From e4b14213b4b99e07973a91545dcaf17d95bd059a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Nov 2017 11:35:49 -0500 Subject: [PATCH] delete old log files. new log files are approved by @athomps --- examples/gcmc/log.6Jul17.gcmc.co2.g++.1 | 193 ---------------- examples/gcmc/log.6Jul17.gcmc.co2.g++.4 | 193 ---------------- examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 | 294 ------------------------ examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 | 294 ------------------------ examples/gcmc/log.6Jul17.gcmc.lj.g++.1 | 137 ----------- examples/gcmc/log.6Jul17.gcmc.lj.g++.4 | 137 ----------- 6 files changed, 1248 deletions(-) delete mode 100644 examples/gcmc/log.6Jul17.gcmc.co2.g++.1 delete mode 100644 examples/gcmc/log.6Jul17.gcmc.co2.g++.4 delete mode 100644 examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 delete mode 100644 examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 delete mode 100644 examples/gcmc/log.6Jul17.gcmc.lj.g++.1 delete mode 100644 examples/gcmc/log.6Jul17.gcmc.lj.g++.4 diff --git a/examples/gcmc/log.6Jul17.gcmc.co2.g++.1 b/examples/gcmc/log.6Jul17.gcmc.co2.g++.1 deleted file mode 100644 index 38bfa0bb87..0000000000 --- a/examples/gcmc/log.6Jul17.gcmc.co2.g++.1 +++ /dev/null @@ -1,193 +0,0 @@ -LAMMPS (22 Sep 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - 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 1 by 1 MPI processor grid -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00136113 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 all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt all 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 -fix_modify myrigidnvt dynamic/dof no - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all 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 all var carbon -dynamic group carbon defined -group oxygen dynamic all 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) -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 ... -WARNING: 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:445) -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:476) -Neighbor list info ... - update every 1 steps, delay 10 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) = 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 -WARNING: Using kspace solver on system with no charge (../kspace.cpp:289) - 1000 420.43475 1722.4052 -9.6956122 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16 - 2000 302.29516 -547.83642 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20 - 3000 316.6934 -1080.2673 -8.2218902 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14 - 4000 246.81614 -679.83628 -14.57724 10.299968 0.65771539 27 0.1568939 0.15860229 0 0 9 18 - 5000 260.23291 -896.27949 -16.097524 10.859868 0.65771539 27 0.13138744 0.13547049 0 0 9 18 - 6000 291.64889 -1524.1007 -22.306243 13.619816 0.73079488 30 0.12615476 0.12717694 0 0 10 20 - 7000 235.90417 -565.40879 -27.600934 13.360525 0.87695385 36 0.119703 0.12145398 0 0 12 24 - 8000 483.381 2017.6258 -7.1315833 15.369247 0.51155641 21 0.10942279 0.11082908 0 0 7 14 - 9000 468.87446 -285.22545 -0.22330095 0.93175047 0.073079488 3 0.13029748 0.13349433 0 0 1 2 - 10000 245.34708 -254.65444 -16.192443 11.457551 0.73079488 30 0.15023549 0.15176828 0 0 10 20 - 11000 233.27704 523.81197 -24.29051 12.052812 0.80387436 33 0.1438083 0.14547187 0 0 11 22 - 12000 230.75966 -2161.9134 -23.812352 11.922746 0.80387436 33 0.1338274 0.13534617 0 0 11 22 - 13000 216.09982 -930.72014 -23.138263 11.16531 0.80387436 33 0.12480714 0.12612138 0 0 11 22 - 14000 343.12403 -327.36241 -16.995149 16.023672 0.73079488 30 0.12006081 0.12108416 0 0 10 20 - 15000 369.60805 581.40471 -11.495738 13.588021 0.5846359 24 0.11372814 0.11534691 0 0 8 16 - 16000 221.23125 -918.58249 -30.702491 