7 arm64 7.0.1+dfsg1-2 [171 kB] 174s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 174s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libsuitesparseconfig7 arm64 1:7.10.1+dfsg-1 [21.5 kB] 174s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd3 arm64 1:7.10.1+dfsg-1 [34.3 kB] 174s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcamd3 arm64 1:7.10.1+dfsg-1 [30.8 kB] 174s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 libccolamd3 arm64 1:7.10.1+dfsg-1 [33.6 kB] 174s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolamd3 arm64 1:7.10.1+dfsg-1 [26.5 kB] 174s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 174s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 174s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcholmod5 arm64 1:7.10.1+dfsg-1 [622 kB] 174s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 libumfpack6 arm64 1:7.10.1+dfsg-1 [258 kB] 174s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfetk1.9t64 arm64 3.4.1-6build2 [592 kB] 174s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapbs3t64 arm64 3.4.1-6build2 [271 kB] 174s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 174s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 174s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 libarpack2t64 arm64 3.9.1-6 [94.9 kB] 174s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10build1 [97.5 kB] 174s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10build1 [8272 B] 174s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 librdmacm1t64 arm64 56.1-1ubuntu1 [71.4 kB] 174s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfabric1 arm64 2.1.0-1.1 [622 kB] 174s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc15 arm64 2.12.2-1 [169 kB] 174s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 libllvm17t64 arm64 1:17.0.6-22build1 [24.8 MB] 175s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build3 [14.0 MB] 175s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.125-1 [21.6 kB] 175s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsakmt1 arm64 6.2.4+ds-1 [64.7 kB] 175s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhsa-runtime64-1 arm64 6.1.2-3 [305 kB] 175s Get:31 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamdhip64-5 arm64 5.7.1-6 [9707 kB] 176s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libibumad3 arm64 56.1-1ubuntu1 [31.3 kB] 176s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libibmad5 arm64 56.1-1ubuntu1 [44.1 kB] 176s Get:34 http://ftpmaster.internal/ubuntu resolute/universe arm64 libucx0 arm64 1.19.0+ds-1 [1242 kB] 176s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libpciaccess0 arm64 0.18.1-1ubuntu2 [19.4 kB] 176s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 176s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.2 kB] 176s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhwloc-plugins arm64 2.12.2-1 [16.6 kB] 176s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 libopenmpi40 arm64 5.0.8-8ubuntu1 [3274 kB] 176s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 libspqr4 arm64 1:7.10.1+dfsg-1 [138 kB] 176s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 apbs arm64 3.4.1-6build2 [75.6 kB] 176s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 176s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 176s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 176s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 176s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 176s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 apbs-doc all 3.4.1-6build2 [5850 kB] 176s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapbs-dev arm64 3.4.1-6build2 [99.5 kB] 176s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmaloc-dev arm64 1.5-2 [904 kB] 176s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfetk-dev arm64 3.4.1-6build2 [144 kB] 176s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-apbslib arm64 3.4.1-6build2 [207 kB] 177s Fetched 81.8 MB in 3s (24.6 MB/s) 177s Selecting previously unselected package fonts-lato. 177s (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 ... 83359 files and directories currently installed.) 177s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... 177s Unpacking fonts-lato (2.015-1) ... 177s Selecting previously unselected package apbs-data. 177s Preparing to unpack .../01-apbs-data_3.4.1-6build2_all.deb ... 177s Unpacking apbs-data (3.4.1-6build2) ... 177s Selecting previously unselected package libmaloc1:arm64. 177s Preparing to unpack .../02-libmaloc1_1.5-2_arm64.deb ... 177s Unpacking libmaloc1:arm64 (1.5-2) ... 177s Selecting previously unselected package libblas3:arm64. 177s Preparing to unpack .../03-libblas3_3.12.1-6build1_arm64.deb ... 177s Unpacking libblas3:arm64 (3.12.1-6build1) ... 177s Selecting previously unselected package libsuperlu7:arm64. 177s Preparing to unpack .../04-libsuperlu7_7.0.1+dfsg1-2_arm64.deb ... 177s Unpacking libsuperlu7:arm64 (7.0.1+dfsg1-2) ... 177s Selecting previously unselected package libgomp1:arm64. 177s Preparing to unpack .../05-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 177s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 178s Selecting previously unselected package libsuitesparseconfig7:arm64. 178s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libsuitesparseconfig7:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libamd3:arm64. 178s Preparing to unpack .../07-libamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libamd3:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libcamd3:arm64. 178s Preparing to unpack .../08-libcamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libcamd3:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libccolamd3:arm64. 178s Preparing to unpack .../09-libccolamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libccolamd3:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libcolamd3:arm64. 178s Preparing to unpack .../10-libcolamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libcolamd3:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libgfortran5:arm64. 178s Preparing to unpack .../11-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 178s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 178s Selecting previously unselected package liblapack3:arm64. 178s Preparing to unpack .../12-liblapack3_3.12.1-6build1_arm64.deb ... 178s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 178s Selecting previously unselected package libcholmod5:arm64. 178s Preparing to unpack .../13-libcholmod5_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libcholmod5:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libumfpack6:arm64. 178s Preparing to unpack .../14-libumfpack6_1%3a7.10.1+dfsg-1_arm64.deb ... 178s Unpacking libumfpack6:arm64 (1:7.10.1+dfsg-1) ... 178s Selecting previously unselected package libfetk1.9t64:arm64. 178s Preparing to unpack .../15-libfetk1.9t64_3.4.1-6build2_arm64.deb ... 178s Unpacking libfetk1.9t64:arm64 (3.4.1-6build2) ... 178s Selecting previously unselected package libapbs3t64:arm64. 178s Preparing to unpack .../16-libapbs3t64_3.4.1-6build2_arm64.deb ... 178s Unpacking libapbs3t64:arm64 (3.4.1-6build2) ... 178s Selecting previously unselected package fonts-mathjax. 178s Preparing to unpack .../17-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 178s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 178s Selecting previously unselected package libjs-mathjax. 178s Preparing to unpack .../18-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 178s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 179s Selecting previously unselected package libarpack2t64:arm64. 179s Preparing to unpack .../19-libarpack2t64_3.9.1-6_arm64.deb ... 179s Unpacking libarpack2t64:arm64 (3.9.1-6) ... 179s Selecting previously unselected package libevent-core-2.1-7t64:arm64. 179s Preparing to unpack .../20-libevent-core-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 179s Unpacking libevent-core-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 179s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 179s Preparing to unpack .../21-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_arm64.deb ... 179s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 179s Selecting previously unselected package librdmacm1t64:arm64. 179s Preparing to unpack .../22-librdmacm1t64_56.1-1ubuntu1_arm64.deb ... 179s Unpacking librdmacm1t64:arm64 (56.1-1ubuntu1) ... 179s Selecting previously unselected 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/usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 182s Setting up libllvm17t64:arm64 (1:17.0.6-22build1) ... 182s Setting up libhwloc15:arm64 (2.12.2-1) ... 182s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 182s Setting up ocl-icd-libopencl1:arm64 (2.3.3-1) ... 182s Setting up libsuitesparseconfig7:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up librdmacm1t64:arm64 (56.1-1ubuntu1) ... 182s Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 182s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build3) ... 182s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 182s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 182s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 182s Setting up libmaloc-dev (1.5-2) ... 182s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 182s Setting up libdrm-amdgpu1:arm64 (2.4.125-1) ... 182s Setting up libfabric1:arm64 (2.1.0-1.1) ... 182s Setting up liblapack3:arm64 (3.12.1-6build1) ... 182s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 182s Setting up libarpack2t64:arm64 (3.9.1-6) ... 182s Setting up libamd3:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up libcolamd3:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10build1) ... 182s Setting up libhwloc-plugins:arm64 (2.12.2-1) ... 182s Setting up libcamd3:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up libsuperlu7:arm64 (7.0.1+dfsg1-2) ... 182s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 182s Setting up libccolamd3:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... 182s Setting up libcholmod5:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up libspqr4:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up apbs-doc (3.4.1-6build2) ... 182s Setting up libumfpack6:arm64 (1:7.10.1+dfsg-1) ... 182s Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... 182s Setting up libfetk1.9t64:arm64 (3.4.1-6build2) ... 182s Setting up libapbs3t64:arm64 (3.4.1-6build2) ... 182s Setting up libfetk-dev:arm64 (3.4.1-6build2) ... 182s Setting up libamdhip64-5:arm64 (5.7.1-6) ... 182s Setting up libapbs-dev:arm64 (3.4.1-6build2) ... 182s Setting up python3-apbslib (3.4.1-6build2) ... 182s Setting up libucx0:arm64 (1.19.0+ds-1) ... 182s Setting up libopenmpi40:arm64 (5.0.8-8ubuntu1) ... 182s Setting up apbs (3.4.1-6build2) ... 182s Processing triggers for man-db (2.13.1-1) ... 183s Processing triggers for libc-bin (2.42-0ubuntu3) ... 185s autopkgtest [14:50:17]: test test-apbs: [----------------------- 185s TESTING WITH BINARY_NAME:apbs 185s START_DIR:/tmp/autopkgtest.2xe8bK/autopkgtest_tmp/build 185s -------------------------------------------------------------------------------- 185s Testing forces from apbs-forces.in 185s 185s Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000855 seconds 185s -------------------------------------------------------------------------------- 185s -------------------------------------------------------------------------------- 185s Testing input file apbs-mol-auto.in 185s 188s CHECKING:/usr/local/sbin/apbs 188s CHECKING:/usr/local/bin/apbs 188s CHECKING:/usr/sbin/apbs 188s CHECKING:/usr/bin/apbs 188s NOTE: Using apbs binary:/usr/bin/apbs 188s Testing all sections 188s The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv 188s ================================================================================ 188s Running tests for born section 188s BINARY: /usr/bin/apbs 188s INPUT: apbs-mol-auto.in 188s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 188s asc_getToken: Error occurred (bailing out). 188s Vio_scanf: Format problem with input. 188s 188s 188s ---------------------------------------------------------------------- 188s APBS -- Adaptive Poisson-Boltzmann Solver 188s Version APBS 3.4.1 188s 188s Nathan A. Baker (nathan.baker@pnnl.gov) 188s Pacific Northwest National Laboratory 188s 188s Additional contributing authors listed in the code documentation. 188s 188s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 188s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 188s Northwest Division for the U.S. Department of Energy. 188s 188s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 188s Portions Copyright (c) 2002-2020, Nathan A. Baker. 188s Portions Copyright (c) 1999-2002, The Regents of the University of California. 188s Portions Copyright (c) 1995, Michael Holst. 188s All rights reserved. 188s 188s Redistribution and use in source and binary forms, with or without 188s modification, are permitted provided that the following conditions are met: 188s 188s * Redistributions of source code must retain the above copyright notice, this 188s list of conditions and the following disclaimer. 188s 188s * Redistributions in binary form must reproduce the above copyright notice, 188s this list of conditions and the following disclaimer in the documentation 188s and/or other materials provided with the distribution. 188s 188s * Neither the name of the developer nor the names of its contributors may be 188s used to endorse or promote products derived from this software without 188s specific prior written permission. 188s 188s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 188s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 188s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 188s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 188s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 188s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 188s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 188s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 188s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 188s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 188s ---------------------------------------------------------------------- 188s APBS uses FETK (the Finite Element ToolKit) to solve the 188s Poisson-Boltzmann equation numerically. FETK is a portable collection 188s of finite element modeling class libraries developed by the Michael Holst 188s research group and written in an object-oriented form of C. FEtk is 188s designed to solve general coupled systems of nonlinear partial differential 188s equations using adaptive finite element methods, inexact Newton methods, 188s and algebraic multilevel methods. More information about FEtk may be found 188s at . 188s ---------------------------------------------------------------------- 188s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 188s Aqua is a modified form of the Holst group PMG library 188s which has been modified by Patrice Koehl 188s for improved efficiency and 188s memory usage when solving the Poisson-Boltzmann equation. 188s ---------------------------------------------------------------------- 188s Please cite your use of APBS as: 188s 188s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 188s nanosystems: application to microtubules and the ribosome. Proc. 188s Natl. Acad. Sci. USA 98, 10037-10041 2001. 188s 188s 188s This executable compiled on Jan 3 2025 at 11:01:42 188s 188s Parsing input file apbs-mol-auto.in... 188s rank 0 size 1... 188s Parsed input file. 188s Got paths for 1 molecules 188s Reading PQR-format atom data from ion.pqr. 188s 1 atoms 188s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 188s Net charge 1.00e+00 e 188s Preparing to run 6 PBE calculations. 188s ---------------------------------------- 188s CALCULATION #1 (solvated): MULTIGRID 188s Setting up problem... 188s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 188s Debye length: 0 A 188s Current memory usage: 61.280 MB total, 61.280 MB high water 188s Using cubic spline charge discretization. 188s Grid dimensions: 65 x 65 x 65 188s Grid spacings: 0.781 x 0.781 x 0.781 188s Grid lengths: 50.000 x 50.000 x 50.000 188s Grid center: (0.000, 0.000, 0.000) 188s Multigrid levels: 5 188s Molecule ID: 1 188s Linearized traditional PBE 188s Multiple Debye-Huckel sphere boundary conditions 188s 0 ion species (0.000 M ionic strength): 188s Solute dielectric: 1.000 188s Solvent dielectric: 78.540 188s Using "molecular" surface definition; no smoothing 188s Solvent probe radius: 1.400 A 188s Temperature: 298.150 K 188s Electrostatic energies will be calculated 188s Total electrostatic energy = 9.607073836227E+02 kJ/mol 188s Calculating forces... 188s ---------------------------------------- 188s CALCULATION #2 (solvated): MULTIGRID 188s Setting up problem... 188s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 188s Debye length: 0 A 188s Current memory usage: 61.280 MB total, 122.102 MB high water 188s Using cubic spline charge discretization. 188s Grid dimensions: 65 x 65 x 65 188s Grid spacings: 0.383 x 0.383 x 0.383 188s Grid lengths: 24.495 x 24.495 x 24.495 188s Grid center: (0.000, 0.000, 0.000) 188s Multigrid levels: 5 188s Molecule ID: 1 188s Linearized traditional PBE 188s Boundary conditions from focusing 188s 0 ion species (0.000 M ionic strength): 188s Solute dielectric: 1.000 188s Solvent dielectric: 78.540 188s Using "molecular" surface definition; no smoothing 188s Solvent probe radius: 1.400 A 188s Temperature: 298.150 K 188s Electrostatic energies will be calculated 188s Total electrostatic energy = 2.200266567971E+03 kJ/mol 188s Calculating forces... 188s ---------------------------------------- 188s CALCULATION #3 (solvated): MULTIGRID 188s Setting up problem... 188s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 188s Debye length: 0 A 188s Current memory usage: 61.280 MB total, 122.102 MB high water 188s Using cubic spline charge discretization. 188s Grid dimensions: 65 x 65 x 65 188s Grid spacings: 0.188 x 0.188 x 0.188 188s Grid lengths: 12.000 x 12.000 x 12.000 188s Grid center: (0.000, 0.000, 0.000) 188s Multigrid levels: 5 188s Molecule ID: 1 188s Linearized traditional PBE 188s Boundary conditions from focusing 188s 0 ion species (0.000 M ionic strength): 188s Solute dielectric: 1.000 188s Solvent dielectric: 78.540 188s Using "molecular" surface definition; no smoothing 188s Solvent probe radius: 1.400 A 188s Temperature: 298.150 K 188s Electrostatic energies will be calculated 188s Potential to be written to potential.dx.gz 188s Total electrostatic energy = 4.732245131587E+03 kJ/mol 188s Calculating forces... 188s Writing potential to potential-PE0.dx.gz 188s ---------------------------------------- 188s CALCULATION #4 (reference): MULTIGRID 188s Setting up problem... 188s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 188s Debye length: 0 A 188s Current memory usage: 61.207 MB total, 122.102 MB high water 188s Using cubic spline charge discretization. 188s Grid dimensions: 65 x 65 x 65 188s Grid spacings: 0.781 x 0.781 x 0.781 188s Grid lengths: 50.000 x 50.000 x 50.000 188s Grid center: (0.000, 0.000, 0.000) 188s Multigrid levels: 5 188s Molecule ID: 1 188s Linearized traditional PBE 188s Multiple Debye-Huckel sphere boundary conditions 188s 0 ion species (0.000 M ionic strength): 188s Solute dielectric: 1.000 188s Solvent dielectric: 1.000 188s Using "molecular" surface definition; no smoothing 188s Solvent probe radius: 1.400 A 188s Temperature: 298.150 K 188s Electrostatic energies will be calculated 188s Total electrostatic energy = 1.190871482831E+03 kJ/mol 188s Calculating forces... 188s ---------------------------------------- 188s CALCULATION #5 (reference): MULTIGRID 188s Setting up problem... 188s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 188s Debye length: 0 A 188s Current memory usage: 61.207 MB total, 122.102 MB high water 188s Using cubic spline charge discretization. 188s Grid dimensions: 65 x 65 x 65 188s Grid spacings: 0.383 x 0.383 x 0.383 188s Grid lengths: 24.495 x 24.495 x 24.495 188s Grid center: (0.000, 0.000, 0.000) 188s Multigrid levels: 5 188s Molecule ID: 1 188s Linearized traditional PBE 188s Boundary conditions from focusing 188s 0 ion species (0.000 M ionic strength): 188s Solute dielectric: 1.000 188s Solvent dielectric: 1.000 188s Using "molecular" surface definition; no smoothing 188s Solvent probe radius: 1.400 A 188s Temperature: 298.150 K 188s Electrostatic energies will be calculated 188s Total electrostatic energy = 2.430874049735E+03 kJ/mol 188s Calculating forces... 188s [focusFillBound()]: WARNING: 188s Unusually large potential values 188s detected on the focusing boundary! 188s Convergence not guaranteed for NPBE/NRPBE calculations! 188s 188s ---------------------------------------- 188s CALCULATION #6 (reference): MULTIGRID 188s Setting up problem... 188s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 188s Debye length: 0 A 188s Current memory usage: 61.207 MB total, 122.102 MB high water 188s Using cubic spline charge discretization. 188s Grid dimensions: 65 x 65 x 65 188s Grid spacings: 0.188 x 0.188 x 0.188 188s Grid lengths: 12.000 x 12.000 x 12.000 188s Grid center: (0.000, 0.000, 0.000) 188s Multigrid levels: 5 188s Molecule ID: 1 188s Linearized traditional PBE 188s Boundary conditions from focusing 188s 0 ion species (0.000 M ionic strength): 188s Solute dielectric: 1.000 188s Solvent dielectric: 1.000 188s Using "molecular" surface definition; no smoothing 188s Solvent probe radius: 1.400 A 188s Temperature: 298.150 K 188s Electrostatic energies will be calculated 188s Total electrostatic energy = 4.962018684215E+03 kJ/mol 188s Calculating forces... 188s ---------------------------------------- 188s PRINT STATEMENTS 188s 188s print energy 1 (solvated) - 2 (reference) end 188s Local net energy (PE 0) = -2.297735526282E+02 kJ/mol 188s Global net ELEC energy = -2.297735526282E+02 kJ/mol 188s ---------------------------------------- 188s CLEANING UP AND SHUTTING DOWN... 188s Destroying force arrays. 188s No energy arrays to destroy. 188s Destroying multigrid structures. 188s Destroying finite element structures. 188s Destroying 1 molecules 188s Final memory usage: 0.001 MB total, 122.102 MB high water 188s 188s 188s Thanks for using APBS! 188s 188s Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) 188s *** PASSED *** 188s Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) 188s *** PASSED *** 188s Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) 188s *** PASSED *** 188s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 188s *** PASSED *** 188s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 188s *** PASSED *** 188s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 188s *** PASSED *** 188s Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) 188s *** PASSED *** 188s Elapsed time: 3.199594 seconds 188s -------------------------------------------------------------------------------- 188s -------------------------------------------------------------------------------- 188s Testing input file apbs-smol-auto.in 188s 191s Checking for intermediate energies in input file apbs-mol-auto.out 191s EXPECTED COMPUTED: 7 191s EXPECTED EXPECTED: 7 191s COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] 191s EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] 191s COMPUTED RESULT 960.7073836227 191s COMPUTED RESULT 2200.266567971 191s COMPUTED RESULT 4732.245131587 191s COMPUTED RESULT 1190.871482831 191s COMPUTED RESULT 2430.874049735 191s COMPUTED RESULT 4962.018684215 191s COMPUTED RESULT -229.7735526282 191s BINARY: /usr/bin/apbs 191s INPUT: apbs-smol-auto.in 191s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 191s asc_getToken: Error occurred (bailing out). 191s Vio_scanf: Format problem with input. 191s 191s 191s ---------------------------------------------------------------------- 191s APBS -- Adaptive Poisson-Boltzmann Solver 191s Version APBS 3.4.1 191s 191s Nathan A. Baker (nathan.baker@pnnl.gov) 191s Pacific Northwest National Laboratory 191s 191s Additional contributing authors listed in the code documentation. 191s 191s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 191s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 191s Northwest Division for the U.S. Department of Energy. 191s 191s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 191s Portions Copyright (c) 2002-2020, Nathan A. Baker. 191s Portions Copyright (c) 1999-2002, The Regents of the University of California. 191s Portions Copyright (c) 1995, Michael Holst. 191s All rights reserved. 191s 191s Redistribution and use in source and binary forms, with or without 191s modification, are permitted provided that the following conditions are met: 191s 191s * Redistributions of source code must retain the above copyright notice, this 191s list of conditions and the following disclaimer. 191s 191s * Redistributions in binary form must reproduce the above copyright notice, 191s this list of conditions and the following disclaimer in the documentation 191s and/or other materials provided with the distribution. 191s 191s * Neither the name of the developer nor the names of its contributors may be 191s used to endorse or promote products derived from this software without 191s specific prior written permission. 191s 191s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 191s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 191s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 191s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 191s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 191s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 191s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 191s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 191s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 191s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 191s ---------------------------------------------------------------------- 191s APBS uses FETK (the Finite Element ToolKit) to solve the 191s Poisson-Boltzmann equation numerically. FETK is a portable collection 191s of finite element modeling class libraries developed by the Michael Holst 191s research group and written in an object-oriented form of C. FEtk is 191s designed to solve general coupled systems of nonlinear partial differential 191s equations using adaptive finite element methods, inexact Newton methods, 191s and algebraic multilevel methods. More information about FEtk may be found 191s at . 191s ---------------------------------------------------------------------- 191s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 191s Aqua is a modified form of the Holst group PMG library 191s which has been modified by Patrice Koehl 191s for improved efficiency and 191s memory usage when solving the Poisson-Boltzmann equation. 191s ---------------------------------------------------------------------- 191s Please cite your use of APBS as: 191s 191s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 191s nanosystems: application to microtubules and the ribosome. Proc. 191s Natl. Acad. Sci. USA 98, 10037-10041 2001. 191s 191s 191s This executable compiled on Jan 3 2025 at 11:01:42 191s 191s Parsing input file apbs-smol-auto.in... 191s rank 0 size 1... 191s Parsed input file. 191s Got paths for 1 molecules 191s Reading PQR-format atom data from ion.pqr. 191s 1 atoms 191s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 191s Net charge 1.00e+00 e 191s Preparing to run 6 PBE calculations. 191s ---------------------------------------- 191s CALCULATION #1 (solvated): MULTIGRID 191s Setting up problem... 191s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 191s Debye length: 0 A 191s Current memory usage: 61.280 MB total, 61.280 MB high water 191s Using cubic spline charge discretization. 191s Grid dimensions: 65 x 65 x 65 191s Grid spacings: 0.781 x 0.781 x 0.781 191s Grid lengths: 50.000 x 50.000 x 50.000 191s Grid center: (0.000, 0.000, 0.000) 191s Multigrid levels: 5 191s Molecule ID: 1 191s Linearized traditional PBE 191s Multiple Debye-Huckel sphere boundary conditions 191s 0 ion species (0.000 M ionic strength): 191s Solute dielectric: 1.000 191s Solvent dielectric: 78.540 191s Using "molecular" surface definition;harmonic average smoothing 191s Solvent probe radius: 1.400 A 191s Temperature: 298.150 K 191s Electrostatic energies will be calculated 191s Total electrostatic energy = 9.532928767450E+02 kJ/mol 191s Calculating forces... 191s ---------------------------------------- 191s CALCULATION #2 (solvated): MULTIGRID 191s Setting up problem... 191s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 191s Debye length: 0 A 191s Current memory usage: 61.280 MB total, 122.102 MB high water 191s Using cubic spline charge discretization. 191s Grid dimensions: 65 x 65 x 65 191s Grid spacings: 0.383 x 0.383 x 0.383 191s Grid lengths: 24.495 x 24.495 x 24.495 191s Grid center: (0.000, 0.000, 0.000) 191s Multigrid levels: 5 191s Molecule ID: 1 191s Linearized traditional PBE 191s Boundary conditions from focusing 191s 0 ion species (0.000 M ionic strength): 191s Solute dielectric: 1.000 191s Solvent dielectric: 78.540 191s Using "molecular" surface definition;harmonic average smoothing 191s Solvent probe radius: 1.400 A 191s Temperature: 298.150 K 191s Electrostatic energies will be calculated 191s Total electrostatic energy = 2.201243880085E+03 kJ/mol 191s Calculating forces... 191s ---------------------------------------- 191s CALCULATION #3 (solvated): MULTIGRID 191s Setting up problem... 191s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 191s Debye length: 0 A 191s Current memory usage: 61.280 MB total, 122.102 MB high water 191s Using cubic spline charge discretization. 191s Grid dimensions: 65 x 65 x 65 191s Grid spacings: 0.188 x 0.188 x 0.188 191s Grid lengths: 12.000 x 12.000 x 12.000 191s Grid center: (0.000, 0.000, 0.000) 191s Multigrid levels: 5 191s Molecule ID: 1 191s Linearized traditional PBE 191s Boundary conditions from focusing 191s 0 ion species (0.000 M ionic strength): 191s Solute dielectric: 1.000 191s Solvent dielectric: 78.540 191s Using "molecular" surface definition;harmonic average smoothing 191s Solvent probe radius: 1.400 A 191s Temperature: 298.150 K 191s Electrostatic energies will be calculated 191s Total electrostatic energy = 4.733006258977E+03 kJ/mol 191s Calculating forces... 191s ---------------------------------------- 191s CALCULATION #4 (reference): MULTIGRID 191s Setting up problem... 191s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 191s Debye length: 0 A 191s Current memory usage: 61.207 MB total, 122.102 MB high water 191s Using cubic spline charge discretization. 191s Grid dimensions: 65 x 65 x 65 191s Grid spacings: 0.781 x 0.781 x 0.781 191s Grid lengths: 50.000 x 50.000 x 50.000 191s Grid center: (0.000, 0.000, 0.000) 191s Multigrid levels: 5 191s Molecule ID: 1 191s Linearized traditional PBE 191s Multiple Debye-Huckel sphere boundary conditions 191s 0 ion species (0.000 M ionic strength): 191s Solute dielectric: 1.000 191s Solvent dielectric: 1.000 191s Using "molecular" surface definition;harmonic average smoothing 191s Solvent probe radius: 1.400 A 191s Temperature: 298.150 K 191s Electrostatic energies will be calculated 191s Total electrostatic energy = 1.190871482831E+03 kJ/mol 191s Calculating forces... 191s ---------------------------------------- 191s CALCULATION #5 (reference): MULTIGRID 191s Setting up problem... 191s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 191s Debye length: 0 A 191s Current memory usage: 61.207 MB total, 122.102 MB high water 191s Using cubic spline charge discretization. 191s Grid dimensions: 65 x 65 x 65 191s Grid spacings: 0.383 x 0.383 x 0.383 191s Grid lengths: 24.495 x 24.495 x 24.495 191s Grid center: (0.000, 0.000, 0.000) 191s Multigrid levels: 5 191s Molecule ID: 1 191s Linearized traditional PBE 191s Boundary conditions from focusing 191s 0 ion species (0.000 M ionic strength): 191s Solute dielectric: 1.000 191s Solvent dielectric: 1.000 191s Using "molecular" surface definition;harmonic average smoothing 191s Solvent probe radius: 1.400 A 191s Temperature: 298.150 K 191s Electrostatic energies will be calculated 191s Total electrostatic energy = 2.430874049735E+03 kJ/mol 191s Calculating forces... 191s [focusFillBound()]: WARNING: 191s Unusually large potential values 191s detected on the focusing boundary! 191s Convergence not guaranteed for NPBE/NRPBE calculations! 191s 191s ---------------------------------------- 191s CALCULATION #6 (reference): MULTIGRID 191s Setting up problem... 191s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 191s Debye length: 0 A 191s Current memory usage: 61.207 MB total, 122.102 MB high water 191s Using cubic spline charge discretization. 191s Grid dimensions: 65 x 65 x 65 191s Grid spacings: 0.188 x 0.188 x 0.188 191s Grid lengths: 12.000 x 12.000 x 12.000 191s Grid center: (0.000, 0.000, 0.000) 191s Multigrid levels: 5 191s Molecule ID: 1 191s Linearized traditional PBE 191s Boundary conditions from focusing 191s 0 ion species (0.000 M ionic strength): 191s Solute dielectric: 1.000 191s Solvent dielectric: 1.000 191s Using "molecular" surface definition;harmonic average smoothing 191s Solvent probe radius: 1.400 A 191s Temperature: 298.150 K 191s Electrostatic energies will be calculated 191s Total electrostatic energy = 4.962018684215E+03 kJ/mol 191s Calculating forces... 191s ---------------------------------------- 191s PRINT STATEMENTS 191s 191s print energy 1 (solvated) - 2 (reference) end 191s Local net energy (PE 0) = -2.290124252387E+02 kJ/mol 191s Global net ELEC energy = -2.290124252387E+02 kJ/mol 191s ---------------------------------------- 191s CLEANING UP AND SHUTTING DOWN... 191s Destroying force arrays. 191s No energy arrays to destroy. 191s Destroying multigrid structures. 191s Destroying finite element structures. 191s Destroying 1 molecules 191s Final memory usage: 0.001 MB total, 122.102 MB high water 191s 191s 191s Thanks for using APBS! 191s 191s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 191s *** PASSED *** 191s Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) 191s *** PASSED *** 191s Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) 191s *** PASSED *** 191s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 191s *** PASSED *** 191s Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) 191s *** PASSED *** 191s Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) 191s *** PASSED *** 191s Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) 191s *** PASSED *** 191s Elapsed time: 2.286315 seconds 191s -------------------------------------------------------------------------------- 191s -------------------------------------------------------------------------------- 191s Testing input file apbs-mol-parallel.in 191s 191s Splitting the input file into 4 separate files using the inputgen utility 191s 194s Checking for intermediate energies in input file apbs-smol-auto.out 194s EXPECTED COMPUTED: 7 194s EXPECTED EXPECTED: 7 194s COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] 194s EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] 194s COMPUTED RESULT 953.292876745 194s COMPUTED RESULT 2201.243880085 194s COMPUTED RESULT 4733.006258977 194s COMPUTED RESULT 1190.871482831 194s COMPUTED RESULT 2430.874049735 194s COMPUTED RESULT 4962.018684215 194s COMPUTED RESULT -229.0124252387 194s BINARY: /usr/bin/apbs 194s INPUT: apbs-mol-parallel-PE0.in 194s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] 194s asc_getToken: Error occurred (bailing out). 194s Vio_scanf: Format problem with input. 194s 194s 194s ---------------------------------------------------------------------- 194s APBS -- Adaptive Poisson-Boltzmann Solver 194s Version APBS 3.4.1 194s 194s Nathan A. Baker (nathan.baker@pnnl.gov) 194s Pacific Northwest National Laboratory 194s 194s Additional contributing authors listed in the code documentation. 194s 194s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 194s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 194s Northwest Division for the U.S. Department of Energy. 194s 194s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 194s Portions Copyright (c) 2002-2020, Nathan A. Baker. 194s Portions Copyright (c) 1999-2002, The Regents of the University of California. 194s Portions Copyright (c) 1995, Michael Holst. 194s All rights reserved. 194s 194s Redistribution and use in source and binary forms, with or without 194s modification, are permitted provided that the following conditions are met: 194s 194s * Redistributions of source code must retain the above copyright notice, this 194s list of conditions and the following disclaimer. 194s 194s * Redistributions in binary form must reproduce the above copyright notice, 194s this list of conditions and the following disclaimer in the documentation 194s and/or other materials provided with the distribution. 194s 194s * Neither the name of the developer nor the names of its contributors may be 194s used to endorse or promote products derived from this software without 194s specific prior written permission. 194s 194s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 194s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 194s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 194s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 194s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 194s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 194s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 194s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 194s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 194s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 194s ---------------------------------------------------------------------- 194s APBS uses FETK (the Finite Element ToolKit) to solve the 194s Poisson-Boltzmann equation numerically. FETK is a portable collection 194s of finite element modeling class libraries developed by the Michael Holst 194s research group and written in an object-oriented form of C. FEtk is 194s designed to solve general coupled systems of nonlinear partial differential 194s equations using adaptive finite element methods, inexact Newton methods, 194s and algebraic multilevel methods. More information about FEtk may be found 194s at . 194s ---------------------------------------------------------------------- 194s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 194s Aqua is a modified form of the Holst group PMG library 194s which has been modified by Patrice Koehl 194s for improved efficiency and 194s memory usage when solving the Poisson-Boltzmann equation. 194s ---------------------------------------------------------------------- 194s Please cite your use of APBS as: 194s 194s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 194s nanosystems: application to microtubules and the ribosome. Proc. 194s Natl. Acad. Sci. USA 98, 10037-10041 2001. 194s 194s 194s This executable compiled on Jan 3 2025 at 11:01:42 194s 194s Parsing input file apbs-mol-parallel-PE0.in... 194s rank 0 size 1... 194s Parsed input file. 194s Got paths for 1 molecules 194s Reading PQR-format atom data from ion.pqr. 194s 1 atoms 194s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 194s Net charge 1.00e+00 e 194s Preparing to run 6 PBE calculations. 194s ---------------------------------------- 194s CALCULATION #1 (solvated): MULTIGRID 194s Setting up problem... 194s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 194s Debye length: 0 A 194s Current memory usage: 61.280 MB total, 61.280 MB high water 194s Using cubic spline charge discretization. 194s Partition overlap fraction = 0.1 194s Processor array = 2 x 2 x 1 194s Grid dimensions: 65 x 65 x 65 194s Grid spacings: 0.781 x 0.781 x 0.781 194s Grid lengths: 50.000 x 50.000 x 50.000 194s Grid center: (0.000, 0.000, 0.000) 194s Multigrid levels: 5 194s Molecule ID: 1 194s Linearized traditional PBE 194s Multiple Debye-Huckel sphere boundary conditions 194s 0 ion species (0.000 M ionic strength): 194s Solute dielectric: 1.000 194s Solvent dielectric: 78.540 194s Using "molecular" surface definition; no smoothing 194s Solvent probe radius: 1.400 A 194s Temperature: 298.150 K 194s Electrostatic energies will be calculated 194s Total electrostatic energy = 2.401768459022E+02 kJ/mol 194s Calculating forces... 194s ---------------------------------------- 194s CALCULATION #2 (solvated): MULTIGRID 194s Setting up problem... 194s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 194s Debye length: 0 A 194s Current memory usage: 61.280 MB total, 122.102 MB high water 194s Using cubic spline charge discretization. 194s Partition overlap fraction = 0.1 194s Processor array = 2 x 2 x 1 194s Grid dimensions: 65 x 65 x 65 194s Grid spacings: 0.296 x 0.296 x 0.383 194s Grid lengths: 18.944 x 18.944 x 24.495 194s Grid center: (-2.411, -2.411, 0.000) 194s Multigrid levels: 5 194s Molecule ID: 1 194s Linearized traditional PBE 194s Boundary conditions from focusing 194s 0 ion species (0.000 M ionic strength): 194s Solute dielectric: 1.000 194s Solvent dielectric: 78.540 194s Using "molecular" surface definition; no smoothing 194s Solvent probe radius: 1.400 A 194s Temperature: 298.150 K 194s Electrostatic energies will be calculated 194s Total electrostatic energy = 8.142935592471E+02 kJ/mol 194s Calculating forces... 194s [focusFillBound()]: WARNING: 194s Unusually large potential values 194s detected on the focusing boundary! 194s Convergence not guaranteed for NPBE/NRPBE calculations! 194s 194s ---------------------------------------- 194s CALCULATION #3 (solvated): MULTIGRID 194s Setting up problem... 194s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 194s Debye length: 0 A 194s Current memory usage: 61.280 MB total, 122.102 MB high water 194s Using cubic spline charge discretization. 194s Partition overlap fraction = 0.1 194s Processor array = 2 x 2 x 1 194s Grid dimensions: 65 x 65 x 65 194s Grid spacings: 0.112 x 0.112 x 0.188 194s Grid lengths: 7.178 x 7.178 x 12.000 194s Grid center: (-2.411, -2.411, 0.000) 194s Multigrid levels: 5 194s Molecule ID: 1 194s Linearized traditional PBE 194s Boundary conditions from focusing 194s 0 ion species (0.000 M ionic strength): 194s Solute dielectric: 1.000 194s Solvent dielectric: 78.540 194s Using "molecular" surface definition; no smoothing 194s Solvent probe radius: 1.400 A 194s Temperature: 298.150 K 194s Electrostatic energies will be calculated 194s Total electrostatic energy = 1.485255308186E+03 kJ/mol 194s Calculating forces... 194s ---------------------------------------- 194s CALCULATION #4 (reference): MULTIGRID 194s Setting up problem... 194s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 194s Debye length: 0 A 194s Current memory usage: 61.207 MB total, 122.102 MB high water 194s Using cubic spline charge discretization. 194s Partition overlap fraction = 0.1 194s PrProcessor 0 results: 194s ocessor array = 2 x 2 x 1 194s Grid dimensions: 65 x 65 x 65 194s Grid spacings: 0.781 x 0.781 x 0.781 194s Grid lengths: 50.000 x 50.000 x 50.000 194s Grid center: (0.000, 0.000, 0.000) 194s Multigrid levels: 5 194s Molecule ID: 1 194s Linearized traditional PBE 194s Multiple Debye-Huckel sphere boundary conditions 194s 0 ion species (0.000 M ionic strength): 194s Solute dielectric: 1.000 194s Solvent dielectric: 1.000 194s Using "molecular" surface definition; no smoothing 194s Solvent probe radius: 1.400 A 194s Temperature: 298.150 K 194s Electrostatic energies will be calculated 194s Total electrostatic energy = 2.977178707009E+02 kJ/mol 194s Calculating forces... 194s ---------------------------------------- 194s CALCULATION #5 (reference): MULTIGRID 194s Setting up problem... 194s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 194s Debye length: 0 A 194s Current memory usage: 61.207 MB total, 122.102 MB high water 194s Using cubic spline charge discretization. 194s Partition overlap fraction = 0.1 194s Processor array = 2 x 2 x 1 194s Grid dimensions: 65 x 65 x 65 194s Grid spacings: 0.296 x 0.296 x 0.383 194s Grid lengths: 18.944 x 18.944 x 24.495 194s Grid center: (-2.411, -2.411, 0.000) 194s Multigrid levels: 5 194s Molecule ID: 1 194s Linearized traditional PBE 194s Boundary conditions from focusing 194s 0 ion species (0.000 M ionic strength): 194s Solute dielectric: 1.000 194s Solvent dielectric: 1.000 194s Using "molecular" surface definition; no smoothing 194s Solvent probe radius: 1.400 A 194s Temperature: 298.150 K 194s Electrostatic energies will be calculated 194s Total electrostatic energy = 8.799304557588E+02 kJ/mol 194s Calculating forces... 194s [focusFillBound()]: WARNING: 194s Unusually large potential values 194s detected on the focusing boundary! 194s Convergence not guaranteed for NPBE/NRPBE calculations! 194s 194s ---------------------------------------- 194s CALCULATION #6 (reference): MULTIGRID 194s Setting up problem... 194s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 194s Debye length: 0 A 194s Current memory usage: 61.207 MB total, 122.102 MB high water 194s Using cubic spline charge discretization. 194s Partition overlap fraction = 0.1 194s Processor array = 2 x 2 x 1 194s Grid dimensions: 65 x 65 x 65 194s Grid spacings: 0.112 x 0.112 x 0.188 194s Grid lengths: 7.178 x 7.178 x 12.000 194s Grid center: (-2.411, -2.411, 0.000) 194s Multigrid levels: 5 194s Molecule ID: 1 194s Linearized traditional PBE 194s Boundary conditions from focusing 194s 0 ion species (0.000 M ionic strength): 194s Solute dielectric: 1.000 194s Solvent dielectric: 1.000 194s Using "molecular" surface definition; no smoothing 194s Solvent probe radius: 1.400 A 194s Temperature: 298.150 K 194s Electrostatic energies will be calculated 194s Total electrostatic energy = 1.542873949131E+03 kJ/mol 194s Calculating forces... 194s ---------------------------------------- 194s PRINT STATEMENTS 194s 194s print energy 1 (solvated) - 2 (reference) end 194s Local net energy (PE 0) = -5.761864094552E+01 kJ/mol 194s Global net ELEC energy = -5.761864094552E+01 kJ/mol 194s ---------------------------------------- 194s CLEANING UP AND SHUTTING DOWN... 194s Destroying force arrays. 194s No energy arrays to destroy. 194s Destroying multigrid structures. 194s Destroying finite element structures. 194s Destroying 1 molecules 194s Final memory usage: 0.001 MB total, 122.102 MB high water 194s 194s 194s Thanks for using APBS! 194s 194s 2.401768459022e+02 194s 8.142935592471e+02 194s 1.485255308186e+03 194s 2.977178707009e+02 194s 8.799304557588e+02 194s 1.542873949131e+03 194s -5.761864094552e+01 194s 196s Processor 1 results: 196s 2.401768459022e+02 196s 8.142778312125e+02 196s Checking for intermediate energies in input file apbs-mol-parallel-PE0.out 196s BINARY: /usr/bin/apbs 196s INPUT: apbs-mol-parallel-PE1.in 196s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] 196s asc_getToken: Error occurred (bailing out). 196s Vio_scanf: Format problem with input. 196s 196s 196s ---------------------------------------------------------------------- 196s APBS -- Adaptive Poisson-Boltzmann Solver 196s Version APBS 3.4.1 196s 196s Nathan A. Baker (nathan.baker@pnnl.gov) 196s Pacific Northwest National Laboratory 196s 196s Additional contributing authors listed in the code documentation. 196s 196s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 196s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 196s Northwest Division for the U.S. Department of Energy. 196s 196s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 196s Portions Copyright (c) 2002-2020, Nathan A. Baker. 196s Portions Copyright (c) 1999-2002, The Regents of the University of California. 196s Portions Copyright (c) 1995, Michael Holst. 196s All rights reserved. 196s 196s Redistribution and use in source and binary forms, with or without 196s modification, are permitted provided that the following conditions are met: 196s 196s * Redistributions of source code must retain the above copyright notice, this 196s list of conditions and the following disclaimer. 196s 196s * Redistributions in binary form must reproduce the above copyright notice, 196s this list of conditions and the following disclaimer in the documentation 196s and/or other materials provided with the distribution. 196s 196s * Neither the name of the developer nor the names of its contributors may be 196s used to endorse or promote products derived from this software without 196s specific prior written permission. 196s 196s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 196s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 196s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 196s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 196s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 196s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 196s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 196s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 196s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 196s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 196s ---------------------------------------------------------------------- 196s APBS uses FETK (the Finite Element ToolKit) to solve the 196s Poisson-Boltzmann equation numerically. FETK is a portable collection 196s of finite element modeling class libraries developed by the Michael Holst 196s research group and written in an object-oriented form of C. FEtk is 196s designed to solve general coupled systems of nonlinear partial differential 196s equations using adaptive finite element methods, inexact Newton methods, 196s and algebraic multilevel methods. More information about FEtk may be found 196s at . 196s ---------------------------------------------------------------------- 196s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 196s Aqua is a modified form of the Holst group PMG library 196s which has been modified by Patrice Koehl 196s for improved efficiency and 196s memory usage when solving the Poisson-Boltzmann equation. 196s ---------------------------------------------------------------------- 196s Please cite your use of APBS as: 196s 196s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 196s nanosystems: application to microtubules and the ribosome. Proc. 196s Natl. Acad. Sci. USA 98, 10037-10041 2001. 196s 196s 196s This executable compiled on Jan 3 2025 at 11:01:42 196s 196s Parsing input file apbs-mol-parallel-PE1.in... 196s rank 0 size 1... 196s Parsed input file. 196s Got paths for 1 molecules 196s Reading PQR-format atom data from ion.pqr. 196s 1 atoms 196s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 196s Net charge 1.00e+00 e 196s Preparing to run 6 PBE calculations. 196s ---------------------------------------- 196s CALCULATION #1 (solvated): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 61.280 MB total, 61.280 MB high water 196s Using cubic spline charge discretization. 196s Partition overlap fraction = 0.1 196s Processor array = 2 x 2 x 1 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.781 x 0.781 x 0.781 196s Grid lengths: 50.000 x 50.000 x 50.000 196s Grid center: (0.000, 0.000, 0.000) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Multiple Debye-Huckel sphere boundary conditions 196s 0 ion species (0.000 M ionic strength): 196s Solute dielectric: 1.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition; no smoothing 196s Solvent probe radius: 1.400 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 2.401768459022E+02 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #2 (solvated): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 61.280 MB total, 122.102 MB high water 196s Using cubic spline charge discretization. 196s Partition overlap fraction = 0.1 196s Processor array = 2 x 2 x 1 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.296 x 0.296 x 0.383 196s Grid lengths: 18.944 x 18.944 x 24.495 196s Grid center: (2.411, -2.411, 0.000) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 0 ion species (0.000 M ionic strength): 196s Solute dielectric: 1.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition; no smoothing 196s Solvent probe radius: 1.400 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 8.142778312125E+02 kJ/mol 196s Calculating forces... 196s [focusFillBound()]: WARNING: 196s Unusually large potential values 196s detected on the focusing boundary! 196s Convergence not guaranteed for NPBE/NRPBE calculations! 196s 196s ---------------------------------------- 196s CALCULATION #3 (solvated): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 61.280 MB total, 122.102 MB high water 196s Using cubic spline charge discretization. 196s Partition overlap fraction = 0.1 196s Processor array = 2 x 2 x 1 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.112 x 0.112 x 0.188 196s Grid lengths: 7.178 x 7.178 x 12.000 196s Grid center: (2.411, -2.411, 0.000) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 0 ion species (0.000 M ionic strength): 196s Solute dielectric: 1.000 196s Solvent dielectric: 78.540 196s Using "molecular" surface definition; no smoothing 196s Solvent probe radius: 1.400 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.485246667424E+03 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #4 (reference): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 61.207 MB total, 122.102 MB high water 196s Using cubic spline charge discretization. 196s Partition overlap fraction = 0.1 196s Processor array = 2 x 2 x 1 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.781 x 0.781 x 0.781 196s Grid lengths: 50.000 x 50.000 x 50.000 196s Grid center: (0.000, 0.000, 0.000) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Multiple Debye-Huckel sphere boundary conditions 196s 0 ion species (0.000 M ionic strength): 196s Solute dielectric: 1.000 196s Solvent dielectric: 1.000 196s Using "molecular" surface definition; no smoothing 196s Solvent probe radius: 1.400 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 2.977178707009E+02 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s CALCULATION #5 (reference): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 61.207 MB total, 122.102 MB high water 196s Using cubic spline charge discretization. 