From 41e24f6e8be8395cda7e976a0ce991329117e08d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 29 Nov 2018 12:35:07 -0500 Subject: [PATCH] update log files for gcmc example --- ...c.co2.g++.1 => log.27Nov18.gcmc.co2.g++.1} | 86 +++---- ...c.h2o.g++.1 => log.27Nov18.gcmc.h2o.g++.1} | 168 ++++++------- ...cmc.lj.g++.1 => log.27Nov18.gcmc.lj.g++.1} | 22 +- ...cmc.lj.g++.4 => log.27Nov18.gcmc.lj.g++.4} | 22 +- examples/gcmc/log.30Mar18.gcmc.co2.g++.4 | 131 ---------- examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 | 237 ------------------ 6 files changed, 149 insertions(+), 517 deletions(-) rename examples/gcmc/{log.30Mar18.gcmc.co2.g++.1 => log.27Nov18.gcmc.co2.g++.1} (60%) rename examples/gcmc/{log.30Mar18.gcmc.h2o.g++.1 => log.27Nov18.gcmc.h2o.g++.1} (54%) rename examples/gcmc/{log.30Mar18.gcmc.lj.g++.1 => log.27Nov18.gcmc.lj.g++.1} (90%) rename examples/gcmc/{log.30Mar18.gcmc.lj.g++.4 => log.27Nov18.gcmc.lj.g++.4} (90%) delete mode 100644 examples/gcmc/log.30Mar18.gcmc.co2.g++.4 delete mode 100644 examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 diff --git a/examples/gcmc/log.30Mar18.gcmc.co2.g++.1 b/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 similarity index 60% rename from examples/gcmc/log.30Mar18.gcmc.co2.g++.1 rename to examples/gcmc/log.27Nov18.gcmc.co2.g++.1 index 46afe5ea2a..4ed9056d04 100644 --- a/examples/gcmc/log.30Mar18.gcmc.co2.g++.1 +++ b/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics # Rigid CO2 TraPPE model @@ -46,7 +46,7 @@ Read molecule co2mol: 0 impropers with max type 0 create_atoms 0 box mol co2mol 464563 units box Created 24 atoms - Time spent = 0.00241756 secs + Time spent = 0.00134993 secs # rigid CO2 TraPPE model @@ -118,16 +118,16 @@ thermo 1000 run 20000 Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.164636 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) +WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -143,54 +143,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 - 1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18 - 2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20 - 3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4 - 4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18 - 5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18 - 6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22 - 7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20 - 8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20 - 9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24 - 10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22 - 11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22 - 12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12 - 13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8 - 14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16 - 15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14 - 16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8 - 17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10 - 18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18 - 19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12 - 20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20 -Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms + 1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10 + 2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12 + 3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24 + 4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24 + 5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18 + 6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12 + 7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4 + 8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16 + 9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14 + 10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16 + 11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20 + 12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28 + 13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10 + 14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10 + 15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22 + 16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2 + 17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18 + 18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6 + 19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10 + 20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18 +Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms -Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s +98.