12.529519 0.87695385 36 0.11489536 0.11560548 0 0 12 24 - 17000 301.82269 -450.56586 -14.373996 12.595466 0.65771539 27 0.11226626 0.11350321 0 0 9 18 - 18000 1065.1385 474.31881 -0.45476519 7.4082761 0.14615898 6 0.11419593 0.11580815 0 0 2 4 - 19000 217.29422 -1111.0114 -12.048289 7.988458 0.5846359 24 0.12564213 0.1261457 0 0 8 16 - 20000 353.35515 465.29269 -6.8428553 9.4795613 0.43847693 18 0.12529827 0.12590018 0 0 6 12 -Loop time of 14.604 on 1 procs for 20000 steps with 18 atoms - -Performance: 118.323 ns/day, 0.203 hours/ns, 1369.484 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.8966 | 1.8966 | 1.8966 | 0.0 | 12.99 -Bond | 0.019538 | 0.019538 | 0.019538 | 0.0 | 0.13 -Kspace | 0.14784 | 0.14784 | 0.14784 | 0.0 | 1.01 -Neigh | 0.070002 | 0.070002 | 0.070002 | 0.0 | 0.48 -Comm | 0.15055 | 0.15055 | 0.15055 | 0.0 | 1.03 -Output | 0.0017672 | 0.0017672 | 0.0017672 | 0.0 | 0.01 -Modify | 12.287 | 12.287 | 12.287 | 0.0 | 84.13 -Other | | 0.03089 | | | 0.21 - -Nlocal: 18 ave 18 max 18 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1335 ave 1335 max 1335 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2797 ave 2797 max 2797 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2797 -Ave neighs/atom = 155.389 -Ave special neighs/atom = 2 -Neighbor list builds = 20401 -Dangerous builds = 0 - -Total wall time: 0:00:14 diff --git a/examples/gcmc/log.6Jul17.gcmc.co2.g++.4 b/examples/gcmc/log.6Jul17.gcmc.co2.g++.4 deleted file mode 100644 index 6b39fda263..0000000000 --- a/examples/gcmc/log.6Jul17.gcmc.co2.g++.4 +++ /dev/null @@ -1,193 +0,0 @@ -LAMMPS (22 Sep 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - 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 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00223303 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 all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt all 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 -fix_modify myrigidnvt dynamic/dof no - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all 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 all var carbon -dynamic group carbon defined -group oxygen dynamic all 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) -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 ... -WARNING: 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:445) -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:476) -Neighbor list info ... - update every 1 steps, delay 10 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) = 15.41 | 15.41 | 15.41 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO - 0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16 -WARNING: Using kspace solver on system with no charge (../kspace.cpp:289) - 1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10 - 2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6 - 3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26 - 4000 182.70803 -1059.2265 -43.04484 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28 - 5000 234.00901 -1821.0459 -46.047939 15.578313 1.0231128 42 0.13498091 0.13704201 0 0 14 28 - 6000 163.42358 -774.64962 -49.686149 11.691232 1.0961923 45 0.11401677 0.11296973 0 0 15 30 - 7000 171.36765 -359.28792 -49.34022 12.259546 1.0961923 45 0.098302308 0.098552065 0 0 15 30 - 8000 215.2905 -905.73479 -38.206404 13.262629 0.95003334 39 0.086608098 0.086135456 0 0 13 26 - 9000 185.19905 -2320.8255 -52.964346 13.249037 1.0961923 45 0.077379246 0.077059206 0 0 15 30 - 10000 241.5783 -1410.8134 -51.37248 17.282377 1.0961923 45 0.069600048 0.069395413 0 0 15 30 - 11000 153.38332 -2647.9572 -53.967244 10.972957 1.0961923 45 0.063207938 0.06315287 0 0 15 30 - 12000 188.93059 -1639.9304 -52.218219 13.515989 1.0961923 45 0.05816163 0.058001715 0 0 15 30 - 13000 243.39974 -1127.2881 -44.54519 16.203468 