196s Partition overlap fraction = 0.1 196s Processor array = 2 x 2 x 1 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.296 x 0.296 x 0.383 196s Grid lengths: 18.944 x 18.944 x 24.495 196s Grid center: (2.411, -2.411, 0.000) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 0 ion species (0.000 M ionic strength): 196s Solute dielectric: 1.000 196s Solvent dielectric: 1.000 196s Using "molecular" surface definition; no smoothing 196s Solvent probe radius: 1.400 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 8.799304557588E+02 kJ/mol 196s Calculating forces... 196s [focusFillBound()]: WARNING: 196s Unusually large potential values 196s detected on the focusing boundary! 196s Convergence not guaranteed for NPBE/NRPBE calculations! 196s 196s ---------------------------------------- 196s CALCULATION #6 (reference): MULTIGRID 196s Setting up problem... 196s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 196s Debye length: 0 A 196s Current memory usage: 61.207 MB total, 122.102 MB high water 196s Using cubic spline charge discretization. 196s Partition overlap fraction = 0.1 196s Processor array = 2 x 2 x 1 196s Grid dimensions: 65 x 65 x 65 196s Grid spacings: 0.112 x 0.112 x 0.188 196s Grid lengths: 7.178 x 7.178 x 12.000 196s Grid center: (2.411, -2.411, 0.000) 196s Multigrid levels: 5 196s Molecule ID: 1 196s Linearized traditional PBE 196s Boundary conditions from focusing 196s 0 ion species (0.000 M ionic strength): 196s Solute dielectric: 1.000 196s Solvent dielectric: 1.000 196s Using "molecular" surface definition; no smoothing 196s Solvent probe radius: 1.400 A 196s Temperature: 298.150 K 196s Electrostatic energies will be calculated 196s Total electrostatic energy = 1.542873949131E+03 kJ/mol 196s Calculating forces... 196s ---------------------------------------- 196s PRINT STATEMENTS 196s 196s print energy 1 (solvated) - 2 (reference) end 196s Local net energy (PE 0) = -5.762728170718E+01 kJ/mol 196s Global net ELEC energy = -5.762728170718E+01 kJ/mol 196s ---------------------------------------- 196s CLEANING UP AND SHUTTING DOWN... 196s Destroying force arrays. 196s No energy arrays to destroy. 196s Destroying multigrid structures. 196s Destroying finite element structures. 196s Destroying 1 molecules 196s Final memory usage: 0.001 MB total, 122.102 MB high water 196s 196s 196s Thanks for using APBS! 196s 196s 1.485246667424e+03 196s 2.977178707009e+02 196s 8.799304557588e+02 196s 1.542873949131e+03 196s -5.762728170718e+01 196s 199s Processor 2 results: 199s 2.401768459091e+02 199s 8.142935605695e+02 199s Checking for intermediate energies in input file apbs-mol-parallel-PE1.out 199s BINARY: /usr/bin/apbs 199s INPUT: apbs-mol-parallel-PE2.in 199s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] 199s asc_getToken: Error occurred (bailing out). 199s Vio_scanf: Format problem with input. 199s 199s 199s ---------------------------------------------------------------------- 199s APBS -- Adaptive Poisson-Boltzmann Solver 199s Version APBS 3.4.1 199s 199s Nathan A. Baker (nathan.baker@pnnl.gov) 199s Pacific Northwest National Laboratory 199s 199s Additional contributing authors listed in the code documentation. 199s 199s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 199s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 199s Northwest Division for the U.S. Department of Energy. 199s 199s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 199s Portions Copyright (c) 2002-2020, Nathan A. Baker. 199s Portions Copyright (c) 1999-2002, The Regents of the University of California. 199s Portions Copyright (c) 1995, Michael Holst. 199s All rights reserved. 199s 199s Redistribution and use in source and binary forms, with or without 199s modification, are permitted provided that the following conditions are met: 199s 199s * Redistributions of source code must retain the above copyright notice, this 199s list of conditions and the following disclaimer. 199s 199s * Redistributions in binary form must reproduce the above copyright notice, 199s this list of conditions and the following disclaimer in the documentation 199s and/or other materials provided with the distribution. 199s 199s * Neither the name of the developer nor the names of its contributors may be 199s used to endorse or promote products derived from this software without 199s specific prior written permission. 199s 199s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 199s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 199s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 199s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 199s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 199s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 199s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 199s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 199s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 199s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 199s ---------------------------------------------------------------------- 199s APBS uses FETK (the Finite Element ToolKit) to solve the 199s Poisson-Boltzmann equation numerically. FETK is a portable collection 199s of finite element modeling class libraries developed by the Michael Holst 199s research group and written in an object-oriented form of C. FEtk is 199s designed to solve general coupled systems of nonlinear partial differential 199s equations using adaptive finite element methods, inexact Newton methods, 199s and algebraic multilevel methods. More information about FEtk may be found 199s at . 199s ---------------------------------------------------------------------- 199s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 199s Aqua is a modified form of the Holst group PMG library 199s which has been modified by Patrice Koehl 199s for improved efficiency and 199s memory usage when solving the Poisson-Boltzmann equation. 199s ---------------------------------------------------------------------- 199s Please cite your use of APBS as: 199s 199s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 199s nanosystems: application to microtubules and the ribosome. Proc. 199s Natl. Acad. Sci. USA 98, 10037-10041 2001. 199s 199s 199s This executable compiled on Jan 3 2025 at 11:01:42 199s 199s Parsing input file apbs-mol-parallel-PE2.in... 199s rank 0 size 1... 199s Parsed input file. 199s Got paths for 1 molecules 199s Reading PQR-format atom data from ion.pqr. 199s 1 atoms 199s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 199s Net charge 1.00e+00 e 199s Preparing to run 6 PBE calculations. 199s ---------------------------------------- 199s CALCULATION #1 (solvated): MULTIGRID 199s Setting up problem... 199s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 199s Debye length: 0 A 199s Current memory usage: 61.280 MB total, 61.280 MB high water 199s Using cubic spline charge discretization. 199s Partition overlap fraction = 0.1 199s Processor array = 2 x 2 x 1 199s Grid dimensions: 65 x 65 x 65 199s Grid spacings: 0.781 x 0.781 x 0.781 199s Grid lengths: 50.000 x 50.000 x 50.000 199s Grid center: (0.000, 0.000, 0.000) 199s Multigrid levels: 5 199s Molecule ID: 1 199s Linearized traditional PBE 199s Multiple Debye-Huckel sphere boundary conditions 199s 0 ion species (0.000 M ionic strength): 199s Solute dielectric: 1.000 199s Solvent dielectric: 78.540 199s Using "molecular" surface definition; no smoothing 199s Solvent probe radius: 1.400 A 199s Temperature: 298.150 K 199s Electrostatic energies will be calculated 199s Total electrostatic energy = 2.401768459091E+02 kJ/mol 199s Calculating forces... 199s ---------------------------------------- 199s CALCULATION #2 (solvated): MULTIGRID 199s Setting up problem... 199s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 199s Debye length: 0 A 199s Current memory usage: 61.280 MB total, 122.102 MB high water 199s Using cubic spline charge discretization. 199s Partition overlap fraction = 0.1 199s Processor array = 2 x 2 x 1 199s Grid dimensions: 65 x 65 x 65 199s Grid spacings: 0.296 x 0.296 x 0.383 199s Grid lengths: 18.944 x 18.944 x 24.495 199s Grid center: (-2.411, 2.411, 0.000) 199s Multigrid levels: 5 199s Molecule ID: 1 199s Linearized traditional PBE 199s Boundary conditions from focusing 199s 0 ion species (0.000 M ionic strength): 199s Solute dielectric: 1.000 199s Solvent dielectric: 78.540 199s Using "molecular" surface definition; no smoothing 199s Solvent probe radius: 1.400 A 199s Temperature: 298.150 K 199s Electrostatic energies will be calculated 199s Total electrostatic energy = 8.142935605695E+02 kJ/mol 199s Calculating forces... 199s [focusFillBound()]: WARNING: 199s Unusually large potential values 199s detected on the focusing boundary! 199s Convergence not guaranteed for NPBE/NRPBE calculations! 199s 199s ---------------------------------------- 199s CALCULATION #3 (solvated): MULTIGRID 199s Setting up problem... 199s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 199s Debye length: 0 A 199s Current memory usage: 61.280 MB total, 122.102 MB high water 199s Using cubic spline charge discretization. 199s Partition overlap fraction = 0.1 199s Processor array = 2 x 2 x 1 199s Grid dimensions: 65 x 65 x 65 199s Grid spacings: 0.112 x 0.112 x 0.188 199s Grid lengths: 7.178 x 7.178 x 12.000 199s Grid center: (-2.411, 2.411, 0.000) 199s Multigrid levels: 5 199s Molecule ID: 1 199s Linearized traditional PBE 199s Boundary conditions from focusing 199s 0 ion species (0.000 M ionic strength): 199s Solute dielectric: 1.000 199s Solvent dielectric: 78.540 199s Using "molecular" surface definition; no smoothing 199s Solvent probe radius: 1.400 A 199s Temperature: 298.150 K 199s Electrostatic energies will be calculated 199s Total electrostatic energy = 1.485255306569E+03 kJ/mol 199s Calculating forces... 199s ---------------------------------------- 199s CALCULATION #4 (reference): MULTIGRID 199s Setting up problem... 199s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 199s Debye length: 0 A 199s Current memory usage: 61.207 MB total, 122.102 MB high water 199s Using cubic spline charge discretization. 199s Partition overlap fraction = 0.1 199s Processor array = 2 x 2 x 1 199s Grid dimensions: 65 x 65 x 65 199s Grid spacings: 0.781 x 0.781 x 0.781 199s Grid lengths: 50.000 x 50.000 x 50.000 199s Grid center: (0.000, 0.000, 0.000) 199s Multigrid levels: 5 199s Molecule ID: 1 199s Linearized traditional PBE 199s Multiple Debye-Huckel sphere boundary conditions 199s 0 ion species (0.000 M ionic strength): 199s Solute dielectric: 1.000 199s Solvent dielectric: 1.000 199s Using "molecular" surface definition; no smoothing 199s Solvent probe radius: 1.400 A 199s Temperature: 298.150 K 199s Electrostatic energies will be calculated 199s Total electrostatic energy = 2.977178707146E+02 kJ/mol 199s Calculating forces... 199s ---------------------------------------- 199s CALCULATION #5 (reference): MULTIGRID 199s Setting up problem... 199s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 199s Debye length: 0 A 199s Current memory usage: 61.207 MB total, 122.102 MB high water 199s Using cubic spline charge discretization. 199s Partition overlap fraction = 0.1 199s Processor array = 2 x 2 x 1 199s Grid dimensions: 65 x 65 x 65 199s Grid spacings: 0.296 x 0.296 x 0.383 199s Grid lengths: 18.944 x 18.944 x 24.495 199s Grid center: (-2.411, 2.411, 0.000) 199s Multigrid levels: 5 199s Molecule ID: 1 199s Linearized traditional PBE 199s Boundary conditions from focusing 199s 0 ion species (0.000 M ionic strength): 199s Solute dielectric: 1.000 199s Solvent dielectric: 1.000 199s Using "molecular" surface definition; no smoothing 199s Solvent probe radius: 1.400 A 199s Temperature: 298.150 K 199s Electrostatic energies will be calculated 199s Total electrostatic energy = 8.799304557596E+02 kJ/mol 199s Calculating forces... 199s [focusFillBound()]: WARNING: 199s Unusually large potential values 199s detected on the focusing boundary! 199s Convergence not guaranteed for NPBE/NRPBE calculations! 199s 199s ---------------------------------------- 199s CALCULATION #6 (reference): MULTIGRID 199s Setting up problem... 199s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 199s Debye length: 0 A 199s Current memory usage: 61.207 MB total, 122.102 MB high water 199s Using cubic spline charge discretization. 199s Partition overlap fraction = 0.1 199s Processor array = 2 x 2 x 1 199s Grid dimensions: 65 x 65 x 65 199s Grid spacings: 0.112 x 0.112 x 0.188 199s Grid lengths: 7.178 x 7.178 x 12.000 199s Grid center: (-2.411, 2.411, 0.000) 199s Multigrid levels: 5 199s Molecule ID: 1 199s Linearized traditional PBE 199s Boundary conditions from focusing 199s 0 ion species (0.000 M ionic strength): 199s Solute dielectric: 1.000 199s Solvent dielectric: 1.000 199s Using "molecular" surface definition; no smoothing 199s Solvent probe radius: 1.400 A 199s Temperature: 298.150 K 199s Electrostatic energies will be calculated 199s Total electrostatic energy = 1.542873949141E+03 kJ/mol 199s Calculating forces... 199s ---------------------------------------- 199s PRINT STATEMENTS 199s 199s print energy 1 (solvated) - 2 (reference) end 199s Local net energy (PE 0) = -5.761864257239E+01 kJ/mol 199s Global net ELEC energy = -5.761864257239E+01 kJ/mol 199s ---------------------------------------- 199s CLEANING UP AND SHUTTING DOWN... 199s Destroying force arrays. 199s No energy arrays to destroy. 199s Destroying multigrid structures. 199s Destroying finite element structures. 199s Destroying 1 molecules 199s Final memory usage: 0.001 MB total, 122.102 MB high water 199s 199s 199s Thanks for using APBS! 199s 199s 1.485255306569e+03 199s 2.977178707146e+02 199s 8.799304557596e+02 199s 1.542873949141e+03 199s -5.761864257239e+01 199s 202s Processor 3 results: 202s 2.401768459091e+02 202s 8.142778325440e+02 202s 1.485246665692e+03 202s 2.977178707146e+02 202s 8.799304557596e+02 202s 1.542873949141e+03 202s -5.762728344953e+01 202s 202s Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) 202s *** PASSED *** 202s Checking for intermediate energies in input file apbs-mol-parallel-PE2.out 202s BINARY: /usr/bin/apbs 202s INPUT: apbs-mol-parallel-PE3.in 202s COMMAND: ['/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] 202s asc_getToken: Error occurred (bailing out). 202s Vio_scanf: Format problem with input. 202s 202s 202s ---------------------------------------------------------------------- 202s APBS -- Adaptive Poisson-Boltzmann Solver 202s Version APBS 3.4.1 202s 202s Nathan A. Baker (nathan.baker@pnnl.gov) 202s Pacific Northwest National Laboratory 202s 202s Additional contributing authors listed in the code documentation. 202s 202s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 202s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 202s Northwest Division for the U.S. Department of Energy. 202s 202s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 202s Portions Copyright (c) 2002-2020, Nathan A. Baker. 202s Portions Copyright (c) 1999-2002, The Regents of the University of California. 202s Portions Copyright (c) 1995, Michael Holst. 202s All rights reserved. 202s 202s Redistribution and use in source and binary forms, with or without 202s modification, are permitted provided that the following conditions are met: 202s 202s * Redistributions of source code must retain the above copyright notice, this 202s list of conditions and the following disclaimer. 202s 202s * Redistributions in binary form must reproduce the above copyright notice, 202s this list of conditions and the following disclaimer in the documentation 202s and/or other materials provided with the distribution. 202s 202s * Neither the name of the developer nor the names of its contributors may be 202s used to endorse or promote products derived from this software without 202s specific prior written permission. 202s 202s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 202s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 202s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 202s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 202s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 202s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 202s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 202s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 202s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 202s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 202s ---------------------------------------------------------------------- 202s APBS uses FETK (the Finite Element ToolKit) to solve the 202s Poisson-Boltzmann equation numerically. FETK is a portable collection 202s of finite element modeling class libraries developed by the Michael Holst 202s research group and written in an object-oriented form of C. FEtk is 202s designed to solve general coupled systems of nonlinear partial differential 202s equations using adaptive finite element methods, inexact Newton methods, 202s and algebraic multilevel methods. More information about FEtk may be found 202s at . 202s ---------------------------------------------------------------------- 202s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 202s Aqua is a modified form of the Holst group PMG library 202s which has been modified by Patrice Koehl 202s for improved efficiency and 202s memory usage when solving the Poisson-Boltzmann equation. 202s ---------------------------------------------------------------------- 202s Please cite your use of APBS as: 202s 202s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 202s nanosystems: application to microtubules and the ribosome. Proc. 202s Natl. Acad. Sci. USA 98, 10037-10041 2001. 202s 202s 202s This executable compiled on Jan 3 2025 at 11:01:42 202s 202s Parsing input file apbs-mol-parallel-PE3.in... 202s rank 0 size 1... 202s Parsed input file. 202s Got paths for 1 molecules 202s Reading PQR-format atom data from ion.pqr. 202s 1 atoms 202s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 202s Net charge 1.00e+00 e 202s Preparing to run 6 PBE calculations. 202s ---------------------------------------- 202s CALCULATION #1 (solvated): MULTIGRID 202s Setting up problem... 202s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 202s Debye length: 0 A 202s Current memory usage: 61.280 MB total, 61.280 MB high water 202s Using cubic spline charge discretization. 202s Partition overlap fraction = 0.1 202s Processor array = 2 x 2 x 1 202s Grid dimensions: 65 x 65 x 65 202s Grid spacings: 0.781 x 0.781 x 0.781 202s Grid lengths: 50.000 x 50.000 x 50.000 202s Grid center: (0.000, 0.000, 0.000) 202s Multigrid levels: 5 202s Molecule ID: 1 202s Linearized traditional PBE 202s Multiple Debye-Huckel sphere boundary conditions 202s 0 ion species (0.000 M ionic strength): 202s Solute dielectric: 1.000 202s Solvent dielectric: 78.540 202s Using "molecular" surface definition; no smoothing 202s Solvent probe radius: 1.400 A 202s Temperature: 298.150 K 202s Electrostatic energies will be calculated 202s Total electrostatic energy = 2.401768459091E+02 kJ/mol 202s Calculating forces... 202s ---------------------------------------- 202s CALCULATION #2 (solvated): MULTIGRID 202s Setting up problem... 202s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 202s Debye length: 0 A 202s Current memory usage: 61.280 MB total, 122.102 MB high water 202s Using cubic spline charge discretization. 202s Partition overlap fraction = 0.1 202s Processor array = 2 x 2 x 1 202s Grid dimensions: 65 x 65 x 65 202s Grid spacings: 0.296 x 0.296 x 0.383 202s Grid lengths: 18.944 x 18.944 x 24.495 202s Grid center: (2.411, 2.411, 0.000) 202s Multigrid levels: 5 202s Molecule ID: 1 202s Linearized traditional PBE 202s Boundary conditions from focusing 202s 0 ion species (0.000 M ionic strength): 202s Solute dielectric: 1.000 202s Solvent dielectric: 78.540 202s Using "molecular" surface definition; no smoothing 202s Solvent probe radius: 1.400 A 202s Temperature: 298.150 K 202s Electrostatic energies will be calculated 202s Total electrostatic energy = 8.142778325440E+02 kJ/mol 202s Calculating forces... 202s [focusFillBound()]: WARNING: 202s Unusually large potential values 202s detected on the focusing boundary! 202s Convergence not guaranteed for NPBE/NRPBE calculations! 202s 202s ---------------------------------------- 202s CALCULATION #3 (solvated): MULTIGRID 202s Setting up problem... 202s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 202s Debye length: 0 A 202s Current memory usage: 61.280 MB total, 122.102 MB high water 202s Using cubic spline charge discretization. 202s Partition overlap fraction = 0.1 202s Processor array = 2 x 2 x 1 202s Grid dimensions: 65 x 65 x 65 202s Grid spacings: 0.112 x 0.112 x 0.188 202s Grid lengths: 7.178 x 7.178 x 12.000 202s Grid center: (2.411, 2.411, 0.000) 202s Multigrid levels: 5 202s Molecule ID: 1 202s Linearized traditional PBE 202s Boundary conditions from focusing 202s 0 ion species (0.000 M ionic strength): 202s Solute dielectric: 1.000 202s Solvent dielectric: 78.540 202s Using "molecular" surface definition; no smoothing 202s Solvent probe radius: 1.400 A 202s Temperature: 298.150 K 202s Electrostatic energies will be calculated 202s Total electrostatic energy = 1.485246665692E+03 kJ/mol 202s Calculating forces... 202s ---------------------------------------- 202s CALCULATION #4 (reference): MULTIGRID 202s Setting up problem... 202s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 202s Debye length: 0 A 202s Current memory usage: 61.207 MB total, 122.102 MB high water 202s Using cubic spline charge discretization. 202s Partition overlap fraction = 0.1 202s Processor array = 2 x 2 x 1 202s Grid dimensions: 65 x 65 x 65 202s Grid spacings: 0.781 x 0.781 x 0.781 202s Grid lengths: 50.000 x 50.000 x 50.000 202s Grid center: (0.000, 0.000, 0.000) 202s Multigrid levels: 5 202s Molecule ID: 1 202s Linearized traditional PBE 202s Multiple Debye-Huckel sphere boundary conditions 202s 0 ion species (0.000 M ionic strength): 202s Solute dielectric: 1.000 202s Solvent dielectric: 1.000 202s Using "molecular" surface definition; no smoothing 202s Solvent probe radius: 1.400 A 202s Temperature: 298.150 K 202s Electrostatic energies will be calculated 202s Total electrostatic energy = 2.977178707146E+02 kJ/mol 202s Calculating forces... 202s ---------------------------------------- 202s CALCULATION #5 (reference): MULTIGRID 202s Setting up problem... 202s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 202s Debye length: 0 A 202s Current memory usage: 61.207 MB total, 122.102 MB high water 202s Using cubic spline charge discretization. 202s Partition overlap fraction = 0.1 202s Processor array = 2 x 2 x 1 202s Grid dimensions: 65 x 65 x 65 202s Grid spacings: 0.296 x 0.296 x 0.383 202s Grid lengths: 18.944 x 18.944 x 24.495 202s Grid center: (2.411, 2.411, 0.000) 202s Multigrid levels: 5 202s Molecule ID: 1 202s Linearized traditional PBE 202s Boundary conditions from focusing 202s 0 ion species (0.000 M ionic strength): 202s Solute dielectric: 1.000 202s Solvent dielectric: 1.000 202s Using "molecular" surface definition; no smoothing 202s Solvent probe radius: 1.400 A 202s Temperature: 298.150 K 202s Electrostatic energies will be calculated 202s Total electrostatic energy = 8.799304557596E+02 kJ/mol 202s Calculating forces... 202s [focusFillBound()]: WARNING: 202s Unusually large potential values 202s detected on the focusing boundary! 202s Convergence not guaranteed for NPBE/NRPBE calculations! 202s 202s ---------------------------------------- 202s CALCULATION #6 (reference): MULTIGRID 202s Setting up problem... 202s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 202s Debye length: 0 A 202s Current memory usage: 61.207 MB total, 122.102 MB high water 202s Using cubic spline charge discretization. 202s Partition overlap fraction = 0.1 202s Processor array = 2 x 2 x 1 202s Grid dimensions: 65 x 65 x 65 202s Grid spacings: 0.112 x 0.112 x 0.188 202s Grid lengths: 7.178 x 7.178 x 12.000 202s Grid center: (2.411, 2.411, 0.000) 202s Multigrid levels: 5 202s Molecule ID: 1 202s Linearized traditional PBE 202s Boundary conditions from focusing 202s 0 ion species (0.000 M ionic strength): 202s Solute dielectric: 1.000 202s Solvent dielectric: 1.000 202s Using "molecular" surface definition; no smoothing 202s Solvent probe radius: 1.400 A 202s Temperature: 298.150 K 202s Electrostatic energies will be calculated 202s Total electrostatic energy = 1.542873949141E+03 kJ/mol 202s Calculating forces... 202s ---------------------------------------- 202s PRINT STATEMENTS 202s 202s print energy 1 (solvated) - 2 (reference) end 202s Local net energy (PE 0) = -5.762728344953E+01 kJ/mol 202s Global net ELEC energy = -5.762728344953E+01 kJ/mol 202s ---------------------------------------- 202s CLEANING UP AND SHUTTING DOWN... 202s Destroying force arrays. 202s No energy arrays to destroy. 202s Destroying multigrid structures. 202s Destroying finite element structures. 202s Destroying 1 molecules 202s Final memory usage: 0.001 MB total, 122.102 MB high water 202s 202s 202s Thanks for using APBS! 202s 202s Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) 202s *** PASSED *** 202s Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) 202s *** PASSED *** 202s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 202s *** PASSED *** 202s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 202s *** PASSED *** 202s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 202s *** PASSED *** 202s Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) 202s *** PASSED *** 202s Elapsed time: 10.882152 seconds 202s -------------------------------------------------------------------------------- 202s -------------------------------------------------------------------------------- 202s Testing input file apbs-smol-parallel.in 202s 202s Splitting the input file into 4 separate files using the inputgen utility 202s 204s Checking for intermediate energies in input file apbs-mol-parallel-PE3.out 204s EXPECTED COMPUTED: 7 204s EXPECTED EXPECTED: 7 204s COMPUTED: [960.7073836226, 3257.1427835730997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 204s EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] 204s COMPUTED RESULT 960.7073836226 204s COMPUTED RESULT 3257.1427835730997 204s COMPUTED RESULT 5941.0039478710005 204s COMPUTED RESULT 1190.8714828309999 204s COMPUTED RESULT 3519.7218230368003 204s COMPUTED RESULT 6171.495796544 204s COMPUTED RESULT -230.49184867462003 204s BINARY: /usr/bin/apbs 204s INPUT: apbs-smol-parallel-PE0.in 204s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] 204s asc_getToken: Error occurred (bailing out). 204s Vio_scanf: Format problem with input. 204s 204s 204s ---------------------------------------------------------------------- 204s APBS -- Adaptive Poisson-Boltzmann Solver 204s Version APBS 3.4.1 204s 204s Nathan A. Baker (nathan.baker@pnnl.gov) 204s Pacific Northwest National Laboratory 204s 204s Additional contributing authors listed in the code documentation. 204s 204s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 204s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 204s Northwest Division for the U.S. Department of Energy. 204s 204s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 204s Portions Copyright (c) 2002-2020, Nathan A. Baker. 204s Portions Copyright (c) 1999-2002, The Regents of the University of California. 204s Portions Copyright (c) 1995, Michael Holst. 204s All rights reserved. 204s 204s Redistribution and use in source and binary forms, with or without 204s modification, are permitted provided that the following conditions are met: 204s 204s * Redistributions of source code must retain the above copyright notice, this 204s list of conditions and the following disclaimer. 204s 204s * Redistributions in binary form must reproduce the above copyright notice, 204s this list of conditions and the following disclaimer in the documentation 204s and/or other materials provided with the distribution. 204s 204s * Neither the name of the developer nor the names of its contributors may be 204s used to endorse or promote products derived from this software without 204s specific prior written permission. 204s 204s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 204s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 204s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 204s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 204s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 204s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 204s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 204s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 204s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 204s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 204s ---------------------------------------------------------------------- 204s APBS uses FETK (the Finite Element ToolKit) to solve the 204s Poisson-Boltzmann equation numerically. FETK is a portable collection 204s of finite element modeling class libraries developed by the Michael Holst 204s research group and written in an object-oriented form of C. FEtk is 204s designed to solve general coupled systems of nonlinear partial differential 204s equations using adaptive finite element methods, inexact Newton methods, 204s and algebraic multilevel methods. More information about FEtk may be found 204s at . 204s ---------------------------------------------------------------------- 204s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 204s Aqua is a modified form of the Holst group PMG library 204s which has been modified by Patrice Koehl 204s for improved efficiency and 204s memory usage when solving the Poisson-Boltzmann equation. 204s ---------------------------------------------------------------------- 204s Please cite your use of APBS as: 204s 204s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 204s nanosystems: application to microtubules and the ribosome. Proc. 204s Natl. Acad. Sci. USA 98, 10037-10041 2001. 204s 204s 204s This executable compiled on Jan 3 2025 at 11:01:42 204s 204s Parsing input file apbs-smol-parallel-PE0.in... 204s rank 0 size 1... 204s Parsed input file. 204s Got paths for 1 molecules 204s Reading PQR-format atom data from ion.pqr. 204s 1 atoms 204s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 204s Net charge 1.00e+00 e 204s Preparing to run 6 PBE calculations. 204s ---------------------------------------- 204s CALCULATION #1 (solvated): MULTIGRID 204s Setting up problem... 204s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 204s Debye length: 0 A 204s Current memory usage: 61.280 MB total, 61.280 MB high water 204s Using cubic spline charge discretization. 204s Partition overlap fraction = 0.1 204s Processor array = 2 x 2 x 1 204s Grid dimensions: 65 x 65 x 65 204s Grid spacings: 0.781 x 0.781 x 0.781 204s Grid lengths: 50.000 x 50.000 x 50.000 204s Grid center: (0.000, 0.000, 0.000) 204s Multigrid levels: 5 204s Molecule ID: 1 204s Linearized traditional PBE 204s Multiple Debye-Huckel sphere boundary conditions 204s 0 ion species (0.000 M ionic strength): 204s Solute dielectric: 1.000 204s Solvent dielectric: 78.540 204s Using "molecular" surface definition;harmonic average smoothing 204s Solvent probe radius: 1.400 A 204s Temperature: 298.150 K 204s Electrostatic energies will be calculated 204s Total electrostatic energy = 2.383232191816E+02 kJ/mol 204s Calculating forces... 204s ---------------------------------------- 204s CALCULATION #2 (solvated): MULTIGRID 204s Setting up problem... 204s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 204s Debye length: 0 A 204s Current memory usage: 61.280 MB total, 122.102 MB high water 204s Using cubic spline charge discretization. 204s Partition overlap fraction = 0.1 204s Processor array = 2 x 2 x 1 204s Grid dimensions: 65 x 65 x 65 204s Grid spacings: 0.296 x 0.296 x 0.383 204s Grid lengths: 18.944 x 18.944 x 24.495 204s Grid center: (-2.411, -2.411, 0.000) 204s Multigrid levels: 5 204s Molecule ID: 1 204s Linearized traditional PBE 204s Boundary conditions from focusing 204s 0 ion species (0.000 M ionic strength): 204s Solute dielectric: 1.000 204s Solvent dielectric: 78.540 204s Using "molecular" surface definition;harmonic average smoothing 204s Solvent probe radius: 1.400 A 204s Temperature: 298.150 K 204s Electrostatic energies will be calculated 204s Total electrostatic energy = 8.145369591602E+02 kJ/mol 204s Calculating forces... 204s [focusFillBound()]: WARNING: 204s Unusually large potential values 204s detected on the focusing boundary! 204s Convergence not guaranteed for NPBE/NRPBE calculations! 204s 204s ---------------------------------------- 204s CALCULATION #3 (solvated): MULTIGRID 204s Setting up problem... 204s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 204s Debye length: 0 A 204s Current memory usage: 61.280 MB total, 122.102 MB high water 204s Using cubic spline charge discretization. 204s Partition overlap fraction = 0.1 204s Processor array = 2 x 2 x 1 204s Grid dimensions: 65 x 65 x 65 204s Grid spacings: 0.112 x 0.112 x 0.188 204s Grid lengths: 7.178 x 7.178 x 12.000 204s Grid center: (-2.411, -2.411, 0.000) 204s Multigrid levels: 5 204s Molecule ID: 1 204s Linearized traditional PBE 204s Boundary conditions from focusing 204s 0 ion species (0.000 M ionic strength): 204s Solute dielectric: 1.000 204s Solvent dielectric: 78.540 204s Using "molecular" surface definition;harmonic average smoothing 204s Solvent probe radius: 1.400 A 204s Temperature: 298.150 K 204s Electrostatic energies will be calculated 204s Total electrostatic energy = 1.485524998001E+03 kJ/mol 204s Calculating forces... 204s ---------------------------------------- 204s CALCULATION #4 (reference): MULTIGRID 204s Setting up problem... 204s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 204s Debye length: 0 A 204s Current memory usage: 61.207 MB total, 122.102 MB high water 204s Using cubic spline charge discretization. 204s Partition overlap fraction = 0.1 204s Processor array = 2 x 2 x 1 204s Grid dimensions: 65 x 65 x 65 204s Grid spacings: 0.781 x 0.781 x 0.781 204s Grid lengths: 50.000 x 50.000 x 50.000 204s Grid center: (0.000, 0.000, 0.000) 204s Multigrid levels: 5 204s Molecule ID: 1 204s Linearized traditional PBE 204s Multiple Debye-Huckel sphere boundary conditions 204s 0 ion species (0.000 M ionic strength): 204s Solute dielectric: 1.000 204s Solvent dielectric: 1.000 204s Using "molecular" surface definition;harmonic average smoothing 204s Solvent probe radius: 1.400 A 204s Temperature: 298.150 K 204s Electrostatic energies will be calculated 204s Total electrostatic energy = 2.977178707009E+02 kJ/mol 204s Calculating forces... 204s ---------------------------------------- 204s CALCULATION #5 (reference): MULTIGRID 204s Setting up problem... 204s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 204s Debye length: 0 A 204s Current memory usage: 61.207 MB total, 122.102 MB high water 204s Using cubic spline charge discretization. 204s Partition overlap fraction = 0.1 204s Processor array = 2 x 2 x 1 204s Grid dimensions: 65 x 65 x 65 204s Grid spacings: 0.296 x 0.296 x 0.383 204s Grid lengths: 18.944 x 18.944 x 24.495 204s Grid center: (-2.411, -2.411, 0.000) 204s Multigrid levels: 5 204s Molecule ID: 1 204s Linearized traditional PBE 204s Boundary conditions from focusing 204s 0 ion species (0.000 M ionic strength): 204s Solute dielectric: 1.000 204s Solvent dielectric: 1.000 204s Using "molecular" surface definition;harmonic average smoothing 204s Solvent probe radius: 1.400 A 204s Temperature: 298.150 K 204s Electrostatic energies will be calculated 204s Total electrostatic energy = 8.799304557588E+02 kJ/mol 204s Calculating forces... 204s [focusFillBound()]: WARNING: 204s Unusually large potential values 204s detected on the focusing boundary! 204s Convergence not guaranteed for NPBE/NRPBE calculations! 204s 204s ---------------------------------------- 204s CALCULATION #6 (reference): MULTIGRID 204s Setting up problem... 204s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 204s Debye length: 0 A 204s Current memory usage: 61.207 MB total, 122.102 MB high water 204s Using cubic spline charge discretization. 204s Partition overlap fraction = 0.1 204s Processor array = 2 x 2 x 1 204s Grid dimensions: 65 x 65 x 65 204s Grid spacings: 0.112 x 0.112 x 0.188 204s Grid lengths: 7.178 x 7.178 x 12.000 204s Grid center: (-2.411, -2.411, 0.000) 204s Multigrid levels: 5 204s Molecule ID: 1 204s Linearized traditional PBE 204s Boundary conditions from focusing 204s 0 ion species (0.000 M ionic strength): 204s Solute dielectric: 1.000 204s Solvent dielectric: 1.000 204s Using "molecular" surface definition;harmonic average smoothing 204s Solvent probe radius: 1.400 A 204s Temperature: 298.150 K 204s Electrostatic energies will be calculated 204s Total electrostatic energy = 1.542873949131E+03 kJ/mol 204s Calculating forces... 204s ---------------------------------------- 204s PRINT STATEMENTS 204s 204s print energy 1 (solvated) - 2 (reference) end 204s Local net energy (PE 0) = -5.734895113069E+01 kJ/mol 204s Global net ELEC energy = -5.734895113069E+01 kJ/mol 204s ---------------------------------------- 204s CLEANING UP AND SHUTTING DOWN... 204s Destroying force arrays. 204s No energy arrays to destroy. 204s Destroying multigrid structures. 204s Destroying finite element structures. 204s Destroying 1 molecules 204s Final memory usage: 0.001 MB total, 122.102 MB high water 204s 204s 204s Thanks for using APBS! 204s 204s Processor 0 results: 204s 2.383232191816e+02 204s 8.145369591602e+02 204s 1.485524998001e+03 204s 2.977178707009e+02 204s 8.799304557588e+02 204s 1.542873949131e+03 204s -5.734895113069e+01 204s 207s Checking for intermediate energies in input file apbs-smol-parallel-PE0.out 207s BINARY: /usr/bin/apbs 207s INPUT: apbs-smol-parallel-PE1.in 207s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] 207s Processor 1 results: 207s 2.383232191816e+02 207s 8.145419898332e+02 207s 1.485529328612e+03 207s 2.977178707009e+02 207s 8.799304557588e+02 207s 1.542873949131e+03 207s -5.734462051928e+01 207s 207s asc_getToken: Error occurred (bailing out). 207s Vio_scanf: Format problem with input. 207s 207s 207s ---------------------------------------------------------------------- 207s APBS -- Adaptive Poisson-Boltzmann Solver 207s Version APBS 3.4.1 207s 207s Nathan A. Baker (nathan.baker@pnnl.gov) 207s Pacific Northwest National Laboratory 207s 207s Additional contributing authors listed in the code documentation. 207s 207s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 207s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 207s Northwest Division for the U.S. Department of Energy. 207s 207s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 207s Portions Copyright (c) 2002-2020, Nathan A. Baker. 207s Portions Copyright (c) 1999-2002, The Regents of the University of California. 207s Portions Copyright (c) 1995, Michael Holst. 207s All rights reserved. 207s 207s Redistribution and use in source and binary forms, with or without 207s modification, are permitted provided that the following conditions are met: 207s 207s * Redistributions of source code must retain the above copyright notice, this 207s list of conditions and the following disclaimer. 207s 207s * Redistributions in binary form must reproduce the above copyright notice, 207s this list of conditions and the following disclaimer in the documentation 207s and/or other materials provided with the distribution. 207s 207s * Neither the name of the developer nor the names of its contributors may be 207s used to endorse or promote products derived from this software without 207s specific prior written permission. 207s 207s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 207s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 207s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 207s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 207s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 207s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 207s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 207s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 207s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 207s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 207s ---------------------------------------------------------------------- 207s APBS uses FETK (the Finite Element ToolKit) to solve the 207s Poisson-Boltzmann equation numerically. FETK is a portable collection 207s of finite element modeling class libraries developed by the Michael Holst 207s research group and written in an object-oriented form of C. FEtk is 207s designed to solve general coupled systems of nonlinear partial differential 207s equations using adaptive finite element methods, inexact Newton methods, 207s and algebraic multilevel methods. More information about FEtk may be found 207s at . 207s ---------------------------------------------------------------------- 207s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 207s Aqua is a modified form of the Holst group PMG library 207s which has been modified by Patrice Koehl 207s for improved efficiency and 207s memory usage when solving the Poisson-Boltzmann equation. 207s ---------------------------------------------------------------------- 207s Please cite your use of APBS as: 207s 207s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 207s nanosystems: application to microtubules and the ribosome. Proc. 207s Natl. Acad. Sci. USA 98, 10037-10041 2001. 207s 207s 207s This executable compiled on Jan 3 2025 at 11:01:42 207s 207s Parsing input file apbs-smol-parallel-PE1.in... 207s rank 0 size 1... 207s Parsed input file. 207s Got paths for 1 molecules 207s Reading PQR-format atom data from ion.pqr. 207s 1 atoms 207s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 207s Net charge 1.00e+00 e 207s Preparing to run 6 PBE calculations. 207s ---------------------------------------- 207s CALCULATION #1 (solvated): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 61.280 MB total, 61.280 MB high water 207s Using cubic spline charge discretization. 207s Partition overlap fraction = 0.1 207s Processor array = 2 x 2 x 1 207s Grid dimensions: 65 x 65 x 65 207s Grid spacings: 0.781 x 0.781 x 0.781 207s Grid lengths: 50.000 x 50.000 x 50.000 207s Grid center: (0.000, 0.000, 0.000) 207s Multigrid levels: 5 207s Molecule ID: 1 207s Linearized traditional PBE 207s Multiple Debye-Huckel sphere boundary conditions 207s 0 ion species (0.000 M ionic strength): 207s Solute dielectric: 1.000 207s Solvent dielectric: 78.540 207s Using "molecular" surface definition;harmonic average smoothing 207s Solvent probe radius: 1.400 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 2.383232191816E+02 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s CALCULATION #2 (solvated): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 61.280 MB total, 122.102 MB high water 207s Using cubic spline charge discretization. 207s Partition overlap fraction = 0.1 207s Processor array = 2 x 2 x 1 207s Grid dimensions: 65 x 65 x 65 207s Grid spacings: 0.296 x 0.296 x 0.383 207s Grid lengths: 18.944 x 18.944 x 24.495 207s Grid center: (2.411, -2.411, 0.000) 207s Multigrid levels: 5 207s Molecule ID: 1 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 0 ion species (0.000 M ionic strength): 207s Solute dielectric: 1.000 207s Solvent dielectric: 78.540 207s Using "molecular" surface definition;harmonic average smoothing 207s Solvent probe radius: 1.400 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 8.145419898332E+02 kJ/mol 207s Calculating forces... 207s [focusFillBound()]: WARNING: 207s Unusually large potential values 207s detected on the focusing boundary! 207s Convergence not guaranteed for NPBE/NRPBE calculations! 207s 207s ---------------------------------------- 207s CALCULATION #3 (solvated): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 61.280 MB total, 122.102 MB high water 207s Using cubic spline charge discretization. 207s Partition overlap fraction = 0.1 207s Processor array = 2 x 2 x 1 207s Grid dimensions: 65 x 65 x 65 207s Grid spacings: 0.112 x 0.112 x 0.188 207s Grid lengths: 7.178 x 7.178 x 12.000 207s Grid center: (2.411, -2.411, 0.000) 207s Multigrid levels: 5 207s Molecule ID: 1 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 0 ion species (0.000 M ionic strength): 207s Solute dielectric: 1.000 207s Solvent dielectric: 78.540 207s Using "molecular" surface definition;harmonic average smoothing 207s Solvent probe radius: 1.400 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 1.485529328612E+03 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s CALCULATION #4 (reference): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 61.207 MB total, 122.102 MB high water 207s Using cubic spline charge discretization. 207s Partition overlap fraction = 0.1 207s Processor array = 2 x 2 x 1 207s Grid dimensions: 65 x 65 x 65 207s Grid spacings: 0.781 x 0.781 x 0.781 207s Grid lengths: 50.000 x 50.000 x 50.000 207s Grid center: (0.000, 0.000, 0.000) 207s Multigrid levels: 5 207s Molecule ID: 1 207s Linearized traditional PBE 207s Multiple Debye-Huckel sphere boundary conditions 207s 0 ion species (0.000 M ionic strength): 207s Solute dielectric: 1.000 207s Solvent dielectric: 1.000 207s Using "molecular" surface definition;harmonic average smoothing 207s Solvent probe radius: 1.400 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 2.977178707009E+02 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s CALCULATION #5 (reference): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 61.207 MB total, 122.102 MB high water 207s Using cubic spline charge discretization. 207s Partition overlap fraction = 0.1 207s Processor array = 2 x 2 x 1 207s Grid dimensions: 65 x 65 x 65 207s Grid spacings: 0.296 x 0.296 x 0.383 207s Grid lengths: 18.944 x 18.944 x 24.495 207s Grid center: (2.411, -2.411, 0.000) 207s Multigrid levels: 5 207s Molecule ID: 1 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 0 ion species (0.000 M ionic strength): 207s Solute dielectric: 1.000 207s Solvent dielectric: 1.000 207s Using "molecular" surface definition;harmonic average smoothing 207s Solvent probe radius: 1.400 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 8.799304557588E+02 kJ/mol 207s Calculating forces... 207s [focusFillBound()]: WARNING: 207s Unusually large potential values 207s detected on the focusing boundary! 207s Convergence not guaranteed for NPBE/NRPBE calculations! 207s 207s ---------------------------------------- 207s CALCULATION #6 (reference): MULTIGRID 207s Setting up problem... 207s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 207s Debye length: 0 A 207s Current memory usage: 61.207 MB total, 122.102 MB high water 207s Using cubic spline charge discretization. 207s Partition overlap fraction = 0.1 207s Processor array = 2 x 2 x 1 207s Grid dimensions: 65 x 65 x 65 207s Grid spacings: 0.112 x 0.112 x 0.188 207s Grid lengths: 7.178 x 7.178 x 12.000 207s Grid center: (2.411, -2.411, 0.000) 207s Multigrid levels: 5 207s Molecule ID: 1 207s Linearized traditional PBE 207s Boundary conditions from focusing 207s 0 ion species (0.000 M ionic strength): 207s Solute dielectric: 1.000 207s Solvent dielectric: 1.000 207s Using "molecular" surface definition;harmonic average smoothing 207s Solvent probe radius: 1.400 A 207s Temperature: 298.150 K 207s Electrostatic energies will be calculated 207s Total electrostatic energy = 1.542873949131E+03 kJ/mol 207s Calculating forces... 207s ---------------------------------------- 207s PRINT STATEMENTS 207s 207s print energy 1 (solvated) - 2 (reference) end 207s Local net energy (PE 0) = -5.734462051928E+01 kJ/mol 207s Global net ELEC energy = -5.734462051928E+01 kJ/mol 207s ---------------------------------------- 207s CLEANING UP AND SHUTTING DOWN... 207s Destroying force arrays. 207s No energy arrays to destroy. 207s Destroying multigrid structures. 207s Destroying finite element structures. 207s Destroying 1 molecules 207s Final memory usage: 0.001 MB total, 122.102 MB high water 207s 207s 207s Thanks for using APBS! 207s 209s Checking for intermediate energies in input file apbs-smol-parallel-PE1.out 209s BINARY: /usr/bin/apbs 209s INPUT: apbs-smol-parallel-PE2.in 209s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] 209s Processor 2 results: 209s asc_getToken: Error occurred (bailing out). 209s Vio_scanf: Format problem with input. 209s 209s 209s ---------------------------------------------------------------------- 209s APBS -- Adaptive Poisson-Boltzmann Solver 209s Version APBS 3.4.1 209s 209s Nathan A. Baker (nathan.baker@pnnl.gov) 209s Pacific Northwest National Laboratory 209s 209s Additional contributing authors listed in the code documentation. 209s 209s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 209s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 209s Northwest Division for the U.S. Department of Energy. 209s 209s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 209s Portions Copyright (c) 2002-2020, Nathan A. Baker. 209s Portions Copyright (c) 1999-2002, The Regents of the University of California. 209s Portions Copyright (c) 1995, Michael Holst. 209s All rights reserved. 209s 209s Redistribution and use in source and binary forms, with or without 209s modification, are permitted provided that the following conditions are met: 209s 209s * Redistributions of source code must retain the above copyright notice, this 209s list of conditions and the following disclaimer. 209s 209s * Redistributions in binary form must reproduce the above copyright notice, 209s this list of conditions and the following disclaimer in the documentation 209s and/or other materials provided with the distribution. 209s 209s * Neither the name of the developer nor the names of its contributors may be 209s used to endorse or promote products derived from this software without 209s specific prior written permission. 209s 209s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 209s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 209s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 209s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 209s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 209s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 209s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 209s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 209s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 209s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 209s ---------------------------------------------------------------------- 209s APBS uses FETK (the Finite Element ToolKit) to solve the 209s Poisson-Boltzmann equation numerically. FETK is a portable collection 209s of finite element modeling class libraries developed by the Michael Holst 209s research group and written in an object-oriented form of C. FEtk is 209s designed to solve general coupled systems of nonlinear partial differential 209s equations using adaptive finite element methods, inexact Newton methods, 209s and algebraic multilevel methods. More information about FEtk may be found 209s at . 209s ---------------------------------------------------------------------- 209s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 209s Aqua is a modified form of the Holst group PMG library 209s which has been modified by Patrice Koehl 209s for improved efficiency and 209s memory usage when solving the Poisson-Boltzmann equation. 209s ---------------------------------------------------------------------- 209s Please cite your use of APBS as: 209s 209s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 209s nanosystems: application to microtubules and the ribosome. Proc. 209s Natl. Acad. Sci. USA 98, 10037-10041 2001. 209s 209s 209s This executable compiled on Jan 3 2025 at 11:01:42 209s 209s Parsing input file apbs-smol-parallel-PE2.in... 209s rank 0 size 1... 209s Parsed input file. 209s Got paths for 1 molecules 209s Reading PQR-format atom data from ion.pqr. 209s 1 atoms 209s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 209s Net charge 1.00e+00 e 209s Preparing to run 6 PBE calculations. 209s ---------------------------------------- 209s CALCULATION #1 (solvated): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.280 MB total, 61.280 MB high water 209s Using cubic spline charge discretization. 209s Partition overlap fraction = 0.1 209s Processor array = 2 x 2 x 1 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.781 x 0.781 x 0.781 209s Grid lengths: 50.000 x 50.000 x 50.000 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 1.000 209s Solvent dielectric: 78.540 209s Using "molecular" surface definition;harmonic average smoothing 209s Solvent probe radius: 1.400 A 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 2.383232191909E+02 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #2 (solvated): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.280 MB total, 122.102 MB high water 209s Using cubic spline charge discretization. 209s Partition overlap fraction = 0.1 209s Processor array = 2 x 2 x 1 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.296 x 0.296 x 0.383 209s Grid lengths: 18.944 x 18.944 x 24.495 209s Grid center: (-2.411, 2.411, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Boundary conditions from focusing 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 1.000 209s Solvent dielectric: 78.540 209s Using "molecular" surface definition;harmonic average smoothing 209s Solvent probe radius: 1.400 A 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 8.145369593489E+02 kJ/mol 209s Calculating forces... 