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.8955 | 1.8955 | 1.8955 | 0.0 | 11.49 -Bond | 0.026564 | 0.026564 | 0.026564 | 0.0 | 0.16 -Kspace | 0.21215 | 0.21215 | 0.21215 | 0.0 | 1.29 -Neigh | 0.088336 | 0.088336 | 0.088336 | 0.0 | 0.54 -Comm | 0.19828 | 0.19828 | 0.19828 | 0.0 | 1.20 -Output | 0.001025 | 0.001025 | 0.001025 | 0.0 | 0.01 -Modify | 14.024 | 14.024 | 14.024 | 0.0 | 85.02 -Other | | 0.0491 | | | 0.30 +Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63 +Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11 +Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80 +Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54 +Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28 +Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01 +Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45 +Other | | 0.03692 | | | 0.18 -Nlocal: 30 ave 30 max 30 min +Nlocal: 27 ave 27 max 27 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2094 ave 2094 max 2094 min +Nghost: 2081 ave 2081 max 2081 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7664 ave 7664 max 7664 min +Neighs: 6264 ave 6264 max 6264 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 7664 -Ave neighs/atom = 255.467 +Total # of neighbors = 6264 +Ave neighs/atom = 232 Ave special neighs/atom = 2 -Neighbor list builds = 20076 +Neighbor list builds = 20177 Dangerous builds = 0 -Total wall time: 0:00:16 +Total wall time: 0:00:21 diff --git a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 b/examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 similarity index 54% rename from examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 rename to examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 index 2f11cb116e..86b8fa7b45 100644 --- a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 +++ b/examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # fix gcmc example with fix shake @@ -43,7 +43,7 @@ Read molecule h2omol: 0 impropers with max type 0 create_atoms 0 box mol h2omol 464563 units box Created 24 atoms - Time spent = 0.00204968 secs + Time spent = 0.00128841 secs # rigid SPC/E water model @@ -69,9 +69,9 @@ velocity all create 338.0 54654 timestep 1.0 minimize 0.0 0.0 100 1000 -WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 @@ -92,41 +92,41 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 338 -4.1890564 9.2628112e-06 18.98377 739.06991 - 100 338 -30.182886 0.85607237 -6.1539961 -2535.3207 -Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms + 100 338 -36.122455 0.67828405 -12.271354 573.22675 +Loop time of 0.0461962 on 1 procs for 100 steps with 24 atoms -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = - -4.18904713252 -28.9258064504 -29.3268133965 - Force two-norm initial, final = 18.0027 42.4511 - Force max component initial, final = 5.8993 16.0523 - Final line search alpha, max atom move = 0.00353207 0.056698 - Iterations, force evaluations = 100 238 + -4.18904713252 -34.586018764 -35.4441713339 + Force two-norm initial, final = 18.0027 42.115 + Force max component initial, final = 5.8993 15.4907 + Final line search alpha, max atom move = 0.00127226 0.0197082 + Iterations, force evaluations = 100 239 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04 -Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92 -Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81 -Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90 -Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65 -Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04 +Pair | 0.038526 | 0.038526 | 0.038526 | 0.0 | 83.40 +Bond | 0.00031209 | 0.00031209 | 0.00031209 | 0.0 | 0.68 +Kspace | 0.0019636 | 0.0019636 | 0.0019636 | 0.0 | 4.25 +Neigh | 0.00055456 | 0.00055456 | 0.00055456 | 0.0 | 1.20 +Comm | 0.0040288 | 0.0040288 | 0.0040288 | 0.0 | 8.72 +Output | 1.5259e-05 | 1.5259e-05 | 1.5259e-05 | 0.0 | 0.03 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0008392 | | | 1.64 +Other | | 0.0007958 | | | 1.72 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2047 ave 2047 max 2047 min +Nghost: 2011 ave 2011 max 2011 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4936 ave 4936 max 4936 min +Neighs: 4921 ave 4921 max 4921 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 4936 -Ave neighs/atom = 205.667 +Total # of neighbors = 4921 +Ave neighs/atom = 205.042 Ave special neighs/atom = 2 Neighbor list builds = 2 Dangerous builds = 0 @@ -150,7 +150,7 @@ compute_modify mynvt_temp dynamic/dof yes run 1000 Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 @@ -158,36 +158,36 @@ Ewald initialization ... kxmax kymax kzmax = 2 2 2 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp E_pair E_mol TotEng Press - 0 518.26667 -30.182886 0 -7.0100684 993.1985 - 1000 326.9865 -62.258443 0 -47.638173 -5.3439918 -Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms + 0 518.26667 -36.122455 0 -12.949638 703.43827 + 1000 260.39219 -55.141232 0 -43.498537 -1698.672 +Loop time of 0.140376 on 1 procs for 1000 steps with 24 atoms -Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 615.489 ns/day, 0.039 hours/ns, 7123.720 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94 -Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11 -Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99 -Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29 -Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17 -Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01 -Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11 -Other | | 0.001914 | | | 1.37 +Pair | 0.10434 | 0.10434 | 0.10434 | 0.0 | 74.33 +Bond | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.09 +Kspace | 0.008199 | 0.008199 | 0.008199 | 0.0 | 5.84 +Neigh | 0.0061581 | 0.0061581 | 0.0061581 | 0.0 | 4.39 +Comm | 0.015352 | 0.015352 | 0.015352 | 0.0 | 10.94 +Output | 1.4305e-05 | 1.4305e-05 | 1.4305e-05 | 0.0 | 0.01 +Modify | 0.004544 | 0.004544 | 0.004544 | 0.0 | 3.24 +Other | | 0.001639 | | | 1.17 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1660 ave 1660 max 1660 min +Nghost: 1776 ave 1776 max 1776 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5112 ave 5112 max 5112 min +Neighs: 5073 ave 5073 max 5073 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 5112 -Ave neighs/atom = 213 +Total # of neighbors = 5073 +Ave neighs/atom = 211.375 Ave special neighs/atom = 2 -Neighbor list builds = 25 +Neighbor list builds = 27 Dangerous builds = 0 reset_timestep 0 @@ -224,67 +224,67 @@ thermo 1000 run 20000 Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) +WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH - 0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16 - 1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50 - 2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54 - 3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66 - 4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66 - 5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68 - 6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68 - 7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70 - 8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70 - 9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70 - 10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70 - 11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72 - 12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72 - 13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72 - 14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72 - 15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72 - 16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74 - 17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74 - 18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74 - 19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74 - 20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74 -Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms + 0 260.39219 -1699.3643 -55.141232 11.642695 0.23910963 24 0 0 0 0 8 16 + 1000 340.44409 -2560.1501 -280.70157 53.784356 0.80699501 81 0.054205983 0.015933081 0 0 27 54 + 2000 302.57602 592.41718 -310.37771 53.213377 0.89666113 90 0.030546787 0.0078577743 0 0 30 60 + 3000 270.18045 -817.18659 -346.75773 50.737466 0.95643854 96 0.021969243 0.0060076096 0 0 32 64 + 4000 334.17192 1153.3017 -335.25519 62.75449 0.95643854 96 0.016400775 0.0045269353 0 0 32 64 + 5000 360.36872 -647.99689 -336.2928 67.674015 0.95643854 96 0.012996731 0.0036569014 0 0 32 64 + 6000 282.37822 -986.51765 -341.91848 53.028098 0.95643854 96 0.010941282 0.0030159847 0 0 32 64 + 7000 363.01448 2952.0391 -358.72963 70.335018 0.98632724 99 0.0098923151 0.0028884203 0 0 33 66 + 8000 331.70391 323.34886 -382.04165 68.223498 1.0461046 105 0.0092083323 0.0025112378 0 0 35 70 + 9000 337.2032 -3637.5257 -390.66472 69.35457 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70 + 10000 373.67063 3081.3271 -380.5107 76.855041 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70 + 11000 336.64665 5535.9451 -405.21548 71.247059 1.0759934 108 0.0068442571 0.0018355023 0 0 36 72 + 12000 306.51164 1448.1757 -410.3655 64.869362 1.0759934 108 0.0062798499 0.0016809265 0 0 36 72 + 13000 319.03497 177.44405 -406.17113 67.519768 1.0759934 108 0.0057952448 0.0015520479 0 0 36 72 + 14000 309.89701 -1022.6798 -384.20239 65.585833 1.0759934 108 0.005391524 0.0014384143 0 0 36 72 + 15000 398.91559 2058.9251 -404.32604 84.425503 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72 + 16000 318.98778 873.46142 -392.13338 67.50978 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72 + 17000 333.16025 2347.0215 -387.73943 70.509206 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72 + 18000 353.23789 -2305.787 -382.1633 74.758389 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72 + 19000 322.70939 5619.9631 -381.81328 68.297412 1.0759934 108 0.0039877848 0.0010558436 0 0 36 72 + 20000 371.07261 3916.1113 -389.76357 78.532884 1.0759934 108 0.0037874635 0.0010033009 0 0 36 72 +Loop time of 242.59 on 1 procs for 20000 steps with 108 atoms -Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 7.123 ns/day, 3.369 hours/ns, 82.444 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 39.09 | 39.09 | 39.09 | 0.0 | 16.90 -Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04 -Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38 -Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71 -Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46 -Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00 -Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43 -Other | | 0.1892 | | | 0.08 +Pair | 38.279 | 38.279 | 38.279 | 0.0 | 15.78 +Bond | 0.055672 | 0.055672 | 0.055672 | 0.0 | 0.02 +Kspace | 0.60623 | 0.60623 | 0.60623 | 0.0 | 0.25 +Neigh | 4.4189 | 4.4189 | 4.4189 | 0.0 | 1.82 +Comm | 1.2719 | 1.2719 | 1.2719 | 0.0 | 0.52 +Output | 0.00096583 | 0.00096583 | 0.00096583 | 0.0 | 0.00 +Modify | 197.85 | 