1.0231128 42 0.053682268 0.053700858 0 0 14 28 - 14000 200.88474 -272.11992 -41.725507 13.373183 1.0231128 42 0.050212054 0.050071222 0 0 14 28 - 15000 204.6505 -1616.9057 -44.631997 13.623875 1.0231128 42 0.046944632 0.046920585 0 0 14 28 - 16000 169.22546 105.40991 -42.46103 11.26558 1.0231128 42 0.044460451 0.044287314 0 0 14 28 - 17000 163.55389 -783.34837 -36.841459 10.075477 0.95003334 39 0.042304052 0.042283048 0 0 13 26 - 18000 499.48334 -503.24838 -8.94456 15.881226 0.51155641 21 0.04035334 0.040870565 0 0 7 14 - 19000 658.81004 391.68747 -2.6979013 11.12813 0.29231795 12 0.055391781 0.056188676 0 0 4 8 - 20000 489.87356 -122.40743 -13.636951 18.00938 0.5846359 24 0.061378424 0.061821941 0 0 8 16 -Loop time of 17.1274 on 4 procs for 20000 steps with 24 atoms - -Performance: 100.891 ns/day, 0.238 hours/ns, 1167.718 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.81646 | 1.1504 | 1.4937 | 23.0 | 6.72 -Bond | 0.011878 | 0.012255 | 0.013296 | 0.5 | 0.07 -Kspace | 0.23802 | 0.58086 | 0.91304 | 32.3 | 3.39 -Neigh | 0.04321 | 0.043291 | 0.043372 | 0.0 | 0.25 -Comm | 0.90855 | 0.90959 | 0.91112 | 0.1 | 5.31 -Output | 0.0011697 | 0.0012506 | 0.001482 | 0.4 | 0.01 -Modify | 14.362 | 14.365 | 14.367 | 0.1 | 83.87 -Other | | 0.06436 | | | 0.38 - -Nlocal: 6 ave 8 max 4 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 1465.25 ave 1556 max 1376 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 1243.5 ave 1726 max 748 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 4974 -Ave neighs/atom = 207.25 -Ave special neighs/atom = 2 -Neighbor list builds = 20375 -Dangerous builds = 0 - -Total wall time: 0:00:17 diff --git a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 b/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 deleted file mode 100644 index a40760d25f..0000000000 --- a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 +++ /dev/null @@ -1,294 +0,0 @@ -LAMMPS (22 Sep 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - 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 1 by 1 MPI processor grid - -# we can load multiple molecule templates, but don't have to use them all -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -molecule h2omol H2O.txt -Read molecule h2omol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -create_atoms 0 box mol h2omol 464563 units box -Created 24 atoms - Time spent = 0.00136209 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 ... -WARNING: 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) = 11.88 | 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 -27.771871 0.61137788 -3.9876753 -2259.9107 -Loop time of 0.0333829 on 1 procs for 100 steps with 24 atoms - -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -4.18904713252 -26.8589493819 -27.1604926722 - Force two-norm initial, final = 18.0027 28.6823 - Force max component initial, final = 5.8993 11.77 - Final line search alpha, max atom move = 0.00301381 0.0354725 - Iterations, force evaluations = 100 239 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.028252 | 0.028252 | 0.028252 | 0.0 | 84.63 -Bond | 0.00025415 | 0.00025415 | 0.00025415 | 0.0 | 0.76 -Kspace | 0.0017328 | 0.0017328 | 0.0017328 | 0.0 | 5.19 -Neigh | 0.00038004 | 0.00038004 | 0.00038004 | 0.0 | 1.14 -Comm | 0.0022359 | 0.0022359 | 0.0022359 | 0.0 | 6.70 -Output | 2.1935e-05 | 2.1935e-05 | 2.1935e-05 | 0.0 | 0.07 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0005062 | | | 1.52 - -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 -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4939 ave 4939 max 4939 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4939 -Ave neighs/atom = 205.792 -Ave special neighs/atom = 2 -Neighbor list builds = 2 -Dangerous builds = 0 -reset_timestep 0 -# rigid constraints with thermostat - -fix mynvt