209s [focusFillBound()]: WARNING: 209s Unusually large potential values 209s detected on the focusing boundary! 209s Convergence not guaranteed for NPBE/NRPBE calculations! 209s 209s ---------------------------------------- 209s CALCULATION #3 (solvated): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.280 MB total, 122.102 MB high water 209s Using cubic spline charge discretization. 209s Partition overlap fraction = 0.1 209s Processor array = 2 x 2 x 1 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.112 x 0.112 x 0.188 209s Grid lengths: 7.178 x 7.178 x 12.000 209s Grid center: (-2.411, 2.411, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Boundary conditions from focusing 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 1.000 209s Solvent dielectric: 78.540 209s Using "molecular" surface definition;harmonic average smoothing 209s Solvent probe radius: 1.400 A 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 1.485524997676E+03 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #4 (reference): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.207 MB total, 122.102 MB high water 209s Using cubic spline charge discretization. 209s Partition overlap fraction = 0.1 209s Processor array = 2 x 2 x 1 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.781 x 0.781 x 0.781 209s Grid lengths: 50.000 x 50.000 x 50.000 209s Grid center: (0.000, 0.000, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Multiple Debye-Huckel sphere boundary conditions 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 1.000 209s Solvent dielectric: 1.000 209s Using "molecular" surface definition;harmonic average smoothing 209s Solvent probe radius: 1.400 A 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 2.977178707146E+02 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s CALCULATION #5 (reference): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.207 MB total, 122.102 MB high water 209s Using cubic spline charge discretization. 209s Partition overlap fraction = 0.1 209s Processor array = 2 x 2 x 1 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.296 x 0.296 x 0.383 209s Grid lengths: 18.944 x 18.944 x 24.495 209s Grid center: (-2.411, 2.411, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Boundary conditions from focusing 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 1.000 209s Solvent dielectric: 1.000 209s Using "molecular" surface definition;harmonic average smoothing 209s Solvent probe radius: 1.400 A 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 8.799304557596E+02 kJ/mol 209s Calculating forces... 209s [focusFillBound()]: WARNING: 209s Unusually large potential values 209s detected on the focusing boundary! 209s Convergence not guaranteed for NPBE/NRPBE calculations! 209s 209s ---------------------------------------- 209s CALCULATION #6 (reference): MULTIGRID 209s Setting up problem... 209s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 209s Debye length: 0 A 209s Current memory usage: 61.207 MB total, 122.102 MB high water 209s Using cubic spline charge discretization. 209s Partition overlap fraction = 0.1 209s Processor array = 2 x 2 x 1 209s Grid dimensions: 65 x 65 x 65 209s Grid spacings: 0.112 x 0.112 x 0.188 209s Grid lengths: 7.178 x 7.178 x 12.000 209s Grid center: (-2.411, 2.411, 0.000) 209s Multigrid levels: 5 209s Molecule ID: 1 209s Linearized traditional PBE 209s Boundary conditions from focusing 209s 0 ion species (0.000 M ionic strength): 209s Solute dielectric: 1.000 209s Solvent dielectric: 1.000 209s Using "molecular" surface definition;harmonic average smoothing 209s Solvent probe radius: 1.400 A 209s Temperature: 298.150 K 209s Electrostatic energies will be calculated 209s Total electrostatic energy = 1.542873949141E+03 kJ/mol 209s Calculating forces... 209s ---------------------------------------- 209s PRINT STATEMENTS 209s 209s print energy 1 (solvated) - 2 (reference) end 209s Local net energy (PE 0) = -5.734895146550E+01 kJ/mol 209s Global net ELEC energy = -5.734895146550E+01 kJ/mol 209s ---------------------------------------- 209s CLEANING UP AND SHUTTING DOWN... 209s Destroying force arrays. 209s No energy arrays to destroy. 209s Destroying multigrid structures. 209s Destroying finite element structures. 209s Destroying 1 molecules 209s Final memory usage: 0.001 MB total, 122.102 MB high water 209s 209s 209s Thanks for using APBS! 209s 209s 2.383232191909e+02 209s 8.145369593489e+02 209s 1.485524997676e+03 209s 2.977178707146e+02 209s 8.799304557596e+02 209s 1.542873949141e+03 209s -5.734895146550e+01 209s 212s Checking for intermediate energies in input file apbs-smol-parallel-PE2.out 212s BINARY: /usr/bin/apbs 212s INPUT: apbs-smol-parallel-PE3.in 212s COMMAND: ['/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] 212s asc_getToken: Error occurred (bailing out). 212s Vio_scanf: Format problem with input. 212s 212s 212s ---------------------------------------------------------------------- 212s APBS -- Adaptive Poisson-Boltzmann Solver 212s Version APBS 3.4.1 212s 212s Nathan A. Baker (nathan.baker@pnnl.gov) 212s Pacific Northwest National Laboratory 212s 212s Additional contributing authors listed in the code documentation. 212s 212s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 212s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 212s Northwest Division for the U.S. Department of Energy. 212s 212s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 212s Portions Copyright (c) 2002-2020, Nathan A. Baker. 212s Portions Copyright (c) 1999-2002, The Regents of the University of California. 212s Portions Copyright (c) 1995, Michael Holst. 212s All rights reserved. 212s 212s Redistribution and use in source and binary forms, with or without 212s modification, are permitted provided that the following conditions are met: 212s 212s * Redistributions of source code must retain the above copyright notice, this 212s list of conditions and the following disclaimer. 212s 212s * Redistributions in binary form must reproduce the above copyright notice, 212s this list of conditions and the following disclaimer in the documentation 212s and/or other materials provided with the distribution. 212s 212s * Neither the name of the developer nor the names of its contributors may be 212s used to endorse or promote products derived from this software without 212s specific prior written permission. 212s 212s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 212s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 212s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 212s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 212s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 212s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 212s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 212s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 212s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 212s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 212s ---------------------------------------------------------------------- 212s APBS uses FETK (the Finite Element ToolKit) to solve the 212s Poisson-Boltzmann equation numerically. FETK is a portable collection 212s of finite element modeling class libraries developed by the Michael Holst 212s research group and written in an object-oriented form of C. FEtk is 212s designed to solve general coupled systems of nonlinear partial differential 212s equations using adaptive finite element methods, inexact Newton methods, 212s and algebraic multilevel methods. More information about FEtk may be found 212s at . 212s ---------------------------------------------------------------------- 212s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 212s Aqua is a modified form of the Holst group PMG library 212s which has been modified by Patrice Koehl 212s for improved efficiency and 212s memory usage when solving the Poisson-Boltzmann equation. 212s ---------------------------------------------------------------------- 212s Please cite your use of APBS as: 212s 212s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 212s nanosystems: application to microtubules and the ribosome. Proc. 212s Natl. Acad. Sci. USA 98, 10037-10041 2001. 212s 212s 212s This executable compiled on Jan 3 2025 at 11:01:42 212s 212s Parsing input file apbs-smol-parallel-PE3.in... 212s rank 0 size 1... 212s Parsed input file. 212s Got paths for 1 molecules 212s Reading PQR-format atom data from ion.pqr. 212s 1 atoms 212s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 212s Net charge 1.00e+00 e 212s Preparing to run 6 PBE calculations. 212s ---------------------------------------- 212s CALCULATION #1 (solvated): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 61.280 MB total, 61.280 MB high water 212s Using cubic spline charge discretization. 212s Partition overlap fraction = 0.1 212s Processor array = 2 x 2 x 1 212s Grid dimensions: 65 x 65 x 65 212s Grid spacings: 0.781 x 0.781 x 0.781 212s Grid lengths: 50.000 x 50.000 x 50.000 212s Grid center: (0.000, 0.000, 0.000) 212s Multigrid levels: 5 212s Molecule ID: 1 212s Linearized traditional PBE 212s Multiple Debye-Huckel sphere boundary conditions 212s 0 ion species (0.000 M ionic strength): 212s Solute dielectric: 1.000 212s Solvent dielectric: 78.540 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 1.400 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 2.383232191909E+02 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s CALCULATION #2 (solvated): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 61.280 MB total, 122.102 MB high water 212s Using cubic spline charge discretization. 212s Partition overlap fraction = 0.1 212s Processor array = 2 x 2 x 1 212s Grid dimensions: 65 x 65 x 65 212s Grid spacings: 0.296 x 0.296 x 0.383 212s Grid lengths: 18.944 x 18.944 x 24.495 212s Grid center: (2.411, 2.411, 0.000) 212s Multigrid levels: 5 212s Molecule ID: 1 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 0 ion species (0.000 M ionic strength): 212s Solute dielectric: 1.000 212s Solvent dielectric: 78.540 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 1.400 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 8.145419900310E+02 kJ/mol 212s Calculating forces... 212s [focusFillBound()]: WARNING: 212s Unusually large potential values 212s detected on the focusing boundary! 212s Convergence not guaranteed for NPBE/NRPBE calculations! 212s 212s ---------------------------------------- 212s CALCULATION #3 (solvated): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 61.280 MB total, 122.102 MB high water 212s Using cubic spline charge discretization. 212s Partition overlap fraction = 0.1 212s Processor array = 2 x 2 x 1 212s Grid dimensions: 65 x 65 x 65 212s Grid spacings: 0.112 x 0.112 x 0.188 212s Grid lengths: 7.178 x 7.178 x 12.000 212s Grid center: (2.411, 2.411, 0.000) 212s Multigrid levels: 5 212s Molecule ID: 1 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 0 ion species (0.000 M ionic strength): 212s Solute dielectric: 1.000 212s Solvent dielectric: 78.540 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 1.400 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 1.485529328301E+03 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s CALCULATION #4 (reference): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 61.207 MB total, 122.102 MB high water 212s Using cubic spline charge discretization. 212s Partition overlap fraction = 0.1 212s Processor array = 2 x 2 x 1 212s Grid dimensions: 65 x 65 x 65 212s Grid spacings: 0.781 x 0.781 x 0.781 212s Grid lengths: 50.000 x 50.000 x 50.000 212s Grid center: (0.000, 0.000, 0.000) 212s Multigrid levels: 5 212s Molecule ID: 1 212s Linearized traditional PBE 212s Multiple Debye-Huckel sphere boundary conditions 212s 0 ion species (0.000 M ionic strength): 212s Solute dielectric: 1.000 212s Solvent dielectric: 1.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 1.400 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 2.977178707146E+02 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s CALCULATION #5 (reference): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 61.207 MB total, 122.102 MB high water 212s Using cubic spline charge discretization. 212s Partition overlap fraction = 0.1 212s Processor array = 2 x 2 x 1 212s Grid dimensions: 65 x 65 x 65 212s Grid spacings: 0.296 x 0.296 x 0.383 212s Grid lengths: 18.944 x 18.944 x 24.495 212s Grid center: (2.411, 2.411, 0.000) 212s Multigrid levels: 5 212s Molecule ID: 1 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 0 ion species (0.000 M ionic strength): 212s Solute dielectric: 1.000 212s Solvent dielectric: 1.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 1.400 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 8.799304557596E+02 kJ/mol 212s Calculating forces... 212s [focusFillBound()]: WARNING: 212s Unusually large potential values 212s detected on the focusing boundary! 212s Convergence not guaranteed for NPBE/NRPBE calculations! 212s 212s ---------------------------------------- 212s CALCULATION #6 (reference): MULTIGRID 212s Setting up problem... 212s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 212s Debye length: 0 A 212s Current memory usage: 61.207 MB total, 122.102 MB high water 212s Using cubic spline charge discretization. 212s Partition overlap fraction = 0.1 212s Processor array = 2 x 2 x 1 212s Grid dimensions: 65 x 65 x 65 212s Grid spacings: 0.112 x 0.112 x 0.188 212s Grid lengths: 7.178 x 7.178 x 12.000 212s Grid center: (2.411, 2.411, 0.000) 212s Multigrid levels: 5 212s Molecule ID: 1 212s Linearized traditional PBE 212s Boundary conditions from focusing 212s 0 ion species (0.000 M ionic strength): 212s Solute dielectric: 1.000 212s Solvent dielectric: 1.000 212s Using "molecular" surface definition;harmonic average smoothing 212s Solvent probe radius: 1.400 A 212s Temperature: 298.150 K 212s Electrostatic energies will be calculated 212s Total electrostatic energy = 1.542873949141E+03 kJ/mol 212s Calculating forces... 212s ---------------------------------------- 212s PRINT STATEMENTS 212s 212s print energy 1 (solvated) - 2 (reference) end 212s Local net energy (PE 0) = -5.734462084052E+01 kJ/mol 212s Global net ELEC energy = -5.734462084052E+01 kJ/mol 212s ---------------------------------------- 212s CLEANING UP AND SHUTTING DOWN... 212s Destroying force arrays. 212s No energy arrays to destroy. 212s Destroying multigrid structures. 212s Destroying finite element structures. 212s Destroying 1 molecules 212s Final memory usage: 0.001 MB total, 122.102 MB high water 212s 212s 212s Thanks for using APBS! 212s 212s Processor 3 results: 212s 2.383232191909e+02 212s 8.145419900310e+02 212s 1.485529328301e+03 212s 2.977178707146e+02 212s 8.799304557596e+02 212s 1.542873949141e+03 212s -5.734462084052e+01 212s 212s Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) 212s *** PASSED *** 212s Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) 212s *** PASSED *** 212s Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) 212s *** PASSED *** 212s Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) 212s *** PASSED *** 212s Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) 212s *** PASSED *** 212s Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) 212s *** PASSED *** 212s Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) 212s *** PASSED *** 212s Elapsed time: 10.074222 seconds 212s -------------------------------------------------------------------------------- 212s Total elapsed time: 26.443138 seconds 212s Test results have been logged 212s -------------------------------------------------------------------------------- 212s -------------------------------------------------------------------------------- 212s Testing input file apbs-mol-auto.in 212s 305s Checking for intermediate energies in input file apbs-smol-parallel-PE3.out 305s EXPECTED COMPUTED: 7 305s EXPECTED EXPECTED: 7 305s COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] 305s EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] 305s COMPUTED RESULT 953.292876745 305s COMPUTED RESULT 3258.1578983732998 305s COMPUTED RESULT 5942.108652589999 305s COMPUTED RESULT 1190.8714828309999 305s COMPUTED RESULT 3519.7218230368003 305s COMPUTED RESULT 6171.495796544 305s COMPUTED RESULT -229.38714395599 305s Running tests for actin-dimer-auto section 305s BINARY: /usr/bin/apbs 305s INPUT: apbs-mol-auto.in 305s COMMAND: ['/usr/bin/apbs', 'apbs-mol-auto.in'] 305s asc_getToken: Error occurred (bailing out). 305s Vio_scanf: Format problem with input. 305s 305s 305s ---------------------------------------------------------------------- 305s APBS -- Adaptive Poisson-Boltzmann Solver 305s Version APBS 3.4.1 305s 305s Nathan A. Baker (nathan.baker@pnnl.gov) 305s Pacific Northwest National Laboratory 305s 305s Additional contributing authors listed in the code documentation. 305s 305s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 305s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 305s Northwest Division for the U.S. Department of Energy. 305s 305s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 305s Portions Copyright (c) 2002-2020, Nathan A. Baker. 305s Portions Copyright (c) 1999-2002, The Regents of the University of California. 305s Portions Copyright (c) 1995, Michael Holst. 305s All rights reserved. 305s 305s Redistribution and use in source and binary forms, with or without 305s modification, are permitted provided that the following conditions are met: 305s 305s * Redistributions of source code must retain the above copyright notice, this 305s list of conditions and the following disclaimer. 305s 305s * Redistributions in binary form must reproduce the above copyright notice, 305s this list of conditions and the following disclaimer in the documentation 305s and/or other materials provided with the distribution. 305s 305s * Neither the name of the developer nor the names of its contributors may be 305s used to endorse or promote products derived from this software without 305s specific prior written permission. 305s 305s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 305s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 305s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 305s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 305s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 305s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 305s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 305s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 305s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 305s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 305s ---------------------------------------------------------------------- 305s APBS uses FETK (the Finite Element ToolKit) to solve the 305s Poisson-Boltzmann equation numerically. FETK is a portable collection 305s of finite element modeling class libraries developed by the Michael Holst 305s research group and written in an object-oriented form of C. FEtk is 305s designed to solve general coupled systems of nonlinear partial differential 305s equations using adaptive finite element methods, inexact Newton methods, 305s and algebraic multilevel methods. More information about FEtk may be found 305s at . 305s ---------------------------------------------------------------------- 305s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 305s Aqua is a modified form of the Holst group PMG library 305s which has been modified by Patrice Koehl 305s for improved efficiency and 305s memory usage when solving the Poisson-Boltzmann equation. 305s ---------------------------------------------------------------------- 305s Please cite your use of APBS as: 305s 305s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 305s nanosystems: application to microtubules and the ribosome. Proc. 305s Natl. Acad. Sci. USA 98, 10037-10041 2001. 305s 305s 305s This executable compiled on Jan 3 2025 at 11:01:42 305s 305s Parsing input file apbs-mol-auto.in... 305s rank 0 size 1... 305s Parsed input file. 305s Got paths for 3 molecules 305s Reading PQR-format atom data from mol1.pqr. 305s asc_getToken: Error occurred (bailing out). 305s Vio_scanf: Format problem with input. 305s 5877 atoms 305s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 305s Net charge -1.20e+01 e 305s Reading PQR-format atom data from mol2.pqr. 305s asc_getToken: Error occurred (bailing out). 305s Vio_scanf: Format problem with input. 305s 5877 atoms 305s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 305s Net charge -1.20e+01 e 305s Reading PQR-format atom data from complex.pqr. 305s 11754 atoms 305s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 305s Net charge -2.40e+01 e 305s Preparing to run 6 PBE calculations. 305s ---------------------------------------- 305s CALCULATION #1 (mol1): MULTIGRID 305s Setting up problem... 305s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 305s Debye length: 13.5959 A 305s Current memory usage: 1028.322 MB total, 1028.322 MB high water 305s Using linear spline charge discretization. 305s Grid dimensions: 161 x 161 x 161 305s Grid spacings: 0.975 x 0.756 x 1.012 305s Grid lengths: 156.000 x 121.000 x 162.000 305s Grid center: (2.518, -2.465, 16.742) 305s Multigrid levels: 4 305s Molecule ID: 1 305s Nonlinear traditional PBE 305s Single Debye-Huckel sphere boundary conditions 305s 2 ion species (0.050 M ionic strength): 305s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 305s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 305s Solute dielectric: 2.000 305s Solvent dielectric: 78.400 305s Using "molecular" surface definition; no smoothing 305s Solvent probe radius: 1.400 A 305s Temperature: 298.150 K 305s Electrostatic energies will be calculated 305s Total electrostatic energy = 1.527617850342E+05 kJ/mol 305s Calculating forces... 305s ---------------------------------------- 305s CALCULATION #2 (mol1): MULTIGRID 305s Setting up problem... 305s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 305s Debye length: 13.5959 A 305s Current memory usage: 1028.322 MB total, 2042.113 MB high water 305s Using linear spline charge discretization. 305s Grid dimensions: 161 x 161 x 161 305s Grid spacings: 0.700 x 0.569 x 0.725 305s Grid lengths: 112.000 x 91.000 x 116.000 305s Grid center: (2.518, -2.465, 16.742) 305s Multigrid levels: 4 305s Molecule ID: 1 305s Nonlinear traditional PBE 305s Boundary conditions from focusing 305s 2 ion species (0.050 M ionic strength): 305s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 305s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 305s Solute dielectric: 2.000 305s Solvent dielectric: 78.400 305s Using "molecular" surface definition; no smoothing 305s Solvent probe radius: 1.400 A 305s Temperature: 298.150 K 305s Electrostatic energies will be calculated 305s Total electrostatic energy = 2.919510754196E+05 kJ/mol 305s Calculating forces... 305s ---------------------------------------- 305s CALCULATION #3 (mol2): MULTIGRID 305s Setting up problem... 305s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 305s Debye length: 13.5959 A 305s Current memory usage: 1030.291 MB total, 2042.113 MB high water 305s Using linear spline charge discretization. 305s Grid dimensions: 161 x 161 x 161 305s Grid spacings: 0.975 x 0.756 x 1.012 305s Grid lengths: 156.000 x 121.000 x 162.000 305s Grid center: (2.518, -2.465, 16.742) 305s Multigrid levels: 4 305s Molecule ID: 2 305s Nonlinear traditional PBE 305s Single Debye-Huckel sphere boundary conditions 305s 2 ion species (0.050 M ionic strength): 305s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 305s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 305s Solute dielectric: 2.000 305s Solvent dielectric: 78.400 305s Using "molecular" surface definition; no smoothing 305s Solvent probe radius: 1.400 A 305s Temperature: 298.150 K 305s Electrostatic energies will be calculated 305s Total electrostatic energy = 1.527671844880E+05 kJ/mol 305s Calculating forces... 305s ---------------------------------------- 305s CALCULATION #4 (mol2): MULTIGRID 305s Setting up problem... 305s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 305s Debye length: 13.5959 A 305s Current memory usage: 1030.291 MB total, 2046.048 MB high water 305s Using linear spline charge discretization. 305s Grid dimensions: 161 x 161 x 161 305s Grid spacings: 0.700 x 0.569 x 0.725 305s Grid lengths: 112.000 x 91.000 x 116.000 305s Grid center: (2.518, -2.465, 16.742) 305s Multigrid levels: 4 305s Molecule ID: 2 305s Nonlinear traditional PBE 305s Boundary conditions from focusing 305s 2 ion species (0.050 M ionic strength): 305s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 305s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 305s Solute dielectric: 2.000 305s Solvent dielectric: 78.400 305s Using "molecular" surface definition; no smoothing 305s Solvent probe radius: 1.400 A 305s Temperature: 298.150 K 305s Electrostatic energies will be calculated 305s Total electrostatic energy = 2.915468859278E+05 kJ/mol 305s Calculating forces... 305s ---------------------------------------- 305s CALCULATION #5 (complex): MULTIGRID 305s Setting up problem... 305s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 305s Debye length: 13.5959 A 305s Current memory usage: 1046.446 MB total, 2046.048 MB high water 305s Using linear spline charge discretization. 305s Grid dimensions: 161 x 161 x 161 305s Grid spacings: 0.975 x 0.756 x 1.012 305s Grid lengths: 156.000 x 121.000 x 162.000 305s Grid center: (2.518, -2.465, 16.742) 305s Multigrid levels: 4 305s Molecule ID: 3 305s Nonlinear traditional PBE 305s Single Debye-Huckel sphere boundary conditions 305s 2 ion species (0.050 M ionic strength): 305s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 305s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 305s Solute dielectric: 2.000 305s Solvent dielectric: 78.400 305s Using "molecular" surface definition; no smoothing 305s Solvent probe radius: 1.400 A 305s Temperature: 298.150 K 305s Electrostatic energies will be calculated 305s Total electrostatic energy = 3.056317807611E+05 kJ/mol 305s Calculating forces... 305s ---------------------------------------- 305s CALCULATION #6 (complex): MULTIGRID 305s Setting up problem... 305s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 305s Debye length: 13.5959 A 305s Current memory usage: 1046.446 MB total, 2069.492 MB high water 305s Using linear spline charge discretization. 305s Grid dimensions: 161 x 161 x 161 305s Grid spacings: 0.700 x 0.569 x 0.725 305s Grid lengths: 112.000 x 91.000 x 116.000 305s Grid center: (2.518, -2.465, 16.742) 305s Multigrid levels: 4 305s Molecule ID: 3 305s Nonlinear traditional PBE 305s Boundary conditions from focusing 305s 2 ion species (0.050 M ionic strength): 305s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 305s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 305s Solute dielectric: 2.000 305s Solvent dielectric: 78.400 305s Using "molecular" surface definition; no smoothing 305s Solvent probe radius: 1.400 A 305s Temperature: 298.150 K 305s Electrostatic energies will be calculated 305s Total electrostatic energy = 5.836028296532E+05 kJ/mol 305s Calculating forces... 305s ---------------------------------------- 305s PRINT STATEMENTS 305s 305s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 305s Local net energy (PE 0) = 1.048683058621E+02 kJ/mol 305s Global net ELEC energy = 1.048683058621E+02 kJ/mol 305s ---------------------------------------- 305s CLEANING UP AND SHUTTING DOWN... 305s Destroying force arrays. 305s No energy arrays to destroy. 305s Destroying multigrid structures. 305s Destroying finite element structures. 305s Destroying 3 molecules 305s Final memory usage: 0.001 MB total, 2069.492 MB high water 305s 305s 305s Thanks for using APBS! 305s 305s Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) 305s *** PASSED *** 305s Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) 305s *** PASSED *** 305s Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) 305s *** PASSED *** 305s Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) 305s *** PASSED *** 305s Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) 305s *** PASSED *** 305s Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) 305s *** PASSED *** 305s Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02) 305s *** PASSED *** 305s Elapsed time: 92.867913 seconds 305s -------------------------------------------------------------------------------- 305s -------------------------------------------------------------------------------- 305s Testing input file apbs-smol-auto.in 305s 376s Checking for intermediate energies in input file apbs-mol-auto.out 376s EXPECTED COMPUTED: 7 376s EXPECTED EXPECTED: 7 376s COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058621] 376s EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] 376s COMPUTED RESULT 152761.7850342 376s COMPUTED RESULT 291951.0754196 376s COMPUTED RESULT 152767.184488 376s COMPUTED RESULT 291546.8859278 376s COMPUTED RESULT 305631.7807611 376s COMPUTED RESULT 583602.8296532 376s COMPUTED RESULT 104.8683058621 376s BINARY: /usr/bin/apbs 376s INPUT: apbs-smol-auto.in 376s COMMAND: ['/usr/bin/apbs', 'apbs-smol-auto.in'] 376s asc_getToken: Error occurred (bailing out). 376s Vio_scanf: Format problem with input. 376s 376s 376s ---------------------------------------------------------------------- 376s APBS -- Adaptive Poisson-Boltzmann Solver 376s Version APBS 3.4.1 376s 376s Nathan A. Baker (nathan.baker@pnnl.gov) 376s Pacific Northwest National Laboratory 376s 376s Additional contributing authors listed in the code documentation. 376s 376s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 376s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 376s Northwest Division for the U.S. Department of Energy. 376s 376s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 376s Portions Copyright (c) 2002-2020, Nathan A. Baker. 376s Portions Copyright (c) 1999-2002, The Regents of the University of California. 376s Portions Copyright (c) 1995, Michael Holst. 376s All rights reserved. 376s 376s Redistribution and use in source and binary forms, with or without 376s modification, are permitted provided that the following conditions are met: 376s 376s * Redistributions of source code must retain the above copyright notice, this 376s list of conditions and the following disclaimer. 376s 376s * Redistributions in binary form must reproduce the above copyright notice, 376s this list of conditions and the following disclaimer in the documentation 376s and/or other materials provided with the distribution. 376s 376s * Neither the name of the developer nor the names of its contributors may be 376s used to endorse or promote products derived from this software without 376s specific prior written permission. 376s 376s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 376s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 376s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 376s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 376s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 376s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 376s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 376s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 376s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 376s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 376s ---------------------------------------------------------------------- 376s APBS uses FETK (the Finite Element ToolKit) to solve the 376s Poisson-Boltzmann equation numerically. FETK is a portable collection 376s of finite element modeling class libraries developed by the Michael Holst 376s research group and written in an object-oriented form of C. FEtk is 376s designed to solve general coupled systems of nonlinear partial differential 376s equations using adaptive finite element methods, inexact Newton methods, 376s and algebraic multilevel methods. More information about FEtk may be found 376s at . 376s ---------------------------------------------------------------------- 376s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 376s Aqua is a modified form of the Holst group PMG library 376s which has been modified by Patrice Koehl 376s for improved efficiency and 376s memory usage when solving the Poisson-Boltzmann equation. 376s ---------------------------------------------------------------------- 376s Please cite your use of APBS as: 376s 376s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 376s nanosystems: application to microtubules and the ribosome. Proc. 376s Natl. Acad. Sci. USA 98, 10037-10041 2001. 376s 376s 376s This executable compiled on Jan 3 2025 at 11:01:42 376s 376s Parsing input file apbs-smol-auto.in... 376s rank 0 size 1... 376s Parsed input file. 376s Got paths for 3 molecules 376s Reading PQR-format atom data from mol1.pqr. 376s asc_getToken: Error occurred (bailing out). 376s Vio_scanf: Format problem with input. 376s 5877 atoms 376s Centered at (1.535e+01, -3.100e-02, 2.993e+00) 376s Net charge -1.20e+01 e 376s Reading PQR-format atom data from mol2.pqr. 376s asc_getToken: Error occurred (bailing out). 376s Vio_scanf: Format problem with input. 376s 5877 atoms 376s Centered at (-1.404e+01, -3.356e+00, 3.049e+01) 376s Net charge -1.20e+01 e 376s Reading PQR-format atom data from complex.pqr. 376s 11754 atoms 376s Centered at (2.518e+00, -2.465e+00, 1.674e+01) 376s Net charge -2.40e+01 e 376s Preparing to run 6 PBE calculations. 376s ---------------------------------------- 376s CALCULATION #1 (mol1): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 13.5959 A 376s Current memory usage: 1028.322 MB total, 1028.322 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 161 x 161 x 161 376s Grid spacings: 0.975 x 0.756 x 1.012 376s Grid lengths: 156.000 x 121.000 x 162.000 376s Grid center: (2.518, -2.465, 16.742) 376s Multigrid levels: 4 376s Molecule ID: 1 376s Nonlinear traditional PBE 376s Single Debye-Huckel sphere boundary conditions 376s 2 ion species (0.050 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.400 376s Using "molecular" surface definition;harmonic average smoothing 376s Solvent probe radius: 1.400 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.528632421825E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #2 (mol1): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 13.5959 A 376s Current memory usage: 1028.322 MB total, 2042.113 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 161 x 161 x 161 376s Grid spacings: 0.700 x 0.569 x 0.725 376s Grid lengths: 112.000 x 91.000 x 116.000 376s Grid center: (2.518, -2.465, 16.742) 376s Multigrid levels: 4 376s Molecule ID: 1 376s Nonlinear traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.050 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.400 376s Using "molecular" surface definition;harmonic average smoothing 376s Solvent probe radius: 1.400 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 2.920618662320E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #3 (mol2): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 13.5959 A 376s Current memory usage: 1030.291 MB total, 2042.113 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 161 x 161 x 161 376s Grid spacings: 0.975 x 0.756 x 1.012 376s Grid lengths: 156.000 x 121.000 x 162.000 376s Grid center: (2.518, -2.465, 16.742) 376s Multigrid levels: 4 376s Molecule ID: 2 376s Nonlinear traditional PBE 376s Single Debye-Huckel sphere boundary conditions 376s 2 ion species (0.050 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.400 376s Using "molecular" surface definition;harmonic average smoothing 376s Solvent probe radius: 1.400 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 1.529297900572E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #4 (mol2): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 13.5959 A 376s Current memory usage: 1030.291 MB total, 2046.048 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 161 x 161 x 161 376s Grid spacings: 0.700 x 0.569 x 0.725 376s Grid lengths: 112.000 x 91.000 x 116.000 376s Grid center: (2.518, -2.465, 16.742) 376s Multigrid levels: 4 376s Molecule ID: 2 376s Nonlinear traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.050 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.400 376s Using "molecular" surface definition;harmonic average smoothing 376s Solvent probe radius: 1.400 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 2.916592202835E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #5 (complex): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 13.5959 A 376s Current memory usage: 1046.446 MB total, 2046.048 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 161 x 161 x 161 376s Grid spacings: 0.975 x 0.756 x 1.012 376s Grid lengths: 156.000 x 121.000 x 162.000 376s Grid center: (2.518, -2.465, 16.742) 376s Multigrid levels: 4 376s Molecule ID: 3 376s Nonlinear traditional PBE 376s Single Debye-Huckel sphere boundary conditions 376s 2 ion species (0.050 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.400 376s Using "molecular" surface definition;harmonic average smoothing 376s Solvent probe radius: 1.400 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 3.059244262535E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s CALCULATION #6 (complex): MULTIGRID 376s Setting up problem... 376s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 376s Debye length: 13.5959 A 376s Current memory usage: 1046.446 MB total, 2069.492 MB high water 376s Using linear spline charge discretization. 376s Grid dimensions: 161 x 161 x 161 376s Grid spacings: 0.700 x 0.569 x 0.725 376s Grid lengths: 112.000 x 91.000 x 116.000 376s Grid center: (2.518, -2.465, 16.742) 376s Multigrid levels: 4 376s Molecule ID: 3 376s Nonlinear traditional PBE 376s Boundary conditions from focusing 376s 2 ion species (0.050 M ionic strength): 376s 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 376s 2.000 A-radius, -1.000 e-charge, 0.050 M concentration 376s Solute dielectric: 2.000 376s Solvent dielectric: 78.400 376s Using "molecular" surface definition;harmonic average smoothing 376s Solvent probe radius: 1.400 A 376s Temperature: 298.150 K 376s Electrostatic energies will be calculated 376s Total electrostatic energy = 5.838306706232E+05 kJ/mol 376s Calculating forces... 376s ---------------------------------------- 376s PRINT STATEMENTS 376s 376s print energy 3 (complex) - 2 (mol2) - 1 (mol1) end 376s Local net energy (PE 0) = 1.095841077688E+02 kJ/mol 376s Global net ELEC energy = 1.095841077688E+02 kJ/mol 376s ---------------------------------------- 376s CLEANING UP AND SHUTTING DOWN... 376s Destroying force arrays. 376s No energy arrays to destroy. 376s Destroying multigrid structures. 376s Destroying finite element structures. 376s Destroying 3 molecules 376s Final memory usage: 0.001 MB total, 2069.492 MB high water 376s 376s 376s Thanks for using APBS! 376s 376s Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) 376s *** PASSED *** 376s Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) 376s *** PASSED *** 376s Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) 376s *** PASSED *** 376s Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) 376s *** PASSED *** 376s Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) 376s *** PASSED *** 376s Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) 376s *** PASSED *** 376s Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02) 376s *** PASSED *** 376s Elapsed time: 71.286157 seconds 376s -------------------------------------------------------------------------------- 376s Total elapsed time: 164.15407 seconds 376s Test results have been logged 376s -------------------------------------------------------------------------------- 376s -------------------------------------------------------------------------------- 376s Testing input file alkanes.in 376s 386s Checking for intermediate energies in input file apbs-smol-auto.out 386s EXPECTED COMPUTED: 7 386s EXPECTED EXPECTED: 7 386s COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077688] 386s EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] 386s COMPUTED RESULT 152863.2421825 386s COMPUTED RESULT 292061.866232 386s COMPUTED RESULT 152929.7900572 386s COMPUTED RESULT 291659.2202835 386s COMPUTED RESULT 305924.4262535 386s COMPUTED RESULT 583830.6706232 386s COMPUTED RESULT 109.5841077688 386s Running tests for alkanes section 386s BINARY: /usr/bin/apbs 386s INPUT: alkanes.in 386s COMMAND: ['/usr/bin/apbs', 'alkanes.in'] 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 386s 386s ---------------------------------------------------------------------- 386s APBS -- Adaptive Poisson-Boltzmann Solver 386s Version APBS 3.4.1 386s 386s Nathan A. Baker (nathan.baker@pnnl.gov) 386s Pacific Northwest National Laboratory 386s 386s Additional contributing authors listed in the code documentation. 386s 386s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 386s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 386s Northwest Division for the U.S. Department of Energy. 386s 386s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 386s Portions Copyright (c) 2002-2020, Nathan A. Baker. 386s Portions Copyright (c) 1999-2002, The Regents of the University of California. 386s Portions Copyright (c) 1995, Michael Holst. 386s All rights reserved. 386s 386s Redistribution and use in source and binary forms, with or without 386s modification, are permitted provided that the following conditions are met: 386s 386s * Redistributions of source code must retain the above copyright notice, this 386s list of conditions and the following disclaimer. 386s 386s * Redistributions in binary form must reproduce the above copyright notice, 386s this list of conditions and the following disclaimer in the documentation 386s and/or other materials provided with the distribution. 386s 386s * Neither the name of the developer nor the names of its contributors may be 386s used to endorse or promote products derived from this software without 386s specific prior written permission. 386s 386s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 386s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 386s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 386s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 386s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 386s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 386s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 386s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 386s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 386s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 386s ---------------------------------------------------------------------- 386s APBS uses FETK (the Finite Element ToolKit) to solve the 386s Poisson-Boltzmann equation numerically. FETK is a portable collection 386s of finite element modeling class libraries developed by the Michael Holst 386s research group and written in an object-oriented form of C. FEtk is 386s designed to solve general coupled systems of nonlinear partial differential 386s equations using adaptive finite element methods, inexact Newton methods, 386s and algebraic multilevel methods. More information about FEtk may be found 386s at . 386s ---------------------------------------------------------------------- 386s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 386s Aqua is a modified form of the Holst group PMG library 386s which has been modified by Patrice Koehl 386s for improved efficiency and 386s memory usage when solving the Poisson-Boltzmann equation. 386s ---------------------------------------------------------------------- 386s Please cite your use of APBS as: 386s 386s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 386s nanosystems: application to microtubules and the ribosome. Proc. 386s Natl. Acad. Sci. USA 98, 10037-10041 2001. 386s 386s 386s This executable compiled on Jan 3 2025 at 11:01:42 386s 386s Parsing input file alkanes.in... 386s rank 0 size 1... 386s Parsed input file. 386s Reading parameter data from parm.dat. 386s Got paths for 11 molecules 386s Reading PDB-format atom data from 2-methylbutane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 17 atoms 386s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 386s Net charge 4.33e+00 e 386s Reading PDB-format atom data from butane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 14 atoms 386s Centered at (3.917e+00, 7.025e-01, -8.575e+00) 386s Net charge 3.51e+00 e 386s Reading PDB-format atom data from cyclohexane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 18 atoms 386s Centered at (1.123e+00, 5.880e-01, 7.680e-01) 386s Net charge 4.93e+00 e 386s Reading PDB-format atom data from cyclopentane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 13 atoms 386s Centered at (1.320e+00, 5.255e-01, 1.289e+00) 386s Net charge 3.88e+00 e 386s Reading PDB-format atom data from ethane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 8 atoms 386s Centered at (2.210e-01, -2.100e-02, 7.650e-01) 386s Net charge 1.87e+00 e 386s Reading PDB-format atom data from hexane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 20 atoms 386s Centered at (4.951e+00, -9.500e-03, -8.406e+00) 386s Net charge 5.16e+00 e 386s Reading PDB-format atom data from isobutane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 14 atoms 386s Centered at (1.859e+01, 1.864e+01, 1.921e+01) 386s Net charge 3.51e+00 e 386s Reading PDB-format atom data from methane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 5 atoms 386s Centered at (1.803e+01, 1.779e+01, 1.782e+01) 386s Net charge 1.05e+00 e 386s Reading PDB-format atom data from neopentane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 17 atoms 386s Centered at (1.867e+01, 1.894e+01, 1.920e+01) 386s Net charge 4.33e+00 e 386s Reading PDB-format atom data from pentane.pdb. 386s asc_getToken: Error occurred (bailing out). 386s Vio_scanf: Format problem with input. 386s 17 atoms 386s Centered at (4.460e+00, 1.615e-01, -8.566e+00) 386s Net charge 4.33e+00 e 386s Reading PDB-format atom data from propane.pdb. 386s 11 atoms 386s Centered at (1.836e+01, 1.896e+01, 1.861e+01) 386s Net charge 2.69e+00 e 386s Preparing to run 11 PBE calculations. 