diff --git a/examples/relres/in.22DMH.relres b/examples/relres/in.22DMH.relres index 1c0d44433e..26e2d933e6 100644 --- a/examples/relres/in.22DMH.relres +++ b/examples/relres/in.22DMH.relres @@ -5,17 +5,17 @@ dielectric 1 special_bonds lj/coul 0.0 0.0 0.5 pair_style lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9 -bond_style harmonic -angle_style harmonic -dihedral_style fourier +bond_style harmonic +angle_style harmonic +dihedral_style fourier read_data Data.22DMH.in.relres -pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 -pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 -pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 -pair_modify shift yes +pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 +pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 +pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 +pair_modify shift yes neighbor 2.0e-10 bin neigh_modify every 2 delay 4 check yes @@ -26,6 +26,6 @@ fix 2 all nvt temp 290 290 2.0e-13 run 1000 #write_data Data.22DMH.out.relres pair ij -pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 -pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 -pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 +#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 +#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 +#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 diff --git a/examples/relres/log.relres b/examples/relres/log.09Feb21.22DMH.relres.g++.1 similarity index 63% rename from examples/relres/log.relres rename to examples/relres/log.09Feb21.22DMH.relres.g++.1 index e723ed0020..da3368e6e0 100644 --- a/examples/relres/log.relres +++ b/examples/relres/log.09Feb21.22DMH.relres.g++.1 @@ -1,5 +1,4 @@ LAMMPS (24 Dec 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task units si atom_style molecular @@ -10,11 +9,11 @@ special_bonds lj/coul 0.0 0.0 0.5 pair_style lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9 bond_style harmonic angle_style harmonic -dihedral_style fourier +dihedral_style fourier read_data Data.22DMH.in.relres Reading data file ... orthogonal box = (3.7421629e-10 3.7421629e-10 3.7421629e-10) to (6.8257837e-09 6.8257837e-09 6.8257837e-09) - 1 by 1 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 8000 atoms reading velocities ... @@ -38,15 +37,15 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors - special bonds CPU = 0.003 seconds - read_data CPU = 0.062 seconds -pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 -pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 -pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 -pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 -pair_modify shift yes + special bonds CPU = 0.019 seconds + read_data CPU = 0.168 seconds +pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 +pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 +pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 +pair_modify shift yes neighbor 2.0e-10 bin neigh_modify every 2 delay 4 check yes @@ -68,7 +67,7 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 19.53 | 19.53 | 19.53 Mbytes +Per MPI rank memory allocation (min/avg/max) = 20.39 | 20.39 | 20.39 Mbytes Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 0 286.85659 -21390710 2.6345656e-17 4.7519899e-17 7.3865555e-17 -3.3260066e-17 5.9605722e-17 2.685318e-25 100 292.25165 10716172 2.5245584e-17 4.841363e-17 7.3659214e-17 -3.2561964e-17 5.7807548e-17 2.685318e-25 @@ -81,27 +80,27 @@ Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume 800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25 900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25 1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25 -Loop time of 7.07676 on 2 procs for 1000 steps with 8000 atoms +Loop time of 20.1906 on 1 procs for 1000 steps with 8000 atoms -99.7% CPU use with 2 MPI tasks x 1 OpenMP threads +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 | 5.1275 | 5.1852 | 5.243 | 2.5 | 73.27 -Bond | 1.0056 | 1.0072 | 1.0087 | 0.2 | 14.23 -Neigh | 0.38261 | 0.38263 | 0.38266 | 0.0 | 5.41 -Comm | 0.25513 | 0.31266 | 0.37018 | 10.3 | 4.42 -Output | 0.00042391 | 0.00044036 | 0.00045681 | 0.0 | 0.01 -Modify | 0.14501 | 0.14643 | 0.14785 | 0.4 | 2.07 -Other | | 0.04219 | | | 0.60 +Pair | 15.751 | 15.751 | 15.751 | 0.0 | 78.01 +Bond | 1.7612 | 1.7612 | 1.7612 | 0.0 | 8.72 +Neigh | 1.4937 | 1.4937 | 1.4937 | 0.0 | 7.40 +Comm | 0.404 | 0.404 | 0.404 | 0.0 | 2.00 +Output | 0.0013139 | 0.0013139 | 0.0013139 | 0.0 | 0.01 +Modify | 0.72282 | 0.72282 | 0.72282 | 0.0 | 3.58 +Other | | 0.05691 | | | 0.28 -Nlocal: 4000.00 ave 4000 max 4000 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Nghost: 13887.5 ave 13896 max 13879 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 217142.0 ave 217471 max 216812 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 8000.00 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 18912.0 ave 18912 max 18912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 434283.0 ave 434283 max 434283 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 434283 Ave neighs/atom = 54.285375 @@ -109,13 +108,10 @@ Ave special neighs/atom = 5.2500000 Neighbor