all nvt temp ${temp} ${temp} 100 -fix mynvt all nvt temp 338.0 ${temp} 100 -fix mynvt all nvt temp 338.0 338.0 100 -fix wshake all 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 -# gcmc - - - -run 1000 -Ewald initialization ... -WARNING: 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) = 11.63 | 11.63 | 11.63 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 518.26667 -27.771871 0 -4.5990532 3.1322213 - 1000 277.5448 -45.272615 0 -32.86299 -1575.2641 -Loop time of 0.101694 on 1 procs for 1000 steps with 24 atoms - -Performance: 849.609 ns/day, 0.028 hours/ns, 9833.435 timesteps/s -99.2% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.078345 | 0.078345 | 0.078345 | 0.0 | 77.04 -Bond | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.10 -Kspace | 0.0079424 | 0.0079424 | 0.0079424 | 0.0 | 7.81 -Neigh | 0.003454 | 0.003454 | 0.003454 | 0.0 | 3.40 -Comm | 0.0080469 | 0.0080469 | 0.0080469 | 0.0 | 7.91 -Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.02 -Modify | 0.0026064 | 0.0026064 | 0.0026064 | 0.0 | 2.56 -Other | | 0.001179 | | | 1.16 - -Nlocal: 24 ave 24 max 24 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1688 ave 1688 max 1688 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4952 ave 4952 max 4952 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4952 -Ave neighs/atom = 206.333 -Ave special neighs/atom = 2 -Neighbor list builds = 26 -Dangerous builds = 0 - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all 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) -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_nO v_nH -thermo 1000 - -# run - -run 20000 -Ewald initialization ... -WARNING: 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:445) -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:476) -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 - 1000 277.5448 -1575.1516 -45.272615 12.409625 0.23910963 24 0 0 0 0 8 16 - 2000 84.31104 -7419.6538 -330.36966 13.319705 0.80699501 81 0.048183096 0.0099581757 0 0 27 54 - 3000 79.654082 -7034.6542 -345.84563 13.058853 0.83688372 84 0.027492109 0.0068755525 0 0 28 56 - 4000 73.831702 -3905.1456 -380.27757 12.984619 0.89666113 90 0.020637774 0.0060076096 0 0 30 60 - 5000 95.397292 -3523.6886 -414.9618 18.483479 0.98632724 99 0.016897769 0.0045269353 0 0 33 66 - 6000 74.46018 -4913.3009 -425.33102 14.426857 0.98632724 99 0.013390571 0.0036569014 0 0 33 66 - 7000 59.601812 -3108.7781 -425.91441 11.548009 0.98632724 99 0.01160439 0.0033510941 0 0 33 66 - 8000 74.104787 -1710.7687 -444.03326 14.799784 1.0162159 102 0.010174953 0.0028884203 0 0 34 68 - 9000 92.497957 -1255.2193 -435.57266 18.473162 1.0162159 102 0.0089594585 0.0025112378 0 0 34 68 - 10000 71.075249 -3191.4633 -454.19438 14.618465 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70 - 11000 60.402203 -2011.6602 -461.68383 12.423277 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70 - 12000 92.903919 -3023.4452 -462.20701 19.108096 1.0461046 105 0.0066641451 0.0018355023 0 0 35 70 - 13000 51.285407 -1016.3672 -466.29402 10.548172 1.0461046 105 0.0061145907 0.0016809265 0 0 35 70 - 14000 72.733554 -3284.3632 -463.38578 14.959539 1.0461046 105 0.0056427384 0.0015520479 0 0 35 70 - 15000 76.324778 -1795.0839 -477.59722 16.153186 1.0759934 108 0.005391524 0.0014384143 0 0 36 72 - 16000 78.185379 345.92387 -481.1903 16.546959 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72 - 17000 79.868226 -3095.839 -478.59141 16.903113 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72 - 18000 69.578814 -1884.4164 -482.28013 14.725487 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72 - 19000 73.973471 -1943.8906 -480.82986 15.655561 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72 - 20000 59.614528 -2439.1076 -485.78451 12.616671 1.0759934 108 0.0040927265 