386s ---------------------------------------- 386s CALCULATION #1 (solvated-2-methylbutane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 3.815624614267E+00 386s SASA for atom 1: 0.000000000000E+00 386s SASA for atom 2: 6.122920124655E-01 386s SASA for atom 3: 3.957497153740E+00 386s SASA for atom 4: 4.308445014544E+00 386s SASA for atom 5: 1.843264951960E+01 386s SASA for atom 6: 1.837011296483E+01 386s SASA for atom 7: 1.666599184724E+01 386s SASA for atom 8: 1.480031796315E+01 386s SASA for atom 9: 1.603020354037E+01 386s SASA for atom 10: 1.473778140838E+01 386s SASA for atom 11: 1.611879699297E+01 386s SASA for atom 12: 1.810954398660E+01 386s SASA for atom 13: 1.420100931324E+01 386s SASA for atom 14: 1.437298483886E+01 386s SASA for atom 15: 1.814081226399E+01 386s SASA for atom 16: 2.152820898091E+01 386s 386s Total solvent accessible surface area: 214.202 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 3.243280922127E-02 386s Surface tension*area energy for atom 1: 0.000000000000E+00 386s Surface tension*area energy for atom 2: 5.204482105957E-03 386s Surface tension*area energy for atom 3: 3.363872580679E-02 386s Surface tension*area energy for atom 4: 3.662178262362E-02 386s Surface tension*area energy for atom 5: 1.566775209166E-01 386s Surface tension*area energy for atom 6: 1.561459602010E-01 386s Surface tension*area energy for atom 7: 1.416609307015E-01 386s Surface tension*area energy for atom 8: 1.258027026868E-01 386s Surface tension*area energy for atom 9: 1.362567300932E-01 386s Surface tension*area energy for atom 10: 1.252711419712E-01 386s Surface tension*area energy for atom 11: 1.370097744402E-01 386s Surface tension*area energy for atom 12: 1.539311238861E-01 386s Surface tension*area energy for atom 13: 1.207085791625E-01 386s Surface tension*area energy for atom 14: 1.221703711303E-01 386s Surface tension*area energy for atom 15: 1.541969042439E-01 386s Surface tension*area energy for atom 16: 1.829897763377E-01 386s 386s Total surface tension energy: 1.82072 kJ/mol 386s 386s Total solvent accessible volume: 253.665 A^3 386s 386s Total pressure*volume energy: 60.7274 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.271287875274E+00 386s WCA energy for atom 1: -5.600872869478E+00 386s WCA energy for atom 2: -5.773775123943E+00 386s WCA energy for atom 3: -6.072801488986E+00 386s WCA energy for atom 4: -6.378470721845E+00 386s WCA energy for atom 5: -1.573474558351E+00 386s WCA energy for atom 6: -1.582338715648E+00 386s WCA energy for atom 7: -1.504044838266E+00 386s WCA energy for atom 8: -1.351002262819E+00 386s WCA energy for atom 9: -1.437367175239E+00 386s WCA energy for atom 10: -1.384626257493E+00 386s WCA energy for atom 11: -1.468867560891E+00 386s WCA energy for atom 12: -1.557005662832E+00 386s WCA energy for atom 13: -1.473759654043E+00 386s WCA energy for atom 14: -1.502261431335E+00 386s WCA energy for atom 15: -1.550940901474E+00 386s WCA energy for atom 16: -1.667828659696E+00 386s 386s Total WCA energy: -48.1507 kJ/mol 386s 386s Total non-polar energy = 1.439739455792E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #2 (solvated-butane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 4.405515699447E+00 386s SASA for atom 1: 8.213673337951E-01 386s SASA for atom 2: 8.064333822716E-01 386s SASA for atom 3: 4.375647796400E+00 386s SASA for atom 4: 1.855251124959E+01 386s SASA for atom 5: 2.147609518526E+01 386s SASA for atom 6: 1.852645435176E+01 386s SASA for atom 7: 1.660345529247E+01 386s SASA for atom 8: 1.658782115377E+01 386s SASA for atom 9: 1.658260977421E+01 386s SASA for atom 10: 1.658260977421E+01 386s SASA for atom 11: 2.145003828744E+01 386s SASA for atom 12: 1.852124297220E+01 386s SASA for atom 13: 1.856293400871E+01 386s 386s Total solvent accessible surface area: 193.855 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 3.744688344530E-02 386s Surface tension*area energy for atom 1: 6.981622337259E-03 386s Surface tension*area energy for atom 2: 6.854683749309E-03 386s Surface tension*area energy for atom 3: 3.719300626940E-02 386s Surface tension*area energy for atom 4: 1.576963456215E-01 386s Surface tension*area energy for atom 5: 1.825468090747E-01 386s Surface tension*area energy for atom 6: 1.574748619900E-01 386s Surface tension*area energy for atom 7: 1.411293699860E-01 386s Surface tension*area energy for atom 8: 1.409964798071E-01 386s Surface tension*area energy for atom 9: 1.409521830808E-01 386s Surface tension*area energy for atom 10: 1.409521830808E-01 386s Surface tension*area energy for atom 11: 1.823253254433E-01 386s Surface tension*area energy for atom 12: 1.574305652637E-01 386s Surface tension*area energy for atom 13: 1.577849390741E-01 386s 386s Total surface tension energy: 1.64777 kJ/mol 386s 386s Total solvent accessible volume: 217.863 A^3 386s 386s Total pressure*volume energy: 52.1564 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.728858147814E+00 386s WCA energy for atom 1: -6.204037472587E+00 386s WCA energy for atom 2: -6.202937735018E+00 386s WCA energy for atom 3: -6.728762249931E+00 386s WCA energy for atom 4: -1.623549989062E+00 386s WCA energy for atom 5: -1.709092300778E+00 386s WCA energy for atom 6: -1.625196457114E+00 386s WCA energy for atom 7: -1.484289341167E+00 386s WCA energy for atom 8: -1.485410538626E+00 386s WCA energy for atom 9: -1.485593139015E+00 386s WCA energy for atom 10: -1.484878734279E+00 386s WCA energy for atom 11: -1.708585062695E+00 386s WCA energy for atom 12: -1.625094916482E+00 386s WCA energy for atom 13: -1.624416805392E+00 386s 386s Total WCA energy: -41.7207 kJ/mol 386s 386s Total non-polar energy = 1.208346456826E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #3 (solvated-cyclohexane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 7.840324549863E-01 386s SASA for atom 1: 8.064333822716E-01 386s SASA for atom 2: 8.288343095569E-01 386s SASA for atom 3: 7.840324549863E-01 386s SASA for atom 4: 7.989664065098E-01 386s SASA for atom 5: 8.363012853187E-01 386s SASA for atom 6: 2.001169752764E+01 386s SASA for atom 7: 1.616048802948E+01 386s SASA for atom 8: 2.001169752764E+01 386s SASA for atom 9: 1.619175630687E+01 386s SASA for atom 10: 1.616048802948E+01 386s SASA for atom 11: 1.993352683418E+01 386s SASA for atom 12: 2.001169752764E+01 386s SASA for atom 13: 1.618133354774E+01 386s SASA for atom 14: 1.617091078861E+01 386s SASA for atom 15: 2.001690890721E+01 386s SASA for atom 16: 1.993873821374E+01 386s SASA for atom 17: 1.617091078861E+01 386s 386s Total solvent accessible surface area: 221.799 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 6.664275867383E-03 386s Surface tension*area energy for atom 1: 6.854683749309E-03 386s Surface tension*area energy for atom 2: 7.045091631234E-03 386s Surface tension*area energy for atom 3: 6.664275867383E-03 386s Surface tension*area energy for atom 4: 6.791214455333E-03 386s Surface tension*area energy for atom 5: 7.108560925209E-03 386s Surface tension*area energy for atom 6: 1.700994289850E-01 386s Surface tension*area energy for atom 7: 1.373641482506E-01 386s Surface tension*area energy for atom 8: 1.700994289850E-01 386s Surface tension*area energy for atom 9: 1.376299286084E-01 386s Surface tension*area energy for atom 10: 1.373641482506E-01 386s Surface tension*area energy for atom 11: 1.694349780905E-01 386s Surface tension*area energy for atom 12: 1.700994289850E-01 386s Surface tension*area energy for atom 13: 1.375413351558E-01 386s Surface tension*area energy for atom 14: 1.374527417032E-01 386s Surface tension*area energy for atom 15: 1.701437257113E-01 386s Surface tension*area energy for atom 16: 1.694792748168E-01 386s Surface tension*area energy for atom 17: 1.374527417032E-01 386s 386s Total surface tension energy: 1.88529 kJ/mol 386s 386s Total solvent accessible volume: 267.435 A^3 386s 386s Total pressure*volume energy: 64.0239 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -5.793234697241E+00 386s WCA energy for atom 1: -5.784370526583E+00 386s WCA energy for atom 2: -5.791799130412E+00 386s WCA energy for atom 3: -5.788504399087E+00 386s WCA energy for atom 4: -5.797319672490E+00 386s WCA energy for atom 5: -5.787358035342E+00 386s WCA energy for atom 6: -1.523887929614E+00 386s WCA energy for atom 7: -1.413678912317E+00 386s WCA energy for atom 8: -1.521751604392E+00 386s WCA energy for atom 9: -1.414741802525E+00 386s WCA energy for atom 10: -1.413367854344E+00 386s WCA energy for atom 11: -1.523407238081E+00 386s WCA energy for atom 12: -1.523000623583E+00 386s WCA energy for atom 13: -1.413922068538E+00 386s WCA energy for atom 14: -1.416316744211E+00 386s WCA energy for atom 15: -1.524577474659E+00 386s WCA energy for atom 16: -1.523300410052E+00 386s WCA energy for atom 17: -1.414522566061E+00 386s 386s Total WCA energy: -52.3691 kJ/mol 386s 386s Total non-polar energy = 1.354016672221E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #4 (solvated-cyclopentane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 9.490526193215E+00 386s SASA for atom 1: 9.512927120500E+00 386s SASA for atom 2: 2.299828534626E+00 386s SASA for atom 3: 1.919012770776E+00 386s SASA for atom 4: 2.307295510388E+00 386s SASA for atom 5: 2.325838699632E+01 386s SASA for atom 6: 2.325838699632E+01 386s SASA for atom 7: 2.045987617019E+01 386s SASA for atom 8: 2.067875411190E+01 386s SASA for atom 9: 2.028790064456E+01 386s SASA for atom 10: 1.897463299431E+01 386s SASA for atom 11: 2.048593306801E+01 386s SASA for atom 12: 2.070481100972E+01 386s 386s Total solvent accessible surface area: 193.638 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 8.066947264233E-02 386s Surface tension*area energy for atom 1: 8.085988052425E-02 386s Surface tension*area energy for atom 2: 1.954854254432E-02 386s Surface tension*area energy for atom 3: 1.631160855160E-02 386s Surface tension*area energy for atom 4: 1.961201183830E-02 386s Surface tension*area energy for atom 5: 1.976962894687E-01 386s Surface tension*area energy for atom 6: 1.976962894687E-01 386s Surface tension*area energy for atom 7: 1.739089474466E-01 386s Surface tension*area energy for atom 8: 1.757694099511E-01 386s Surface tension*area energy for atom 9: 1.724471554788E-01 386s Surface tension*area energy for atom 10: 1.612843804516E-01 386s Surface tension*area energy for atom 11: 1.741304310781E-01 386s Surface tension*area energy for atom 12: 1.759908935826E-01 386s 386s Total surface tension energy: 1.64593 kJ/mol 386s 386s Total solvent accessible volume: 217.998 A^3 386s 386s Total pressure*volume energy: 52.1887 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.343496616804E+00 386s WCA energy for atom 1: -6.327869601807E+00 386s WCA energy for atom 2: -6.334858040579E+00 386s WCA energy for atom 3: -6.296075406417E+00 386s WCA energy for atom 4: -6.345600816761E+00 386s WCA energy for atom 5: -1.663697465126E+00 386s WCA energy for atom 6: -1.662444032853E+00 386s WCA energy for atom 7: -1.572325104493E+00 386s WCA energy for atom 8: -1.604626551065E+00 386s WCA energy for atom 9: -1.586431484963E+00 386s WCA energy for atom 10: -1.554291291374E+00 386s WCA energy for atom 11: -1.574315220751E+00 386s WCA energy for atom 12: -1.604941679892E+00 386s 386s Total WCA energy: -44.471 kJ/mol 386s 386s Total non-polar energy = 9.363673200142E+00 kJ/mol 386s ---------------------------------------- 386s CALCULATION #5 (solvated-ethane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 5.995981536705E+00 386s SASA for atom 1: 5.966113633657E+00 386s SASA for atom 2: 2.121552620704E+01 386s SASA for atom 3: 2.124158310486E+01 386s SASA for atom 4: 2.125200586399E+01 386s SASA for atom 5: 2.123116034573E+01 386s SASA for atom 6: 2.125200586399E+01 386s SASA for atom 7: 2.127285138225E+01 386s 386s Total solvent accessible surface area: 139.427 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 5.096584306199E-02 386s Surface tension*area energy for atom 1: 5.071196588609E-02 386s Surface tension*area energy for atom 2: 1.803319727598E-01 386s Surface tension*area energy for atom 3: 1.805534563913E-01 386s Surface tension*area energy for atom 4: 1.806420498439E-01 386s Surface tension*area energy for atom 5: 1.804648629387E-01 386s Surface tension*area energy for atom 6: 1.806420498439E-01 386s Surface tension*area energy for atom 7: 1.808192367491E-01 386s 386s Total surface tension energy: 1.18513 kJ/mol 386s 386s Total solvent accessible volume: 140.346 A^3 386s 386s Total pressure*volume energy: 33.5988 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -7.360066353115E+00 386s WCA energy for atom 1: -7.355483516201E+00 386s WCA energy for atom 2: -1.776106201066E+00 386s WCA energy for atom 3: -1.773973940651E+00 386s WCA energy for atom 4: -1.775401936843E+00 386s WCA energy for atom 5: -1.773464835521E+00 386s WCA energy for atom 6: -1.774382856097E+00 386s WCA energy for atom 7: -1.772366599434E+00 386s 386s Total WCA energy: -25.3612 kJ/mol 386s 386s Total non-polar energy = 9.422717598546E+00 kJ/mol 386s ---------------------------------------- 386s CALCULATION #6 (solvated-hexane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 4.405515699447E+00 386s SASA for atom 1: 8.213673337951E-01 386s SASA for atom 2: 3.285469335181E-01 386s SASA for atom 3: 2.986790304710E-01 386s SASA for atom 4: 1.855251124959E+01 386s SASA for atom 5: 2.147609518526E+01 386s SASA for atom 6: 1.852645435176E+01 386s SASA for atom 7: 1.655655287639E+01 386s SASA for atom 8: 1.655134149682E+01 386s SASA for atom 9: 1.360170066332E+01 386s SASA for atom 10: 1.357043238593E+01 386s SASA for atom 11: 1.381536722546E+01 386s SASA for atom 12: 1.384142412329E+01 386s SASA for atom 13: 7.765654792245E-01 386s SASA for atom 14: 1.684839013200E+01 386s SASA for atom 15: 1.682233323417E+01 386s SASA for atom 16: 4.166572475070E+00 386s SASA for atom 17: 2.179398933870E+01 386s SASA for atom 18: 1.877660057086E+01 386s SASA for atom 19: 1.876096643216E+01 386s 386s Total solvent accessible surface area: 250.291 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 3.744688344530E-02 386s Surface tension*area energy for atom 1: 6.981622337259E-03 386s Surface tension*area energy for atom 2: 2.792648934903E-03 386s Surface tension*area energy for atom 3: 2.538771759003E-03 386s Surface tension*area energy for atom 4: 1.576963456215E-01 386s Surface tension*area energy for atom 5: 1.825468090747E-01 386s Surface tension*area energy for atom 6: 1.574748619900E-01 386s Surface tension*area energy for atom 7: 1.407306994493E-01 386s Surface tension*area energy for atom 8: 1.406864027230E-01 386s Surface tension*area energy for atom 9: 1.156144556382E-01 386s Surface tension*area energy for atom 10: 1.153486752804E-01 386s Surface tension*area energy for atom 11: 1.174306214164E-01 386s Surface tension*area energy for atom 12: 1.176521050479E-01 386s Surface tension*area energy for atom 13: 6.600806573408E-03 386s Surface tension*area energy for atom 14: 1.432113161220E-01 386s Surface tension*area energy for atom 15: 1.429898324905E-01 386s Surface tension*area energy for atom 16: 3.541586603809E-02 386s Surface tension*area energy for atom 17: 1.852489093789E-01 386s Surface tension*area energy for atom 18: 1.596011048523E-01 386s Surface tension*area energy for atom 19: 1.594682146734E-01 386s 386s Total surface tension energy: 2.12748 kJ/mol 386s 386s Total solvent accessible volume: 298.053 A^3 386s 386s Total pressure*volume energy: 71.3539 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.635406071935E+00 386s WCA energy for atom 1: -5.957247427848E+00 386s WCA energy for atom 2: -5.524801144538E+00 386s WCA energy for atom 3: -5.522294168859E+00 386s WCA energy for atom 4: -1.605314409440E+00 386s WCA energy for atom 5: -1.701051761776E+00 386s WCA energy for atom 6: -1.606669162773E+00 386s WCA energy for atom 7: -1.442505934938E+00 386s WCA energy for atom 8: -1.443059002759E+00 386s WCA energy for atom 9: -1.328947132810E+00 386s WCA energy for atom 10: -1.328906972440E+00 386s WCA energy for atom 11: -1.331566344214E+00 386s WCA energy for atom 12: -1.328041776815E+00 386s WCA energy for atom 13: -5.937562025661E+00 386s WCA energy for atom 14: -1.442277774427E+00 386s WCA energy for atom 15: -1.442777091510E+00 386s WCA energy for atom 16: -6.602262542378E+00 386s WCA energy for atom 17: -1.698172146664E+00 386s WCA energy for atom 18: -1.600970858835E+00 386s WCA energy for atom 19: -1.600841970217E+00 386s 386s Total WCA energy: -57.0807 kJ/mol 386s 386s Total non-polar energy = 1.640068943201E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #7 (solvated-isobutane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 3.464676753463E+00 386s SASA for atom 1: 1.984493338158E+01 386s SASA for atom 2: 1.778643845361E+01 386s SASA for atom 3: 1.671289426332E+01 386s SASA for atom 4: 0.000000000000E+00 386s SASA for atom 5: 3.531879535319E+00 386s SASA for atom 6: 1.673895116114E+01 386s SASA for atom 7: 1.793756846098E+01 386s SASA for atom 8: 1.973549441072E+01 386s SASA for atom 9: 1.710895911022E+01 386s SASA for atom 10: 4.599657069253E+00 386s SASA for atom 11: 1.937069784121E+01 386s SASA for atom 12: 1.654613011726E+01 386s SASA for atom 13: 1.936548646165E+01 386s 386s Total solvent accessible surface area: 192.744 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 2.944975240444E-02 386s Surface tension*area energy for atom 1: 1.686819337434E-01 386s Surface tension*area energy for atom 2: 1.511847268556E-01 386s Surface tension*area energy for atom 3: 1.420596012382E-01 386s Surface tension*area energy for atom 4: 0.000000000000E+00 386s Surface tension*area energy for atom 5: 3.002097605021E-02 386s Surface tension*area energy for atom 6: 1.422810848697E-01 386s Surface tension*area energy for atom 7: 1.524693319183E-01 386s Surface tension*area energy for atom 8: 1.677517024912E-01 386s Surface tension*area energy for atom 9: 1.454261524369E-01 386s Surface tension*area energy for atom 10: 3.909708508865E-02 386s Surface tension*area energy for atom 11: 1.646509316503E-01 386s Surface tension*area energy for atom 12: 1.406421059967E-01 386s Surface tension*area energy for atom 13: 1.646066349240E-01 386s 386s Total surface tension energy: 1.63832 kJ/mol 386s 386s Total solvent accessible volume: 218.943 A^3 386s 386s Total pressure*volume energy: 52.415 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.381016335247E+00 386s WCA energy for atom 1: -1.612317964554E+00 386s WCA energy for atom 2: -1.588013719598E+00 386s WCA energy for atom 3: -1.532162371190E+00 386s WCA energy for atom 4: -5.987950445279E+00 386s WCA energy for atom 5: -6.393089030861E+00 386s WCA energy for atom 6: -1.533454887042E+00 386s WCA energy for atom 7: -1.587650918485E+00 386s WCA energy for atom 8: -1.614083521570E+00 386s WCA energy for atom 9: -1.442402031577E+00 386s WCA energy for atom 10: -6.408813541353E+00 386s WCA energy for atom 11: -1.605830214390E+00 386s WCA energy for atom 12: -1.529385873788E+00 386s WCA energy for atom 13: -1.605662490385E+00 386s 386s Total WCA energy: -40.8218 kJ/mol 386s 386s Total non-polar energy = 1.323144287435E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #8 (solvated-methane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 1.231304303117E+01 386s SASA for atom 1: 2.323233009850E+01 386s SASA for atom 2: 2.345641941977E+01 386s SASA for atom 3: 2.377431357320E+01 386s SASA for atom 4: 2.264344420771E+01 386s 386s Total solvent accessible surface area: 105.42 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 1.046608657649E-01 386s Surface tension*area energy for atom 1: 1.974748058372E-01 386s Surface tension*area energy for atom 2: 1.993795650680E-01 386s Surface tension*area energy for atom 3: 2.020816653722E-01 386s Surface tension*area energy for atom 4: 1.924692757655E-01 386s 386s Total surface tension energy: 0.896066 kJ/mol 386s 386s Total solvent accessible volume: 95.985 A^3 386s 386s Total pressure*volume energy: 22.9788 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -8.133807570805E+00 386s WCA energy for atom 1: -1.962181541765E+00 386s WCA energy for atom 2: -1.964078319162E+00 386s WCA energy for atom 3: -1.963015006647E+00 386s WCA energy for atom 4: -1.957425549100E+00 386s 386s Total WCA energy: -15.9805 kJ/mol 386s 386s Total non-polar energy = 7.894367190329E+00 kJ/mol 386s ---------------------------------------- 386s CALCULATION #9 (solvated-neopentane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 2.441701074100E+00 386s SASA for atom 1: 1.663993494942E+01 386s SASA for atom 2: 1.715586152630E+01 386s SASA for atom 3: 1.645753666466E+01 386s SASA for atom 4: 0.000000000000E+00 386s SASA for atom 5: 2.389432243768E+00 386s SASA for atom 6: 1.638457735076E+01 386s SASA for atom 7: 1.667641460637E+01 386s SASA for atom 8: 1.721839808108E+01 386s SASA for atom 9: 2.419300146815E+00 386s SASA for atom 10: 1.640021148945E+01 386s SASA for atom 11: 1.666599184724E+01 386s SASA for atom 12: 1.719234118325E+01 386s SASA for atom 13: 2.449168049862E+00 386s SASA for atom 14: 1.723403221977E+01 386s SASA for atom 15: 1.639500010989E+01 386s SASA for atom 16: 1.663472356985E+01 386s 386s Total solvent accessible surface area: 210.755 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 2.075445912985E-02 386s Surface tension*area energy for atom 1: 1.414394470700E-01 386s Surface tension*area energy for atom 2: 1.458248229736E-01 386s Surface tension*area energy for atom 3: 1.398890616496E-01 386s Surface tension*area energy for atom 4: 0.000000000000E+00 386s Surface tension*area energy for atom 5: 2.031017407203E-02 386s Surface tension*area energy for atom 6: 1.392689074814E-01 386s Surface tension*area energy for atom 7: 1.417495241541E-01 386s Surface tension*area energy for atom 8: 1.463563836891E-01 386s Surface tension*area energy for atom 9: 2.056405124793E-02 386s Surface tension*area energy for atom 10: 1.394017976603E-01 386s Surface tension*area energy for atom 11: 1.416609307015E-01 386s Surface tension*area energy for atom 12: 1.461349000577E-01 386s Surface tension*area energy for atom 13: 2.081792842383E-02 386s Surface tension*area energy for atom 14: 1.464892738680E-01 386s Surface tension*area energy for atom 15: 1.393575009340E-01 386s Surface tension*area energy for atom 16: 1.413951503437E-01 386s 386s Total surface tension energy: 1.79141 kJ/mol 386s 386s Total solvent accessible volume: 251.127 A^3 386s 386s Total pressure*volume energy: 60.1198 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.011082520236E+00 386s WCA energy for atom 1: -1.497367782613E+00 386s WCA energy for atom 2: -1.498546483218E+00 386s WCA energy for atom 3: -1.492562171495E+00 386s WCA energy for atom 4: -5.447325863939E+00 386s WCA energy for atom 5: -6.004516149175E+00 386s WCA energy for atom 6: -1.492776531092E+00 386s WCA energy for atom 7: -1.496078170066E+00 386s WCA energy for atom 8: -1.501529655270E+00 386s WCA energy for atom 9: -5.996267554365E+00 386s WCA energy for atom 10: -1.492194267752E+00 386s WCA energy for atom 11: -1.496027211216E+00 386s WCA energy for atom 12: -1.500561393960E+00 386s WCA energy for atom 13: -6.000218612907E+00 386s WCA energy for atom 14: -1.500859921426E+00 386s WCA energy for atom 15: -1.492908499790E+00 386s WCA energy for atom 16: -1.494057174414E+00 386s 386s Total WCA energy: -47.4149 kJ/mol 386s 386s Total non-polar energy = 1.449633815052E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #10 (solvated-pentane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 4.405515699447E+00 386s SASA for atom 1: 8.213673337951E-01 386s SASA for atom 2: 3.285469335181E-01 386s SASA for atom 3: 7.466975761774E-01 386s SASA for atom 4: 1.855251124959E+01 386s SASA for atom 5: 2.147609518526E+01 386s SASA for atom 6: 1.852645435176E+01 386s SASA for atom 7: 1.655655287639E+01 386s SASA for atom 8: 1.655134149682E+01 386s SASA for atom 9: 1.360170066332E+01 386s SASA for atom 10: 1.357043238593E+01 386s SASA for atom 11: 1.685881289113E+01 386s SASA for atom 12: 1.687444702982E+01 386s SASA for atom 13: 4.196440378117E+00 386s SASA for atom 14: 1.881308022781E+01 386s SASA for atom 15: 1.882350298694E+01 386s SASA for atom 16: 2.182004623652E+01 386s 386s Total solvent accessible surface area: 222.524 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 3.744688344530E-02 386s Surface tension*area energy for atom 1: 6.981622337259E-03 386s Surface tension*area energy for atom 2: 2.792648934903E-03 386s Surface tension*area energy for atom 3: 6.346929397508E-03 386s Surface tension*area energy for atom 4: 1.576963456215E-01 386s Surface tension*area energy for atom 5: 1.825468090747E-01 386s Surface tension*area energy for atom 6: 1.574748619900E-01 386s Surface tension*area energy for atom 7: 1.407306994493E-01 386s Surface tension*area energy for atom 8: 1.406864027230E-01 386s Surface tension*area energy for atom 9: 1.156144556382E-01 386s Surface tension*area energy for atom 10: 1.153486752804E-01 386s Surface tension*area energy for atom 11: 1.432999095746E-01 386s Surface tension*area energy for atom 12: 1.434327997535E-01 386s Surface tension*area energy for atom 13: 3.566974321399E-02 386s Surface tension*area energy for atom 14: 1.599111819364E-01 386s Surface tension*area energy for atom 15: 1.599997753890E-01 386s Surface tension*area energy for atom 16: 1.854703930104E-01 386s 386s Total surface tension energy: 1.89145 kJ/mol 386s 386s Total solvent accessible volume: 258.93 A^3 386s 386s Total pressure*volume energy: 61.9878 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.655804319869E+00 386s WCA energy for atom 1: -6.027315962813E+00 386s WCA energy for atom 2: -5.696430965386E+00 386s WCA energy for atom 3: -6.016749084714E+00 386s WCA energy for atom 4: -1.608595384643E+00 386s WCA energy for atom 5: -1.703300955380E+00 386s WCA energy for atom 6: -1.609931495887E+00 386s WCA energy for atom 7: -1.457107525189E+00 386s WCA energy for atom 8: -1.457741620594E+00 386s WCA energy for atom 9: -1.354235498709E+00 386s WCA energy for atom 10: -1.354106470090E+00 386s WCA energy for atom 11: -1.456736412636E+00 386s WCA energy for atom 12: -1.455995435596E+00 386s WCA energy for atom 13: -6.633650611186E+00 386s WCA energy for atom 14: -1.605996088477E+00 386s WCA energy for atom 15: -1.606549890103E+00 386s WCA energy for atom 16: -1.700042300035E+00 386s 386s Total WCA energy: -49.4003 kJ/mol 386s 386s Total non-polar energy = 1.447900211546E+01 kJ/mol 386s ---------------------------------------- 386s CALCULATION #11 (solvated-propane): APOLAR 386s 386s Solvent Accessible Surface Area (SASA) for each atom: 386s SASA for atom 0: 3.173464698754E+00 386s SASA for atom 1: 1.931858404557E+01 386s SASA for atom 2: 2.014198201675E+01 386s SASA for atom 3: 2.149694070352E+01 386s SASA for atom 4: 1.904078819252E+00 386s SASA for atom 5: 2.067354273233E+01 386s SASA for atom 6: 1.937590922077E+01 386s SASA for atom 7: 3.098794941136E+00 386s SASA for atom 8: 1.942802301642E+01 386s SASA for atom 9: 1.973028303116E+01 386s SASA for atom 10: 2.204934693736E+01 386s 386s Total solvent accessible surface area: 170.391 A^2 386s 386s Surface tension*area energies (gamma * SASA) for each atom: 386s Surface tension*area energy for atom 0: 2.697444993941E-02 386s Surface tension*area energy for atom 1: 1.642079643873E-01 386s Surface tension*area energy for atom 2: 1.712068471424E-01 386s Surface tension*area energy for atom 3: 1.827239959799E-01 386s Surface tension*area energy for atom 4: 1.618466996365E-02 386s Surface tension*area energy for atom 5: 1.757251132248E-01 386s Surface tension*area energy for atom 6: 1.646952283766E-01 386s Surface tension*area energy for atom 7: 2.633975699966E-02 386s Surface tension*area energy for atom 8: 1.651381956396E-01 386s Surface tension*area energy for atom 9: 1.677074057649E-01 386s Surface tension*area energy for atom 10: 1.874194489675E-01 386s 386s Total surface tension energy: 1.44832 kJ/mol 386s 386s Total solvent accessible volume: 183.573 A^3 386s 386s Total pressure*volume energy: 43.9474 kJ/mol 386s 386s WCA dispersion Energies for each atom: 386s WCA energy for atom 0: -6.818670105515E+00 386s WCA energy for atom 1: -1.641297645338E+00 386s WCA energy for atom 2: -1.649584120441E+00 386s WCA energy for atom 3: -1.711408141255E+00 386s WCA energy for atom 4: -6.624720142882E+00 386s WCA energy for atom 5: -1.610117050515E+00 386s WCA energy for atom 6: -1.596858009746E+00 386s WCA energy for atom 7: -6.816460624835E+00 386s WCA energy for atom 8: -1.642782751806E+00 386s WCA energy for atom 9: -1.645779566650E+00 386s WCA energy for atom 10: -1.714436154542E+00 386s 386s Total WCA energy: -33.4721 kJ/mol 386s 386s Total non-polar energy = 1.192358496286E+01 kJ/mol 386s ---------------------------------------- 386s PRINT STATEMENTS 386s 386s print APOL energy 1 (solvated-2-methylbutane) end 386s Global net APOL energy = 1.439739455792E+01 kJ/mol 386s 386s print APOL energy 2 (solvated-butane) end 386s Global net APOL energy = 1.208346456826E+01 kJ/mol 386s 386s print APOL energy 3 (solvated-cyclohexane) end 386s Global net APOL energy = 1.354016672221E+01 kJ/mol 386s 386s print APOL energy 4 (solvated-cyclopentane) end 386s Global net APOL energy = 9.363673200142E+00 kJ/mol 386s 386s print APOL energy 5 (solvated-ethane) end 386s Global net APOL energy = 9.422717598546E+00 kJ/mol 386s 386s print APOL energy 6 (solvated-hexane) end 386s Global net APOL energy = 1.640068943201E+01 kJ/mol 386s 386s print APOL energy 7 (solvated-isobutane) end 386s Global net APOL energy = 1.323144287435E+01 kJ/mol 386s 386s print APOL energy 8 (solvated-methane) end 386s Global net APOL energy = 7.894367190329E+00 kJ/mol 386s 386s print APOL energy 9 (solvated-neopentane) end 386s Global net APOL energy = 1.449633815052E+01 kJ/mol 386s 386s print APOL energy 10 (solvated-pentane) end 386s Global net APOL energy = 1.447900211546E+01 kJ/mol 386s 386s print APOL energy 11 (solvated-propane) end 386s Global net APOL energy = 1.192358496286E+01 kJ/mol 386s ---------------------------------------- 386s CLEANING UP AND SHUTTING DOWN... 386s Destroying force arrays. 386s No energy arrays to destroy. 386s Destroying multigrid structures. 386s Destroying finite element structures. 386s Destroying 11 molecules 386s Final memory usage: 0.001 MB total, 2.267 MB high water 386s 386s 386s Thanks for using APBS! 386s 386s Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) 386s *** PASSED *** 386s Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) 386s *** PASSED *** 386s Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) 386s *** PASSED *** 386s Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) 386s *** PASSED *** 386s Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) 386s *** PASSED *** 386s Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) 386s *** PASSED *** 386s Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) 386s *** PASSED *** 386s Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) 386s *** PASSED *** 386s Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) 386s *** PASSED *** 386s Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) 386s *** PASSED *** 386s Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) 386s *** PASSED *** 386s Elapsed time: 10.384314 seconds 386s -------------------------------------------------------------------------------- 386s Total elapsed time: 10.384314 seconds 386s Test results have been logged 386s -------------------------------------------------------------------------------- 386s -------------------------------------------------------------------------------- 386s Testing input file 1d7h-dmso-mol.in 386s 397s Checking for intermediate energies in input file alkanes.out 397s EXPECTED COMPUTED: 11 397s EXPECTED EXPECTED: 11 397s COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] 397s 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'] 397s COMPUTED RESULT 14.39739455792 397s COMPUTED RESULT 12.08346456826 397s COMPUTED RESULT 13.54016672221 397s COMPUTED RESULT 9.363673200142 397s COMPUTED RESULT 9.422717598546 397s COMPUTED RESULT 16.40068943201 397s COMPUTED RESULT 13.23144287435 397s COMPUTED RESULT 7.894367190329 397s COMPUTED RESULT 14.49633815052 397s COMPUTED RESULT 14.47900211546 397s COMPUTED RESULT 11.92358496286 397s Running tests for FKBP section 397s BINARY: /usr/bin/apbs 397s INPUT: 1d7h-dmso-mol.in 397s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-mol.in'] 397s asc_getToken: Error occurred (bailing out). 397s Vio_scanf: Format problem with input. 397s 397s 397s ---------------------------------------------------------------------- 397s APBS -- Adaptive Poisson-Boltzmann Solver 397s Version APBS 3.4.1 397s 397s Nathan A. Baker (nathan.baker@pnnl.gov) 397s Pacific Northwest National Laboratory 397s 397s Additional contributing authors listed in the code documentation. 397s 397s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 397s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 397s Northwest Division for the U.S. Department of Energy. 397s 397s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 397s Portions Copyright (c) 2002-2020, Nathan A. Baker. 397s Portions Copyright (c) 1999-2002, The Regents of the University of California. 397s Portions Copyright (c) 1995, Michael Holst. 397s All rights reserved. 397s 397s Redistribution and use in source and binary forms, with or without 397s modification, are permitted provided that the following conditions are met: 397s 397s * Redistributions of source code must retain the above copyright notice, this 397s list of conditions and the following disclaimer. 397s 397s * Redistributions in binary form must reproduce the above copyright notice, 397s this list of conditions and the following disclaimer in the documentation 397s and/or other materials provided with the distribution. 397s 397s * Neither the name of the developer nor the names of its contributors may be 397s used to endorse or promote products derived from this software without 397s specific prior written permission. 397s 397s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 397s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 397s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 397s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 397s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 397s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 397s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 397s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 397s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 397s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 397s ---------------------------------------------------------------------- 397s APBS uses FETK (the Finite Element ToolKit) to solve the 397s Poisson-Boltzmann equation numerically. FETK is a portable collection 397s of finite element modeling class libraries developed by the Michael Holst 397s research group and written in an object-oriented form of C. FEtk is 397s designed to solve general coupled systems of nonlinear partial differential 397s equations using adaptive finite element methods, inexact Newton methods, 397s and algebraic multilevel methods. More information about FEtk may be found 397s at . 397s ---------------------------------------------------------------------- 397s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 397s Aqua is a modified form of the Holst group PMG library 397s which has been modified by Patrice Koehl 397s for improved efficiency and 397s memory usage when solving the Poisson-Boltzmann equation. 397s ---------------------------------------------------------------------- 397s Please cite your use of APBS as: 397s 397s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 397s nanosystems: application to microtubules and the ribosome. Proc. 397s Natl. Acad. Sci. USA 98, 10037-10041 2001. 397s 397s 397s This executable compiled on Jan 3 2025 at 11:01:42 397s 397s Parsing input file 1d7h-dmso-mol.in... 397s rank 0 size 1... 397s Parsed input file. 397s Got paths for 3 molecules 397s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 397s asc_getToken: Error occurred (bailing out). 397s Vio_scanf: Format problem with input. 397s 1673 atoms 397s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 397s Net charge 9.91e-01 e 397s Reading PQR-format atom data from dmso-min.pqr. 397s asc_getToken: Error occurred (bailing out). 397s Vio_scanf: Format problem with input. 397s 10 atoms 397s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 397s Net charge 2.78e-17 e 397s Reading PQR-format atom data from 1d7h-min.pqr. 397s 1663 atoms 397s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 397s Net charge 9.91e-01 e 397s Preparing to run 12 PBE calculations. 397s ---------------------------------------- 397s CALCULATION #1 (complex-solv-coarse): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 30.4176 A 397s Current memory usage: 122.059 MB total, 122.059 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 1.500 x 1.500 x 1.500 397s Grid lengths: 96.000 x 96.000 x 96.000 397s Grid center: (25.875, 18.349, 19.112) 397s Multigrid levels: 5 397s Molecule ID: 1 397s Linearized traditional PBE 397s Multiple Debye-Huckel sphere boundary conditions 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 78.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 1.060899690259E+04 kJ/mol 397s Calculating forces... 397s [focusFillBound()]: WARNING: 397s Unusually large potential values 397s detected on the focusing boundary! 397s Convergence not guaranteed for NPBE/NRPBE calculations! 397s 397s ---------------------------------------- 397s CALCULATION #2 (complex-solv-fine): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 30.4176 A 397s Current memory usage: 122.059 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 0.225 x 0.225 x 0.225 397s Grid lengths: 14.400 x 14.400 x 14.400 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 1 397s Linearized traditional PBE 397s Boundary conditions from focusing 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 78.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 4.276523673491E+04 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #3 (complex-ref-coarse): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 4.87072 A 397s Current memory usage: 122.059 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 1.500 x 1.500 x 1.500 397s Grid lengths: 96.000 x 96.000 x 96.000 397s Grid center: (25.875, 18.349, 19.112) 397s Multigrid levels: 5 397s Molecule ID: 1 397s Linearized traditional PBE 397s Multiple Debye-Huckel sphere boundary conditions 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 2.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 1.399234956777E+04 kJ/mol 397s Calculating forces... 397s [focusFillBound()]: WARNING: 397s Unusually large potential values 397s detected on the focusing boundary! 397s Convergence not guaranteed for NPBE/NRPBE calculations! 397s 397s ---------------------------------------- 397s CALCULATION #4 (complex-ref-fine): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 4.87072 A 397s Current memory usage: 122.059 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 0.225 x 0.225 x 0.225 397s Grid lengths: 14.400 x 14.400 x 14.400 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 1 397s Linearized traditional PBE 397s Boundary conditions from focusing 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 2.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 4.610066575192E+04 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 30.4176 A 397s Current memory usage: 62.428 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 1.500 x 1.500 x 1.500 397s Grid lengths: 96.000 x 96.000 x 96.000 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 2 397s Linearized traditional PBE 397s Multiple Debye-Huckel sphere boundary conditions 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 78.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 3.961107503213E+01 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #6 (dmso-solv-fine): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 30.4176 A 397s Current memory usage: 62.428 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 0.225 x 0.225 x 0.225 397s Grid lengths: 14.400 x 14.400 x 14.400 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 2 397s Linearized traditional PBE 397s Boundary conditions from focusing 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 78.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 7.121048606059E+02 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 4.87072 A 397s Current memory usage: 62.428 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 1.500 x 1.500 x 1.500 397s Grid lengths: 96.000 x 96.000 x 96.000 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 2 397s Linearized traditional PBE 397s Multiple Debye-Huckel sphere boundary conditions 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 2.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 6.751571424823E+01 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #8 (dmso-ref-fine): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 4.87072 A 397s Current memory usage: 62.428 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 0.225 x 0.225 x 0.225 397s Grid lengths: 14.400 x 14.400 x 14.400 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 2 397s Linearized traditional PBE 397s Boundary conditions from focusing 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 2.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 7.339101343121E+02 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 30.4176 A 397s Current memory usage: 121.736 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 1.500 x 1.500 x 1.500 397s Grid lengths: 96.000 x 96.000 x 96.000 397s Grid center: (25.875, 18.349, 19.112) 397s Multigrid levels: 5 397s Molecule ID: 3 397s Linearized traditional PBE 397s Multiple Debye-Huckel sphere boundary conditions 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 78.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 1.058410584089E+04 kJ/mol 397s Calculating forces... 397s [focusFillBound()]: WARNING: 397s Unusually large potential values 397s detected on the focusing boundary! 397s Convergence not guaranteed for NPBE/NRPBE calculations! 397s 397s ---------------------------------------- 397s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 30.4176 A 397s Current memory usage: 121.736 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 0.225 x 0.225 x 0.225 397s Grid lengths: 14.400 x 14.400 x 14.400 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 3 397s Linearized traditional PBE 397s Boundary conditions from focusing 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 78.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 4.205385249581E+04 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 4.87072 A 397s Current memory usage: 121.736 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 1.500 x 1.500 x 1.500 397s Grid lengths: 96.000 x 96.000 x 96.000 397s Grid center: (25.875, 18.349, 19.112) 397s Multigrid levels: 5 397s Molecule ID: 3 397s Linearized traditional PBE 397s Multiple Debye-Huckel sphere boundary conditions 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 2.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 1.395961902233E+04 kJ/mol 397s Calculating forces... 397s [focusFillBound()]: WARNING: 397s Unusually large potential values 397s detected on the focusing boundary! 397s Convergence not guaranteed for NPBE/NRPBE calculations! 397s 397s ---------------------------------------- 397s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 397s Setting up problem... 397s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 397s Debye length: 4.87072 A 397s Current memory usage: 121.736 MB total, 221.696 MB high water 397s Using linear spline charge discretization. 397s Grid dimensions: 65 x 65 x 65 397s Grid spacings: 0.225 x 0.225 x 0.225 397s Grid lengths: 14.400 x 14.400 x 14.400 397s Grid center: (17.751, 17.770, 20.492) 397s Multigrid levels: 5 397s Molecule ID: 3 397s Linearized traditional PBE 397s Boundary conditions from focusing 397s 2 ion species (0.010 M ionic strength): 397s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 397s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 397s Solute dielectric: 2.000 397s Solvent dielectric: 2.000 397s Using "molecular" surface definition; no smoothing 397s Solvent probe radius: 0.000 A 397s Temperature: 300.000 K 397s Electrostatic energies will be calculated 397s Total electrostatic energy = 4.538248433997E+04 kJ/mol 397s Calculating forces... 397s ---------------------------------------- 397s PRINT STATEMENTS 397s 397s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 397s Local net energy (PE 0) = -3.335429017008E+03 kJ/mol 397s Global net ELEC energy = -3.335429017008E+03 kJ/mol 397s 397s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 397s Local net energy (PE 0) = -2.180527370616E+01 kJ/mol 397s Global net ELEC energy = -2.180527370616E+01 kJ/mol 397s 397s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 397s Local net energy (PE 0) = -3.328631844166E+03 kJ/mol 397s Global net ELEC energy = -3.328631844166E+03 kJ/mol 397s 397s 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 397s Local net energy (PE 0) = 1.500810086373E+01 kJ/mol 397s Global net ELEC energy = 1.500810086373E+01 kJ/mol 397s ---------------------------------------- 397s CLEANING UP AND SHUTTING DOWN... 397s Destroying force arrays. 397s No energy arrays to destroy. 397s Destroying multigrid structures. 397s Destroying finite element structures. 397s Destroying 3 molecules 397s Final memory usage: 0.001 MB total, 221.696 MB high water 397s 397s 397s Thanks for using APBS! 397s 397s Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) 397s *** PASSED *** 397s Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) 397s *** PASSED *** 397s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 397s *** PASSED *** 397s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 397s *** PASSED *** 397s Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) 397s *** PASSED *** 397s Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) 397s *** PASSED *** 397s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 397s *** PASSED *** 397s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 397s *** PASSED *** 397s Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) 397s *** PASSED *** 397s Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) 397s *** PASSED *** 397s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 397s *** PASSED *** 397s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 397s *** PASSED *** 397s Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01) 397s *** PASSED *** 397s Elapsed time: 11.045099 seconds 397s -------------------------------------------------------------------------------- 397s -------------------------------------------------------------------------------- 397s Testing input file 1d7h-dmso-smol.in 397s 407s Checking for intermediate energies in input file 1d7h-dmso-mol.out 407s EXPECTED COMPUTED: 16 407s EXPECTED EXPECTED: 16 407s 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] 407s 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'] 407s COMPUTED RESULT 10608.99690259 407s COMPUTED RESULT 42765.23673491 407s COMPUTED RESULT 13992.34956777 407s COMPUTED RESULT 46100.66575192 407s COMPUTED RESULT 39.61107503213 407s COMPUTED RESULT 712.1048606059 407s COMPUTED RESULT 67.51571424823 407s COMPUTED RESULT 733.9101343121 407s COMPUTED RESULT 10584.10584089 407s COMPUTED RESULT 42053.85249581 407s COMPUTED RESULT 13959.61902233 407s COMPUTED RESULT 45382.48433997 407s COMPUTED RESULT -3335.429017008 407s COMPUTED RESULT -21.80527370616 407s COMPUTED RESULT -3328.631844166 407s COMPUTED RESULT 15.00810086373 407s BINARY: /usr/bin/apbs 407s INPUT: 1d7h-dmso-smol.in 407s COMMAND: ['/usr/bin/apbs', '1d7h-dmso-smol.in'] 407s asc_getToken: Error occurred (bailing out). 407s Vio_scanf: Format problem with input. 407s 407s 407s ---------------------------------------------------------------------- 407s APBS -- Adaptive Poisson-Boltzmann Solver 407s Version APBS 3.4.1 407s 407s Nathan A. Baker (nathan.baker@pnnl.gov) 407s Pacific Northwest National Laboratory 407s 407s Additional contributing authors listed in the code documentation. 407s 407s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 407s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 407s Northwest Division for the U.S. Department of Energy. 407s 407s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 407s Portions Copyright (c) 2002-2020, Nathan A. Baker. 407s Portions Copyright (c) 1999-2002, The Regents of the University of California. 407s Portions Copyright (c) 1995, Michael Holst. 407s All rights reserved. 407s 407s Redistribution and use in source and binary forms, with or without 407s modification, are permitted provided that the following conditions are met: 407s 407s * Redistributions of source code must retain the above copyright notice, this 407s list of conditions and the following disclaimer. 407s 407s * Redistributions in binary form must reproduce the above copyright notice, 407s this list of conditions and the following disclaimer in the documentation 407s and/or other materials provided with the distribution. 407s 407s * Neither the name of the developer nor the names of its contributors may be 407s used to endorse or promote products derived from this software without 407s specific prior written permission. 407s 407s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 407s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 407s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 407s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 407s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 407s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 407s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 407s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 407s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 407s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 407s ---------------------------------------------------------------------- 407s APBS uses FETK (the Finite Element ToolKit) to solve the 407s Poisson-Boltzmann equation numerically. FETK is a portable collection 407s of finite element modeling class libraries developed by the Michael Holst 407s research group and written in an object-oriented form of C. FEtk is 407s designed to solve general coupled systems of nonlinear partial differential 407s equations using adaptive finite element methods, inexact Newton methods, 407s and algebraic multilevel methods. More information about FEtk may be found 407s at . 407s ---------------------------------------------------------------------- 407s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 407s Aqua is a modified form of the Holst group PMG library 407s which has been modified by Patrice Koehl 407s for improved efficiency and 407s memory usage when solving the Poisson-Boltzmann equation. 407s ---------------------------------------------------------------------- 407s Please cite your use of APBS as: 407s 407s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 407s nanosystems: application to microtubules and the ribosome. Proc. 407s Natl. Acad. Sci. USA 98, 10037-10041 2001. 407s 407s 407s This executable compiled on Jan 3 2025 at 11:01:42 407s 407s Parsing input file 1d7h-dmso-smol.in... 407s rank 0 size 1... 407s Parsed input file. 407s Got paths for 3 molecules 407s Reading PQR-format atom data from 1d7h-dmso-complex.pqr. 407s asc_getToken: Error occurred (bailing out). 407s Vio_scanf: Format problem with input. 407s 1673 atoms 407s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 407s Net charge 9.91e-01 e 407s Reading PQR-format atom data from dmso-min.pqr. 407s asc_getToken: Error occurred (bailing out). 407s Vio_scanf: Format problem with input. 407s 10 atoms 407s Centered at (1.775e+01, 1.777e+01, 2.049e+01) 407s Net charge 2.78e-17 e 407s Reading PQR-format atom data from 1d7h-min.pqr. 407s 1663 atoms 407s Centered at (2.587e+01, 1.835e+01, 1.911e+01) 407s Net charge 9.91e-01 e 407s Preparing to run 12 PBE calculations. 407s ---------------------------------------- 407s CALCULATION #1 (complex-solv-coarse): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 30.4176 A 407s Current memory usage: 122.059 MB total, 122.059 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 1.500 x 1.500 x 1.500 407s Grid lengths: 96.000 x 96.000 x 96.000 407s Grid center: (25.875, 18.349, 19.112) 407s Multigrid levels: 5 407s Molecule ID: 1 407s Linearized traditional PBE 407s Multiple Debye-Huckel sphere boundary conditions 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 78.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 1.074948704824E+04 kJ/mol 407s Calculating forces... 407s [focusFillBound()]: WARNING: 407s Unusually large potential values 407s detected on the focusing boundary! 407s Convergence not guaranteed for NPBE/NRPBE calculations! 407s 407s ---------------------------------------- 407s CALCULATION #2 (complex-solv-fine): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 30.4176 A 407s Current memory usage: 122.059 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 0.225 x 0.225 x 0.225 407s Grid lengths: 14.400 x 14.400 x 14.400 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 1 407s Linearized traditional PBE 407s Boundary conditions from focusing 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 78.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 4.289487256481E+04 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #3 (complex-ref-coarse): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 4.87072 A 407s Current memory usage: 122.059 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 1.500 x 1.500 x 1.500 407s Grid lengths: 96.000 x 96.000 x 96.000 407s Grid center: (25.875, 18.349, 19.112) 407s Multigrid levels: 5 407s Molecule ID: 1 407s Linearized traditional PBE 407s Multiple Debye-Huckel sphere boundary conditions 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 2.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 1.399234956777E+04 kJ/mol 407s Calculating forces... 407s [focusFillBound()]: WARNING: 407s Unusually large potential values 407s detected on the focusing boundary! 407s Convergence not guaranteed for NPBE/NRPBE calculations! 407s 407s ---------------------------------------- 407s CALCULATION #4 (complex-ref-fine): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 4.87072 A 407s Current memory usage: 122.059 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 0.225 x 0.225 x 0.225 407s Grid lengths: 14.400 x 14.400 x 14.400 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 1 407s Linearized traditional PBE 407s Boundary conditions from focusing 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 2.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 4.610066575192E+04 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #5 (dmso-solv-coarse): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 30.4176 A 407s Current memory usage: 62.428 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 1.500 x 1.500 x 1.500 407s Grid lengths: 96.000 x 96.000 x 96.000 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 2 407s Linearized traditional PBE 407s Multiple Debye-Huckel sphere boundary conditions 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 78.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 3.719709905887E+01 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #6 (dmso-solv-fine): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 30.4176 A 407s Current memory usage: 62.428 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 0.225 x 0.225 x 0.225 407s Grid lengths: 14.400 x 14.400 x 14.400 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 2 407s Linearized traditional PBE 407s Boundary conditions from focusing 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 78.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 7.125747080979E+02 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #7 (dmso-ref-coarse): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 4.87072 A 407s Current memory usage: 62.428 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 1.500 x 1.500 x 1.500 407s Grid lengths: 96.000 x 96.000 x 96.000 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 2 407s Linearized traditional PBE 407s Multiple Debye-Huckel sphere boundary conditions 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 2.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 6.751571424823E+01 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #8 (dmso-ref-fine): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 4.87072 A 407s Current memory usage: 62.428 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 0.225 x 0.225 x 0.225 407s Grid lengths: 14.400 x 14.400 x 14.400 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 2 407s Linearized traditional PBE 407s Boundary conditions from focusing 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 2.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 7.339101343121E+02 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #9 (1d7h-solv-coarse): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 30.4176 A 407s Current memory usage: 121.736 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 1.500 x 1.500 x 1.500 407s Grid lengths: 96.000 x 96.000 x 96.000 407s Grid center: (25.875, 18.349, 19.112) 407s Multigrid levels: 5 407s Molecule ID: 3 407s Linearized traditional PBE 407s Multiple Debye-Huckel sphere boundary conditions 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 78.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 1.071654753674E+04 kJ/mol 407s Calculating forces... 407s [focusFillBound()]: WARNING: 407s Unusually large potential values 407s detected on the focusing boundary! 407s Convergence not guaranteed for NPBE/NRPBE calculations! 407s 407s ---------------------------------------- 407s CALCULATION #10 (1d7h-solv-fine): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 30.4176 A 407s Current memory usage: 121.736 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 0.225 x 0.225 x 0.225 407s Grid lengths: 14.400 x 14.400 x 14.400 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 3 407s Linearized traditional PBE 407s Boundary conditions from focusing 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 78.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 4.218178203716E+04 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s CALCULATION #11 (1d7h-ref-coarse): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 4.87072 A 407s Current memory usage: 121.736 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 1.500 x 1.500 x 1.500 407s Grid lengths: 96.000 x 96.000 x 96.000 407s Grid center: (25.875, 18.349, 19.112) 407s Multigrid levels: 5 407s Molecule ID: 3 407s Linearized traditional PBE 407s Multiple Debye-Huckel sphere boundary conditions 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 2.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 1.395961902233E+04 kJ/mol 407s Calculating forces... 407s [focusFillBound()]: WARNING: 407s Unusually large potential values 407s detected on the focusing boundary! 407s Convergence not guaranteed for NPBE/NRPBE calculations! 407s 407s ---------------------------------------- 407s CALCULATION #12 (1d7h-ref-fine): MULTIGRID 407s Setting up problem... 407s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 407s Debye length: 4.87072 A 407s Current memory usage: 121.736 MB total, 221.696 MB high water 407s Using linear spline charge discretization. 407s Grid dimensions: 65 x 65 x 65 407s Grid spacings: 0.225 x 0.225 x 0.225 407s Grid lengths: 14.400 x 14.400 x 14.400 407s Grid center: (17.751, 17.770, 20.492) 407s Multigrid levels: 5 407s Molecule ID: 3 407s Linearized traditional PBE 407s Boundary conditions from focusing 407s 2 ion species (0.010 M ionic strength): 407s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 407s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 407s Solute dielectric: 2.000 407s Solvent dielectric: 2.000 407s Using "molecular" surface definition;harmonic average smoothing 407s Solvent probe radius: 0.000 A 407s Temperature: 300.000 K 407s Electrostatic energies will be calculated 407s Total electrostatic energy = 4.538248433997E+04 kJ/mol 407s Calculating forces... 407s ---------------------------------------- 407s PRINT STATEMENTS 407s 407s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 407s Local net energy (PE 0) = -3.205793187109E+03 kJ/mol 407s Global net ELEC energy = -3.205793187109E+03 kJ/mol 407s 407s print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end 407s Local net energy (PE 0) = -2.133542621421E+01 kJ/mol 407s Global net ELEC energy = -2.133542621421E+01 kJ/mol 407s 407s print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end 407s Local net energy (PE 0) = -3.200702302816E+03 kJ/mol 407s Global net ELEC energy = -3.200702302816E+03 kJ/mol 407s 407s 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 407s Local net energy (PE 0) = 1.624454192074E+01 kJ/mol 407s Global net ELEC energy = 1.624454192074E+01 kJ/mol 407s ---------------------------------------- 407s CLEANING UP AND SHUTTING DOWN... 407s Destroying force arrays. 