list builds = 13 Dangerous builds = 0 #write_data Data.22DMH.out.relres pair ij -pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 -Creating table file potential.relres with DATE: 2021-02-05 -pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 -Appending to table file potential.relres with DATE: 2021-02-05 -pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 -Appending to table file potential.relres with DATE: 2021-02-05 +#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 +#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 +#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:07 +Total wall time: 0:00:20 diff --git a/examples/relres/log.09Feb21.22DMH.relres.g++.4 b/examples/relres/log.09Feb21.22DMH.relres.g++.4 new file mode 100644 index 0000000000..969b47463a --- /dev/null +++ b/examples/relres/log.09Feb21.22DMH.relres.g++.4 @@ -0,0 +1,117 @@ +LAMMPS (24 Dec 2020) + using 1 OpenMP thread(s) per MPI task +units si +atom_style molecular +boundary p p p +dielectric 1 +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/relres 0.675e-9 .725e-9 1.2e-9 1.4e-9 +bond_style harmonic +angle_style harmonic +dihedral_style fourier +read_data Data.22DMH.in.relres +Reading data file ... + orthogonal box = (3.7421629e-10 3.7421629e-10 3.7421629e-10) to (6.8257837e-09 6.8257837e-09 6.8257837e-09) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8000 atoms + reading velocities ... + 8000 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 3 = max dihedrals/atom + reading bonds ... + 7000 bonds + reading angles ... + 9000 angles + reading dihedrals ... + 5000 dihedrals +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0.5 + special bond factors coul: 0 0 0.5 + 4 = max # of 1-2 neighbors + 4 = max # of 1-3 neighbors + 5 = max # of 1-4 neighbors + 7 = max # of special neighbors + special bonds CPU = 0.010 seconds + read_data CPU = 0.145 seconds +pair_coeff 6 6 1.21585e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 4 4 0.819828e-21 0.3905e-9 0 0.3905e-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 2 2 0.819828e-21 0.3905e-9 8.48872E-21 0.3905E-9 0.575e-9 0.625e-9 1.2e-9 1.4e-9 +pair_coeff 5 5 1.00742E-21 0.396E-9 0 0.396E-9 +pair_coeff 3 3 0.819828e-21 0.3905e-9 0 0.3905e-9 +pair_coeff 1 1 0.347385E-21 0.38E-9 20.2372E-21 0.39309E-9 +pair_modify shift yes +neighbor 2.0e-10 bin +neigh_modify every 2 delay 4 check yes + +timestep 1.0e-15 +thermo 100 +thermo_style custom step temp press pe ke etotal epair emol vol +fix 2 all nvt temp 290 290 2.0e-13 + +run 1000 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.6e-09 + ghost atom cutoff = 1.6e-09 + binsize = 8e-10, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/relres, 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) = 10.33 | 10.33 | 10.34 Mbytes +Step Temp Press PotEng KinEng TotEng E_pair E_mol Volume + 0 286.85659 -21390710 2.6345656e-17 4.7519899e-17 7.3865555e-17 -3.3260066e-17 5.9605722e-17 2.685318e-25 + 100 292.25165 10716172 2.5245584e-17 4.841363e-17 7.3659214e-17 -3.2561964e-17 5.7807548e-17 2.685318e-25 + 200 291.6011 48774461 2.4897987e-17 4.8305863e-17 7.320385e-17 -3.3268705e-17 5.8166692e-17 2.685318e-25 + 300 291.50656 37655969 2.4389062e-17 4.8290201e-17 7.2679262e-17 -3.3428236e-17 5.7817297e-17 2.685318e-25 + 400 287.23427 25920755 2.4747225e-17 4.7582464e-17 7.2329689e-17 -3.3065908e-17 5.7813133e-17 2.685318e-25 + 500 288.56911 -9297451 2.4379025e-17 4.7803591e-17 7.2182615e-17 -3.3515426e-17 5.7894451e-17 2.685318e-25 + 600 291.82949 20083719 2.3686904e-17 4.8343696e-17 7.2030599e-17 -3.3468666e-17 5.7155569e-17 2.685318e-25 + 700 290.64445 60535932 2.3704156e-17 4.8147386e-17 7.1851542e-17 -3.3299994e-17 5.700415e-17 2.685318e-25 + 800 293.01243 38119194 2.3163674e-17 4.8539659e-17 7.1703333e-17 -3.3641284e-17 5.6804958e-17 2.685318e-25 + 900 289.1191 32514067 2.3608264e-17 4.7894701e-17 7.1502965e-17 -3.3787865e-17 5.7396129e-17 2.685318e-25 + 1000 292.45834 -714652.68 2.2885394e-17 4.8447871e-17 7.1333265e-17 -3.3864138e-17 5.6749532e-17 2.685318e-25 +Loop time of 5.79033 on 4 procs for 1000 steps with 8000 atoms + +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0309 | 4.0713 | 4.1247 | 1.7 | 70.31 +Bond | 0.45193 | 0.46562 | 0.49307 | 2.4 | 8.04 +Neigh | 0.40834 | 0.40848 | 0.40871 | 0.0 | 7.05 +Comm | 0.48313 | 0.56787 | 0.60777 | 6.6 | 9.81 +Output | 0.00049329 | 0.0010571 | 0.0020971 | 1.9 | 0.02 +Modify | 0.22813 | 0.25523 | 0.27164 | 3.2 | 4.41 +Other | | 0.02078 | | | 0.36 + +Nlocal: 2000.00 ave 2013 max 1987 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 9887.00 ave 9898 max 9865 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 108571.0 ave 110054 max 107417 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 434283 +Ave neighs/atom = 54.285375 +Ave special neighs/atom = 5.2500000 +Neighbor list builds = 13 +Dangerous builds = 0 +#write_data Data.22DMH.out.relres pair ij +#pair_write 1 1 1201 r 0.2e-9 1.4e-9 potential.relres LJ11 +#pair_write 2 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ22 +#pair_write 1 2 1201 r 0.2e-9 1.4e-9 potential.relres LJ12 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:06