0.0011614279 0 0 36 72 - 21000 89.393596 -728.94872 -484.62787 18.919038 1.0759934 108 0.0038871336 0.0011036309 0 0 36 72 -Loop time of 148.361 on 1 procs for 20000 steps with 108 atoms - -Performance: 11.647 ns/day, 2.061 hours/ns, 134.806 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 26.404 | 26.404 | 26.404 | 0.0 | 17.80 -Bond | 0.058909 | 0.058909 | 0.058909 | 0.0 | 0.04 -Kspace | 0.58222 | 0.58222 | 0.58222 | 0.0 | 0.39 -Neigh | 0.81976 | 0.81976 | 0.81976 | 0.0 | 0.55 -Comm | 0.60514 | 0.60514 | 0.60514 | 0.0 | 0.41 -Output | 0.00070596 | 0.00070596 | 0.00070596 | 0.0 | 0.00 -Modify | 119.77 | 119.77 | 119.77 | 0.0 | 80.73 -Other | | 0.1157 | | | 0.08 - -Nlocal: 108 ave 108 max 108 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7908 ave 7908 max 7908 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 99854 ave 99854 max 99854 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 99854 -Ave neighs/atom = 924.574 -Ave special neighs/atom = 2 -Neighbor list builds = 20442 -Dangerous builds = 0 - -Total wall time: 0:02:28 diff --git a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 b/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 deleted file mode 100644 index 9dcc60f849..0000000000 --- a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 +++ /dev/null @@ -1,294 +0,0 @@ -LAMMPS (22 Sep 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - 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 - -# we can load multiple molecule templates, but don't have to use them all -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -molecule h2omol H2O.txt -Read molecule h2omol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -create_atoms 0 box mol h2omol 464563 units box -Created 24 atoms - Time spent = 0.00236797 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 ... -WARNING: 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 -15.815905 0.10936727 7.4662793 -278.75864 -Loop time of 0.0389402 on 4 procs for 100 steps with 24 atoms - -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -4.96106135393 -15.696637101 -15.7065379926 - Force two-norm initial, final = 15.474 4.38071 - Force max component initial, final = 5.80042 2.01432 - Final line search alpha, max atom move = 0.00468711 0.00944132 - Iterations, force evaluations = 100 346 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0067904 | 0.012084 | 0.019882 | 4.5 | 31.03 -Bond | 0.0001657 | 0.00019389 | 0.00022459 | 0.0 | 0.50 -Kspace | 0.0032685 | 0.010629 | 0.015032 | 4.4 | 27.30 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013826 | 0.014182 | 0.015051 | 0.4 | 36.42 -Output | 2.0027e-05 | 2.2769e-05 | 3.0994e-05 | 0.0 | 0.06 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.001829 | | | 4.70 - -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 all nvt temp ${temp} ${temp} 100 -fix mynvt all nvt temp 338.0 ${temp} 100 -fix mynvt all nvt temp 338.0 338.0 100 -fix wshake all 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 -# gcmc - - - -run 1000 -Ewald initialization ... -WARNING: 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 -15.815905 0 7.3569121 -385.7767 - 1000 240.84589 -44.723106 0 -33.954368 61.365522 -Loop time of 0.0971818 on 4 procs for 1000 steps with 24 atoms - -Performance: 889.055 ns/day, 0.027 hours/ns, 10289.993 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.010939 | 0.020819 | 0.033432 | 5.8 | 21.42 -Bond | 9.5129e-05 | 0.00010997 | 0.0001266 | 0.0 | 0.11 -Kspace | 0.0058987 | 0.017954 | 0.027383 | 5.9 | 18.47 -Neigh | 0.0018289 | 0.001851 | 0.0018759 | 0.0 | 1.90 -Comm | 0.033144 | 0.033717 | 0.034395 | 0.3 | 34.69 -Output | 1.3113e-05 | 1.6809e-05 | 2.5988e-05 | 0.0 | 0.02 -Modify | 0.020795 | 0.020843 | 0.020866 | 0.0 | 21.45 -Other | | 0.001872 | | | 1.93 - -Nlocal: 6 ave 9 max 1 