407s No energy arrays to destroy. 407s Destroying multigrid structures. 407s Destroying finite element structures. 407s Destroying 3 molecules 407s Final memory usage: 0.001 MB total, 221.696 MB high water 407s 407s 407s Thanks for using APBS! 407s 407s Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) 407s *** PASSED *** 407s Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) 407s *** PASSED *** 407s Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) 407s *** PASSED *** 407s Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) 407s *** PASSED *** 407s Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) 407s *** PASSED *** 407s Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) 407s *** PASSED *** 407s Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) 407s *** PASSED *** 407s Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) 407s *** PASSED *** 407s Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) 407s *** PASSED *** 407s Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) 407s *** PASSED *** 407s Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) 407s *** PASSED *** 407s Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) 407s *** PASSED *** 407s Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01) 407s *** PASSED *** 407s Elapsed time: 9.540746 seconds 407s -------------------------------------------------------------------------------- 407s -------------------------------------------------------------------------------- 407s Testing input file 1d7i-dss-mol.in 407s 417s Checking for intermediate energies in input file 1d7h-dmso-smol.out 417s EXPECTED COMPUTED: 16 417s EXPECTED EXPECTED: 16 417s 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] 417s 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'] 417s COMPUTED RESULT 10749.48704824 417s COMPUTED RESULT 42894.87256481 417s COMPUTED RESULT 13992.34956777 417s COMPUTED RESULT 46100.66575192 417s COMPUTED RESULT 37.19709905887 417s COMPUTED RESULT 712.5747080979 417s COMPUTED RESULT 67.51571424823 417s COMPUTED RESULT 733.9101343121 417s COMPUTED RESULT 10716.54753674 417s COMPUTED RESULT 42181.78203716 417s COMPUTED RESULT 13959.61902233 417s COMPUTED RESULT 45382.48433997 417s COMPUTED RESULT -3205.793187109 417s COMPUTED RESULT -21.33542621421 417s COMPUTED RESULT -3200.702302816 417s COMPUTED RESULT 16.24454192074 417s BINARY: /usr/bin/apbs 417s INPUT: 1d7i-dss-mol.in 417s COMMAND: ['/usr/bin/apbs', '1d7i-dss-mol.in'] 418s asc_getToken: Error occurred (bailing out). 418s Vio_scanf: Format problem with input. 418s 418s 418s ---------------------------------------------------------------------- 418s APBS -- Adaptive Poisson-Boltzmann Solver 418s Version APBS 3.4.1 418s 418s Nathan A. Baker (nathan.baker@pnnl.gov) 418s Pacific Northwest National Laboratory 418s 418s Additional contributing authors listed in the code documentation. 418s 418s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 418s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 418s Northwest Division for the U.S. Department of Energy. 418s 418s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 418s Portions Copyright (c) 2002-2020, Nathan A. Baker. 418s Portions Copyright (c) 1999-2002, The Regents of the University of California. 418s Portions Copyright (c) 1995, Michael Holst. 418s All rights reserved. 418s 418s Redistribution and use in source and binary forms, with or without 418s modification, are permitted provided that the following conditions are met: 418s 418s * Redistributions of source code must retain the above copyright notice, this 418s list of conditions and the following disclaimer. 418s 418s * Redistributions in binary form must reproduce the above copyright notice, 418s this list of conditions and the following disclaimer in the documentation 418s and/or other materials provided with the distribution. 418s 418s * Neither the name of the developer nor the names of its contributors may be 418s used to endorse or promote products derived from this software without 418s specific prior written permission. 418s 418s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 418s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 418s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 418s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 418s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 418s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 418s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 418s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 418s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 418s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 418s ---------------------------------------------------------------------- 418s APBS uses FETK (the Finite Element ToolKit) to solve the 418s Poisson-Boltzmann equation numerically. FETK is a portable collection 418s of finite element modeling class libraries developed by the Michael Holst 418s research group and written in an object-oriented form of C. FEtk is 418s designed to solve general coupled systems of nonlinear partial differential 418s equations using adaptive finite element methods, inexact Newton methods, 418s and algebraic multilevel methods. More information about FEtk may be found 418s at . 418s ---------------------------------------------------------------------- 418s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 418s Aqua is a modified form of the Holst group PMG library 418s which has been modified by Patrice Koehl 418s for improved efficiency and 418s memory usage when solving the Poisson-Boltzmann equation. 418s ---------------------------------------------------------------------- 418s Please cite your use of APBS as: 418s 418s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 418s nanosystems: application to microtubules and the ribosome. Proc. 418s Natl. Acad. Sci. USA 98, 10037-10041 2001. 418s 418s 418s This executable compiled on Jan 3 2025 at 11:01:42 418s 418s Parsing input file 1d7i-dss-mol.in... 418s rank 0 size 1... 418s Parsed input file. 418s Got paths for 3 molecules 418s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 418s asc_getToken: Error occurred (bailing out). 418s Vio_scanf: Format problem with input. 418s 1677 atoms 418s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 418s Net charge 9.91e-01 e 418s Reading PQR-format atom data from dss-min.pqr. 418s asc_getToken: Error occurred (bailing out). 418s Vio_scanf: Format problem with input. 418s 14 atoms 418s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 418s Net charge -8.33e-17 e 418s Reading PQR-format atom data from 1d7i-min.pqr. 418s 1663 atoms 418s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 418s Net charge 9.91e-01 e 418s Preparing to run 12 PBE calculations. 418s ---------------------------------------- 418s CALCULATION #1 (complex-solv-coarse): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 30.4176 A 418s Current memory usage: 122.425 MB total, 122.425 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 1.500 x 1.500 x 1.500 418s Grid lengths: 96.000 x 96.000 x 96.000 418s Grid center: (25.264, 18.988, 19.122) 418s Multigrid levels: 5 418s Molecule ID: 1 418s Linearized traditional PBE 418s Multiple Debye-Huckel sphere boundary conditions 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 78.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 9.160578033846E+03 kJ/mol 418s Calculating forces... 418s [focusFillBound()]: WARNING: 418s Unusually large potential values 418s detected on the focusing boundary! 418s Convergence not guaranteed for NPBE/NRPBE calculations! 418s 418s ---------------------------------------- 418s CALCULATION #2 (complex-solv-fine): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 30.4176 A 418s Current memory usage: 122.425 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 0.225 x 0.225 x 0.225 418s Grid lengths: 14.400 x 14.400 x 14.400 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 1 418s Linearized traditional PBE 418s Boundary conditions from focusing 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 78.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 3.955701871716E+04 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #3 (complex-ref-coarse): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 4.87072 A 418s Current memory usage: 122.425 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 1.500 x 1.500 x 1.500 418s Grid lengths: 96.000 x 96.000 x 96.000 418s Grid center: (25.264, 18.988, 19.122) 418s Multigrid levels: 5 418s Molecule ID: 1 418s Linearized traditional PBE 418s Multiple Debye-Huckel sphere boundary conditions 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 2.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 1.264965939588E+04 kJ/mol 418s Calculating forces... 418s [focusFillBound()]: WARNING: 418s Unusually large potential values 418s detected on the focusing boundary! 418s Convergence not guaranteed for NPBE/NRPBE calculations! 418s 418s ---------------------------------------- 418s CALCULATION #4 (complex-ref-fine): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 4.87072 A 418s Current memory usage: 122.425 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 0.225 x 0.225 x 0.225 418s Grid lengths: 14.400 x 14.400 x 14.400 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 1 418s Linearized traditional PBE 418s Boundary conditions from focusing 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 2.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 4.301801664829E+04 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #5 (dss-solv-coarse): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 30.4176 A 418s Current memory usage: 62.528 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 1.500 x 1.500 x 1.500 418s Grid lengths: 96.000 x 96.000 x 96.000 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 2 418s Linearized traditional PBE 418s Multiple Debye-Huckel sphere boundary conditions 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 78.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 9.431133325426E+01 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #6 (dss-solv-fine): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 30.4176 A 418s Current memory usage: 62.528 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 0.225 x 0.225 x 0.225 418s Grid lengths: 14.400 x 14.400 x 14.400 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 2 418s Linearized traditional PBE 418s Boundary conditions from focusing 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 78.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 1.677348113184E+03 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #7 (dss-ref-coarse): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 4.87072 A 418s Current memory usage: 62.528 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 1.500 x 1.500 x 1.500 418s Grid lengths: 96.000 x 96.000 x 96.000 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 2 418s Linearized traditional PBE 418s Multiple Debye-Huckel sphere boundary conditions 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 2.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 1.171079106781E+02 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #8 (dss-ref-fine): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 4.87072 A 418s Current memory usage: 62.528 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 0.225 x 0.225 x 0.225 418s Grid lengths: 14.400 x 14.400 x 14.400 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 2 418s Linearized traditional PBE 418s Boundary conditions from focusing 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 2.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 1.697869784185E+03 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 30.4176 A 418s Current memory usage: 121.977 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 1.500 x 1.500 x 1.500 418s Grid lengths: 96.000 x 96.000 x 96.000 418s Grid center: (25.264, 18.988, 19.122) 418s Multigrid levels: 5 418s Molecule ID: 3 418s Linearized traditional PBE 418s Multiple Debye-Huckel sphere boundary conditions 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 78.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 9.040108332204E+03 kJ/mol 418s Calculating forces... 418s [focusFillBound()]: WARNING: 418s Unusually large potential values 418s detected on the focusing boundary! 418s Convergence not guaranteed for NPBE/NRPBE calculations! 418s 418s ---------------------------------------- 418s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 30.4176 A 418s Current memory usage: 121.977 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 0.225 x 0.225 x 0.225 418s Grid lengths: 14.400 x 14.400 x 14.400 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 3 418s Linearized traditional PBE 418s Boundary conditions from focusing 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 78.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 3.787747796627E+04 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 4.87072 A 418s Current memory usage: 121.977 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 1.500 x 1.500 x 1.500 418s Grid lengths: 96.000 x 96.000 x 96.000 418s Grid center: (25.264, 18.988, 19.122) 418s Multigrid levels: 5 418s Molecule ID: 3 418s Linearized traditional PBE 418s Multiple Debye-Huckel sphere boundary conditions 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 2.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 1.252495566243E+04 kJ/mol 418s Calculating forces... 418s [focusFillBound()]: WARNING: 418s Unusually large potential values 418s detected on the focusing boundary! 418s Convergence not guaranteed for NPBE/NRPBE calculations! 418s 418s ---------------------------------------- 418s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 418s Setting up problem... 418s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 418s Debye length: 4.87072 A 418s Current memory usage: 121.977 MB total, 222.305 MB high water 418s Using linear spline charge discretization. 418s Grid dimensions: 65 x 65 x 65 418s Grid spacings: 0.225 x 0.225 x 0.225 418s Grid lengths: 14.400 x 14.400 x 14.400 418s Grid center: (17.340, 19.211, 20.503) 418s Multigrid levels: 5 418s Molecule ID: 3 418s Linearized traditional PBE 418s Boundary conditions from focusing 418s 2 ion species (0.010 M ionic strength): 418s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 418s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 418s Solute dielectric: 2.000 418s Solvent dielectric: 2.000 418s Using "molecular" surface definition; no smoothing 418s Solvent probe radius: 0.000 A 418s Temperature: 300.000 K 418s Electrostatic energies will be calculated 418s Total electrostatic energy = 4.133237922574E+04 kJ/mol 418s Calculating forces... 418s ---------------------------------------- 418s PRINT STATEMENTS 418s 418s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 418s Local net energy (PE 0) = -3.460997931137E+03 kJ/mol 418s Global net ELEC energy = -3.460997931137E+03 kJ/mol 418s 418s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 418s Local net energy (PE 0) = -2.052167100108E+01 kJ/mol 418s Global net ELEC energy = -2.052167100108E+01 kJ/mol 418s 418s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 418s Local net energy (PE 0) = -3.454901259473E+03 kJ/mol 418s Global net ELEC energy = -3.454901259473E+03 kJ/mol 418s 418s 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 418s Local net energy (PE 0) = 1.442499933664E+01 kJ/mol 418s Global net ELEC energy = 1.442499933664E+01 kJ/mol 418s ---------------------------------------- 418s CLEANING UP AND SHUTTING DOWN... 418s Destroying force arrays. 418s No energy arrays to destroy. 418s Destroying multigrid structures. 418s Destroying finite element structures. 418s Destroying 3 molecules 418s Final memory usage: 0.001 MB total, 222.305 MB high water 418s 418s 418s Thanks for using APBS! 418s 418s Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) 418s *** PASSED *** 418s Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) 418s *** PASSED *** 418s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 418s *** PASSED *** 418s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 418s *** PASSED *** 418s Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) 418s *** PASSED *** 418s Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) 418s *** PASSED *** 418s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 418s *** PASSED *** 418s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 418s *** PASSED *** 418s Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) 418s *** PASSED *** 418s Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) 418s *** PASSED *** 418s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 418s *** PASSED *** 418s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 418s *** PASSED *** 418s Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01) 418s *** PASSED *** 418s Elapsed time: 10.612711000000001 seconds 418s -------------------------------------------------------------------------------- 418s -------------------------------------------------------------------------------- 418s Testing input file 1d7i-dss-smol.in 418s 427s Checking for intermediate energies in input file 1d7i-dss-mol.out 427s EXPECTED COMPUTED: 16 427s EXPECTED EXPECTED: 16 427s 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] 427s 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'] 427s COMPUTED RESULT 9160.578033846 427s COMPUTED RESULT 39557.01871716 427s COMPUTED RESULT 12649.65939588 427s COMPUTED RESULT 43018.01664829 427s COMPUTED RESULT 94.31133325426 427s COMPUTED RESULT 1677.348113184 427s COMPUTED RESULT 117.1079106781 427s COMPUTED RESULT 1697.869784185 427s COMPUTED RESULT 9040.108332204 427s COMPUTED RESULT 37877.47796627 427s COMPUTED RESULT 12524.95566243 427s COMPUTED RESULT 41332.37922574 427s COMPUTED RESULT -3460.997931137 427s COMPUTED RESULT -20.52167100108 427s COMPUTED RESULT -3454.901259473 427s COMPUTED RESULT 14.42499933664 427s BINARY: /usr/bin/apbs 427s INPUT: 1d7i-dss-smol.in 427s COMMAND: ['/usr/bin/apbs', '1d7i-dss-smol.in'] 427s asc_getToken: Error occurred (bailing out). 427s Vio_scanf: Format problem with input. 427s 427s 427s ---------------------------------------------------------------------- 427s APBS -- Adaptive Poisson-Boltzmann Solver 427s Version APBS 3.4.1 427s 427s Nathan A. Baker (nathan.baker@pnnl.gov) 427s Pacific Northwest National Laboratory 427s 427s Additional contributing authors listed in the code documentation. 427s 427s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 427s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 427s Northwest Division for the U.S. Department of Energy. 427s 427s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 427s Portions Copyright (c) 2002-2020, Nathan A. Baker. 427s Portions Copyright (c) 1999-2002, The Regents of the University of California. 427s Portions Copyright (c) 1995, Michael Holst. 427s All rights reserved. 427s 427s Redistribution and use in source and binary forms, with or without 427s modification, are permitted provided that the following conditions are met: 427s 427s * Redistributions of source code must retain the above copyright notice, this 427s list of conditions and the following disclaimer. 427s 427s * Redistributions in binary form must reproduce the above copyright notice, 427s this list of conditions and the following disclaimer in the documentation 427s and/or other materials provided with the distribution. 427s 427s * Neither the name of the developer nor the names of its contributors may be 427s used to endorse or promote products derived from this software without 427s specific prior written permission. 427s 427s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 427s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 427s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 427s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 427s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 427s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 427s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 427s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 427s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 427s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 427s ---------------------------------------------------------------------- 427s APBS uses FETK (the Finite Element ToolKit) to solve the 427s Poisson-Boltzmann equation numerically. FETK is a portable collection 427s of finite element modeling class libraries developed by the Michael Holst 427s research group and written in an object-oriented form of C. FEtk is 427s designed to solve general coupled systems of nonlinear partial differential 427s equations using adaptive finite element methods, inexact Newton methods, 427s and algebraic multilevel methods. More information about FEtk may be found 427s at . 427s ---------------------------------------------------------------------- 427s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 427s Aqua is a modified form of the Holst group PMG library 427s which has been modified by Patrice Koehl 427s for improved efficiency and 427s memory usage when solving the Poisson-Boltzmann equation. 427s ---------------------------------------------------------------------- 427s Please cite your use of APBS as: 427s 427s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 427s nanosystems: application to microtubules and the ribosome. Proc. 427s Natl. Acad. Sci. USA 98, 10037-10041 2001. 427s 427s 427s This executable compiled on Jan 3 2025 at 11:01:42 427s 427s Parsing input file 1d7i-dss-smol.in... 427s rank 0 size 1... 427s Parsed input file. 427s Got paths for 3 molecules 427s Reading PQR-format atom data from 1d7i-dss-complex.pqr. 427s asc_getToken: Error occurred (bailing out). 427s Vio_scanf: Format problem with input. 427s 1677 atoms 427s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 427s Net charge 9.91e-01 e 427s Reading PQR-format atom data from dss-min.pqr. 427s asc_getToken: Error occurred (bailing out). 427s Vio_scanf: Format problem with input. 427s 14 atoms 427s Centered at (1.734e+01, 1.921e+01, 2.050e+01) 427s Net charge -8.33e-17 e 427s Reading PQR-format atom data from 1d7i-min.pqr. 427s 1663 atoms 427s Centered at (2.526e+01, 1.899e+01, 1.912e+01) 427s Net charge 9.91e-01 e 427s Preparing to run 12 PBE calculations. 427s ---------------------------------------- 427s CALCULATION #1 (complex-solv-coarse): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 30.4176 A 427s Current memory usage: 122.425 MB total, 122.425 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 1.500 x 1.500 x 1.500 427s Grid lengths: 96.000 x 96.000 x 96.000 427s Grid center: (25.264, 18.988, 19.122) 427s Multigrid levels: 5 427s Molecule ID: 1 427s Linearized traditional PBE 427s Multiple Debye-Huckel sphere boundary conditions 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 78.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 9.634884642408E+03 kJ/mol 427s Calculating forces... 427s [focusFillBound()]: WARNING: 427s Unusually large potential values 427s detected on the focusing boundary! 427s Convergence not guaranteed for NPBE/NRPBE calculations! 427s 427s ---------------------------------------- 427s CALCULATION #2 (complex-solv-fine): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 30.4176 A 427s Current memory usage: 122.425 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 0.225 x 0.225 x 0.225 427s Grid lengths: 14.400 x 14.400 x 14.400 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 1 427s Linearized traditional PBE 427s Boundary conditions from focusing 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 78.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 4.003177540425E+04 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #3 (complex-ref-coarse): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 4.87072 A 427s Current memory usage: 122.425 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 1.500 x 1.500 x 1.500 427s Grid lengths: 96.000 x 96.000 x 96.000 427s Grid center: (25.264, 18.988, 19.122) 427s Multigrid levels: 5 427s Molecule ID: 1 427s Linearized traditional PBE 427s Multiple Debye-Huckel sphere boundary conditions 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 2.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 1.264965939588E+04 kJ/mol 427s Calculating forces... 427s [focusFillBound()]: WARNING: 427s Unusually large potential values 427s detected on the focusing boundary! 427s Convergence not guaranteed for NPBE/NRPBE calculations! 427s 427s ---------------------------------------- 427s CALCULATION #4 (complex-ref-fine): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 4.87072 A 427s Current memory usage: 122.425 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 0.225 x 0.225 x 0.225 427s Grid lengths: 14.400 x 14.400 x 14.400 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 1 427s Linearized traditional PBE 427s Boundary conditions from focusing 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 2.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 4.301801664829E+04 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #5 (dss-solv-coarse): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 30.4176 A 427s Current memory usage: 62.528 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 1.500 x 1.500 x 1.500 427s Grid lengths: 96.000 x 96.000 x 96.000 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 2 427s Linearized traditional PBE 427s Multiple Debye-Huckel sphere boundary conditions 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 78.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 7.942232645345E+01 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #6 (dss-solv-fine): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 30.4176 A 427s Current memory usage: 62.528 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 0.225 x 0.225 x 0.225 427s Grid lengths: 14.400 x 14.400 x 14.400 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 2 427s Linearized traditional PBE 427s Boundary conditions from focusing 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 78.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 1.677798535473E+03 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #7 (dss-ref-coarse): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 4.87072 A 427s Current memory usage: 62.528 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 1.500 x 1.500 x 1.500 427s Grid lengths: 96.000 x 96.000 x 96.000 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 2 427s Linearized traditional PBE 427s Multiple Debye-Huckel sphere boundary conditions 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 2.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 1.171079106781E+02 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #8 (dss-ref-fine): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 4.87072 A 427s Current memory usage: 62.528 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 0.225 x 0.225 x 0.225 427s Grid lengths: 14.400 x 14.400 x 14.400 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 2 427s Linearized traditional PBE 427s Boundary conditions from focusing 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 2.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 1.697869784185E+03 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #9 (1d7i-solv-coarse): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 30.4176 A 427s Current memory usage: 121.977 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 1.500 x 1.500 x 1.500 427s Grid lengths: 96.000 x 96.000 x 96.000 427s Grid center: (25.264, 18.988, 19.122) 427s Multigrid levels: 5 427s Molecule ID: 3 427s Linearized traditional PBE 427s Multiple Debye-Huckel sphere boundary conditions 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 78.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 9.507068451372E+03 kJ/mol 427s Calculating forces... 427s [focusFillBound()]: WARNING: 427s Unusually large potential values 427s detected on the focusing boundary! 427s Convergence not guaranteed for NPBE/NRPBE calculations! 427s 427s ---------------------------------------- 427s CALCULATION #10 (1d7i-solv-fine): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 30.4176 A 427s Current memory usage: 121.977 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 0.225 x 0.225 x 0.225 427s Grid lengths: 14.400 x 14.400 x 14.400 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 3 427s Linearized traditional PBE 427s Boundary conditions from focusing 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 78.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 3.835075772299E+04 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s CALCULATION #11 (1d7i-ref-coarse): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 4.87072 A 427s Current memory usage: 121.977 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 1.500 x 1.500 x 1.500 427s Grid lengths: 96.000 x 96.000 x 96.000 427s Grid center: (25.264, 18.988, 19.122) 427s Multigrid levels: 5 427s Molecule ID: 3 427s Linearized traditional PBE 427s Multiple Debye-Huckel sphere boundary conditions 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 2.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 1.252495566243E+04 kJ/mol 427s Calculating forces... 427s [focusFillBound()]: WARNING: 427s Unusually large potential values 427s detected on the focusing boundary! 427s Convergence not guaranteed for NPBE/NRPBE calculations! 427s 427s ---------------------------------------- 427s CALCULATION #12 (1d7i-ref-fine): MULTIGRID 427s Setting up problem... 427s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 427s Debye length: 4.87072 A 427s Current memory usage: 121.977 MB total, 222.305 MB high water 427s Using linear spline charge discretization. 427s Grid dimensions: 65 x 65 x 65 427s Grid spacings: 0.225 x 0.225 x 0.225 427s Grid lengths: 14.400 x 14.400 x 14.400 427s Grid center: (17.340, 19.211, 20.503) 427s Multigrid levels: 5 427s Molecule ID: 3 427s Linearized traditional PBE 427s Boundary conditions from focusing 427s 2 ion species (0.010 M ionic strength): 427s 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 427s 2.000 A-radius, -1.000 e-charge, 0.010 M concentration 427s Solute dielectric: 2.000 427s Solvent dielectric: 2.000 427s Using "molecular" surface definition;harmonic average smoothing 427s Solvent probe radius: 0.000 A 427s Temperature: 300.000 K 427s Electrostatic energies will be calculated 427s Total electrostatic energy = 4.133237922574E+04 kJ/mol 427s Calculating forces... 427s ---------------------------------------- 427s PRINT STATEMENTS 427s 427s print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end 427s Local net energy (PE 0) = -2.986241244040E+03 kJ/mol 427s Global net ELEC energy = -2.986241244040E+03 kJ/mol 427s 427s print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end 427s Local net energy (PE 0) = -2.007124871262E+01 kJ/mol 427s Global net ELEC energy = -2.007124871262E+01 kJ/mol 427s 427s print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end 427s Local net energy (PE 0) = -2.981621502756E+03 kJ/mol 427s Global net ELEC energy = -2.981621502756E+03 kJ/mol 427s 427s 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 427s Local net energy (PE 0) = 1.545150742843E+01 kJ/mol 427s Global net ELEC energy = 1.545150742843E+01 kJ/mol 427s ---------------------------------------- 427s CLEANING UP AND SHUTTING DOWN... 427s Destroying force arrays. 427s No energy arrays to destroy. 427s Destroying multigrid structures. 427s Destroying finite element structures. 427s Destroying 3 molecules 427s Final memory usage: 0.001 MB total, 222.305 MB high water 427s 427s 427s Thanks for using APBS! 427s 427s Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) 427s *** PASSED *** 427s Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) 427s *** PASSED *** 427s Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) 427s *** PASSED *** 427s Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) 427s *** PASSED *** 427s Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) 427s *** PASSED *** 427s Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) 427s *** PASSED *** 427s Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) 427s *** PASSED *** 427s Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) 427s *** PASSED *** 427s Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) 427s *** PASSED *** 427s Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) 427s *** PASSED *** 427s Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) 427s *** PASSED *** 427s Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) 427s *** PASSED *** 427s Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01) 427s *** PASSED *** 427s Elapsed time: 9.194619 seconds 427s -------------------------------------------------------------------------------- 427s Total elapsed time: 40.393175 seconds 427s Test results have been logged 427s -------------------------------------------------------------------------------- 427s -------------------------------------------------------------------------------- 427s Testing input file apbs-mol.in 427s 436s Checking for intermediate energies in input file 1d7i-dss-smol.out 436s EXPECTED COMPUTED: 16 436s EXPECTED EXPECTED: 16 436s 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] 436s 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'] 436s COMPUTED RESULT 9634.884642408 436s COMPUTED RESULT 40031.77540425 436s COMPUTED RESULT 12649.65939588 436s COMPUTED RESULT 43018.01664829 436s COMPUTED RESULT 79.42232645345 436s COMPUTED RESULT 1677.798535473 436s COMPUTED RESULT 117.1079106781 436s COMPUTED RESULT 1697.869784185 436s COMPUTED RESULT 9507.068451372 436s COMPUTED RESULT 38350.75772299 436s COMPUTED RESULT 12524.95566243 436s COMPUTED RESULT 41332.37922574 436s COMPUTED RESULT -2986.24124404 436s COMPUTED RESULT -20.07124871262 436s COMPUTED RESULT -2981.621502756 436s COMPUTED RESULT 15.45150742843 436s Running tests for hca-bind section 436s BINARY: /usr/bin/apbs 436s INPUT: apbs-mol.in 436s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 436s asc_getToken: Error occurred (bailing out). 436s Vio_scanf: Format problem with input. 436s 436s 436s ---------------------------------------------------------------------- 436s APBS -- Adaptive Poisson-Boltzmann Solver 436s Version APBS 3.4.1 436s 436s Nathan A. Baker (nathan.baker@pnnl.gov) 436s Pacific Northwest National Laboratory 436s 436s Additional contributing authors listed in the code documentation. 436s 436s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 436s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 436s Northwest Division for the U.S. Department of Energy. 436s 436s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 436s Portions Copyright (c) 2002-2020, Nathan A. Baker. 436s Portions Copyright (c) 1999-2002, The Regents of the University of California. 436s Portions Copyright (c) 1995, Michael Holst. 436s All rights reserved. 436s 436s Redistribution and use in source and binary forms, with or without 436s modification, are permitted provided that the following conditions are met: 436s 436s * Redistributions of source code must retain the above copyright notice, this 436s list of conditions and the following disclaimer. 436s 436s * Redistributions in binary form must reproduce the above copyright notice, 436s this list of conditions and the following disclaimer in the documentation 436s and/or other materials provided with the distribution. 436s 436s * Neither the name of the developer nor the names of its contributors may be 436s used to endorse or promote products derived from this software without 436s specific prior written permission. 436s 436s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 436s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 436s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 436s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 436s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 436s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 436s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 436s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 436s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 436s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 436s ---------------------------------------------------------------------- 436s APBS uses FETK (the Finite Element ToolKit) to solve the 436s Poisson-Boltzmann equation numerically. FETK is a portable collection 436s of finite element modeling class libraries developed by the Michael Holst 436s research group and written in an object-oriented form of C. FEtk is 436s designed to solve general coupled systems of nonlinear partial differential 436s equations using adaptive finite element methods, inexact Newton methods, 436s and algebraic multilevel methods. More information about FEtk may be found 436s at . 436s ---------------------------------------------------------------------- 436s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 436s Aqua is a modified form of the Holst group PMG library 436s which has been modified by Patrice Koehl 436s for improved efficiency and 436s memory usage when solving the Poisson-Boltzmann equation. 436s ---------------------------------------------------------------------- 436s Please cite your use of APBS as: 436s 436s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 436s nanosystems: application to microtubules and the ribosome. Proc. 436s Natl. Acad. Sci. USA 98, 10037-10041 2001. 436s 436s 436s This executable compiled on Jan 3 2025 at 11:01:42 436s 436s Parsing input file apbs-mol.in... 436s rank 0 size 1... 436s Parsed input file. 436s Got paths for 3 molecules 436s Reading PQR-format atom data from acet.pqr. 436s asc_getToken: Error occurred (bailing out). 436s Vio_scanf: Format problem with input. 436s 18 atoms 436s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 436s Net charge -1.00e+00 e 436s Reading PQR-format atom data from hca.pqr. 436s asc_getToken: Error occurred (bailing out). 436s Vio_scanf: Format problem with input. 436s 2482 atoms 436s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 436s Net charge 1.00e+00 e 436s Reading PQR-format atom data from complex.pqr. 436s 2500 atoms 436s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 436s Net charge -1.02e-14 e 436s Preparing to run 9 PBE calculations. 436s ---------------------------------------- 436s CALCULATION #1 (acet): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 62.727 MB total, 62.727 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 1.500 x 1.500 x 1.500 436s Grid lengths: 96.000 x 96.000 x 96.000 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 1 436s Linearized traditional PBE 436s Single Debye-Huckel sphere boundary conditions 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 2.213600726771E+02 kJ/mol 436s Calculating forces... 436s ---------------------------------------- 436s CALCULATION #2 (acet): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 62.727 MB total, 123.701 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 0.581 x 0.581 x 0.581 436s Grid lengths: 37.181 x 37.181 x 37.181 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 1 436s Linearized traditional PBE 436s Boundary conditions from focusing 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 1.825764811255E+03 kJ/mol 436s Calculating forces... 436s ---------------------------------------- 436s CALCULATION #3 (acet): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 62.727 MB total, 123.701 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 0.225 x 0.225 x 0.225 436s Grid lengths: 14.400 x 14.400 x 14.400 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 1 436s Linearized traditional PBE 436s Boundary conditions from focusing 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 6.458471211905E+03 kJ/mol 436s Calculating forces... 436s ---------------------------------------- 436s CALCULATION #4 (hca): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 146.516 MB total, 146.516 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 1.500 x 1.500 x 1.500 436s Grid lengths: 96.000 x 96.000 x 96.000 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 2 436s Linearized traditional PBE 436s Single Debye-Huckel sphere boundary conditions 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 2.093606095527E+04 kJ/mol 436s Calculating forces... 436s [focusFillBound()]: WARNING: 436s Unusually large potential values 436s detected on the focusing boundary! 436s Convergence not guaranteed for NPBE/NRPBE calculations! 436s 436s ---------------------------------------- 436s CALCULATION #5 (hca): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 146.516 MB total, 245.092 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 0.581 x 0.581 x 0.581 436s Grid lengths: 37.181 x 37.181 x 37.181 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 2 436s Linearized traditional PBE 436s Boundary conditions from focusing 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 1.515433544464E+05 kJ/mol 436s Calculating forces... 436s [focusFillBound()]: WARNING: 436s Unusually large potential values 436s detected on the focusing boundary! 436s Convergence not guaranteed for NPBE/NRPBE calculations! 436s 436s ---------------------------------------- 436s CALCULATION #6 (hca): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 146.516 MB total, 245.092 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 0.225 x 0.225 x 0.225 436s Grid lengths: 14.400 x 14.400 x 14.400 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 2 436s Linearized traditional PBE 436s Boundary conditions from focusing 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 1.786369323561E+05 kJ/mol 436s Calculating forces... 436s ---------------------------------------- 436s CALCULATION #7 (complex): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 146.926 MB total, 245.092 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 1.500 x 1.500 x 1.500 436s Grid lengths: 96.000 x 96.000 x 96.000 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 3 436s Linearized traditional PBE 436s Single Debye-Huckel sphere boundary conditions 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 2.105322784838E+04 kJ/mol 436s Calculating forces... 436s [focusFillBound()]: WARNING: 436s Unusually large potential values 436s detected on the focusing boundary! 436s Convergence not guaranteed for NPBE/NRPBE calculations! 436s 436s ---------------------------------------- 436s CALCULATION #8 (complex): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 146.926 MB total, 245.725 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 0.581 x 0.581 x 0.581 436s Grid lengths: 37.181 x 37.181 x 37.181 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 3 436s Linearized traditional PBE 436s Boundary conditions from focusing 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 1.533304996252E+05 kJ/mol 436s Calculating forces... 436s [focusFillBound()]: WARNING: 436s Unusually large potential values 436s detected on the focusing boundary! 436s Convergence not guaranteed for NPBE/NRPBE calculations! 436s 436s ---------------------------------------- 436s CALCULATION #9 (complex): MULTIGRID 436s Setting up problem... 436s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 436s Debye length: 0 A 436s Current memory usage: 146.926 MB total, 245.725 MB high water 436s Using linear spline charge discretization. 436s Grid dimensions: 65 x 65 x 65 436s Grid spacings: 0.225 x 0.225 x 0.225 436s Grid lengths: 14.400 x 14.400 x 14.400 436s Grid center: (-6.028, 3.898, 15.179) 436s Multigrid levels: 5 436s Molecule ID: 3 436s Linearized traditional PBE 436s Boundary conditions from focusing 436s 2 ion species (0.000 M ionic strength): 436s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 436s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 436s Solute dielectric: 2.000 436s Solvent dielectric: 78.540 436s Using "molecular" surface definition; no smoothing 436s Solvent probe radius: 0.000 A 436s Temperature: 298.150 K 436s Electrostatic energies will be calculated 436s Total electrostatic energy = 1.850429388099E+05 kJ/mol 436s Calculating forces... 436s ---------------------------------------- 436s PRINT STATEMENTS 436s 436s print energy 3 (complex) - 1 (acet) - 2 (hca) end 436s Local net energy (PE 0) = -5.246475812684E+01 kJ/mol 436s Global net ELEC energy = -5.246475812684E+01 kJ/mol 436s ---------------------------------------- 436s CLEANING UP AND SHUTTING DOWN... 436s Destroying force arrays. 436s No energy arrays to destroy. 436s Destroying multigrid structures. 436s Destroying finite element structures. 436s Destroying 3 molecules 436s Final memory usage: 0.001 MB total, 245.725 MB high water 436s 436s 436s Thanks for using APBS! 436s 436s Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) 436s *** PASSED *** 436s Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) 436s *** PASSED *** 436s Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) 436s *** PASSED *** 436s Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) 436s *** PASSED *** 436s Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) 436s *** PASSED *** 436s Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) 436s *** PASSED *** 436s Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) 436s *** PASSED *** 436s Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) 436s *** PASSED *** 436s Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) 436s *** PASSED *** 436s Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01) 436s *** PASSED *** 436s Elapsed time: 9.477113 seconds 436s -------------------------------------------------------------------------------- 436s -------------------------------------------------------------------------------- 436s Testing input file apbs-smol.in 436s 444s Checking for intermediate energies in input file apbs-mol.out 444s EXPECTED COMPUTED: 10 444s EXPECTED EXPECTED: 10 444s COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812684] 444s 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'] 444s COMPUTED RESULT 221.3600726771 444s COMPUTED RESULT 1825.764811255 444s COMPUTED RESULT 6458.471211905 444s COMPUTED RESULT 20936.06095527 444s COMPUTED RESULT 151543.3544464 444s COMPUTED RESULT 178636.9323561 444s COMPUTED RESULT 21053.22784838 444s COMPUTED RESULT 153330.4996252 444s COMPUTED RESULT 185042.9388099 444s COMPUTED RESULT -52.46475812684 444s BINARY: /usr/bin/apbs 444s INPUT: apbs-smol.in 444s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 444s Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) 444s *** PASSED *** 444s Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) 444s *** PASSED *** 444s Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) 444s *** PASSED *** 444s Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) 444s *** PASSED *** 444s Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) 444s *** PASSED *** 444s Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) 444s *** PASSED *** 444s Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) 444s *** PASSED *** 444s Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) 444s *** PASSED *** 444s Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) 444s *** PASSED *** 444s Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01) 444s *** PASSED *** 444s Elapsed time: 8.040716 seconds 444s -------------------------------------------------------------------------------- 444s Total elapsed time: 17.517829 seconds 444s Test results have been logged 444s -------------------------------------------------------------------------------- 444s -------------------------------------------------------------------------------- 444s Testing input file apbs-mol.in 444s 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 444s 444s ---------------------------------------------------------------------- 444s APBS -- Adaptive Poisson-Boltzmann Solver 444s Version APBS 3.4.1 444s 444s Nathan A. Baker (nathan.baker@pnnl.gov) 444s Pacific Northwest National Laboratory 444s 444s Additional contributing authors listed in the code documentation. 444s 444s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 444s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 444s Northwest Division for the U.S. Department of Energy. 444s 444s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 444s Portions Copyright (c) 2002-2020, Nathan A. Baker. 444s Portions Copyright (c) 1999-2002, The Regents of the University of California. 444s Portions Copyright (c) 1995, Michael Holst. 444s All rights reserved. 444s 444s Redistribution and use in source and binary forms, with or without 444s modification, are permitted provided that the following conditions are met: 444s 444s * Redistributions of source code must retain the above copyright notice, this 444s list of conditions and the following disclaimer. 444s 444s * Redistributions in binary form must reproduce the above copyright notice, 444s this list of conditions and the following disclaimer in the documentation 444s and/or other materials provided with the distribution. 444s 444s * Neither the name of the developer nor the names of its contributors may be 444s used to endorse or promote products derived from this software without 444s specific prior written permission. 444s 444s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 444s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 444s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 444s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 444s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 444s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 444s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 444s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 444s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 444s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 444s ---------------------------------------------------------------------- 444s APBS uses FETK (the Finite Element ToolKit) to solve the 444s Poisson-Boltzmann equation numerically. FETK is a portable collection 444s of finite element modeling class libraries developed by the Michael Holst 444s research group and written in an object-oriented form of C. FEtk is 444s designed to solve general coupled systems of nonlinear partial differential 444s equations using adaptive finite element methods, inexact Newton methods, 444s and algebraic multilevel methods. More information about FEtk may be found 444s at . 444s ---------------------------------------------------------------------- 444s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 444s Aqua is a modified form of the Holst group PMG library 444s which has been modified by Patrice Koehl 444s for improved efficiency and 444s memory usage when solving the Poisson-Boltzmann equation. 444s ---------------------------------------------------------------------- 444s Please cite your use of APBS as: 444s 444s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 444s nanosystems: application to microtubules and the ribosome. Proc. 444s Natl. Acad. Sci. USA 98, 10037-10041 2001. 444s 444s 444s This executable compiled on Jan 3 2025 at 11:01:42 444s 444s Parsing input file apbs-smol.in... 444s rank 0 size 1... 444s Parsed input file. 444s Got paths for 3 molecules 444s Reading PQR-format atom data from acet.pqr. 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 18 atoms 444s Centered at (-6.028e+00, 3.898e+00, 1.518e+01) 444s Net charge -1.00e+00 e 444s Reading PQR-format atom data from hca.pqr. 444s asc_getToken: Error occurred (bailing out). 444s Vio_scanf: Format problem with input. 444s 2482 atoms 444s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 444s Net charge 1.00e+00 e 444s Reading PQR-format atom data from complex.pqr. 444s 2500 atoms 444s Centered at (-7.196e+00, 4.070e-01, 1.704e+01) 444s Net charge -1.02e-14 e 444s Preparing to run 9 PBE calculations. 444s ---------------------------------------- 444s CALCULATION #1 (acet): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 62.727 MB total, 62.727 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 1.500 x 1.500 x 1.500 444s Grid lengths: 96.000 x 96.000 x 96.000 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 1 444s Linearized traditional PBE 444s Single Debye-Huckel sphere boundary conditions 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.884888131017E+02 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #2 (acet): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 62.727 MB total, 123.701 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.581 x 0.581 x 0.581 444s Grid lengths: 37.181 x 37.181 x 37.181 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 1 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.820045922544E+03 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #3 (acet): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 62.727 MB total, 123.701 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.225 x 0.225 x 0.225 444s Grid lengths: 14.400 x 14.400 x 14.400 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 1 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 6.460002606908E+03 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #4 (hca): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 146.516 MB total, 146.516 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 1.500 x 1.500 x 1.500 444s Grid lengths: 96.000 x 96.000 x 96.000 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 2 444s Linearized traditional PBE 444s Single Debye-Huckel sphere boundary conditions 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 2.189161497021E+04 kJ/mol 444s Calculating forces... 