197.85 | 197.85 | 0.0 | 81.56 +Other | | 0.1098 | | | 0.05 -Nlocal: 111 ave 111 max 111 min +Nlocal: 108 ave 108 max 108 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 8070 ave 8070 max 8070 min +Nghost: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 105469 ave 105469 max 105469 min +Neighs: 100006 ave 100006 max 100006 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 105469 -Ave neighs/atom = 950.171 +Total # of neighbors = 100006 +Ave neighs/atom = 925.981 Ave special neighs/atom = 2 -Neighbor list builds = 20910 +Neighbor list builds = 20903 Dangerous builds = 0 -Total wall time: 0:03:51 +Total wall time: 0:04:02 diff --git a/examples/gcmc/log.30Mar18.gcmc.lj.g++.1 b/examples/gcmc/log.27Nov18.gcmc.lj.g++.1 similarity index 90% rename from examples/gcmc/log.30Mar18.gcmc.lj.g++.1 rename to examples/gcmc/log.27Nov18.gcmc.lj.g++.1 index 20a25c0f95..1a6651fd4e 100644 --- a/examples/gcmc/log.30Mar18.gcmc.lj.g++.1 +++ b/examples/gcmc/log.27Nov18.gcmc.lj.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # GCMC for LJ simple fluid, no dynamics # T = 2.0 @@ -112,20 +112,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v 8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43 9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23 10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44 -Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms +Loop time of 27.8547 on 1 procs for 10000 steps with 64 atoms -Performance: 203381.368 tau/day, 470.790 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 155090.656 tau/day, 359.006 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.45931 | 0.45931 | 0.45931 | 0.0 | 2.16 -Neigh | 1.1637 | 1.1637 | 1.1637 | 0.0 | 5.48 -Comm | 0.17294 | 0.17294 | 0.17294 | 0.0 | 0.81 -Output | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.00 -Modify | 19.416 | 19.416 | 19.416 | 0.0 | 91.41 -Other | | 0.02919 | | | 0.14 +Pair | 0.43892 | 0.43892 | 0.43892 | 0.0 | 1.58 +Neigh | 1.278 | 1.278 | 1.278 | 0.0 | 4.59 +Comm | 0.24105 | 0.24105 | 0.24105 | 0.0 | 0.87 +Output | 0.00032067 | 0.00032067 | 0.00032067 | 0.0 | 0.00 +Modify | 25.88 | 25.88 | 25.88 | 0.0 | 92.91 +Other | | 0.01693 | | | 0.06 Nlocal: 64 ave 64 max 64 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -138,4 +138,4 @@ Total # of neighbors = 2423 Ave neighs/atom = 37.8594 Neighbor list builds = 10000 Dangerous builds = 0 -Total wall time: 0:00:21 +Total wall time: 0:00:27 diff --git a/examples/gcmc/log.30Mar18.gcmc.lj.g++.4 b/examples/gcmc/log.27Nov18.gcmc.lj.g++.4 similarity index 90% rename from examples/gcmc/log.30Mar18.gcmc.lj.g++.4 rename to examples/gcmc/log.27Nov18.gcmc.lj.g++.4 index 819d0ed086..6e59f3d484 100644 --- a/examples/gcmc/log.30Mar18.gcmc.lj.g++.4 +++ b/examples/gcmc/log.27Nov18.gcmc.lj.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # GCMC for LJ simple fluid, no dynamics # T = 2.0 @@ -112,20 +112,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v 8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45 9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73 10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04 -Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms +Loop time of 26.0069 on 4 procs for 10000 steps with 60 atoms -Performance: 147733.999 tau/day, 341.977 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 166109.741 tau/day, 384.513 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.11648 | 0.1221 | 0.13001 | 1.5 | 0.42 -Neigh | 0.34452 | 0.35618 | 0.36328 | 1.2 | 1.22 -Comm | 0.63561 | 0.65617 | 0.67542 | 1.8 | 2.24 -Output | 0.00056601 | 0.00069755 | 0.00074744 | 0.0 | 0.00 -Modify | 28.069 | 28.076 | 28.082 | 0.1 | 96.01 -Other | | 0.03094 | | | 0.11 +Pair | 0.10309 | 0.115 | 0.1225 | 2.2 | 0.44 +Neigh | 0.3907 | 0.40447 | 0.41957 | 1.7 | 1.56 +Comm | 0.44236 | 0.46678 | 0.49472 | 2.8 | 1.79 +Output | 0.0011411 | 0.0062903 | 0.0080109 | 3.7 | 0.02 +Modify | 25 | 25.002 | 25.005 | 0.0 | 96.14 +Other | | 0.01231 | | | 0.05 Nlocal: 15 ave 16 max 14 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -138,4 +138,4 @@ Total # of neighbors = 2116 Ave neighs/atom = 35.2667 Neighbor list builds = 10000 Dangerous builds = 0 -Total wall time: 0:00:29 +Total wall time: 0:00:26 diff --git a/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 b/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 deleted file mode 100644 index a824945cbf..0000000000 --- a/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 +++ /dev/null @@ -1,131 +0,0 @@ -LAMMPS (30 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics -# Rigid CO2 TraPPE model -# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of -# mixtures containing alkanes, carbon dioxide and -# nitrogen AIChE J., 47,1676-1682 (2001)]. - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with max type 2 - 2 bonds with max type 1 - 1 angles with max type 1 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00257635 secs - -# rigid CO2 TraPPE model - -pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 - -# masses - -mass 1 12.0107 -mass 2 15.9994 - -# MD settings - -group co2 type 1 2 -24 atoms in group co2 -neighbor 2.0 bin -neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -# rigid constraints with thermostat - -fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol -8 rigid bodies with 24 atoms - 1.16 = max distance from body owner to body atom - -# dynamically update fix rigid/nvt/small temperature ndof -fix_modify myrigidnvt dynamic/dof yes - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt - -# atom counts - -variable carbon atom "type==1" -variable oxygen atom "type==2" -group carbon dynamic co2 var carbon -dynamic group carbon defined -group oxygen dynamic co2 var oxygen -dynamic group oxygen defined -variable nC equal count(carbon) -variable nO equal count(oxygen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) - -# dynamically update default temperature ndof -compute_modify thermo_temp dynamic/dof yes - -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO -thermo 1000 - -# run - -run 20000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.164636 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721) -Last command: run 20000 diff --git a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 deleted file mode 100644 index c5caf57113..0000000000 --- a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 +++ /dev/null @@ -1,237 +0,0 @@ -LAMMPS (30 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# fix gcmc example with fix shake - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid - -molecule h2omol H2O.txt -Read molecule h2omol: - 3 atoms with max type 2 - 2 bonds with max type 1 - 1 angles with max type 1 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -create_atoms 0 box mol h2omol 464563 units box -Created 24 atoms - Time spent = 0.00285625 secs - -# rigid SPC/E water model - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_coeff 1 1000 1.0 -angle_coeff 1 100 109.47 - -# masses - -mass 1 15.9994 -mass 2 1.0 - -# MD settings - -group h2o type 1 2 -24 atoms in group h2o -neighbor 2.0 bin -neigh_modify every 1 delay 1 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -minimize 0.0 0.0 100 1000 -WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 2 2 2 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791 - 100 338 -15.742442 0.14954269 7.579918 -637.49568 -Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms - -94.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -4.96106135393 -15.5388622715 -15.592899346 - Force two-norm initial, final = 15.474 18.1478 - Force max component initial, final = 5.80042 7.56514 - Final line search alpha, max atom move = 0.00151131 0.0114333 - Iterations, force evaluations = 100 328 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34 -Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61 -Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08 -Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.006672 | | | 9.59 - -Nlocal: 6 ave 8 max 3 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 1722 ave 1725 max 1720 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 1256.75 ave 2101 max 667 min -Histogram: 1 0 1 0 1 0 0 0 0 1 - -Total # of neighbors = 5027 -Ave neighs/atom = 209.458 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 -reset_timestep 0 - -# rigid constraints with thermostat - -fix mynvt h2o nvt temp ${temp} ${temp} 100 -fix mynvt h2o nvt temp 338.0 ${temp} 100 -fix mynvt h2o nvt temp 338.0 338.0 100 -fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 8 = # of frozen angles - -# important to make temperature dofs dynamic - -compute_modify thermo_temp dynamic/dof yes -compute_modify mynvt_temp dynamic/dof yes - -run 1000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 518.26667 -15.742442 0 7.4303753 -613.0781 - 1000 369.81793 -54.202682 0 -37.667327 294.98832 -Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms - -Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s -96.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13 -Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14 -Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00 -Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35 -Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58 -Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03 -Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04 -Other | | 0.005226 | | | 2.73 - -Nlocal: 6 ave 8 max 3 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 1331.5 ave 1369 max 1290 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 1259.75 ave 1642 max 428 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 5039 -Ave neighs/atom = 209.958 -Ave special neighs/atom = 2 -Neighbor list builds = 27 -Dangerous builds = 0 -reset_timestep 0 - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake - -# atom counts - -variable oxygen atom "type==1" -variable hydrogen atom "type==2" -group oxygen dynamic all var oxygen -dynamic group oxygen defined -group hydrogen dynamic all var hydrogen -dynamic group hydrogen defined -variable nO equal count(oxygen) -variable nH equal count(hydrogen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH -thermo 1000 - -# run - -run 20000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721) -Last command: run 20000