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 1375.25 ave 1495 max 1251 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 1263.25 ave 2045 max 122 min -Histogram: 1 0 0 0 0 0 2 0 0 1 - -Total # of neighbors = 5053 -Ave neighs/atom = 210.542 -Ave special neighs/atom = 2 -Neighbor list builds = 30 -Dangerous builds = 0 - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all 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) -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_nO v_nH -thermo 1000 - -# run - -run 20000 -Ewald initialization ... -WARNING: 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:445) -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:476) -Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH - 1000 240.84589 61.724018 -44.723106 10.768738 0.23910963 24 0 0 0 0 8 16 - 2000 90.409434 -6561.5238 -333.25624 14.822134 0.83688372 84 0.050190725 0.0099581757 0 0 28 56 - 3000 67.305679 -341.32154 -396.19372 12.238152 0.92654983 93 0.030546787 0.0068755525 0 0 31 62 - 4000 70.339514 -2575.9146 -419.94752 13.628467 0.98632724 99 0.021303508 0.0046725853 0 0 33 66 - 5000 85.676845 -3904.0268 -427.45932 17.110889 1.0162159 102 0.016400775 0.0035209497 0 0 34 68 - 6000 55.817537 -2067.5498 -448.02732 11.147559 1.0162159 102 0.012996731 0.0028442566 0 0 34 68 - 7000 87.59123 -3931.0089 -442.0299 17.493219 1.0162159 102 0.01160439 0.0030159847 0 0 34 68 - 8000 77.695862 -1684.9299 -461.16897 15.980166 1.0461046 105 0.010174953 0.0025995783 0 0 35 70 - 9000 70.375873 -6250.5951 -467.15813 14.474621 1.0461046 105 0.0089594585 0.002260114 0 0 35 70 - 10000 85.004974 -3406.0315 -464.23871 17.483474 1.0461046 105 0.007938083 0.0020156323 0 0 35 70 - 11000 55.459986 -3437.3858 -470.38117 11.406782 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70 - 12000 80.59057 -2145.2149 -464.5658 16.575538 1.0461046 105 0.0064840331 0.0016519521 0 0 35 70 - 13000 52.183725 -3956.875 -470.42779 10.732934 1.0461046 105 0.0059493315 0.0015128339 0 0 35 70 - 14000 78.482417 -4895.8977 -465.0452 16.141941 1.0461046 105 0.005490232 0.0013968431 0 0 35 70 - 15000 61.802226 -6148.8506 -469.41496 12.711228 1.0461046 105 0.0051077595 0.0012945729 0 0 35 70 - 16000 69.59917 -5755.4737 -462.37636 14.314872 1.0461046 105 0.004761212 0.0012098238 0 0 35 70 - 17000 78.44382 -4103.8449 -461.5505 16.134003 1.0461046 105 0.0044719941 0.0011320612 0 0 35 70 - 18000 76.04971 -3994.5995 -464.26842 15.641592 1.0461046 105 0.0042070328 0.0010659592 0 0 35 70 - 19000 70.676514 -4558.507 -463.40477 14.536455 1.0461046 105 0.0039804956 0.0010049017 0 0 35 70 - 20000 79.682951 -3876.5977 -462.70391 16.388862 1.0461046 105 0.0037779014 0.00095025921 0 0 35 70 - 21000 56.755378 -4224.8128 -465.66199 11.673213 1.0461046 105 0.0035881233 0.00090297077 0 0 35 70 -Loop time of 63.5274 on 4 procs for 20000 steps with 105 atoms - -Performance: 27.201 ns/day, 0.882 hours/ns, 314.825 timesteps/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 6.7399 | 8.4644 | 10.565 | 49.0 | 13.32 -Bond | 0.021824 | 0.024522 | 0.0278 | 1.4 | 0.04 -Kspace | 0.47207 | 2.5646 | 4.286 | 88.8 | 4.04 -Neigh | 0.25299 | 0.2535 | 0.25374 | 0.1 | 0.40 -Comm | 2.011 | 2.0187 | 2.0311 | 0.5 | 3.18 -Output | 0.00063848 | 0.00072688 | 0.00099015 | 0.0 | 0.00 -Modify | 50.025 | 50.035 | 50.051 | 0.1 | 78.76 -Other | | 0.166 | | | 0.26 - -Nlocal: 26.25 ave 30 max 24 min -Histogram: 1 1 0 1 0 0 0 0 0 1 -Nghost: 5965 ave 6026 max 5911 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 23614.8 ave 29343 max 16281 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 94459 -Ave neighs/atom = 899.61 -Ave special neighs/atom = 2 -Neighbor list builds = 20437 -Dangerous builds = 0 - -Total wall time: 0:01:03 diff --git a/examples/gcmc/log.6Jul17.gcmc.lj.g++.1 b/examples/gcmc/log.6Jul17.gcmc.lj.g++.1 