444s [focusFillBound()]: WARNING: 444s Unusually large potential values 444s detected on the focusing boundary! 444s Convergence not guaranteed for NPBE/NRPBE calculations! 444s 444s ---------------------------------------- 444s CALCULATION #5 (hca): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 146.516 MB total, 245.092 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.581 x 0.581 x 0.581 444s Grid lengths: 37.181 x 37.181 x 37.181 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 2 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.520000494925E+05 kJ/mol 444s Calculating forces... 444s [focusFillBound()]: WARNING: 444s Unusually large potential values 444s detected on the focusing boundary! 444s Convergence not guaranteed for NPBE/NRPBE calculations! 444s 444s ---------------------------------------- 444s CALCULATION #6 (hca): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 146.516 MB total, 245.092 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.225 x 0.225 x 0.225 444s Grid lengths: 14.400 x 14.400 x 14.400 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 2 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.790436191580E+05 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s CALCULATION #7 (complex): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 146.926 MB total, 245.092 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 1.500 x 1.500 x 1.500 444s Grid lengths: 96.000 x 96.000 x 96.000 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 3 444s Linearized traditional PBE 444s Single Debye-Huckel sphere boundary conditions 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 2.195842512312E+04 kJ/mol 444s Calculating forces... 444s [focusFillBound()]: WARNING: 444s Unusually large potential values 444s detected on the focusing boundary! 444s Convergence not guaranteed for NPBE/NRPBE calculations! 444s 444s ---------------------------------------- 444s CALCULATION #8 (complex): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 146.926 MB total, 245.725 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.581 x 0.581 x 0.581 444s Grid lengths: 37.181 x 37.181 x 37.181 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 3 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.537771604355E+05 kJ/mol 444s Calculating forces... 444s [focusFillBound()]: WARNING: 444s Unusually large potential values 444s detected on the focusing boundary! 444s Convergence not guaranteed for NPBE/NRPBE calculations! 444s 444s ---------------------------------------- 444s CALCULATION #9 (complex): MULTIGRID 444s Setting up problem... 444s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 444s Debye length: 0 A 444s Current memory usage: 146.926 MB total, 245.725 MB high water 444s Using linear spline charge discretization. 444s Grid dimensions: 65 x 65 x 65 444s Grid spacings: 0.225 x 0.225 x 0.225 444s Grid lengths: 14.400 x 14.400 x 14.400 444s Grid center: (-6.028, 3.898, 15.179) 444s Multigrid levels: 5 444s Molecule ID: 3 444s Linearized traditional PBE 444s Boundary conditions from focusing 444s 2 ion species (0.000 M ionic strength): 444s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 444s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 444s Solute dielectric: 2.000 444s Solvent dielectric: 78.540 444s Using "molecular" surface definition;harmonic average smoothing 444s Solvent probe radius: 0.000 A 444s Temperature: 298.150 K 444s Electrostatic energies will be calculated 444s Total electrostatic energy = 1.854495619747E+05 kJ/mol 444s Calculating forces... 444s ---------------------------------------- 444s PRINT STATEMENTS 444s 444s print energy 3 (complex) - 1 (acet) - 2 (hca) end 444s Local net energy (PE 0) = -5.405979017059E+01 kJ/mol 444s Global net ELEC energy = -5.405979017059E+01 kJ/mol 444s ---------------------------------------- 444s CLEANING UP AND SHUTTING DOWN... 444s Destroying force arrays. 444s No energy arrays to destroy. 444s Destroying multigrid structures. 444s Destroying finite element structures. 444s Destroying 3 molecules 444s Final memory usage: 0.001 MB total, 245.725 MB high water 444s 444s 444s Thanks for using APBS! 444s 449s Checking for intermediate energies in input file apbs-smol.out 449s EXPECTED COMPUTED: 10 449s EXPECTED EXPECTED: 10 449s COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017059] 449s 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'] 449s COMPUTED RESULT 188.4888131017 449s COMPUTED RESULT 1820.045922544 449s COMPUTED RESULT 6460.002606908 449s COMPUTED RESULT 21891.61497021 449s COMPUTED RESULT 152000.0494925 449s COMPUTED RESULT 179043.619158 449s COMPUTED RESULT 21958.42512312 449s COMPUTED RESULT 153777.1604355 449s COMPUTED RESULT 185449.5619747 449s COMPUTED RESULT -54.05979017059 449s Running tests for ionize section 449s BINARY: /usr/bin/apbs 449s INPUT: apbs-mol.in 449s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 449s asc_getToken: Error occurred (bailing out). 449s Vio_scanf: Format problem with input. 449s 449s 449s ---------------------------------------------------------------------- 449s APBS -- Adaptive Poisson-Boltzmann Solver 449s Version APBS 3.4.1 449s 449s Nathan A. Baker (nathan.baker@pnnl.gov) 449s Pacific Northwest National Laboratory 449s 449s Additional contributing authors listed in the code documentation. 449s 449s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 449s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 449s Northwest Division for the U.S. Department of Energy. 449s 449s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 449s Portions Copyright (c) 2002-2020, Nathan A. Baker. 449s Portions Copyright (c) 1999-2002, The Regents of the University of California. 449s Portions Copyright (c) 1995, Michael Holst. 449s All rights reserved. 449s 449s Redistribution and use in source and binary forms, with or without 449s modification, are permitted provided that the following conditions are met: 449s 449s * Redistributions of source code must retain the above copyright notice, this 449s list of conditions and the following disclaimer. 449s 449s * Redistributions in binary form must reproduce the above copyright notice, 449s this list of conditions and the following disclaimer in the documentation 449s and/or other materials provided with the distribution. 449s 449s * Neither the name of the developer nor the names of its contributors may be 449s used to endorse or promote products derived from this software without 449s specific prior written permission. 449s 449s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 449s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 449s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 449s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 449s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 449s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 449s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 449s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 449s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 449s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 449s ---------------------------------------------------------------------- 449s APBS uses FETK (the Finite Element ToolKit) to solve the 449s Poisson-Boltzmann equation numerically. FETK is a portable collection 449s of finite element modeling class libraries developed by the Michael Holst 449s research group and written in an object-oriented form of C. FEtk is 449s designed to solve general coupled systems of nonlinear partial differential 449s equations using adaptive finite element methods, inexact Newton methods, 449s and algebraic multilevel methods. More information about FEtk may be found 449s at . 449s ---------------------------------------------------------------------- 449s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 449s Aqua is a modified form of the Holst group PMG library 449s which has been modified by Patrice Koehl 449s for improved efficiency and 449s memory usage when solving the Poisson-Boltzmann equation. 449s ---------------------------------------------------------------------- 449s Please cite your use of APBS as: 449s 449s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 449s nanosystems: application to microtubules and the ribosome. Proc. 449s Natl. Acad. Sci. USA 98, 10037-10041 2001. 449s 449s 449s This executable compiled on Jan 3 2025 at 11:01:42 449s 449s Parsing input file apbs-mol.in... 449s rank 0 size 1... 449s Parsed input file. 449s Got paths for 3 molecules 449s Reading PQR-format atom data from acetic-acid.pqr. 449s asc_getToken: Error occurred (bailing out). 449s Vio_scanf: Format problem with input. 449s 8 atoms 449s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 449s Net charge -1.67e-16 e 449s Reading PQR-format atom data from acetate.pqr. 449s asc_getToken: Error occurred (bailing out). 449s Vio_scanf: Format problem with input. 449s 8 atoms 449s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 449s Net charge -1.00e+00 e 449s Reading PQR-format atom data from proton.pqr. 449s 1 atoms 449s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 449s Net charge 1.00e+00 e 449s Preparing to run 12 PBE calculations. 449s ---------------------------------------- 449s CALCULATION #1 (acetic-solv): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 7.76163 A 449s Current memory usage: 61.598 MB total, 61.598 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.188 x 0.188 x 0.188 449s Grid lengths: 12.000 x 12.000 x 12.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 1 449s Linearized traditional PBE 449s Multiple Debye-Huckel sphere boundary conditions 449s 2 ion species (0.150 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 78.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 5.823898055191E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #2 (acetic-solv): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 7.76163 A 449s Current memory usage: 61.598 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.094 x 0.094 x 0.094 449s Grid lengths: 6.000 x 6.000 x 6.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 1 449s Linearized traditional PBE 449s Boundary conditions from focusing 449s 2 ion species (0.150 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 78.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 9.793274462353E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #3 (acetic-ref): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 0 A 449s Current memory usage: 61.422 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.188 x 0.188 x 0.188 449s Grid lengths: 12.000 x 12.000 x 12.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 1 449s Linearized traditional PBE 449s Multiple Debye-Huckel sphere boundary conditions 449s 2 ion species (0.000 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 2.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 5.846917564309E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #4 (acetic-ref): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 0 A 449s Current memory usage: 61.422 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.094 x 0.094 x 0.094 449s Grid lengths: 6.000 x 6.000 x 6.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 1 449s Linearized traditional PBE 449s Boundary conditions from focusing 449s 2 ion species (0.000 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 2.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 9.815953282539E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #5 (acetate-solv): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 7.76163 A 449s Current memory usage: 61.598 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.188 x 0.188 x 0.188 449s Grid lengths: 12.000 x 12.000 x 12.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 2 449s Linearized traditional PBE 449s Multiple Debye-Huckel sphere boundary conditions 449s 2 ion species (0.150 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 78.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 8.219846763777E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #6 (acetate-solv): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 7.76163 A 449s Current memory usage: 61.598 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.094 x 0.094 x 0.094 449s Grid lengths: 6.000 x 6.000 x 6.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 2 449s Linearized traditional PBE 449s Boundary conditions from focusing 449s 2 ion species (0.150 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 78.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 1.392741988698E+04 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #7 (acetate-ref): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 0 A 449s Current memory usage: 61.422 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.188 x 0.188 x 0.188 449s Grid lengths: 12.000 x 12.000 x 12.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 2 449s Linearized traditional PBE 449s Multiple Debye-Huckel sphere boundary conditions 449s 2 ion species (0.000 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 2.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 8.420373979905E+03 kJ/mol 449s Calculating forces... 449s [focusFillBound()]: WARNING: 449s Unusually large potential values 449s detected on the focusing boundary! 449s Convergence not guaranteed for NPBE/NRPBE calculations! 449s 449s ---------------------------------------- 449s CALCULATION #8 (acetate-ref): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 0 A 449s Current memory usage: 61.422 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.094 x 0.094 x 0.094 449s Grid lengths: 6.000 x 6.000 x 6.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 2 449s Linearized traditional PBE 449s Boundary conditions from focusing 449s 2 ion species (0.000 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 2.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 1.412716615065E+04 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #9 (proton-solv): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 7.76163 A 449s Current memory usage: 61.412 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.188 x 0.188 x 0.188 449s Grid lengths: 12.000 x 12.000 x 12.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 3 449s Linearized traditional PBE 449s Multiple Debye-Huckel sphere boundary conditions 449s 2 ion species (0.150 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 78.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 3.862359524598E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #10 (proton-solv): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 7.76163 A 449s Current memory usage: 61.412 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.094 x 0.094 x 0.094 449s Grid lengths: 6.000 x 6.000 x 6.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 3 449s Linearized traditional PBE 449s Boundary conditions from focusing 449s 2 ion species (0.150 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 78.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 6.288156251610E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s CALCULATION #11 (proton-ref): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 0 A 449s Current memory usage: 61.373 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.188 x 0.188 x 0.188 449s Grid lengths: 12.000 x 12.000 x 12.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 3 449s Linearized traditional PBE 449s Multiple Debye-Huckel sphere boundary conditions 449s 2 ion species (0.000 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 2.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 4.162533113906E+03 kJ/mol 449s Calculating forces... 449s [focusFillBound()]: WARNING: 449s Unusually large potential values 449s detected on the focusing boundary! 449s Convergence not guaranteed for NPBE/NRPBE calculations! 449s 449s ---------------------------------------- 449s CALCULATION #12 (proton-ref): MULTIGRID 449s Setting up problem... 449s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 449s Debye length: 0 A 449s Current memory usage: 61.373 MB total, 122.404 MB high water 449s Using linear spline charge discretization. 449s Grid dimensions: 65 x 65 x 65 449s Grid spacings: 0.094 x 0.094 x 0.094 449s GridTesting computed result against expected result (5.823898055191e+03, 5.823898055191e+03) 449s *** PASSED *** 449s Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) 449s *** PASSED *** 449s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 449s *** PASSED *** 449s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 449s *** PASSED *** 449s Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) 449s *** PASSED *** 449s Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) 449s *** PASSED *** 449s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 449s *** PASSED *** 449s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 449s *** PASSED *** 449s Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) 449s *** PASSED *** 449s Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) 449s *** PASSED *** 449s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 449s *** PASSED *** 449s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 449s *** PASSED *** 449s Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) 449s *** PASSED *** 449s Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) 449s *** PASSED *** 449s Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) 449s *** PASSED *** 449s Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) 449s *** PASSED *** 449s Elapsed time: 4.688033 seconds 449s -------------------------------------------------------------------------------- 449s -------------------------------------------------------------------------------- 449s Testing input file apbs-smol.in 449s 449s lengths: 6.000 x 6.000 x 6.000 449s Grid center: (0.000, -0.154, 1.287) 449s Multigrid levels: 5 449s Molecule ID: 3 449s Linearized traditional PBE 449s Boundary conditions from focusing 449s 2 ion species (0.000 M ionic strength): 449s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 449s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 449s Solute dielectric: 2.000 449s Solvent dielectric: 2.000 449s Using "molecular" surface definition; no smoothing 449s Solvent probe radius: 0.000 A 449s Temperature: 293.000 K 449s Electrostatic energies will be calculated 449s Total electrostatic energy = 6.585616091973E+03 kJ/mol 449s Calculating forces... 449s ---------------------------------------- 449s PRINT STATEMENTS 449s 449s print energy 1 (acetic-solv) - 2 (acetic-ref) end 449s Local net energy (PE 0) = -2.267882018629E+01 kJ/mol 449s Global net ELEC energy = -2.267882018629E+01 kJ/mol 449s 449s print energy 3 (acetate-solv) - 4 (acetate-ref) end 449s Local net energy (PE 0) = -1.997462636633E+02 kJ/mol 449s Global net ELEC energy = -1.997462636633E+02 kJ/mol 449s 449s print energy 5 (proton-solv) - 6 (proton-ref) end 449s Local net energy (PE 0) = -2.974598403628E+02 kJ/mol 449s Global net ELEC energy = -2.974598403628E+02 kJ/mol 449s 449s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 449s Local net energy (PE 0) = -4.745272838398E+02 kJ/mol 449s Global net ELEC energy = -4.745272838398E+02 kJ/mol 449s ---------------------------------------- 449s CLEANING UP AND SHUTTING DOWN... 449s Destroying force arrays. 449s No energy arrays to destroy. 449s Destroying multigrid structures. 449s Destroying finite element structures. 449s Destroying 3 molecules 449s Final memory usage: 0.001 MB total, 122.404 MB high water 449s 449s 449s Thanks for using APBS! 449s 453s Checking for intermediate energies in input file apbs-mol.out 453s EXPECTED COMPUTED: 16 453s EXPECTED EXPECTED: 16 453s 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] 453s 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'] 453s COMPUTED RESULT 5823.898055191 453s COMPUTED RESULT 9793.274462353 453s COMPUTED RESULT 5846.917564309 453s COMPUTED RESULT 9815.953282539 453s COMPUTED RESULT 8219.846763777 453s COMPUTED RESULT 13927.41988698 453s COMPUTED RESULT 8420.373979905 453s COMPUTED RESULT 14127.16615065 453s COMPUTED RESULT 3862.359524598 453s COMPUTED RESULT 6288.15625161 453s COMPUTED RESULT 4162.533113906 453s COMPUTED RESULT 6585.616091973 453s COMPUTED RESULT -22.67882018629 453s COMPUTED RESULT -199.7462636633 453s COMPUTED RESULT -297.4598403628 453s COMPUTED RESULT -474.5272838398 453s BINARY: /usr/bin/apbs 453s INPUT: apbs-smol.in 453s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 453s asc_getToken: Error occurred (bailing out). 453s Vio_scanf: Format problem with input. 453s 453s 453s ---------------------------------------------------------------------- 453s APBS -- Adaptive Poisson-Boltzmann Solver 453s Version APBS 3.4.1 453s 453s Nathan A. Baker (nathan.baker@pnnl.gov) 453s Pacific Northwest National Laboratory 453s 453s Additional contributing authors listed in the code documentation. 453s 453s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 453s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 453s Northwest Division for the U.S. Department of Energy. 453s 453s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 453s Portions Copyright (c) 2002-2020, Nathan A. Baker. 453s Portions Copyright (c) 1999-2002, The Regents of the University of California. 453s Portions Copyright (c) 1995, Michael Holst. 453s All rights reserved. 453s 453s Redistribution and use in source and binary forms, with or without 453s modification, are permitted provided that the following conditions are met: 453s 453s * Redistributions of source code must retain the above copyright notice, this 453s list of conditions and the following disclaimer. 453s 453s * Redistributions in binary form must reproduce the above copyright notice, 453s this list of conditions and the following disclaimer in the documentation 453s and/or other materials provided with the distribution. 453s 453s * Neither the name of the developer nor the names of its contributors may be 453s used to endorse or promote products derived from this software without 453s specific prior written permission. 453s 453s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 453s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 453s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 453s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 453s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 453s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 453s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 453s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 453s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 453s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 453s ---------------------------------------------------------------------- 453s APBS uses FETK (the Finite Element ToolKit) to solve the 453s Poisson-Boltzmann equation numerically. FETK is a portable collection 453s of finite element modeling class libraries developed by the Michael Holst 453s research group and written in an object-oriented form of C. FEtk is 453s designed to solve general coupled systems of nonlinear partial differential 453s equations using adaptive finite element methods, inexact Newton methods, 453s and algebraic multilevel methods. More information about FEtk may be found 453s at . 453s ---------------------------------------------------------------------- 453s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 453s Aqua is a modified form of the Holst group PMG library 453s which has been modified by Patrice Koehl 453s for improved efficiency and 453s memory usage when solving the Poisson-Boltzmann equation. 453s ---------------------------------------------------------------------- 453s Please cite your use of APBS as: 453s 453s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 453s nanosystems: application to microtubules and the ribosome. Proc. 453s Natl. Acad. Sci. USA 98, 10037-10041 2001. 453s 453s 453s This executable compiled on Jan 3 2025 at 11:01:42 453s 453s Parsing input file apbs-smol.in... 453s rank 0 size 1... 453s Parsed input file. 453s Got paths for 3 molecules 453s Reading PQR-format atom data from acetic-acid.pqr. 453s asc_getToken: Error occurred (bailing out). 453s Vio_scanf: Format problem with input. 453s 8 atoms 453s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 453s Net charge -1.67e-16 e 453s Reading PQR-format atom data from acetate.pqr. 453s asc_getToken: Error occurred (bailing out). 453s Vio_scanf: Format problem with input. 453s 8 atoms 453s Centered at (0.000e+00, -1.535e-01, 1.287e+00) 453s Net charge -1.00e+00 e 453s Reading PQR-format atom data from proton.pqr. 453s 1 atoms 453s Centered at (1.780e-01, -1.286e+00, 2.937e+00) 453s Net charge 1.00e+00 e 453s Preparing to run 12 PBE calculations. 453s ---------------------------------------- 453s CALCULATION #1 (acetic-solv): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 7.76163 A 453s Current memory usage: 61.598 MB total, 61.598 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.188 x 0.188 x 0.188 453s Grid lengths: 12.000 x 12.000 x 12.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 1 453s Linearized traditional PBE 453s Multiple Debye-Huckel sphere boundary conditions 453s 2 ion species (0.150 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 78.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 5.824172730822E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #2 (acetic-solv): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 7.76163 A 453s Current memory usage: 61.598 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.094 x 0.094 x 0.094 453s Grid lengths: 6.000 x 6.000 x 6.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 1 453s Linearized traditional PBE 453s Boundary conditions from focusing 453s 2 ion species (0.150 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 78.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 9.793622759239E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #3 (acetic-ref): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 0 A 453s Current memory usage: 61.422 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.188 x 0.188 x 0.188 453s Grid lengths: 12.000 x 12.000 x 12.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 1 453s Linearized traditional PBE 453s Multiple Debye-Huckel sphere boundary conditions 453s 2 ion species (0.000 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 2.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 5.846917564309E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #4 (acetic-ref): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 0 A 453s Current memory usage: 61.422 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.094 x 0.094 x 0.094 453s Grid lengths: 6.000 x 6.000 x 6.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 1 453s Linearized traditional PBE 453s Boundary conditions from focusing 453s 2 ion species (0.000 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 2.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 9.815953282539E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #5 (acetate-solv): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 7.76163 A 453s Current memory usage: 61.598 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.188 x 0.188 x 0.188 453s Grid lengths: 12.000 x 12.000 x 12.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 2 453s Linearized traditional PBE 453s Multiple Debye-Huckel sphere boundary conditions 453s 2 ion species (0.150 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 78.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 8.221328580569E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #6 (acetate-solv): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 7.76163 A 453s Current memory usage: 61.598 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.094 x 0.094 x 0.094 453s Grid lengths: 6.000 x 6.000 x 6.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 2 453s Linearized traditional PBE 453s Boundary conditions from focusing 453s 2 ion species (0.150 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 78.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 1.392867783119E+04 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #7 (acetate-ref): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 0 A 453s Current memory usage: 61.422 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.188 x 0.188 x 0.188 453s Grid lengths: 12.000 x 12.000 x 12.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 2 453s Linearized traditional PBE 453s Multiple Debye-Huckel sphere boundary conditions 453s 2 ion species (0.000 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 2.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 8.420373979905E+03 kJ/mol 453s Calculating forces... 453s [focusFillBound()]: WARNING: 453s Unusually large potential values 453s detected on the focusing boundary! 453s Convergence not guaranteed for NPBE/NRPBE calculations! 453s 453s ---------------------------------------- 453s CALCULATION #8 (acetate-ref): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 0 A 453s Current memory usage: 61.422 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.094 x 0.094 x 0.094 453s Grid lengths: 6.000 x 6.000 x 6.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 2 453s Linearized traditional PBE 453s Boundary conditions from focusing 453s 2 ion species (0.000 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 2.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 1.412716615065E+04 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #9 (proton-solv): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 7.76163 A 453s Current memory usage: 61.412 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.188 x 0.188 x 0.188 453s Grid lengths: 12.000 x 12.000 x 12.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 3 453s Linearized traditional PBE 453s Multiple Debye-Huckel sphere boundary conditions 453s 2 ion species (0.150 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 78.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 3.863066835285E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #10 (proton-solv): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 7.76163 A 453s Current memory usage: 61.412 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.094 x 0.094 x 0.094 453s Grid lengths: 6.000 x 6.000 x 6.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 3 453s Linearized traditional PBE 453s Boundary conditions from focusing 453s 2 ion species (0.150 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.150 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 78.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 6.289649216644E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s CALCULATION #11 (proton-ref): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 0 A 453s Current memory usage: 61.373 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.188 x 0.188 x 0.188 453s Grid lengths: 12.000 x 12.000 x 12.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 3 453s Linearized traditional PBE 453s Multiple Debye-Huckel sphere boundary conditions 453s 2 ion species (0.000 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 2.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 4.162533113906E+03 kJ/mol 453s Calculating forces... 453s [focusFillBound()]: WARNING: 453s Unusually large potential values 453s detected on the focusing boundary! 453s Convergence not guaranteed for NPBE/NRPBE calculations! 453s 453s ---------------------------------------- 453s CALCULATION #12 (proton-ref): MULTIGRID 453s Setting up problem... 453s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 453s Debye length: 0 A 453s Current memory usage: 61.373 MB total, 122.404 MB high water 453s Using linear spline charge discretization. 453s Grid dimensions: 65 x 65 x 65 453s Grid spacings: 0.094 x 0.094 x 0.094 453s Grid lengths: 6.000 x 6.000 x 6.000 453s Grid center: (0.000, -0.154, 1.287) 453s Multigrid levels: 5 453s Molecule ID: 3 453s Linearized traditional PBE 453s Boundary conditions from focusing 453s 2 ion species (0.000 M ionic strength): 453s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 453s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 453s Solute dielectric: 2.000 453s Solvent dielectric: 2.000 453s Using "molecular" surface definition;harmonic average smoothing 453s Solvent probe radius: 0.000 A 453s Temperature: 293.000 K 453s Electrostatic energies will be calculated 453s Total electrostatic energy = 6.585616091973E+03 kJ/mol 453s Calculating forces... 453s ---------------------------------------- 453s PRINT STATEMENTS 453s 453s print energy 1 (acetic-solv) - 2 (acetic-ref) end 453s Local net energy (PE 0) = -2.233052329981E+01 kJ/mol 453s Global net ELEC energy = -2.233052329981E+01 kJ/mol 453s 453s print energy 3 (acetate-solv) - 4 (acetate-ref) end 453s Local net energy (PE 0) = -1.984883194538E+02 kJ/mol 453s Global net ELEC energy = -1.984883194538E+02 kJ/mol 453s 453s print energy 5 (proton-solv) - 6 (proton-ref) end 453s Local net energy (PE 0) = -2.959668753288E+02 kJ/mol 453s Global net ELEC energy = -2.959668753288E+02 kJ/mol 453s 453s print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end 453s Local net energy (PE 0) = -4.721246714828E+02 kJ/mol 453s Global net ELEC energy = -4.721246714828E+02 kJ/mol 453s ---------------------------------------- 453s CLEANING UP AND SHUTTING DOWN... 453s Destroying force arrays. 453s No energy arrays to destroy. 453s Destroying multigrid structures. 453s Destroying finite element structures. 453s Destroying 3 molecules 453s Final memory usage: 0.001 MB total, 122.404 MB high water 453s 453s 453s Thanks for using APBS! 453s 453s Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) 453s *** PASSED *** 453s Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) 453s *** PASSED *** 453s Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) 453s *** PASSED *** 453s Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) 453s *** PASSED *** 453s Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) 453s *** PASSED *** 453s Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) 453s *** PASSED *** 453s Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) 453s *** PASSED *** 453s Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) 453s *** PASSED *** 453s Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) 453s *** PASSED *** 453s Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) 453s *** PASSED *** 453s Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) 453s *** PASSED *** 453s Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) 453s *** PASSED *** 453s Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) 453s *** PASSED *** 453s Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) 453s *** PASSED *** 453s Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) 453s *** PASSED *** 453s Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) 453s *** PASSED *** 453s Elapsed time: 4.119905 seconds 453s -------------------------------------------------------------------------------- 453s Total elapsed time: 8.807938 seconds 453s Test results have been logged 453s -------------------------------------------------------------------------------- 453s -------------------------------------------------------------------------------- 453s Testing input file ion-pmf.in 453s 460s Checking for intermediate energies in input file apbs-smol.out 460s EXPECTED COMPUTED: 16 460s EXPECTED EXPECTED: 16 460s 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] 460s 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'] 460s COMPUTED RESULT 5824.172730822 460s COMPUTED RESULT 9793.622759239 460s COMPUTED RESULT 5846.917564309 460s COMPUTED RESULT 9815.953282539 460s COMPUTED RESULT 8221.328580569 460s COMPUTED RESULT 13928.67783119 460s COMPUTED RESULT 8420.373979905 460s COMPUTED RESULT 14127.16615065 460s COMPUTED RESULT 3863.066835285 460s COMPUTED RESULT 6289.649216644 460s COMPUTED RESULT 4162.533113906 460s COMPUTED RESULT 6585.616091973 460s COMPUTED RESULT -22.33052329981 460s COMPUTED RESULT -198.4883194538 460s COMPUTED RESULT -295.9668753288 460s COMPUTED RESULT -472.1246714828 460s Running tests for ion-pmf section 460s BINARY: /usr/bin/apbs 460s INPUT: ion-pmf.in 460s COMMAND: ['/usr/bin/apbs', 'ion-pmf.in'] 460s asc_getToken: Error occurred (bailing out). 460s Vio_scanf: Format problem with input. 460s asc_getToken: Error occurred (bailing out). 460s Vio_scanf: Format problem with input. 460s 460s 460s ---------------------------------------------------------------------- 460s APBS -- Adaptive Poisson-Boltzmann Solver 460s Version APBS 3.4.1 460s 460s Nathan A. Baker (nathan.baker@pnnl.gov) 460s Pacific Northwest National Laboratory 460s 460s Additional contributing authors listed in the code documentation. 460s 460s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 460s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 460s Northwest Division for the U.S. Department of Energy. 460s 460s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 460s Portions Copyright (c) 2002-2020, Nathan A. Baker. 460s Portions Copyright (c) 1999-2002, The Regents of the University of California. 460s Portions Copyright (c) 1995, Michael Holst. 460s All rights reserved. 460s 460s Redistribution and use in source and binary forms, with or without 460s modification, are permitted provided that the following conditions are met: 460s 460s * Redistributions of source code must retain the above copyright notice, this 460s list of conditions and the following disclaimer. 460s 460s * Redistributions in binary form must reproduce the above copyright notice, 460s this list of conditions and the following disclaimer in the documentation 460s and/or other materials provided with the distribution. 460s 460s * Neither the name of the developer nor the names of its contributors may be 460s used to endorse or promote products derived from this software without 460s specific prior written permission. 460s 460s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 460s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 460s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 460s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 460s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 460s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 460s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 460s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 460s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 460s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 460s ---------------------------------------------------------------------- 460s APBS uses FETK (the Finite Element ToolKit) to solve the 460s Poisson-Boltzmann equation numerically. FETK is a portable collection 460s of finite element modeling class libraries developed by the Michael Holst 460s research group and written in an object-oriented form of C. FEtk is 460s designed to solve general coupled systems of nonlinear partial differential 460s equations using adaptive finite element methods, inexact Newton methods, 460s and algebraic multilevel methods. More information about FEtk may be found 460s at . 460s ---------------------------------------------------------------------- 460s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 460s Aqua is a modified form of the Holst group PMG library 460s which has been modified by Patrice Koehl 460s for improved efficiency and 460s memory usage when solving the Poisson-Boltzmann equation. 460s ---------------------------------------------------------------------- 460s Please cite your use of APBS as: 460s 460s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 460s nanosystems: application to microtubules and the ribosome. Proc. 460s Natl. Acad. Sci. USA 98, 10037-10041 2001. 460s 460s 460s This executable compiled on Jan 3 2025 at 11:01:42 460s 460s Parsing input file ion-pmf.in... 460s rank 0 size 1... 460s Parsed input file. 460s Reading parameter data from parm.dat. 460s Got paths for 1 molecules 460s Reading PDB-format atom data from ion-pmf.pdb. 460s Vpmg_ibForce: No force for zero ionic strength! 460s Vpmg_ibForce: No force for zero ionic strength! 460s 2 atoms 460s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 460s Net charge 2.00e+00 e 460s Preparing to run 3 PBE calculations. 460s ---------------------------------------- 460s CALCULATION #1 (solv): MULTIGRID 460s Setting up problem... 460s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 460s Debye length: 0 A 460s Current memory usage: 61.106 MB total, 61.106 MB high water 460s Using cubic spline charge discretization. 460s Grid dimensions: 65 x 65 x 65 460s Grid spacings: 0.210 x 0.210 x 0.210 460s Grid lengths: 13.440 x 13.440 x 13.440 460s Grid center: (0.000, 0.000, 0.000) 460s Multigrid levels: 5 460s Molecule ID: 1 460s Linearized traditional PBE 460s Multiple Debye-Huckel sphere boundary conditions 460s 0 ion species (0.000 M ionic strength): 460s Solute dielectric: 1.000 460s Solvent dielectric: 78.540 460s Using spline-based surface definition;window = 0.300 460s Temperature: 298.150 K 460s Electrostatic energies will be calculated 460s All-atom solvent forces will be calculated 460s Total electrostatic energy = 7.839535983197E+03 kJ/mol 460s Calculating forces... 460s Printing per-atom forces for molecule 1 (kJ/mol/A) 460s Legend: 460s tot n -- total force for atom n 460s qf n -- fixed charge force for atom n 460s db n -- dielectric boundary force for atom n 460s ib n -- ionic boundary force for atom n 460s mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 460s mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 460s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 460s mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 460s mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 460s mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 460s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 460s mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 460s Vpmg_ibForce: No force for zero ionic strength! 460s Vpmg_ibForce: No force for zero ionic strength! 460s ---------------------------------------- 460s CALCULATION #2 (ref): MULTIGRID 460s Setting up problem... 460s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 460s Debye length: 0 A 460s Current memory usage: 61.106 MB total, 61.155 MB high water 460s Using cubic spline charge discretization. 460s Grid dimensions: 65 x 65 x 65 460s Grid spacings: 0.210 x 0.210 x 0.210 460s Grid lengths: 13.440 x 13.440 x 13.440 460s Grid center: (0.000, 0.000, 0.000) 460s Multigrid levels: 5 460s Molecule ID: 1 460s Linearized traditional PBE 460s Multiple Debye-Huckel sphere boundary conditions 460s 0 ion species (0.000 M ionic strength): 460s Solute dielectric: 1.000 460s Solvent dielectric: 1.000 460s Using spline-based surface definition;window = 0.300 460s Temperature: 298.150 K 460s Electrostatic energies will be calculated 460s All-atom solvent forces will be calculated 460s Total electrostatic energy = 8.964727588811E+03 kJ/mol 460s Calculating forces... 460s Printing per-atom forces for molecule 1 (kJ/mol/A) 460s Legend: 460s tot n -- total force for atom n 460s qf n -- fixed charge force for atom n 460s db n -- dielectric boundary force for atom n 460s ib n -- ionic boundary force for atom n 460s mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 460s mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 460s mgF ib 0 0.000e+00 0.000e+00 0.000e+00 460s mgF db 0 0.000e+00 0.000e+00 0.000e+00 460s mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 460s mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 460s mgF ib 1 0.000e+00 0.000e+00 0.000e+00 460s mgF db 1 0.000e+00 0.000e+00 0.000e+00 460s ---------------------------------------- 460s CALCULATION #3 (asolv): APOLAR 460s Printing per atom forces (kJ/mol/A) 460s Legend: 460s tot n -- Total force for atom n 460s sasa n -- SASA force for atom n 460s sav n -- SAV force for atom n 460s wca n -- WCA force for atom n 460s 460s gamma 0.000720 460s pressure 0.000000 460s bconc 0.033000 460s 460s tot 0 2.715e-02 9.130e-07 9.128e-07 460s sasa 0 -1.100e+01 0.000e+00 0.000e+00 460s sav 0 0.000e+00 0.000e+00 0.000e+00 460s wca 0 -5.827e-01 -2.767e-05 -2.766e-05 460s tot 1 -2.723e-02 9.131e-07 9.134e-07 460s sasa 1 1.112e+01 0.000e+00 0.000e+00 460s sav 1 0.000e+00 0.000e+00 0.000e+00 460s wca 1 5.827e-01 -2.767e-05 -2.768e-05 460s 460s 460s Solvent Accessible Surface Area (SASA) for each atom: 460s SASA for atom 0: 1.153275282828E+02 460s SASA for atom 1: 1.153114143344E+02 460s 460s Total solvent accessible surface area: 230.639 A^2 460s 460s Surface tension*area energies (gamma * SASA) for each atom: 460s Surface tension*area energy for atom 0: 8.303582036361E-02 460s Surface tension*area energy for atom 1: 8.302421832080E-02 460s 460s Total surface tension energy: 0.16606 kJ/mol 460s 460s Total solvent accessible volume: 0 A^3 460s 460s Total pressure*volume energy: 0 kJ/mol 460s 460s WCA dispersion Energies for each atom: 460s WCA energy for atom 0: -6.909718345777E+00 460s WCA energy for atom 1: -6.909411348230E+00 460s 460s Total WCA energy: -13.8191 kJ/mol 460s 460s Total non-polar energy = -1.365306965532E+01 kJ/mol 460s ---------------------------------------- 460s PRINT STATEMENTS 460s 460s print energy 1 (solv) - 2 (ref) end 460s Local net energy (PE 0) = -1.125191605614E+03 kJ/mol 460s Global net ELEC energy = -1.125191605614E+03 kJ/mol 460s print force 1 (solv) - 2 (ref) end 460s Printing per-atom forces (kJ/mol/A). 460s Legend: 460s tot n -- Total force for atom n 460s qf n -- Fixed charge force for atom n 460s db n -- Dielectric boundary force for atom n 460s ib n -- Ionic boundary force for atom n 460s tot all -- Total force for system 460s qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 460s ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 460s db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 460s tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 460s qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 460s ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 460s db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 460s tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 460s tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 460s 460s print APOL energy 1 (asolv) end 460s Global net APOL energy = -1.365306965532E+01 kJ/mol 460s 460s print APOL force 1 (asolv) end 460s Printing per atom forces (kJ/mol/A) 460s Legend: 460s tot n -- Total force for atom n 460s sasa n -- SASA force for atom n 460s sav n -- SAV force for atom n 460s wca n -- WCA force for atom n 460s tot all -- Total force for system 460s sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 460s sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 460s wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 460s tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 460s sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 460s sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 460s wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 460s tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 460s tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 460s ---------------------------------------- 460s CLEANING UP AND SHUTTING DOWN... 460s Destroying force arrays. 460s No energy arrays to destroy. 460s Destroying multigrid structures. 460s Destroying finite element structures. 460s Destroying 1 molecules 460s Final memory usage: 60.711 MB total, 62.250 MB high water 460s 460s 460s Thanks for using APBS! 460s 460s Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) 460s *** PASSED *** 460s Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) 460s *** PASSED *** 460s Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) 460s *** PASSED *** 460s Elapsed time: 6.557845 seconds 460s -------------------------------------------------------------------------------- 460s Total elapsed time: 6.557845 seconds 460s Test results have been logged 460s -------------------------------------------------------------------------------- 460s -------------------------------------------------------------------------------- 460s Testing input file apbs-mol-vdw.in 460s 476s Checking for intermediate energies in input file ion-pmf.out 476s EXPECTED COMPUTED: 4 476s EXPECTED EXPECTED: 4 476s COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65306965532] 476s EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] 476s COMPUTED RESULT 7839.535983197 476s COMPUTED RESULT 8964.727588811 476s COMPUTED RESULT -1125.191605614 476s COMPUTED RESULT -13.65306965532 476s Running tests for pka-lig section 476s BINARY: /usr/bin/apbs 476s INPUT: apbs-mol-vdw.in 476s COMMAND: ['/usr/bin/apbs', 'apbs-mol-vdw.in'] 476s asc_getToken: Error occurred (bailing out). 476s Vio_scanf: Format problem with input. 476s 476s 476s ---------------------------------------------------------------------- 476s APBS -- Adaptive Poisson-Boltzmann Solver 476s Version APBS 3.4.1 476s 476s Nathan A. Baker (nathan.baker@pnnl.gov) 476s Pacific Northwest National Laboratory 476s 476s Additional contributing authors listed in the code documentation. 476s 476s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 476s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 476s Northwest Division for the U.S. Department of Energy. 476s 476s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 476s Portions Copyright (c) 2002-2020, Nathan A. Baker. 476s Portions Copyright (c) 1999-2002, The Regents of the University of California. 476s Portions Copyright (c) 1995, Michael Holst. 476s All rights reserved. 476s 476s Redistribution and use in source and binary forms, with or without 476s modification, are permitted provided that the following conditions are met: 476s 476s * Redistributions of source code must retain the above copyright notice, this 476s list of conditions and the following disclaimer. 476s 476s * Redistributions in binary form must reproduce the above copyright notice, 476s this list of conditions and the following disclaimer in the documentation 476s and/or other materials provided with the distribution. 476s 476s * Neither the name of the developer nor the names of its contributors may be 476s used to endorse or promote products derived from this software without 476s specific prior written permission. 476s 476s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 476s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 476s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 476s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 476s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 476s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 476s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 476s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 476s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 476s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 476s ---------------------------------------------------------------------- 476s APBS uses FETK (the Finite Element ToolKit) to solve the 476s Poisson-Boltzmann equation numerically. FETK is a portable collection 476s of finite element modeling class libraries developed by the Michael Holst 476s research group and written in an object-oriented form of C. FEtk is 476s designed to solve general coupled systems of nonlinear partial differential 476s equations using adaptive finite element methods, inexact Newton methods, 476s and algebraic multilevel methods. More information about FEtk may be found 476s at . 476s ---------------------------------------------------------------------- 476s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 476s Aqua is a modified form of the Holst group PMG library 476s which has been modified by Patrice Koehl 476s for improved efficiency and 476s memory usage when solving the Poisson-Boltzmann equation. 476s ---------------------------------------------------------------------- 476s Please cite your use of APBS as: 476s 476s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 476s nanosystems: application to microtubules and the ribosome. Proc. 476s Natl. Acad. Sci. USA 98, 10037-10041 2001. 476s 476s 476s This executable compiled on Jan 3 2025 at 11:01:42 476s 476s Parsing input file apbs-mol-vdw.in... 476s rank 0 size 1... 476s Parsed input file. 476s Got paths for 3 molecules 476s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 476s asc_getToken: Error occurred (bailing out). 476s Vio_scanf: Format problem with input. 476s 47 atoms 476s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 476s Net charge 1.11e-16 e 476s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 476s asc_getToken: Error occurred (bailing out). 476s Vio_scanf: Format problem with input. 476s 3423 atoms 476s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 476s Net charge 1.00e+00 e 476s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 476s 3470 atoms 476s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 476s Net charge 1.00e+00 e 476s Preparing to run 6 PBE calculations. 476s ---------------------------------------- 476s CALCULATION #1 (lig-coarse): MULTIGRID 476s Setting up problem... 476s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 476s Debye length: 0 A 476s Current memory usage: 204.292 MB total, 204.292 MB high water 476s Using linear spline charge discretization. 476s Grid dimensions: 97 x 97 x 97 476s Grid spacings: 0.729 x 0.729 x 0.729 476s Grid lengths: 70.000 x 70.000 x 70.000 476s Grid center: (28.969, -32.507, 27.022) 476s Multigrid levels: 4 476s Molecule ID: 1 476s Linearized traditional PBE 476s Single Debye-Huckel sphere boundary conditions 476s 2 ion species (0.000 M ionic strength): 476s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 476s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 476s Solute dielectric: 2.000 476s Solvent dielectric: 78.000 476s Using "molecular" surface definition; no smoothing 476s Solvent probe radius: 0.000 A 476s Temperature: 298.150 K 476s Electrostatic energies will be calculated 476s Total electrostatic energy = 2.224988750664E+03 kJ/mol 476s Calculating forces... 