deleted file mode 100644 index 7ff7e02f86..0000000000 --- a/examples/gcmc/log.6Jul17.gcmc.lj.g++.1 +++ /dev/null @@ -1,137 +0,0 @@ -LAMMPS (22 Sep 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# GCMC for LJ simple fluid, no dynamics -# T = 2.0 -# rho ~ 0.5 -# p ~ 1.5 -# mu_ex ~ 0.0 -# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8 - -# variables modifiable using -var command line switch - -variable mu index -1.25 -variable temp index 2.0 -variable disp index 1.0 -variable lbox index 5.0 - -# global model settings - -units lj -atom_style atomic -pair_style lj/cut 3.0 -pair_modify tail no # turn of to avoid triggering full_energy - -# box - -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} -region box block 0 5.0 0 ${lbox} 0 ${lbox} -region box block 0 5.0 0 5.0 0 ${lbox} -region box block 0 5.0 0 5.0 0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (5 5 5) - 1 by 1 by 1 MPI processor grid - -# lj parameters - -pair_coeff * * 1.0 1.0 -mass * 1.0 - -# gcmc - -fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0 - -# atom count - -variable type1 atom "type==1" -group type1 dynamic all var type1 -dynamic group type1 defined -variable n1 equal count(type1) - -# averaging - -variable rho equal density -variable p equal press -variable nugget equal 1.0e-8 -variable lambda equal 1.0 -variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget}) -variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget}) -variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget}) -variable muex equal -1.25-2.0*ln(density*1+${nugget}) -variable muex equal -1.25-2.0*ln(density*1+1e-08) -fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat -variable rhoav equal f_ave[1] -variable pav equal f_ave[2] -variable muexav equal f_ave[3] -variable n1av equal f_ave[4] - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget}) -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget}) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget}) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08) -compute_modify thermo_temp dynamic yes -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av -thermo 1000 - -# run - -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.3 - ghost atom cutoff = 3.3 - binsize = 1.65, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av - 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 - 1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98 - 2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97 - 3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5 - 4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17 - 5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15 - 6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37 - 7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33 - 8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29 - 9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87 - 10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2 -Loop time of 13.1886 on 1 procs for 10000 steps with 60 atoms - -Performance: 327555.715 tau/day, 758.231 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.37102 | 0.37102 | 0.37102 | 0.0 | 2.81 -Neigh | 0.86986 | 0.86986 | 0.86986 | 0.0 | 6.60 -Comm | 0.10394 | 0.10394 | 0.10394 | 0.0 | 0.79 -Output | 0.00025702 | 0.00025702 | 0.00025702 | 0.0 | 0.00 -Modify | 11.833 | 11.833 | 11.833 | 0.0 | 89.72 -Other | | 0.01084 | | | 0.08 - -Nlocal: 60 ave 60 max 60 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 663 ave 663 max 663 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2133 ave 2133 max 2133 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2133 -Ave neighs/atom = 35.55 -Neighbor list builds = 10000 -Dangerous builds = 0 -Total wall time: 0:00:13 diff --git a/examples/gcmc/log.6Jul17.gcmc.lj.g++.4 