476s ---------------------------------------- 476s CALCULATION #2 (lig-fine): MULTIGRID 476s Setting up problem... 476s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 476s Debye length: 0 A 476s Current memory usage: 204.292 MB total, 406.001 MB high water 476s Using linear spline charge discretization. 476s Grid dimensions: 97 x 97 x 97 476s Grid spacings: 0.250 x 0.250 x 0.250 476s Grid lengths: 24.000 x 24.000 x 24.000 476s Grid center: (24.822, -33.153, 21.545) 476s Multigrid levels: 4 476s Molecule ID: 1 476s Linearized traditional PBE 476s Boundary conditions from focusing 476s 2 ion species (0.000 M ionic strength): 476s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 476s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 476s Solute dielectric: 2.000 476s Solvent dielectric: 78.000 476s Using "molecular" surface definition; no smoothing 476s Solvent probe radius: 0.000 A 476s Temperature: 298.150 K 476s Electrostatic energies will be calculated 476s Total electrostatic energy = 1.049695084686E+04 kJ/mol 476s Calculating forces... 476s ---------------------------------------- 476s CALCULATION #3 (pka-coarse): MULTIGRID 476s Setting up problem... 476s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 476s Debye length: 0 A 476s Current memory usage: 291.151 MB total, 406.001 MB high water 476s Using linear spline charge discretization. 476s Grid dimensions: 97 x 97 x 97 476s Grid spacings: 0.729 x 0.729 x 0.729 476s Grid lengths: 70.000 x 70.000 x 70.000 476s Grid center: (28.969, -32.507, 27.022) 476s Multigrid levels: 4 476s Molecule ID: 2 476s Linearized traditional PBE 476s Single Debye-Huckel sphere boundary conditions 476s 2 ion species (0.000 M ionic strength): 476s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 476s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 476s Solute dielectric: 2.000 476s Solvent dielectric: 78.000 476s Using "molecular" surface definition; no smoothing 476s Solvent probe radius: 0.000 A 476s Temperature: 298.150 K 476s Electrostatic energies will be calculated 476s Total electrostatic energy = 1.818450789522E+05 kJ/mol 476s Calculating forces... 476s [focusFillBound()]: WARNING: 476s Unusually large potential values 476s detected on the focusing boundary! 476s Convergence not guaranteed for NPBE/NRPBE calculations! 476s 476s ---------------------------------------- 476s CALCULATION #4 (pka-fine): MULTIGRID 476s Setting up problem... 476s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 476s Debye length: 0 A 476s Current memory usage: 291.151 MB total, 533.426 MB high water 476s Using linear spline charge discretization. 476s Grid dimensions: 97 x 97 x 97 476s Grid spacings: 0.250 x 0.250 x 0.250 476s Grid lengths: 24.000 x 24.000 x 24.000 476s Grid center: (24.822, -33.153, 21.545) 476s Multigrid levels: 4 476s Molecule ID: 2 476s Linearized traditional PBE 476s Boundary conditions from focusing 476s 2 ion species (0.000 M ionic strength): 476s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 476s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 476s Solute dielectric: 2.000 476s Solvent dielectric: 78.000 476s Using "molecular" surface definition; no smoothing 476s Solvent probe radius: 0.000 A 476s Temperature: 298.150 K 476s Electrostatic energies will be calculated 476s Total electrostatic energy = 3.008254338259E+05 kJ/mol 476s Calculating forces... 476s ---------------------------------------- 476s CALCULATION #5 (complex-coarse): MULTIGRID 476s Setting up problem... 476s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 476s Debye length: 0 A 476s Current memory usage: 292.063 MB total, 533.426 MB high water 476s Using linear spline charge discretization. 476s Grid dimensions: 97 x 97 x 97 476s Grid spacings: 0.729 x 0.729 x 0.729 476s Grid lengths: 70.000 x 70.000 x 70.000 476s Grid center: (28.969, -32.507, 27.022) 476s Multigrid levels: 4 476s Molecule ID: 3 476s Linearized traditional PBE 476s Single Debye-Huckel sphere boundary conditions 476s 2 ion species (0.000 M ionic strength): 476s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 476s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 476s Solute dielectric: 2.000 476s Solvent dielectric: 78.000 476s Using "molecular" surface definition; no smoothing 476s Solvent probe radius: 0.000 A 476s Temperature: 298.150 K 476s Electrostatic energies will be calculated 476s Total electrostatic energy = 1.840918409896E+05 kJ/mol 476s Calculating forces... 476s [focusFillBound()]: WARNING: 476s Unusually large potential values 476s detected on the focusing boundary! 476s Convergence not guaranteed for NPBE/NRPBE calculations! 476s 476s ---------------------------------------- 476s CALCULATION #6 (complex-fine): MULTIGRID 476s Setting up problem... 476s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 476s Debye length: 0 A 476s Current memory usage: 292.063 MB total, 534.806 MB high water 476s Using linear spline charge discretization. 476s Grid dimensions: 97 x 97 x 97 476s Grid spacings: 0.250 x 0.250 x 0.250 476s Grid lengths: 24.000 x 24.000 x 24.000 476s Grid center: (24.822, -33.153, 21.545) 476s Multigrid levels: 4 476s Molecule ID: 3 476s Linearized traditional PBE 476s Boundary conditions from focusing 476s 2 ion species (0.000 M ionic strength): 476s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 476s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 476s Solute dielectric: 2.000 476s Solvent dielectric: 78.000 476s Using "molecular" surface definition; no smoothing 476s Solvent probe radius: 0.000 A 476s Temperature: 298.150 K 476s Electrostatic energies will be calculated 476s Total electrostatic energy = 3.113304681884E+05 kJ/mol 476s Calculating forces... 476s ---------------------------------------- 476s PRINT STATEMENTS 476s 476s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 476s Local net energy (PE 0) = 8.083515648803E+00 kJ/mol 476s Global net ELEC energy = 8.083515648803E+00 kJ/mol 476s ---------------------------------------- 476s CLEANING UP AND SHUTTING DOWN... 476s Destroying force arrays. 476s No energy arrays to destroy. 476s Destroying multigrid structures. 476s Destroying finite element structures. 476s Destroying 3 molecules 476s Final memory usage: 0.001 MB total, 534.806 MB high water 476s 476s 476s Thanks for using APBS! 476s 476s Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) 476s *** PASSED *** 476s Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) 476s *** PASSED *** 476s Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) 477s *** PASSED *** 477s Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) 477s *** PASSED *** 477s Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) 477s *** PASSED *** 477s Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) 477s *** PASSED *** 477s Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00) 477s *** PASSED *** 477s Elapsed time: 16.947329 seconds 477s -------------------------------------------------------------------------------- 477s -------------------------------------------------------------------------------- 477s Testing input file apbs-smol-vdw.in 477s 489s Checking for intermediate energies in input file apbs-mol-vdw.out 489s EXPECTED COMPUTED: 7 489s EXPECTED EXPECTED: 7 489s COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.083515648803] 489s EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] 489s COMPUTED RESULT 2224.988750664 489s COMPUTED RESULT 10496.95084686 489s COMPUTED RESULT 181845.0789522 489s COMPUTED RESULT 300825.4338259 489s COMPUTED RESULT 184091.8409896 489s COMPUTED RESULT 311330.4681884 489s COMPUTED RESULT 8.083515648803 489s BINARY: /usr/bin/apbs 489s INPUT: apbs-smol-vdw.in 489s COMMAND: ['/usr/bin/apbs', 'apbs-smol-vdw.in'] 489s asc_getToken: Error occurred (bailing out). 489s Vio_scanf: Format problem with input. 489s 489s 489s ---------------------------------------------------------------------- 489s APBS -- Adaptive Poisson-Boltzmann Solver 489s Version APBS 3.4.1 489s 489s Nathan A. Baker (nathan.baker@pnnl.gov) 489s Pacific Northwest National Laboratory 489s 489s Additional contributing authors listed in the code documentation. 489s 489s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 489s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 489s Northwest Division for the U.S. Department of Energy. 489s 489s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 489s Portions Copyright (c) 2002-2020, Nathan A. Baker. 489s Portions Copyright (c) 1999-2002, The Regents of the University of California. 489s Portions Copyright (c) 1995, Michael Holst. 489s All rights reserved. 489s 489s Redistribution and use in source and binary forms, with or without 489s modification, are permitted provided that the following conditions are met: 489s 489s * Redistributions of source code must retain the above copyright notice, this 489s list of conditions and the following disclaimer. 489s 489s * Redistributions in binary form must reproduce the above copyright notice, 489s this list of conditions and the following disclaimer in the documentation 489s and/or other materials provided with the distribution. 489s 489s * Neither the name of the developer nor the names of its contributors may be 489s used to endorse or promote products derived from this software without 489s specific prior written permission. 489s 489s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 489s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 489s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 489s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 489s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 489s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 489s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 489s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 489s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 489s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 489s ---------------------------------------------------------------------- 489s APBS uses FETK (the Finite Element ToolKit) to solve the 489s Poisson-Boltzmann equation numerically. FETK is a portable collection 489s of finite element modeling class libraries developed by the Michael Holst 489s research group and written in an object-oriented form of C. FEtk is 489s designed to solve general coupled systems of nonlinear partial differential 489s equations using adaptive finite element methods, inexact Newton methods, 489s and algebraic multilevel methods. More information about FEtk may be found 489s at . 489s ---------------------------------------------------------------------- 489s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 489s Aqua is a modified form of the Holst group PMG library 489s which has been modified by Patrice Koehl 489s for improved efficiency and 489s memory usage when solving the Poisson-Boltzmann equation. 489s ---------------------------------------------------------------------- 489s Please cite your use of APBS as: 489s 489s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 489s nanosystems: application to microtubules and the ribosome. Proc. 489s Natl. Acad. Sci. USA 98, 10037-10041 2001. 489s 489s 489s This executable compiled on Jan 3 2025 at 11:01:42 489s 489s Parsing input file apbs-smol-vdw.in... 489s rank 0 size 1... 489s Parsed input file. 489s Got paths for 3 molecules 489s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 489s asc_getToken: Error occurred (bailing out). 489s Vio_scanf: Format problem with input. 489s 47 atoms 489s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 489s Net charge 1.11e-16 e 489s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 489s asc_getToken: Error occurred (bailing out). 489s Vio_scanf: Format problem with input. 489s 3423 atoms 489s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 489s Net charge 1.00e+00 e 489s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 489s 3470 atoms 489s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 489s Net charge 1.00e+00 e 489s Preparing to run 6 PBE calculations. 489s ---------------------------------------- 489s CALCULATION #1 (lig-coarse): MULTIGRID 489s Setting up problem... 489s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 489s Debye length: 0 A 489s Current memory usage: 204.292 MB total, 204.292 MB high water 489s Using linear spline charge discretization. 489s Grid dimensions: 97 x 97 x 97 489s Grid spacings: 0.729 x 0.729 x 0.729 489s Grid lengths: 70.000 x 70.000 x 70.000 489s Grid center: (28.969, -32.507, 27.022) 489s Multigrid levels: 4 489s Molecule ID: 1 489s Linearized traditional PBE 489s Single Debye-Huckel sphere boundary conditions 489s 2 ion species (0.000 M ionic strength): 489s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 489s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 489s Solute dielectric: 2.000 489s Solvent dielectric: 78.000 489s Using "molecular" surface definition;harmonic average smoothing 489s Solvent probe radius: 0.000 A 489s Temperature: 298.150 K 489s Electrostatic energies will be calculated 489s Total electrostatic energy = 2.226793167046E+03 kJ/mol 489s Calculating forces... 489s ---------------------------------------- 489s CALCULATION #2 (lig-fine): MULTIGRID 489s Setting up problem... 489s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 489s Debye length: 0 A 489s Current memory usage: 204.292 MB total, 406.001 MB high water 489s Using linear spline charge discretization. 489s Grid dimensions: 97 x 97 x 97 489s Grid spacings: 0.250 x 0.250 x 0.250 489s Grid lengths: 24.000 x 24.000 x 24.000 489s Grid center: (24.822, -33.153, 21.545) 489s Multigrid levels: 4 489s Molecule ID: 1 489s Linearized traditional PBE 489s Boundary conditions from focusing 489s 2 ion species (0.000 M ionic strength): 489s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 489s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 489s Solute dielectric: 2.000 489s Solvent dielectric: 78.000 489s Using "molecular" surface definition;harmonic average smoothing 489s Solvent probe radius: 0.000 A 489s Temperature: 298.150 K 489s Electrostatic energies will be calculated 489s Total electrostatic energy = 1.050504485887E+04 kJ/mol 489s Calculating forces... 489s ---------------------------------------- 489s CALCULATION #3 (pka-coarse): MULTIGRID 489s Setting up problem... 489s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 489s Debye length: 0 A 489s Current memory usage: 291.151 MB total, 406.001 MB high water 489s Using linear spline charge discretization. 489s Grid dimensions: 97 x 97 x 97 489s Grid spacings: 0.729 x 0.729 x 0.729 489s Grid lengths: 70.000 x 70.000 x 70.000 489s Grid center: (28.969, -32.507, 27.022) 489s Multigrid levels: 4 489s Molecule ID: 2 489s Linearized traditional PBE 489s Single Debye-Huckel sphere boundary conditions 489s 2 ion species (0.000 M ionic strength): 489s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 489s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 489s Solute dielectric: 2.000 489s Solvent dielectric: 78.000 489s Using "molecular" surface definition;harmonic average smoothing 489s Solvent probe radius: 0.000 A 489s Temperature: 298.150 K 489s Electrostatic energies will be calculated 489s Total electrostatic energy = 1.827976621645E+05 kJ/mol 489s Calculating forces... 489s [focusFillBound()]: WARNING: 489s Unusually large potential values 489s detected on the focusing boundary! 489s Convergence not guaranteed for NPBE/NRPBE calculations! 489s 489s ---------------------------------------- 489s CALCULATION #4 (pka-fine): MULTIGRID 489s Setting up problem... 489s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 489s Debye length: 0 A 489s Current memory usage: 291.151 MB total, 533.426 MB high water 489s Using linear spline charge discretization. 489s Grid dimensions: 97 x 97 x 97 489s Grid spacings: 0.250 x 0.250 x 0.250 489s Grid lengths: 24.000 x 24.000 x 24.000 489s Grid center: (24.822, -33.153, 21.545) 489s Multigrid levels: 4 489s Molecule ID: 2 489s Linearized traditional PBE 489s Boundary conditions from focusing 489s 2 ion species (0.000 M ionic strength): 489s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 489s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 489s Solute dielectric: 2.000 489s Solvent dielectric: 78.000 489s Using "molecular" surface definition;harmonic average smoothing 489s Solvent probe radius: 0.000 A 489s Temperature: 298.150 K 489s Electrostatic energies will be calculated 489s Total electrostatic energy = 3.017228546773E+05 kJ/mol 489s Calculating forces... 489s ---------------------------------------- 489s CALCULATION #5 (complex-coarse): MULTIGRID 489s Setting up problem... 489s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 489s Debye length: 0 A 489s Current memory usage: 292.063 MB total, 533.426 MB high water 489s Using linear spline charge discretization. 489s Grid dimensions: 97 x 97 x 97 489s Grid spacings: 0.729 x 0.729 x 0.729 489s Grid lengths: 70.000 x 70.000 x 70.000 489s Grid center: (28.969, -32.507, 27.022) 489s Multigrid levels: 4 489s Molecule ID: 3 489s Linearized traditional PBE 489s Single Debye-Huckel sphere boundary conditions 489s 2 ion species (0.000 M ionic strength): 489s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 489s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 489s Solute dielectric: 2.000 489s Solvent dielectric: 78.000 489s Using "molecular" surface definition;harmonic average smoothing 489s Solvent probe radius: 0.000 A 489s Temperature: 298.150 K 489s Electrostatic energies will be calculated 489s Total electrostatic energy = 1.850819075387E+05 kJ/mol 489s Calculating forces... 489s [focusFillBound()]: WARNING: 489s Unusually large potential values 489s detected on the focusing boundary! 489s Convergence not guaranteed for NPBE/NRPBE calculations! 489s 489s ---------------------------------------- 489s CALCULATION #6 (complex-fine): MULTIGRID 489s Setting up problem... 489s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 489s Debye length: 0 A 489s Current memory usage: 292.063 MB total, 534.806 MB high water 489s Using linear spline charge discretization. 489s Grid dimensions: 97 x 97 x 97 489s Grid spacings: 0.250 x 0.250 x 0.250 489s Grid lengths: 24.000 x 24.000 x 24.000 489s Grid center: (24.822, -33.153, 21.545) 489s Multigrid levels: 4 489s Molecule ID: 3 489s Linearized traditional PBE 489s Boundary conditions from focusing 489s 2 ion species (0.000 M ionic strength): 489s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 489s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 489s Solute dielectric: 2.000 489s Solvent dielectric: 78.000 489s Using "molecular" surface definition;harmonic average smoothing 489s Solvent probe radius: 0.000 A 489s Temperature: 298.150 K 489s Electrostatic energies will be calculated 489s Total electrostatic energy = 3.122488625388E+05 kJ/mol 489s Calculating forces... 489s ---------------------------------------- 489s PRINT STATEMENTS 489s 489s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 489s Local net energy (PE 0) = 2.096300255720E+01 kJ/mol 489s Global net ELEC energy = 2.096300255720E+01 kJ/mol 489s ---------------------------------------- 489s CLEANING UP AND SHUTTING DOWN... 489s Destroying force arrays. 489s No energy arrays to destroy. 489s Destroying multigrid structures. 489s Destroying finite element structures. 489s Destroying 3 molecules 489s Final memory usage: 0.001 MB total, 534.806 MB high water 489s 489s 489s Thanks for using APBS! 489s 489s Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) 489s *** PASSED *** 489s Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) 489s *** PASSED *** 489s Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) 489s *** PASSED *** 489s Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) 489s *** PASSED *** 489s Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) 489s *** PASSED *** 489s Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) 489s *** PASSED *** 489s Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01) 489s *** PASSED *** 489s Elapsed time: 12.762612 seconds 489s -------------------------------------------------------------------------------- 489s -------------------------------------------------------------------------------- 489s Testing input file apbs-mol-surf.in 489s 503s Checking for intermediate energies in input file apbs-smol-vdw.out 503s EXPECTED COMPUTED: 7 503s EXPECTED EXPECTED: 7 503s COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.9630025572] 503s EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] 503s COMPUTED RESULT 2226.793167046 503s COMPUTED RESULT 10505.04485887 503s COMPUTED RESULT 182797.6621645 503s COMPUTED RESULT 301722.8546773 503s COMPUTED RESULT 185081.9075387 503s COMPUTED RESULT 312248.8625388 503s COMPUTED RESULT 20.9630025572 503s BINARY: /usr/bin/apbs 503s INPUT: apbs-mol-surf.in 503s COMMAND: ['/usr/bin/apbs', 'apbs-mol-surf.in'] 503s asc_getToken: Error occurred (bailing out). 503s Vio_scanf: Format problem with input. 503s 503s 503s ---------------------------------------------------------------------- 503s APBS -- Adaptive Poisson-Boltzmann Solver 503s Version APBS 3.4.1 503s 503s Nathan A. Baker (nathan.baker@pnnl.gov) 503s Pacific Northwest National Laboratory 503s 503s Additional contributing authors listed in the code documentation. 503s 503s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 503s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 503s Northwest Division for the U.S. Department of Energy. 503s 503s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 503s Portions Copyright (c) 2002-2020, Nathan A. Baker. 503s Portions Copyright (c) 1999-2002, The Regents of the University of California. 503s Portions Copyright (c) 1995, Michael Holst. 503s All rights reserved. 503s 503s Redistribution and use in source and binary forms, with or without 503s modification, are permitted provided that the following conditions are met: 503s 503s * Redistributions of source code must retain the above copyright notice, this 503s list of conditions and the following disclaimer. 503s 503s * Redistributions in binary form must reproduce the above copyright notice, 503s this list of conditions and the following disclaimer in the documentation 503s and/or other materials provided with the distribution. 503s 503s * Neither the name of the developer nor the names of its contributors may be 503s used to endorse or promote products derived from this software without 503s specific prior written permission. 503s 503s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 503s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 503s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 503s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 503s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 503s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 503s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 503s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 503s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 503s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 503s ---------------------------------------------------------------------- 503s APBS uses FETK (the Finite Element ToolKit) to solve the 503s Poisson-Boltzmann equation numerically. FETK is a portable collection 503s of finite element modeling class libraries developed by the Michael Holst 503s research group and written in an object-oriented form of C. FEtk is 503s designed to solve general coupled systems of nonlinear partial differential 503s equations using adaptive finite element methods, inexact Newton methods, 503s and algebraic multilevel methods. More information about FEtk may be found 503s at . 503s ---------------------------------------------------------------------- 503s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 503s Aqua is a modified form of the Holst group PMG library 503s which has been modified by Patrice Koehl 503s for improved efficiency and 503s memory usage when solving the Poisson-Boltzmann equation. 503s ---------------------------------------------------------------------- 503s Please cite your use of APBS as: 503s 503s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 503s nanosystems: application to microtubules and the ribosome. Proc. 503s Natl. Acad. Sci. USA 98, 10037-10041 2001. 503s 503s 503s This executable compiled on Jan 3 2025 at 11:01:42 503s 503s Parsing input file apbs-mol-surf.in... 503s rank 0 size 1... 503s Parsed input file. 503s Got paths for 3 molecules 503s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 503s asc_getToken: Error occurred (bailing out). 503s Vio_scanf: Format problem with input. 503s 47 atoms 503s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 503s Net charge 1.11e-16 e 503s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 503s asc_getToken: Error occurred (bailing out). 503s Vio_scanf: Format problem with input. 503s 3423 atoms 503s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 503s Net charge 1.00e+00 e 503s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 503s 3470 atoms 503s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 503s Net charge 1.00e+00 e 503s Preparing to run 6 PBE calculations. 503s ---------------------------------------- 503s CALCULATION #1 (lig-coarse): MULTIGRID 503s Setting up problem... 503s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 503s Debye length: 0 A 503s Current memory usage: 203.877 MB total, 203.877 MB high water 503s Using linear spline charge discretization. 503s Grid dimensions: 97 x 97 x 97 503s Grid spacings: 0.729 x 0.729 x 0.729 503s Grid lengths: 70.000 x 70.000 x 70.000 503s Grid center: (28.969, -32.507, 27.022) 503s Multigrid levels: 4 503s Molecule ID: 1 503s Linearized traditional PBE 503s Single Debye-Huckel sphere boundary conditions 503s 2 ion species (0.000 M ionic strength): 503s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 503s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 503s Solute dielectric: 2.000 503s Solvent dielectric: 78.000 503s Using "molecular" surface definition; no smoothing 503s Solvent probe radius: 1.400 A 503s Temperature: 298.150 K 503s Electrostatic energies will be calculated 503s Total electrostatic energy = 2.244350164274E+03 kJ/mol 503s Calculating forces... 503s ---------------------------------------- 503s CALCULATION #2 (lig-fine): MULTIGRID 503s Setting up problem... 503s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 503s Debye length: 0 A 503s Current memory usage: 203.877 MB total, 405.586 MB high water 503s Using linear spline charge discretization. 503s Grid dimensions: 97 x 97 x 97 503s Grid spacings: 0.250 x 0.250 x 0.250 503s Grid lengths: 24.000 x 24.000 x 24.000 503s Grid center: (24.822, -33.153, 21.545) 503s Multigrid levels: 4 503s Molecule ID: 1 503s Linearized traditional PBE 503s Boundary conditions from focusing 503s 2 ion species (0.000 M ionic strength): 503s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 503s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 503s Solute dielectric: 2.000 503s Solvent dielectric: 78.000 503s Using "molecular" surface definition; no smoothing 503s Solvent probe radius: 1.400 A 503s Temperature: 298.150 K 503s Electrostatic energies will be calculated 503s Total electrostatic energy = 1.052149475373E+04 kJ/mol 503s Calculating forces... 503s ---------------------------------------- 503s CALCULATION #3 (pka-coarse): MULTIGRID 503s Setting up problem... 503s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 503s Debye length: 0 A 503s Current memory usage: 251.521 MB total, 405.586 MB high water 503s Using linear spline charge discretization. 503s Grid dimensions: 97 x 97 x 97 503s Grid spacings: 0.729 x 0.729 x 0.729 503s Grid lengths: 70.000 x 70.000 x 70.000 503s Grid center: (28.969, -32.507, 27.022) 503s Multigrid levels: 4 503s Molecule ID: 2 503s Linearized traditional PBE 503s Single Debye-Huckel sphere boundary conditions 503s 2 ion species (0.000 M ionic strength): 503s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 503s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 503s Solute dielectric: 2.000 503s Solvent dielectric: 78.000 503s Using "molecular" surface definition; no smoothing 503s Solvent probe radius: 1.400 A 503s Temperature: 298.150 K 503s Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) 503s Electrostatic energies will be calculated 503s Total electrostatic energy = 1.862615690066E+05 kJ/mol 503s Calculating forces... 503s [focusFillBound()]: WARNING: 503s Unusually large potential values 503s detected on the focusing boundary! 503s Convergence not guaranteed for NPBE/NRPBE calculations! 503s 503s ---------------------------------------- 503s CALCULATION #4 (pka-fine): MULTIGRID 503s Setting up problem... 503s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 503s Debye length: 0 A 503s Current memory usage: 251.521 MB total, 493.795 MB high water 503s Using linear spline charge discretization. 503s Grid dimensions: 97 x 97 x 97 503s Grid spacings: 0.250 x 0.250 x 0.250 503s Grid lengths: 24.000 x 24.000 x 24.000 503s Grid center: (24.822, -33.153, 21.545) 503s Multigrid levels: 4 503s Molecule ID: 2 503s Linearized traditional PBE 503s Boundary conditions from focusing 503s 2 ion species (0.000 M ionic strength): 503s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 503s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 503s Solute dielectric: 2.000 503s Solvent dielectric: 78.000 503s Using "molecular" surface definition; no smoothing 503s Solvent probe radius: 1.400 A 503s Temperature: 298.150 K 503s Electrostatic energies will be calculated 503s Total electrostatic energy = 3.051810884053E+05 kJ/mol 503s Calculating forces... 503s ---------------------------------------- 503s CALCULATION #5 (complex-coarse): MULTIGRID 503s Setting up problem... 503s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 503s Debye length: 0 A 503s Current memory usage: 251.858 MB total, 493.795 MB high water 503s Using linear spline charge discretization. 503s Grid dimensions: 97 x 97 x 97 503s Grid spacings: 0.729 x 0.729 x 0.729 503s Grid lengths: 70.000 x 70.000 x 70.000 503s Grid center: (28.969, -32.507, 27.022) 503s Multigrid levels: 4 503s Molecule ID: 3 503s Linearized traditional PBE 503s Single Debye-Huckel sphere boundary conditions 503s 2 ion species (0.000 M ionic strength): 503s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 503s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 503s Solute dielectric: 2.000 503s Solvent dielectric: 78.000 503s Using "molecular" surface definition; no smoothing 503s Solvent probe radius: 1.400 A 503s Temperature: 298.150 K 503s Electrostatic energies will be calculated 503s Total electrostatic energy = 1.886625455219E+05 kJ/mol 503s Calculating forces... 503s [focusFillBound()]: WARNING: 503s Unusually large potential values 503s detected on the focusing boundary! 503s Convergence not guaranteed for NPBE/NRPBE calculations! 503s 503s ---------------------------------------- 503s CALCULATION #6 (complex-fine): MULTIGRID 503s Setting up problem... 503s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 503s Debye length: 0 A 503s Current memory usage: 251.858 MB total, 494.601 MB high water 503s Using linear spline charge discretization. 503s Grid dimensions: 97 x 97 x 97 503s Grid spacings: 0.250 x 0.250 x 0.250 503s Grid lengths: 24.000 x 24.000 x 24.000 503s Grid center: (24.822, -33.153, 21.545) 503s Multigrid levels: 4 503s Molecule ID: 3 503s Linearized traditional PBE 503s Boundary conditions from focusing 503s 2 ion species (0.000 M ionic strength): 503s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 503s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 503s Solute dielectric: 2.000 503s Solvent dielectric: 78.000 503s Using "molecular" surface definition; no smoothing 503s Solvent probe radius: 1.400 A 503s Temperature: 298.150 K 503s Electrostatic energies will be calculated 503s Total electrostatic energy = 3.158218439277E+05 kJ/mol 503s Calculating forces... 503s ---------------------------------------- 503s PRINT STATEMENTS 503s 503s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 503s Local net energy (PE 0) = 1.192607686582E+02 kJ/mol 503s Global net ELEC energy = 1.192607686582E+02 kJ/mol 503s ---------------------------------------- 503s CLEANING UP AND SHUTTING DOWN... 503s Destroying force arrays. 503s No energy arrays to destroy. 503s Destroying multigrid structures. 503s Destroying finite element structures. 503s Destroying 3 molecules 503s Final memory usage: 0.001 MB total, 494.601 MB high water 503s 503s 503s Thanks for using APBS! 503s 503s *** PASSED *** 503s Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) 503s *** PASSED *** 503s Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) 503s *** PASSED *** 503s Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) 503s *** PASSED *** 503s Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) 503s *** PASSED *** 503s Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) 503s *** PASSED *** 503s Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02) 503s *** PASSED *** 503s Elapsed time: 14.151031 seconds 503s -------------------------------------------------------------------------------- 503s -------------------------------------------------------------------------------- 503s Testing input file apbs-smol-surf.in 503s 516s Checking for intermediate energies in input file apbs-mol-surf.out 516s EXPECTED COMPUTED: 7 516s EXPECTED EXPECTED: 7 516s COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686582] 516s EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] 516s COMPUTED RESULT 2244.350164274 516s COMPUTED RESULT 10521.49475373 516s COMPUTED RESULT 186261.5690066 516s COMPUTED RESULT 305181.0884053 516s COMPUTED RESULT 188662.5455219 516s COMPUTED RESULT 315821.8439277 516s COMPUTED RESULT 119.2607686582 516s BINARY: /usr/bin/apbs 516s INPUT: apbs-smol-surf.in 516s COMMAND: ['/usr/bin/apbs', 'apbs-smol-surf.in'] 516s asc_getToken: Error occurred (bailing out). 516s Vio_scanf: Format problem with input. 516s 516s 516s ---------------------------------------------------------------------- 516s APBS -- Adaptive Poisson-Boltzmann Solver 516s Version APBS 3.4.1 516s 516s Nathan A. Baker (nathan.baker@pnnl.gov) 516s Pacific Northwest National Laboratory 516s 516s Additional contributing authors listed in the code documentation. 516s 516s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 516s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 516s Northwest Division for the U.S. Department of Energy. 516s 516s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 516s Portions Copyright (c) 2002-2020, Nathan A. Baker. 516s Portions Copyright (c) 1999-2002, The Regents of the University of California. 516s Portions Copyright (c) 1995, Michael Holst. 516s All rights reserved. 516s 516s Redistribution and use in source and binary forms, with or without 516s modification, are permitted provided that the following conditions are met: 516s 516s * Redistributions of source code must retain the above copyright notice, this 516s list of conditions and the following disclaimer. 516s 516s * Redistributions in binary form must reproduce the above copyright notice, 516s this list of conditions and the following disclaimer in the documentation 516s and/or other materials provided with the distribution. 516s 516s * Neither the name of the developer nor the names of its contributors may be 516s used to endorse or promote products derived from this software without 516s specific prior written permission. 516s 516s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 516s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 516s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 516s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 516s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 516s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 516s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 516s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 516s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 516s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 516s ---------------------------------------------------------------------- 516s APBS uses FETK (the Finite Element ToolKit) to solve the 516s Poisson-Boltzmann equation numerically. FETK is a portable collection 516s of finite element modeling class libraries developed by the Michael Holst 516s research group and written in an object-oriented form of C. FEtk is 516s designed to solve general coupled systems of nonlinear partial differential 516s equations using adaptive finite element methods, inexact Newton methods, 516s and algebraic multilevel methods. More information about FEtk may be found 516s at . 516s ---------------------------------------------------------------------- 516s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 516s Aqua is a modified form of the Holst group PMG library 516s which has been modified by Patrice Koehl 516s for improved efficiency and 516s memory usage when solving the Poisson-Boltzmann equation. 516s ---------------------------------------------------------------------- 516s Please cite your use of APBS as: 516s 516s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 516s nanosystems: application to microtubules and the ribosome. Proc. 516s Natl. Acad. Sci. USA 98, 10037-10041 2001. 516s 516s 516s This executable compiled on Jan 3 2025 at 11:01:42 516s 516s Parsing input file apbs-smol-surf.in... 516s rank 0 size 1... 516s Parsed input file. 516s Got paths for 3 molecules 516s Reading PQR-format atom data from bx6_7_lig_apbs.pqr. 516s asc_getToken: Error occurred (bailing out). 516s Vio_scanf: Format problem with input. 516s 47 atoms 516s Centered at (2.482e+01, -3.315e+01, 2.154e+01) 516s Net charge 1.11e-16 e 516s Reading PQR-format atom data from bx6_7_apo_apbs.pqr. 516s asc_getToken: Error occurred (bailing out). 516s Vio_scanf: Format problem with input. 516s 3423 atoms 516s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 516s Net charge 1.00e+00 e 516s Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 516s 3470 atoms 516s Centered at (2.897e+01, -3.251e+01, 2.702e+01) 516s Net charge 1.00e+00 e 516s Preparing to run 6 PBE calculations. 516s ---------------------------------------- 516s CALCULATION #1 (lig-coarse): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 203.877 MB total, 203.877 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 97 x 97 x 97 516s Grid spacings: 0.729 x 0.729 x 0.729 516s Grid lengths: 70.000 x 70.000 x 70.000 516s Grid center: (28.969, -32.507, 27.022) 516s Multigrid levels: 4 516s Molecule ID: 1 516s Linearized traditional PBE 516s Single Debye-Huckel sphere boundary conditions 516s 2 ion species (0.000 M ionic strength): 516s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 516s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 516s Solute dielectric: 2.000 516s Solvent dielectric: 78.000 516s Using "molecular" surface definition;harmonic average smoothing 516s Solvent probe radius: 1.400 A 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 2.251466789420E+03 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s CALCULATION #2 (lig-fine): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 203.877 MB total, 405.586 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 97 x 97 x 97 516s Grid spacings: 0.250 x 0.250 x 0.250 516s Grid lengths: 24.000 x 24.000 x 24.000 516s Grid center: (24.822, -33.153, 21.545) 516s Multigrid levels: 4 516s Molecule ID: 1 516s Linearized traditional PBE 516s Boundary conditions from focusing 516s 2 ion species (0.000 M ionic strength): 516s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 516s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 516s Solute dielectric: 2.000 516s Solvent dielectric: 78.000 516s Using "molecular" surface definition;harmonic average smoothing 516s Solvent probe radius: 1.400 A 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 1.052814502873E+04 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s CALCULATION #3 (pka-coarse): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 251.521 MB total, 405.586 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 97 x 97 x 97 516s Grid spacings: 0.729 x 0.729 x 0.729 516s Grid lengths: 70.000 x 70.000 x 70.000 516s Grid center: (28.969, -32.507, 27.022) 516s Multigrid levels: 4 516s Molecule ID: 2 516s Linearized traditional PBE 516s Single Debye-Huckel sphere boundary conditions 516s 2 ion species (0.000 M ionic strength): 516s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 516s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 516s Solute dielectric: 2.000 516s Solvent dielectric: 78.000 516s Using "molecular" surface definition;harmonic average smoothing 516s Solvent probe radius: 1.400 A 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 1.864071689626E+05 kJ/mol 516s Calculating forces... 516s [focusFillBound()]: WARNING: 516s Unusually large potential values 516s detected on the focusing boundary! 516s Convergence not guaranteed for NPBE/NRPBE calculations! 516s 516s ---------------------------------------- 516s CALCULATION #4 (pka-fine): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 251.521 MB total, 493.795 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 97 x 97 x 97 516s Grid spacings: 0.250 x 0.250 x 0.250 516s Grid lengths: 24.000 x 24.000 x 24.000 516s Grid center: (24.822, -33.153, 21.545) 516s Multigrid levels: 4 516s Molecule ID: 2 516s Linearized traditional PBE 516s Boundary conditions from focusing 516s 2 ion species (0.000 M ionic strength): 516s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 516s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 516s Solute dielectric: 2.000 516s Solvent dielectric: 78.000 516s Using "molecular" surface definition;harmonic average smoothing 516s Solvent probe radius: 1.400 A 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 3.053319953673E+05 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s CALCULATION #5 (complex-coarse): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 251.858 MB total, 493.795 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 97 x 97 x 97 516s Grid spacings: 0.729 x 0.729 x 0.729 516s Grid lengths: 70.000 x 70.000 x 70.000 516s Grid center: (28.969, -32.507, 27.022) 516s Multigrid levels: 4 516s Molecule ID: 3 516s Linearized traditional PBE 516s Single Debye-Huckel sphere boundary conditions 516s 2 ion species (0.000 M ionic strength): 516s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 516s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 516s Solute dielectric: 2.000 516s Solvent dielectric: 78.000 516s Using "molecular" surface definition;harmonic average smoothing 516s Solvent probe radius: 1.400 A 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 1.888027142979E+05 kJ/mol 516s Calculating forces... 516s [focusFillBound()]: WARNING: 516s Unusually large potential values 516s detected on the focusing boundary! 516s Convergence not guaranteed for NPBE/NRPBE calculations! 516s 516s ---------------------------------------- 516s CALCULATION #6 (complex-fine): MULTIGRID 516s Setting up problem... 516s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 516s Debye length: 0 A 516s Current memory usage: 251.858 MB total, 494.601 MB high water 516s Using linear spline charge discretization. 516s Grid dimensions: 97 x 97 x 97 516s Grid spacings: 0.250 x 0.250 x 0.250 516s Grid lengths: 24.000 x 24.000 x 24.000 516s Grid center: (24.822, -33.153, 21.545) 516s Multigrid levels: 4 516s Molecule ID: 3 516s Linearized traditional PBE 516s Boundary conditions from focusing 516s 2 ion species (0.000 M ionic strength): 516s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 516s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 516s Solute dielectric: 2.000 516s Solvent dielectric: 78.000 516s Using "molecular" surface definition;harmonic average smoothing 516s Solvent probe radius: 1.400 A 516s Temperature: 298.150 K 516s Electrostatic energies will be calculated 516s Total electrostatic energy = 3.159690177241E+05 kJ/mol 516s Calculating forces... 516s ---------------------------------------- 516s PRINT STATEMENTS 516s 516s print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end 516s Local net energy (PE 0) = 1.088773280806E+02 kJ/mol 516s Global net ELEC energy = 1.088773280806E+02 kJ/mol 516s ---------------------------------------- 516s CLEANING UP AND SHUTTING DOWN... 516s Destroying force arrays. 516s No energy arrays to destroy. 516s Destroying multigrid structures. 516s Destroying finite element structures. 516s Destroying 3 molecules 516s Final memory usage: 0.001 MB total, 494.601 MB high water 516s 516s 516s Thanks for using APBS! 516s 516s Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) 516s *** PASSED *** 516s Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) 516s *** PASSED *** 516s Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) 516s *** PASSED *** 516s Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) 516s *** PASSED *** 516s Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) 516s *** PASSED *** 516s Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) 516s *** PASSED *** 516s Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) 516s *** PASSED *** 516s Elapsed time: 12.506112 seconds 516s -------------------------------------------------------------------------------- 516s Total elapsed time: 56.367084 seconds 516s Test results have been logged 516s -------------------------------------------------------------------------------- 516s -------------------------------------------------------------------------------- 516s Testing input file complex-0_1.in 516s 517s Checking for intermediate energies in input file apbs-smol-surf.out 517s EXPECTED COMPUTED: 7 517s EXPECTED EXPECTED: 7 517s COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] 517s EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] 517s COMPUTED RESULT 2251.46678942 517s COMPUTED RESULT 10528.14502873 517s COMPUTED RESULT 186407.1689626 517s COMPUTED RESULT 305331.9953673 517s COMPUTED RESULT 188802.7142979 517s COMPUTED RESULT 315969.0177241 517s COMPUTED RESULT 108.8773280806 517s Running tests for point-pmf section 517s BINARY: /usr/bin/apbs 517s INPUT: complex-0_1.in 517s COMMAND: ['/usr/bin/apbs', 'complex-0_1.in'] 517s asc_getToken: Error occurred (bailing out). 517s Vio_scanf: Format problem with input. 517s 517s 517s ---------------------------------------------------------------------- 517s APBS -- Adaptive Poisson-Boltzmann Solver 517s Version APBS 3.4.1 517s 517s Nathan A. Baker (nathan.baker@pnnl.gov) 517s Pacific Northwest National Laboratory 517s 517s Additional contributing authors listed in the code documentation. 517s 517s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 517s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 517s Northwest Division for the U.S. Department of Energy. 517s 517s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 517s Portions Copyright (c) 2002-2020, Nathan A. Baker. 517s Portions Copyright (c) 1999-2002, The Regents of the University of California. 517s Portions Copyright (c) 1995, Michael Holst. 517s All rights reserved. 517s 517s Redistribution and use in source and binary forms, with or without 517s modification, are permitted provided that the following conditions are met: 517s 517s * Redistributions of source code must retain the above copyright notice, this 517s list of conditions and the following disclaimer. 517s 517s * Redistributions in binary form must reproduce the above copyright notice, 517s this list of conditions and the following disclaimer in the documentation 517s and/or other materials provided with the distribution. 517s 517s * Neither the name of the developer nor the names of its contributors may be 517s used to endorse or promote products derived from this software without 517s specific prior written permission. 517s 517s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 517s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 517s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 517s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 517s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 517s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 517s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 517s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 517s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 517s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 517s ---------------------------------------------------------------------- 517s APBS uses FETK (the Finite Element ToolKit) to solve the 517s Poisson-Boltzmann equation numerically. FETK is a portable collection 517s of finite element modeling class libraries developed by the Michael Holst 517s research group and written in an object-oriented form of C. FEtk is 517s designed to solve general coupled systems of nonlinear partial differential 517s equations using adaptive finite element methods, inexact Newton methods, 517s and algebraic multilevel methods. More information about FEtk may be found 517s at . 517s ---------------------------------------------------------------------- 517s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 517s Aqua is a modified form of the Holst group PMG library 517s which has been modified by Patrice Koehl 517s for improved efficiency and 517s memory usage when solving the Poisson-Boltzmann equation. 517s ---------------------------------------------------------------------- 517s Please cite your use of APBS as: 517s 517s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 517s nanosystems: application to microtubules and the ribosome. Proc. 517s Natl. Acad. Sci. USA 98, 10037-10041 2001. 517s 517s 517s This executable compiled on Jan 3 2025 at 11:01:42 517s 517s Parsing input file complex-0_1.in... 517s rank 0 size 1... 517s Parsed input file. 517s Got paths for 3 molecules 517s Reading PQR-format atom data from mol0.pqr. 517s asc_getToken: Error occurred (bailing out). 517s Vio_scanf: Format problem with input. 517s 1 atoms 517s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 517s Net charge 1.00e+00 e 517s Reading PQR-format atom data from mol1.pqr. 517s asc_getToken: Error occurred (bailing out). 517s Vio_scanf: Format problem with input. 517s 1 atoms 517s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 517s Net charge 1.00e+00 e 517s Reading PQR-format atom data from complex-0_1.pqr. 517s 2 atoms 517s Centered at (-2.500e+00, 0.000e+00, 0.000e+00) 517s Net charge 2.00e+00 e 517s Preparing to run 3 PBE calculations. 517s ---------------------------------------- 517s CALCULATION #1 (point1): MULTIGRID 517s Setting up problem... 517s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 517s Debye length: 0 A 517s Current memory usage: 61.060 MB total, 61.060 MB high water 517s Using linear spline charge discretization. 517s Grid dimensions: 65 x 65 x 65 517s Grid spacings: 0.210 x 0.210 x 0.210 517s Grid lengths: 13.440 x 13.440 x 13.440 517s Grid center: (0.000, 0.000, 0.000) 517s Multigrid levels: 5 517s Molecule ID: 1 517s Linearized traditional PBE 517s Multiple Debye-Huckel sphere boundary conditions 517s 0 ion species (0.000 M ionic strength): 517s Solute dielectric: 78.540 517s Solvent dielectric: 78.540 517s Using spline-based surface definition;window = 0.300 517s Temperature: 298.150 K 517s Electrostatic energies will be calculated 517s Total electrostatic energy = 9.776035707281E+01 kJ/mol 517s Fixed charge energy = 97.7604 kJ/mol 517s Mobile charge energy = 0 kJ/mol 517s Dielectric energy = 96.5336 kJ/mol 517s Per-atom energies: 517s Atom 0: 9.776035707281E+01 kJ/mol 517s Calculating forces... 517s ---------------------------------------- 517s CALCULATION #2 (point2): MULTIGRID 517s Setting up problem... 517s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 517s Debye length: 0 A 517s Current memory usage: 61.060 MB total, 61.067 MB high water 517s Using linear spline charge discretization. 517s Grid dimensions: 65 x 65 x 65 517s Grid spacings: 0.210 x 0.210 x 0.210 517s Grid lengths: 13.440 x 13.440 x 13.440 517s Grid center: (0.000, 0.000, 0.000) 517s Multigrid levels: 5 517s Molecule ID: 2 517s Linearized traditional PBE 517s Multiple Debye-Huckel sphere boundary conditions 517s 0 ion species (0.000 M ionic strength): 517s Solute dielectric: 78.540 517s Solvent dielectric: 78.540 517s Using spline-based surface definition;window = 0.300 517s Temperature: 298.150 K 517s Electrostatic energies will be calculated 517s Total electrostatic energy = 8.975920687031E+01 kJ/mol 517s Fixed charge energy = 89.7592 kJ/mol 517s Mobile charge energy = 0 kJ/mol 517s Dielectric energy = 88.6151 kJ/mol 517s Per-atom energies: 517s Atom 0: 8.975920687031E+01 kJ/mol 517s Calculating forces... 517s ---------------------------------------- 517s CALCULATION #3 (complex): MULTIGRID 517s Setting up problem... 517s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 517s Debye length: 0 A 517s Current memory usage: 61.060 MB total, 61.067 MB high water 517s Using linear spline charge discretization. 