b/examples/gcmc/log.6Jul17.gcmc.lj.g++.4 deleted file mode 100644 index 59ed0462dc..0000000000 --- a/examples/gcmc/log.6Jul17.gcmc.lj.g++.4 +++ /dev/null @@ -1,137 +0,0 @@ -LAMMPS (22 Sep 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# GCMC for LJ simple fluid, no dynamics -# T = 2.0 -# rho ~ 0.5 -# p ~ 1.5 -# mu_ex ~ 0.0 -# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8 - -# variables modifiable using -var command line switch - -variable mu index -1.25 -variable temp index 2.0 -variable disp index 1.0 -variable lbox index 5.0 - -# global model settings - -units lj -atom_style atomic -pair_style lj/cut 3.0 -pair_modify tail no # turn of to avoid triggering full_energy - -# box - -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} -region box block 0 5.0 0 ${lbox} 0 ${lbox} -region box block 0 5.0 0 5.0 0 ${lbox} -region box block 0 5.0 0 5.0 0 5.0 -create_box 1 box -Created orthogonal box = (0 0 0) to (5 5 5) - 1 by 2 by 2 MPI processor grid - -# lj parameters - -pair_coeff * * 1.0 1.0 -mass * 1.0 - -# gcmc - -fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0 - -# atom count - -variable type1 atom "type==1" -group type1 dynamic all var type1 -dynamic group type1 defined -variable n1 equal count(type1) - -# averaging - -variable rho equal density -variable p equal press -variable nugget equal 1.0e-8 -variable lambda equal 1.0 -variable muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget}) -variable muex equal -1.25-${temp}*ln(density*${lambda}+${nugget}) -variable muex equal -1.25-2.0*ln(density*${lambda}+${nugget}) -variable muex equal -1.25-2.0*ln(density*1+${nugget}) -variable muex equal -1.25-2.0*ln(density*1+1e-08) -fix ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat -variable rhoav equal f_ave[1] -variable pav equal f_ave[2] -variable muexav equal f_ave[3] -variable n1av equal f_ave[4] - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget}) -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget}) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget}) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08) -compute_modify thermo_temp dynamic yes -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av -thermo 1000 - -# run - -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.3 - ghost atom cutoff = 3.3 - binsize = 1.65, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av - 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 - 1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44 - 2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19 - 3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23 - 4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57 - 5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56 - 6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76 - 7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2 - 8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03 - 9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36 - 10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24 -Loop time of 13.089 on 4 procs for 10000 steps with 69 atoms - -Performance: 330047.561 tau/day, 763.999 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.088209 | 0.093632 | 0.098849 | 1.4 | 0.72 -Neigh | 0.25982 | 0.26669 | 0.27885 | 1.5 | 2.04 -Comm | 0.27092 | 0.28815 | 0.29998 | 2.1 | 2.20 -Output | 0.00030112 | 0.00035518 | 0.00037479 | 0.0 | 0.00 -Modify | 12.432 | 12.433 | 12.433 | 0.0 | 94.98 -Other | | 0.007692 | | | 0.06 - -Nlocal: 17.25 ave 23 max 10 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Nghost: 506.5 ave 519 max 490 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 705.75 ave 998 max 369 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 2823 -Ave neighs/atom = 40.913 -Neighbor list builds = 10000 -Dangerous builds = 0 -Total wall time: 0:00:13