517s Grid dimensions: 65 x 65 x 65 517s Grid spacings: 0.210 x 0.210 x 0.210 517s Grid lengths: 13.440 x 13.440 x 13.440 517s Grid center: (0.000, 0.000, 0.000) 517s Multigrid levels: 5 517s Molecule ID: 3 517s Linearized traditional PBE 517s Multiple Debye-Huckel sphere boundary conditions 517s 0 ion species (0.000 M ionic strength): 517s Solute dielectric: 78.540 517s Solvent dielectric: 78.540 517s Using spline-based surface definition;window = 0.300 517s Temperature: 298.150 K 517s Electrostatic energies will be calculated 517s Total electrostatic energy = 2.058277719334E+02 kJ/mol 517s Fixed charge energy = 205.828 kJ/mol 517s Mobile charge energy = 0 kJ/mol 517s Dielectric energy = 201.106 kJ/mol 517s Per-atom energies: 517s Atom 0: 1.069144350786E+02 kJ/mol 517s Atom 1: 9.891333685475E+01 kJ/mol 517s Calculating forces... 517s ---------------------------------------- 517s PRINT STATEMENTS 517s 517s print energy 3 (complex) - 1 (point1) - 2 (point2) end 517s Local net energy (PE 0) = 1.830820799027E+01 kJ/mol 517s Global net ELEC energy = 1.830820799027E+01 kJ/mol 517s ---------------------------------------- 517s CLEANING UP AND SHUTTING DOWN... 517s Destroying force arrays. 517s No energy arrays to destroy. 517s Destroying multigrid structures. 517s Destroying finite element structures. 517s Destroying 3 molecules 517s Final memory usage: 0.001 MB total, 61.067 MB high water 517s 517s 517s Thanks for using APBS! 517s 517s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 517s *** PASSED *** 517s Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) 517s *** PASSED *** 517s Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) 517s *** PASSED *** 517s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 517s *** PASSED *** 517s Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) 517s *** PASSED *** 517s Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) 517s *** PASSED *** 517s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 517s *** PASSED *** 517s Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) 517s *** PASSED *** 517s Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) 517s *** PASSED *** 517s Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) 517s *** PASSED *** 517s Elapsed time: 1.099486 seconds 517s -------------------------------------------------------------------------------- 517s -------------------------------------------------------------------------------- 517s Testing input file complex-0_2.in 517s 518s Checking for intermediate energies in input file complex-0_1.out 518s EXPECTED COMPUTED: 13 518s EXPECTED EXPECTED: 13 518s 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] 518s 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'] 518s COMPUTED RESULT 97.76035707281 518s COMPUTED RESULT 89.75920687031 518s COMPUTED RESULT 205.8277719334 518s COMPUTED RESULT 0.0 518s COMPUTED RESULT 0.0 518s COMPUTED RESULT 0.0 518s COMPUTED RESULT 97.7604 518s COMPUTED RESULT 89.7592 518s COMPUTED RESULT 205.828 518s COMPUTED RESULT 96.5336 518s COMPUTED RESULT 88.6151 518s COMPUTED RESULT 201.106 518s COMPUTED RESULT 18.30820799027 518s BINARY: /usr/bin/apbs 518s INPUT: complex-0_2.in 518s COMMAND: ['/usr/bin/apbs', 'complex-0_2.in'] 518s asc_getToken: Error occurred (bailing out). 518s Vio_scanf: Format problem with input. 518s 518s 518s ---------------------------------------------------------------------- 518s APBS -- Adaptive Poisson-Boltzmann Solver 518s Version APBS 3.4.1 518s 518s Nathan A. Baker (nathan.baker@pnnl.gov) 518s Pacific Northwest National Laboratory 518s 518s Additional contributing authors listed in the code documentation. 518s 518s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 518s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 518s Northwest Division for the U.S. Department of Energy. 518s 518s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 518s Portions Copyright (c) 2002-2020, Nathan A. Baker. 518s Portions Copyright (c) 1999-2002, The Regents of the University of California. 518s Portions Copyright (c) 1995, Michael Holst. 518s All rights reserved. 518s 518s Redistribution and use in source and binary forms, with or without 518s modification, are permitted provided that the following conditions are met: 518s 518s * Redistributions of source code must retain the above copyright notice, this 518s list of conditions and the following disclaimer. 518s 518s * Redistributions in binary form must reproduce the above copyright notice, 518s this list of conditions and the following disclaimer in the documentation 518s and/or other materials provided with the distribution. 518s 518s * Neither the name of the developer nor the names of its contributors may be 518s used to endorse or promote products derived from this software without 518s specific prior written permission. 518s 518s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 518s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 518s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 518s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 518s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 518s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 518s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 518s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 518s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 518s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 518s ---------------------------------------------------------------------- 518s APBS uses FETK (the Finite Element ToolKit) to solve the 518s Poisson-Boltzmann equation numerically. FETK is a portable collection 518s of finite element modeling class libraries developed by the Michael Holst 518s research group and written in an object-oriented form of C. FEtk is 518s designed to solve general coupled systems of nonlinear partial differential 518s equations using adaptive finite element methods, inexact Newton methods, 518s and algebraic multilevel methods. More information about FEtk may be found 518s at . 518s ---------------------------------------------------------------------- 518s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 518s Aqua is a modified form of the Holst group PMG library 518s which has been modified by Patrice Koehl 518s for improved efficiency and 518s memory usage when solving the Poisson-Boltzmann equation. 518s ---------------------------------------------------------------------- 518s Please cite your use of APBS as: 518s 518s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 518s nanosystems: application to microtubules and the ribosome. Proc. 518s Natl. Acad. Sci. USA 98, 10037-10041 2001. 518s 518s 518s This executable compiled on Jan 3 2025 at 11:01:42 518s 518s Parsing input file complex-0_2.in... 518s rank 0 size 1... 518s Parsed input file. 518s Got paths for 3 molecules 518s Reading PQR-format atom data from mol0.pqr. 518s asc_getToken: Error occurred (bailing out). 518s Vio_scanf: Format problem with input. 518s 1 atoms 518s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 518s Net charge 1.00e+00 e 518s Reading PQR-format atom data from mol2.pqr. 518s asc_getToken: Error occurred (bailing out). 518s Vio_scanf: Format problem with input. 518s 1 atoms 518s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 518s Net charge 1.00e+00 e 518s Reading PQR-format atom data from complex-0_2.pqr. 518s 2 atoms 518s Centered at (-2.000e+00, 0.000e+00, 0.000e+00) 518s Net charge 2.00e+00 e 518s Preparing to run 3 PBE calculations. 518s ---------------------------------------- 518s CALCULATION #1 (point1): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.060 MB total, 61.060 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.210 x 0.210 x 0.210 518s Grid lengths: 13.440 x 13.440 x 13.440 518s Grid center: (0.000, 0.000, 0.000) 518s Multigrid levels: 5 518s Molecule ID: 1 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 0 ion species (0.000 M ionic strength): 518s Solute dielectric: 78.540 518s Solvent dielectric: 78.540 518s Using spline-based surface definition;window = 0.300 518s Temperature: 298.150 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 9.776035707281E+01 kJ/mol 518s Fixed charge energy = 97.7604 kJ/mol 518s Mobile charge energy = 0 kJ/mol 518s Dielectric energy = 96.5336 kJ/mol 518s Per-atom energies: 518s Atom 0: 9.776035707281E+01 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s CALCULATION #2 (point2): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.060 MB total, 61.067 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.210 x 0.210 x 0.210 518s Grid lengths: 13.440 x 13.440 x 13.440 518s Grid center: (0.000, 0.000, 0.000) 518s Multigrid levels: 5 518s Molecule ID: 2 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 0 ion species (0.000 M ionic strength): 518s Solute dielectric: 78.540 518s Solvent dielectric: 78.540 518s Using spline-based surface definition;window = 0.300 518s Temperature: 298.150 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 1.017611498797E+02 kJ/mol 518s Fixed charge energy = 101.761 kJ/mol 518s Mobile charge energy = 0 kJ/mol 518s Dielectric energy = 100.656 kJ/mol 518s Per-atom energies: 518s Atom 0: 1.017611498797E+02 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s CALCULATION #3 (complex): MULTIGRID 518s Setting up problem... 518s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 518s Debye length: 0 A 518s Current memory usage: 61.060 MB total, 61.068 MB high water 518s Using linear spline charge discretization. 518s Grid dimensions: 65 x 65 x 65 518s Grid spacings: 0.210 x 0.210 x 0.210 518s Grid lengths: 13.440 x 13.440 x 13.440 518s Grid center: (0.000, 0.000, 0.000) 518s Multigrid levels: 5 518s Molecule ID: 3 518s Linearized traditional PBE 518s Multiple Debye-Huckel sphere boundary conditions 518s 0 ion species (0.000 M ionic strength): 518s Solute dielectric: 78.540 518s Solvent dielectric: 78.540 518s Using spline-based surface definition;window = 0.300 518s Temperature: 298.150 K 518s Electrostatic energies will be calculated 518s Total electrostatic energy = 2.084282010393E+02 kJ/mol 518s Fixed charge energy = 208.428 kJ/mol 518s Mobile charge energy = 0 kJ/mol 518s Dielectric energy = 203.83 kJ/mol 518s Per-atom energies: 518s Atom 0: 1.022136878480E+02 kJ/mol 518s Atom 1: 1.062145131913E+02 kJ/mol 518s Calculating forces... 518s ---------------------------------------- 518s PRINT STATEMENTS 518s 518s print energy 3 (complex) - 1 (point1) - 2 (point2) end 518s Local net energy (PE 0) = 8.906694086751E+00 kJ/mol 518s Global net ELEC energy = 8.906694086751E+00 kJ/mol 518s ---------------------------------------- 518s CLEANING UP AND SHUTTING DOWN... 518s Destroying force arrays. 518s No energy arrays to destroy. 518s Destroying multigrid structures. 518s Destroying finite element structures. 518s Destroying 3 molecules 518s Final memory usage: 0.001 MB total, 61.068 MB high water 518s 518s 518s Thanks for using APBS! 518s 518s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 518s *** PASSED *** 518s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 518s *** PASSED *** 518s Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) 518s *** PASSED *** 518s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 518s *** PASSED *** 518s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 518s *** PASSED *** 518s Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) 518s *** PASSED *** 518s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 518s *** PASSED *** 518s Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) 518s *** PASSED *** 518s Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) 518s *** PASSED *** 518s Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00) 518s *** PASSED *** 518s Elapsed time: 1.090422 seconds 518s -------------------------------------------------------------------------------- 518s -------------------------------------------------------------------------------- 518s Testing input file complex-0_3.in 518s 519s Checking for intermediate energies in input file complex-0_2.out 519s EXPECTED COMPUTED: 13 519s EXPECTED EXPECTED: 13 519s 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] 519s 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'] 519s COMPUTED RESULT 97.76035707281 519s COMPUTED RESULT 101.7611498797 519s COMPUTED RESULT 208.4282010393 519s COMPUTED RESULT 0.0 519s COMPUTED RESULT 0.0 519s COMPUTED RESULT 0.0 519s COMPUTED RESULT 97.7604 519s COMPUTED RESULT 101.761 519s COMPUTED RESULT 208.428 519s COMPUTED RESULT 96.5336 519s COMPUTED RESULT 100.656 519s COMPUTED RESULT 203.83 519s COMPUTED RESULT 8.906694086751 519s BINARY: /usr/bin/apbs 519s INPUT: complex-0_3.in 519s COMMAND: ['/usr/bin/apbs', 'complex-0_3.in'] 519s asc_getToken: Error occurred (bailing out). 519s Vio_scanf: Format problem with input. 519s 519s 519s ---------------------------------------------------------------------- 519s APBS -- Adaptive Poisson-Boltzmann Solver 519s Version APBS 3.4.1 519s 519s Nathan A. Baker (nathan.baker@pnnl.gov) 519s Pacific Northwest National Laboratory 519s 519s Additional contributing authors listed in the code documentation. 519s 519s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 519s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 519s Northwest Division for the U.S. Department of Energy. 519s 519s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 519s Portions Copyright (c) 2002-2020, Nathan A. Baker. 519s Portions Copyright (c) 1999-2002, The Regents of the University of California. 519s Portions Copyright (c) 1995, Michael Holst. 519s All rights reserved. 519s 519s Redistribution and use in source and binary forms, with or without 519s modification, are permitted provided that the following conditions are met: 519s 519s * Redistributions of source code must retain the above copyright notice, this 519s list of conditions and the following disclaimer. 519s 519s * Redistributions in binary form must reproduce the above copyright notice, 519s this list of conditions and the following disclaimer in the documentation 519s and/or other materials provided with the distribution. 519s 519s * Neither the name of the developer nor the names of its contributors may be 519s used to endorse or promote products derived from this software without 519s specific prior written permission. 519s 519s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 519s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 519s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 519s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 519s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 519s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 519s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 519s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 519s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 519s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 519s ---------------------------------------------------------------------- 519s APBS uses FETK (the Finite Element ToolKit) to solve the 519s Poisson-Boltzmann equation numerically. FETK is a portable collection 519s of finite element modeling class libraries developed by the Michael Holst 519s research group and written in an object-oriented form of C. FEtk is 519s designed to solve general coupled systems of nonlinear partial differential 519s equations using adaptive finite element methods, inexact Newton methods, 519s and algebraic multilevel methods. More information about FEtk may be found 519s at . 519s ---------------------------------------------------------------------- 519s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 519s Aqua is a modified form of the Holst group PMG library 519s which has been modified by Patrice Koehl 519s for improved efficiency and 519s memory usage when solving the Poisson-Boltzmann equation. 519s ---------------------------------------------------------------------- 519s Please cite your use of APBS as: 519s 519s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 519s nanosystems: application to microtubules and the ribosome. Proc. 519s Natl. Acad. Sci. USA 98, 10037-10041 2001. 519s 519s 519s This executable compiled on Jan 3 2025 at 11:01:42 519s 519s Parsing input file complex-0_3.in... 519s rank 0 size 1... 519s Parsed input file. 519s Got paths for 3 molecules 519s Reading PQR-format atom data from mol0.pqr. 519s asc_getToken: Error occurred (bailing out). 519s Vio_scanf: Format problem with input. 519s 1 atoms 519s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 519s Net charge 1.00e+00 e 519s Reading PQR-format atom data from mol3.pqr. 519s asc_getToken: Error occurred (bailing out). 519s Vio_scanf: Format problem with input. 519s 1 atoms 519s Centered at (0.000e+00, 0.000e+00, 0.000e+00) 519s Net charge 1.00e+00 e 519s Reading PQR-format atom data from complex-0_3.pqr. 519s 2 atoms 519s Centered at (-1.500e+00, 0.000e+00, 0.000e+00) 519s Net charge 2.00e+00 e 519s Preparing to run 3 PBE calculations. 519s ---------------------------------------- 519s CALCULATION #1 (point1): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.060 MB total, 61.060 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.210 x 0.210 x 0.210 519s Grid lengths: 13.440 x 13.440 x 13.440 519s Grid center: (0.000, 0.000, 0.000) 519s Multigrid levels: 5 519s Molecule ID: 1 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 0 ion species (0.000 M ionic strength): 519s Solute dielectric: 78.540 519s Solvent dielectric: 78.540 519s Using spline-based surface definition;window = 0.300 519s Temperature: 298.150 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 9.776035707281E+01 kJ/mol 519s Fixed charge energy = 97.7604 kJ/mol 519s Mobile charge energy = 0 kJ/mol 519s Dielectric energy = 96.5336 kJ/mol 519s Per-atom energies: 519s Atom 0: 9.776035707281E+01 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s CALCULATION #2 (point2): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.060 MB total, 61.067 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.210 x 0.210 x 0.210 519s Grid lengths: 13.440 x 13.440 x 13.440 519s Grid center: (0.000, 0.000, 0.000) 519s Multigrid levels: 5 519s Molecule ID: 2 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 0 ion species (0.000 M ionic strength): 519s Solute dielectric: 78.540 519s Solvent dielectric: 78.540 519s Using spline-based surface definition;window = 0.300 519s Temperature: 298.150 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 1.337661883222E+02 kJ/mol 519s Fixed charge energy = 133.766 kJ/mol 519s Mobile charge energy = 0 kJ/mol 519s Dielectric energy = 132.672 kJ/mol 519s Per-atom energies: 519s Atom 0: 1.337661883222E+02 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s CALCULATION #3 (complex): MULTIGRID 519s Setting up problem... 519s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 519s Debye length: 0 A 519s Current memory usage: 61.060 MB total, 61.068 MB high water 519s Using linear spline charge discretization. 519s Grid dimensions: 65 x 65 x 65 519s Grid spacings: 0.210 x 0.210 x 0.210 519s Grid lengths: 13.440 x 13.440 x 13.440 519s Grid center: (0.000, 0.000, 0.000) 519s Multigrid levels: 5 519s Molecule ID: 3 519s Linearized traditional PBE 519s Multiple Debye-Huckel sphere boundary conditions 519s 0 ion species (0.000 M ionic strength): 519s Solute dielectric: 78.540 519s Solvent dielectric: 78.540 519s Using spline-based surface definition;window = 0.300 519s Temperature: 298.150 K 519s Electrostatic energies will be calculated 519s Total electrostatic energy = 2.374361452120E+02 kJ/mol 519s Fixed charge energy = 237.436 kJ/mol 519s Mobile charge energy = 0 kJ/mol 519s Dielectric energy = 232.924 kJ/mol 519s Per-atom energies: 519s Atom 0: 1.007151570480E+02 kJ/mol 519s Atom 1: 1.367209881640E+02 kJ/mol 519s Calculating forces... 519s ---------------------------------------- 519s PRINT STATEMENTS 519s 519s print energy 3 (complex) - 1 (point1) - 2 (point2) end 519s Local net energy (PE 0) = 5.909599816984E+00 kJ/mol 519s Global net ELEC energy = 5.909599816984E+00 kJ/mol 519s ---------------------------------------- 519s CLEANING UP AND SHUTTING DOWN... 519s Destroying force arrays. 519s No energy arrays to destroy. 519s Destroying multigrid structures. 519s Destroying finite element structures. 519s Destroying 3 molecules 519s Final memory usage: 0.001 MB total, 61.068 MB high water 519s 519s 519s Thanks for using APBS! 519s 519s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 519s *** PASSED *** 519s Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) 519s *** PASSED *** 519s Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) 519s *** PASSED *** 519s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 519s *** PASSED *** 519s Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) 519s *** PASSED *** 519s Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) 519s *** PASSED *** 519s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 519s *** PASSED *** 519s Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) 519s *** PASSED *** 519s Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) 519s *** PASSED *** 519s Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) 519s *** PASSED *** 519s Elapsed time: 1.091305 seconds 519s -------------------------------------------------------------------------------- 519s -------------------------------------------------------------------------------- 519s Testing input file complex-0_4.in 519s 520s Checking for intermediate energies in input file complex-0_3.out 520s EXPECTED COMPUTED: 13 520s EXPECTED EXPECTED: 13 520s 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] 520s 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'] 520s COMPUTED RESULT 97.76035707281 520s COMPUTED RESULT 133.7661883222 520s COMPUTED RESULT 237.436145212 520s COMPUTED RESULT 0.0 520s COMPUTED RESULT 0.0 520s COMPUTED RESULT 0.0 520s COMPUTED RESULT 97.7604 520s COMPUTED RESULT 133.766 520s COMPUTED RESULT 237.436 520s COMPUTED RESULT 96.5336 520s COMPUTED RESULT 132.672 520s COMPUTED RESULT 232.924 520s COMPUTED RESULT 5.909599816984 520s BINARY: /usr/bin/apbs 520s INPUT: complex-0_4.in 520s COMMAND: ['/usr/bin/apbs', 'complex-0_4.in'] 520s asc_getToken: Error occurred (bailing out). 520s Vio_scanf: Format problem with input. 520s 520s 520s ---------------------------------------------------------------------- 520s APBS -- Adaptive Poisson-Boltzmann Solver 520s Version APBS 3.4.1 520s 520s Nathan A. Baker (nathan.baker@pnnl.gov) 520s Pacific Northwest National Laboratory 520s 520s Additional contributing authors listed in the code documentation. 520s 520s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 520s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 520s Northwest Division for the U.S. Department of Energy. 520s 520s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 520s Portions Copyright (c) 2002-2020, Nathan A. Baker. 520s Portions Copyright (c) 1999-2002, The Regents of the University of California. 520s Portions Copyright (c) 1995, Michael Holst. 520s All rights reserved. 520s 520s Redistribution and use in source and binary forms, with or without 520s modification, are permitted provided that the following conditions are met: 520s 520s * Redistributions of source code must retain the above copyright notice, this 520s list of conditions and the following disclaimer. 520s 520s * Redistributions in binary form must reproduce the above copyright notice, 520s this list of conditions and the following disclaimer in the documentation 520s and/or other materials provided with the distribution. 520s 520s * Neither the name of the developer nor the names of its contributors may be 520s used to endorse or promote products derived from this software without 520s specific prior written permission. 520s 520s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 520s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 520s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 520s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 520s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 520s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 520s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 520s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 520s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 520s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 520s ---------------------------------------------------------------------- 520s APBS uses FETK (the Finite Element ToolKit) to solve the 520s Poisson-Boltzmann equation numerically. FETK is a portable collection 520s of finite element modeling class libraries developed by the Michael Holst 520s research group and written in an object-oriented form of C. FEtk is 520s designed to solve general coupled systems of nonlinear partial differential 520s equations using adaptive finite element methods, inexact Newton methods, 520s and algebraic multilevel methods. More information about FEtk may be found 520s at . 520s ---------------------------------------------------------------------- 520s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 520s Aqua is a modified form of the Holst group PMG library 520s which has been modified by Patrice Koehl 520s for improved efficiency and 520s memory usage when solving the Poisson-Boltzmann equation. 520s ---------------------------------------------------------------------- 520s Please cite your use of APBS as: 520s 520s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 520s nanosystems: application to microtubules and the ribosome. Proc. 520s Natl. Acad. Sci. USA 98, 10037-10041 2001. 520s 520s 520s This executable compiled on Jan 3 2025 at 11:01:42 520s 520s Parsing input file complex-0_4.in... 520s rank 0 size 1... 520s Parsed input file. 520s Got paths for 3 molecules 520s Reading PQR-format atom data from mol0.pqr. 520s asc_getToken: Error occurred (bailing out). 520s Vio_scanf: Format problem with input. 520s 1 atoms 520s Centered at (-3.000e+00, 0.000e+00, 0.000e+00) 520s Net charge 1.00e+00 e 520s Reading PQR-format atom data from mol4.pqr. 520s asc_getToken: Error occurred (bailing out). 520s Vio_scanf: Format problem with input. 520s 1 atoms 520s Centered at (1.000e+00, 0.000e+00, 0.000e+00) 520s Net charge 1.00e+00 e 520s Reading PQR-format atom data from complex-0_4.pqr. 520s 2 atoms 520s Centered at (-1.000e+00, 0.000e+00, 0.000e+00) 520s Net charge 2.00e+00 e 520s Preparing to run 3 PBE calculations. 520s ---------------------------------------- 520s CALCULATION #1 (point1): MULTIGRID 520s Setting up problem... 520s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 520s Debye length: 0 A 520s Current memory usage: 61.060 MB total, 61.060 MB high water 520s Using linear spline charge discretization. 520s Grid dimensions: 65 x 65 x 65 520s Grid spacings: 0.210 x 0.210 x 0.210 520s Grid lengths: 13.440 x 13.440 x 13.440 520s Grid center: (0.000, 0.000, 0.000) 520s Multigrid levels: 5 520s Molecule ID: 1 520s Linearized traditional PBE 520s Multiple Debye-Huckel sphere boundary conditions 520s 0 ion species (0.000 M ionic strength): 520s Solute dielectric: 78.540 520s Solvent dielectric: 78.540 520s Using spline-based surface definition;window = 0.300 520s Temperature: 298.150 K 520s Electrostatic energies will be calculated 520s Total electrostatic energy = 9.776035707281E+01 kJ/mol 520s Fixed charge energy = 97.7604 kJ/mol 520s Mobile charge energy = 0 kJ/mol 520s Dielectric energy = 96.5336 kJ/mol 520s Per-atom energies: 520s Atom 0: 9.776035707281E+01 kJ/mol 520s Calculating forces... 520s ---------------------------------------- 520s CALCULATION #2 (point2): MULTIGRID 520s Setting up problem... 520s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 520s Debye length: 0 A 520s Current memory usage: 61.060 MB total, 61.067 MB high water 520s Using linear spline charge discretization. 520s Grid dimensions: 65 x 65 x 65 520s Grid spacings: 0.210 x 0.210 x 0.210 520s Grid lengths: 13.440 x 13.440 x 13.440 520s Grid center: (0.000, 0.000, 0.000) 520s Multigrid levels: 5 520s Molecule ID: 2 520s Linearized traditional PBE 520s Multiple Debye-Huckel sphere boundary conditions 520s 0 ion species (0.000 M ionic strength): 520s Solute dielectric: 78.540 520s Solvent dielectric: 78.540 520s Using spline-based surface definition;window = 0.300 520s Temperature: 298.150 K 520s Electrostatic energies will be calculated 520s Total electrostatic energy = 1.017611498797E+02 kJ/mol 520s Fixed charge energy = 101.761 kJ/mol 520s Mobile charge energy = 0 kJ/mol 520s Dielectric energy = 100.654 kJ/mol 520s Per-atom energies: 520s Atom 0: 1.017611498797E+02 kJ/mol 520s Calculating forces... 520s ---------------------------------------- 520s CALCULATION #3 (complex): MULTIGRID 520s Setting up problem... 520s Vpbe_ctor: Using max ion radius (0 A) for exclusion function 520s Debye length: 0 A 520s Current memory usage: 61.061 MB total, 61.068 MB high water 520s Using linear spline charge discretization. 520s Grid dimensions: 65 x 65 x 65 520s Grid spacings: 0.210 x 0.210 x 0.210 520s Grid lengths: 13.440 x 13.440 x 13.440 520s Grid center: (0.000, 0.000, 0.000) 520s Multigrid levels: 5 520s Molecule ID: 3 520s Linearized traditional PBE 520s Multiple Debye-Huckel sphere boundary conditions 520s 0 ion species (0.000 M ionic strength): 520s Solute dielectric: 78.540 520s Solvent dielectric: 78.540 520s Using spline-based surface definition;window = 0.300 520s Temperature: 298.150 K 520s Electrostatic energies will be calculated 520s Total electrostatic energy = 2.039516519000E+02 kJ/mol 520s Fixed charge energy = 203.952 kJ/mol 520s Mobile charge energy = 0 kJ/mol 520s Dielectric energy = 199.493 kJ/mol 520s Per-atom energies: 520s Atom 0: 9.997541697022E+01 kJ/mol 520s Atom 1: 1.039762349297E+02 kJ/mol 520s Calculating forces... 520s ---------------------------------------- 520s PRINT STATEMENTS 520s 520s print energy 3 (complex) - 1 (point1) - 2 (point2) end 520s Local net energy (PE 0) = 4.430144947418E+00 kJ/mol 520s Global net ELEC energy = 4.430144947418E+00 kJ/mol 520s ---------------------------------------- 520s CLEANING UP AND SHUTTING DOWN... 520s Destroying force arrays. 520s No energy arrays to destroy. 520s Destroying multigrid structures. 520s Destroying finite element structures. 520s Destroying 3 molecules 520s Final memory usage: 0.001 MB total, 61.068 MB high water 520s 520s 520s Thanks for using APBS! 520s 520s Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) 520s *** PASSED *** 520s Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) 520s *** PASSED *** 520s Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) 520s *** PASSED *** 520s Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) 520s *** PASSED *** 520s Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) 520s *** PASSED *** 520s Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) 520s *** PASSED *** 520s Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) 520s *** PASSED *** 520s Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) 520s *** PASSED *** 520s Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) 520s *** PASSED *** 520s Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) 520s *** PASSED *** 520s Elapsed time: 1.080905 seconds 520s -------------------------------------------------------------------------------- 520s Total elapsed time: 4.362118 seconds 520s Test results have been logged 520s -------------------------------------------------------------------------------- 520s -------------------------------------------------------------------------------- 520s Testing input file apbs-mol.in 520s 522s Checking for intermediate energies in input file complex-0_4.out 522s EXPECTED COMPUTED: 13 522s EXPECTED EXPECTED: 13 522s 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] 522s 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'] 522s COMPUTED RESULT 97.76035707281 522s COMPUTED RESULT 101.7611498797 522s COMPUTED RESULT 203.9516519 522s COMPUTED RESULT 0.0 522s COMPUTED RESULT 0.0 522s COMPUTED RESULT 0.0 522s COMPUTED RESULT 97.7604 522s COMPUTED RESULT 101.761 522s COMPUTED RESULT 203.952 522s COMPUTED RESULT 96.5336 522s COMPUTED RESULT 100.654 522s COMPUTED RESULT 199.493 522s COMPUTED RESULT 4.430144947418 522s Running tests for solv section 522s BINARY: /usr/bin/apbs 522s INPUT: apbs-mol.in 522s COMMAND: ['/usr/bin/apbs', 'apbs-mol.in'] 522s asc_getToken: Error occurred (bailing out). 522s Vio_scanf: Format problem with input. 522s 522s 522s ---------------------------------------------------------------------- 522s APBS -- Adaptive Poisson-Boltzmann Solver 522s Version APBS 3.4.1 522s 522s Nathan A. Baker (nathan.baker@pnnl.gov) 522s Pacific Northwest National Laboratory 522s 522s Additional contributing authors listed in the code documentation. 522s 522s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 522s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 522s Northwest Division for the U.S. Department of Energy. 522s 522s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 522s Portions Copyright (c) 2002-2020, Nathan A. Baker. 522s Portions Copyright (c) 1999-2002, The Regents of the University of California. 522s Portions Copyright (c) 1995, Michael Holst. 522s All rights reserved. 522s 522s Redistribution and use in source and binary forms, with or without 522s modification, are permitted provided that the following conditions are met: 522s 522s * Redistributions of source code must retain the above copyright notice, this 522s list of conditions and the following disclaimer. 522s 522s * Redistributions in binary form must reproduce the above copyright notice, 522s this list of conditions and the following disclaimer in the documentation 522s and/or other materials provided with the distribution. 522s 522s * Neither the name of the developer nor the names of its contributors may be 522s used to endorse or promote products derived from this software without 522s specific prior written permission. 522s 522s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 522s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 522s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 522s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 522s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 522s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 522s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 522s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 522s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 522s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 522s ---------------------------------------------------------------------- 522s APBS uses FETK (the Finite Element ToolKit) to solve the 522s Poisson-Boltzmann equation numerically. FETK is a portable collection 522s of finite element modeling class libraries developed by the Michael Holst 522s research group and written in an object-oriented form of C. FEtk is 522s designed to solve general coupled systems of nonlinear partial differential 522s equations using adaptive finite element methods, inexact Newton methods, 522s and algebraic multilevel methods. More information about FEtk may be found 522s at . 522s ---------------------------------------------------------------------- 522s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 522s Aqua is a modified form of the Holst group PMG library 522s which has been modified by Patrice Koehl 522s for improved efficiency and 522s memory usage when solving the Poisson-Boltzmann equation. 522s ---------------------------------------------------------------------- 522s Please cite your use of APBS as: 522s 522s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 522s nanosystems: application to microtubules and the ribosome. Proc. 522s Natl. Acad. Sci. USA 98, 10037-10041 2001. 522s 522s 522s This executable compiled on Jan 3 2025 at 11:01:42 522s 522s Parsing input file apbs-mol.in... 522s rank 0 size 1... 522s Parsed input file. 522s Got paths for 2 molecules 522s Reading PQR-format atom data from methanol.pqr. 522s asc_getToken: Error occurred (bailing out). 522s Vio_scanf: Format problem with input. 522s 3 atoms 522s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 522s Net charge 5.55e-17 e 522s Reading PQR-format atom data from methoxide.pqr. 522s 2 atoms 522s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 522s Net charge -1.00e+00 e 522s Preparing to run 4 PBE calculations. 522s ---------------------------------------- 522s CALCULATION #1 (methanol-solv): MULTIGRID 522s Setting up problem... 522s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 522s Debye length: 0 A 522s Current memory usage: 61.253 MB total, 61.253 MB high water 522s Using linear spline charge discretization. 522s Grid dimensions: 65 x 65 x 65 522s Grid spacings: 0.250 x 0.250 x 0.250 522s Grid lengths: 16.000 x 16.000 x 16.000 522s Grid center: (0.309, 0.000, -0.242) 522s Multigrid levels: 5 522s Molecule ID: 1 522s Linearized traditional PBE 522s Multiple Debye-Huckel sphere boundary conditions 522s 2 ion species (0.000 M ionic strength): 522s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 522s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 522s Solute dielectric: 2.000 522s Solvent dielectric: 78.000 522s Using "molecular" surface definition; no smoothing 522s Solvent probe radius: 0.000 A 522s Temperature: 300.000 K 522s Electrostatic energies will be calculated 522s Total electrostatic energy = 1.847663548071E+03 kJ/mol 522s Calculating forces... 522s ---------------------------------------- 522s CALCULATION #2 (methanol-ref): MULTIGRID 522s Setting up problem... 522s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 522s Debye length: 0 A 522s Current memory usage: 61.253 MB total, 61.328 MB high water 522s Using linear spline charge discretization. 522s Grid dimensions: 65 x 65 x 65 522s Grid spacings: 0.250 x 0.250 x 0.250 522s Grid lengths: 16.000 x 16.000 x 16.000 522s Grid center: (0.309, 0.000, -0.242) 522s Multigrid levels: 5 522s Molecule ID: 1 522s Linearized traditional PBE 522s Multiple Debye-Huckel sphere boundary conditions 522s 2 ion species (0.000 M ionic strength): 522s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 522s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 522s Solute dielectric: 2.000 522s Solvent dielectric: 1.000 522s Using "molecular" surface definition; no smoothing 522s Solvent probe radius: 0.000 A 522s Temperature: 300.000 K 522s Electrostatic energies will be calculated 522s Total electrostatic energy = 1.883912182952E+03 kJ/mol 522s Calculating forces... 522s ---------------------------------------- 522s CALCULATION #3 (methoxide-solv): MULTIGRID 522s Setting up problem... 522s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 522s Debye length: 0 A 522s Current memory usage: 61.250 MB total, 61.328 MB high water 522s Using linear spline charge discretization. 522s Grid dimensions: 65 x 65 x 65 522s Grid spacings: 0.250 x 0.250 x 0.250 522s Grid lengths: 16.000 x 16.000 x 16.000 522s Grid center: (0.000, 0.000, -0.128) 522s Multigrid levels: 5 522s Molecule ID: 2 522s Linearized traditional PBE 522s Multiple Debye-Huckel sphere boundary conditions 522s 2 ion species (0.000 M ionic strength): 522s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 522s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 522s Solute dielectric: 2.000 522s Solvent dielectric: 78.000 522s Using "molecular" surface definition; no smoothing 522s Solvent probe radius: 0.000 A 522s Temperature: 300.000 K 522s Electrostatic energies will be calculated 522s Total electrostatic energy = 2.732623683321E+03 kJ/mol 522s Calculating forces... 522s ---------------------------------------- 522s CALCULATION #4 (methoxide-ref): MULTIGRID 522s Setting up problem... 522s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 522s Debye length: 0 A 522s Current memory usage: 61.250 MB total, 61.328 MB high water 522s Using linear spline charge discretization. 522s Grid dimensions: 65 x 65 x 65 522s Grid spacings: 0.250 x 0.250 x 0.250 522s Grid lengths: 16.000 x 16.000 x 16.000 522s Grid center: (0.000, 0.000, -0.128) 522s Multigrid levels: 5 522s Molecule ID: 2 522s Linearized traditional PBE 522s Multiple Debye-Huckel sphere boundary conditions 522s 2 ion species (0.000 M ionic strength): 522s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 522s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 522s Solute dielectric: 2.000 522s Solvent dielectric: 1.000 522s Using "molecular" surface definition; no smoothing 522s Solvent probe radius: 0.000 A 522s Temperature: 300.000 K 522s Electrostatic energies will be calculated 522s Total electrostatic energy = 3.123035854133E+03 kJ/mol 522s Calculating forces... 522s ---------------------------------------- 522s PRINT STATEMENTS 522s 522s print energy 1 (methanol-solv) - 2 (methanol-ref) end 522s Local net energy (PE 0) = -3.624863488075E+01 kJ/mol 522s Global net ELEC energy = -3.624863488075E+01 kJ/mol 522s 522s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 522s Local net energy (PE 0) = -3.904121708125E+02 kJ/mol 522s Global net ELEC energy = -3.904121708125E+02 kJ/mol 522s 522s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 522s Local net energy (PE 0) = -3.541635359318E+02 kJ/mol 522s Global net ELEC energy = -3.541635359318E+02 kJ/mol 522s ---------------------------------------- 522s CLEANING UP AND SHUTTING DOWN... 522s Destroying force arrays. 522s No energy arrays to destroy. 522s Destroying multigrid structures. 522s Destroying finite element structures. 522s Destroying 2 molecules 522s Final memory usage: 0.001 MB total, 61.328 MB high water 522s 522s 522s Thanks for using APBS! 522s 522s Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) 522s *** PASSED *** 522s Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) 522s *** PASSED *** 522s Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) 522s *** PASSED *** 522s Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) 522s *** PASSED *** 522s Testing computed result against expected result (-3.624863488075e+01, -3.624863445503e+01) 522s *** PASSED *** 522s Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) 522s *** PASSED *** 522s Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) 522s *** PASSED *** 522s Elapsed time: 1.662344 seconds 522s -------------------------------------------------------------------------------- 522s -------------------------------------------------------------------------------- 522s Testing input file apbs-smol.in 522s 523s Checking for intermediate energies in input file apbs-mol.out 523s EXPECTED COMPUTED: 7 523s EXPECTED EXPECTED: 7 523s COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488075, -390.4121708125, -354.1635359318] 523s EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] 523s COMPUTED RESULT 1847.663548071 523s COMPUTED RESULT 1883.912182952 523s COMPUTED RESULT 2732.623683321 523s COMPUTED RESULT 3123.035854133 523s COMPUTED RESULT -36.24863488075 523s COMPUTED RESULT -390.4121708125 523s COMPUTED RESULT -354.1635359318 523s BINARY: /usr/bin/apbs 523s INPUT: apbs-smol.in 523s COMMAND: ['/usr/bin/apbs', 'apbs-smol.in'] 523s asc_getToken: Error occurred (bailing out). 523s Vio_scanf: Format problem with input. 523s 523s 523s ---------------------------------------------------------------------- 523s APBS -- Adaptive Poisson-Boltzmann Solver 523s Version APBS 3.4.1 523s 523s Nathan A. Baker (nathan.baker@pnnl.gov) 523s Pacific Northwest National Laboratory 523s 523s Additional contributing authors listed in the code documentation. 523s 523s Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific 523s Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific 523s Northwest Division for the U.S. Department of Energy. 523s 523s Portions Copyright (c) 2002-2010, Washington University in St. Louis. 523s Portions Copyright (c) 2002-2020, Nathan A. Baker. 523s Portions Copyright (c) 1999-2002, The Regents of the University of California. 523s Portions Copyright (c) 1995, Michael Holst. 523s All rights reserved. 523s 523s Redistribution and use in source and binary forms, with or without 523s modification, are permitted provided that the following conditions are met: 523s 523s * Redistributions of source code must retain the above copyright notice, this 523s list of conditions and the following disclaimer. 523s 523s * Redistributions in binary form must reproduce the above copyright notice, 523s this list of conditions and the following disclaimer in the documentation 523s and/or other materials provided with the distribution. 523s 523s * Neither the name of the developer nor the names of its contributors may be 523s used to endorse or promote products derived from this software without 523s specific prior written permission. 523s 523s THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 523s ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 523s WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 523s DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 523s ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 523s (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 523s LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND 523s ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 523s (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 523s SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 523s ---------------------------------------------------------------------- 523s APBS uses FETK (the Finite Element ToolKit) to solve the 523s Poisson-Boltzmann equation numerically. FETK is a portable collection 523s of finite element modeling class libraries developed by the Michael Holst 523s research group and written in an object-oriented form of C. FEtk is 523s designed to solve general coupled systems of nonlinear partial differential 523s equations using adaptive finite element methods, inexact Newton methods, 523s and algebraic multilevel methods. More information about FEtk may be found 523s at . 523s ---------------------------------------------------------------------- 523s APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. 523s Aqua is a modified form of the Holst group PMG library 523s which has been modified by Patrice Koehl 523s for improved efficiency and 523s memory usage when solving the Poisson-Boltzmann equation. 523s ---------------------------------------------------------------------- 523s Please cite your use of APBS as: 523s 523s Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 523s nanosystems: application to microtubules and the ribosome. Proc. 523s Natl. Acad. Sci. USA 98, 10037-10041 2001. 523s 523s 523s This executable compiled on Jan 3 2025 at 11:01:42 523s 523s Parsing input file apbs-smol.in... 523s rank 0 size 1... 523s Parsed input file. 523s Got paths for 2 molecules 523s Reading PQR-format atom data from methanol.pqr. 523s asc_getToken: Error occurred (bailing out). 523s Vio_scanf: Format problem with input. 523s 3 atoms 523s Centered at (3.086e-01, 0.000e+00, -2.417e-01) 523s Net charge 5.55e-17 e 523s Reading PQR-format atom data from methoxide.pqr. 523s 2 atoms 523s Centered at (0.000e+00, 0.000e+00, -1.279e-01) 523s Net charge -1.00e+00 e 523s Preparing to run 4 PBE calculations. 523s ---------------------------------------- 523s CALCULATION #1 (methanol-solv): MULTIGRID 523s Setting up problem... 523s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 523s Debye length: 0 A 523s Current memory usage: 61.253 MB total, 61.253 MB high water 523s Using linear spline charge discretization. 523s Grid dimensions: 65 x 65 x 65 523s Grid spacings: 0.250 x 0.250 x 0.250 523s Grid lengths: 16.000 x 16.000 x 16.000 523s Grid center: (0.309, 0.000, -0.242) 523s Multigrid levels: 5 523s Molecule ID: 1 523s Linearized traditional PBE 523s Multiple Debye-Huckel sphere boundary conditions 523s 2 ion species (0.000 M ionic strength): 523s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 523s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 523s Solute dielectric: 2.000 523s Solvent dielectric: 78.000 523s Using "molecular" surface definition;harmonic average smoothing 523s Solvent probe radius: 0.000 A 523s Temperature: 300.000 K 523s Electrostatic energies will be calculated 523s Total electrostatic energy = 1.847860440020E+03 kJ/mol 523s Calculating forces... 523s ---------------------------------------- 523s CALCULATION #2 (methanol-ref): MULTIGRID 523s Setting up problem... 523s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 523s Debye length: 0 A 523s Current memory usage: 61.253 MB total, 61.328 MB high water 523s Using linear spline charge discretization. 523s Grid dimensions: 65 x 65 x 65 523s Grid spacings: 0.250 x 0.250 x 0.250 523s Grid lengths: 16.000 x 16.000 x 16.000 523s Grid center: (0.309, 0.000, -0.242) 523s Multigrid levels: 5 523s Molecule ID: 1 523s Linearized traditional PBE 523s Multiple Debye-Huckel sphere boundary conditions 523s 2 ion species (0.000 M ionic strength): 523s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 523s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 523s Solute dielectric: 2.000 523s Solvent dielectric: 1.000 523s Using "molecular" surface definition;harmonic average smoothing 523s Solvent probe radius: 0.000 A 523s Temperature: 300.000 K 523s Electrostatic energies will be calculated 523s Total electrostatic energy = 1.885436377745E+03 kJ/mol 523s Calculating forces... 523s ---------------------------------------- 523s CALCULATION #3 (methoxide-solv): MULTIGRID 523s Setting up problem... 523s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 523s Debye length: 0 A 523s Current memory usage: 61.250 MB total, 61.328 MB high water 523s Using linear spline charge discretization. 523s Grid dimensions: 65 x 65 x 65 523s Grid spacings: 0.250 x 0.250 x 0.250 523s Grid lengths: 16.000 x 16.000 x 16.000 523s Grid center: (0.000, 0.000, -0.128) 523s Multigrid levels: 5 523s Molecule ID: 2 523s Linearized traditional PBE 523s Multiple Debye-Huckel sphere boundary conditions 523s 2 ion species (0.000 M ionic strength): 523s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 523s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 523s Solute dielectric: 2.000 523s Solvent dielectric: 78.000 523s Using "molecular" surface definition;harmonic average smoothing 523s Solvent probe radius: 0.000 A 523s Temperature: 300.000 K 523s Electrostatic energies will be calculated 523s Total electrostatic energy = 2.734040568569E+03 kJ/mol 523s Calculating forces... 523s ---------------------------------------- 523s CALCULATION #4 (methoxide-ref): MULTIGRID 523s Setting up problem... 523s Vpbe_ctor: Using max ion radius (2 A) for exclusion function 523s Debye length: 0 A 523s Current memory usage: 61.250 MB total, 61.328 MB high water 523s Using linear spline charge discretization. 523s Grid dimensions: 65 x 65 x 65 523s Grid spacings: 0.250 x 0.250 x 0.250 523s Grid lengths: 16.000 x 16.000 x 16.000 523s Grid center: (0.000, 0.000, -0.128) 523s Multigrid levels: 5 523s Molecule ID: 2 523s Linearized traditional PBE 523s Multiple Debye-Huckel sphere boundary conditions 523s 2 ion species (0.000 M ionic strength): 523s 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 523s 2.000 A-radius, -1.000 e-charge, 0.000 M concentration 523s Solute dielectric: 2.000 523s Solvent dielectric: 1.000 523s Using "molecular" surface definition;harmonic average smoothing 523s Solvent probe radius: 0.000 A 523s Temperature: 300.000 K 523s Electrostatic energies will be calculated 523s Total electrostatic energy = 3.125279428954E+03 kJ/mol 523s Calculating forces... 523s ---------------------------------------- 523s PRINT STATEMENTS 523s 523s print energy 1 (methanol-solv) - 2 (methanol-ref) end 523s Local net energy (PE 0) = -3.757593772492E+01 kJ/mol 523s Global net ELEC energy = -3.757593772492E+01 kJ/mol 523s 523s print energy 3 (methoxide-solv) - 4 (methoxide-ref) end 523s Local net energy (PE 0) = -3.912388603848E+02 kJ/mol 523s Global net ELEC energy = -3.912388603848E+02 kJ/mol 523s 523s print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end 523s Local net energy (PE 0) = -3.536629226599E+02 kJ/mol 523s Global net ELEC energy = -3.536629226599E+02 kJ/mol 523s ---------------------------------------- 523s CLEANING UP AND SHUTTING DOWN... 523s Destroying force arrays. 523s No energy arrays to destroy. 523s Destroying multigrid structures. 523s Destroying finite element structures. 523s Destroying 2 molecules 523s Final memory usage: 0.001 MB total, 61.328 MB high water 523s 523s 523s Thanks for using APBS! 523s 523s Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) 523s *** PASSED *** 524s Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) 524s *** PASSED *** 524s Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) 524s *** PASSED *** 524s Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) 524s *** PASSED *** 524s Testing computed result against expected result (-3.757593772492e+01, -3.757593797629e+01) 524s *** PASSED *** 524s Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) 524s *** PASSED *** 524s Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) 524s *** PASSED *** 524s Elapsed time: 1.52248 seconds 524s -------------------------------------------------------------------------------- 524s Total elapsed time: 3.184824 seconds 524s Test results have been logged 524s -------------------------------------------------------------------------------- 524s Checking for intermediate energies in input file apbs-smol.out 524s EXPECTED COMPUTED: 7 524s EXPECTED EXPECTED: 7 524s COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772492, -391.2388603848, -353.6629226599] 524s EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] 524s COMPUTED RESULT 1847.86044002 524s COMPUTED RESULT 1885.436377745 524s COMPUTED RESULT 2734.040568569 524s COMPUTED RESULT 3125.279428954 524s COMPUTED RESULT -37.57593772492 524s COMPUTED RESULT -391.2388603848 524s COMPUTED RESULT -353.6629226599 524s autopkgtest [14:55:56]: test test-apbs: -----------------------] 525s test-apbs PASS 525s autopkgtest [14:55:57]: test test-apbs: - - - - - - - - - - results - - - - - - - - - - 525s autopkgtest [14:55:57]: @@@@@@@@@@@@@@@@@@@@ summary 525s test-apbs PASS