From 13e16dc3f14a53f5071d90c2357d722e26fd4d97 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 May 2017 07:52:13 -0400 Subject: [PATCH] update log files for pair style python examples --- ....1 => log.4May17.pair_python_hybrid.g++.1} | 0 ....4 => log.4May17.pair_python_hybrid.g++.4} | 0 ...++.1 => log.4May17.pair_python_melt.g++.1} | 0 ...++.4 => log.4May17.pair_python_melt.g++.4} | 0 .../python/log.4May17.pair_python_spce.g++.1 | 123 ++++++++++++++++++ .../python/log.4May17.pair_python_spce.g++.4 | 123 ++++++++++++++++++ 6 files changed, 246 insertions(+) rename examples/python/{log.4May2017.pair_python_hybrid.g++.1 => log.4May17.pair_python_hybrid.g++.1} (100%) rename examples/python/{log.4May2017.pair_python_hybrid.g++.4 => log.4May17.pair_python_hybrid.g++.4} (100%) rename examples/python/{log.4May2017.pair_python_melt.g++.1 => log.4May17.pair_python_melt.g++.1} (100%) rename examples/python/{log.4May2017.pair_python_melt.g++.4 => log.4May17.pair_python_melt.g++.4} (100%) create mode 100644 examples/python/log.4May17.pair_python_spce.g++.1 create mode 100644 examples/python/log.4May17.pair_python_spce.g++.4 diff --git a/examples/python/log.4May2017.pair_python_hybrid.g++.1 b/examples/python/log.4May17.pair_python_hybrid.g++.1 similarity index 100% rename from examples/python/log.4May2017.pair_python_hybrid.g++.1 rename to examples/python/log.4May17.pair_python_hybrid.g++.1 diff --git a/examples/python/log.4May2017.pair_python_hybrid.g++.4 b/examples/python/log.4May17.pair_python_hybrid.g++.4 similarity index 100% rename from examples/python/log.4May2017.pair_python_hybrid.g++.4 rename to examples/python/log.4May17.pair_python_hybrid.g++.4 diff --git a/examples/python/log.4May2017.pair_python_melt.g++.1 b/examples/python/log.4May17.pair_python_melt.g++.1 similarity index 100% rename from examples/python/log.4May2017.pair_python_melt.g++.1 rename to examples/python/log.4May17.pair_python_melt.g++.1 diff --git a/examples/python/log.4May2017.pair_python_melt.g++.4 b/examples/python/log.4May17.pair_python_melt.g++.4 similarity index 100% rename from examples/python/log.4May2017.pair_python_melt.g++.4 rename to examples/python/log.4May17.pair_python_melt.g++.4 diff --git a/examples/python/log.4May17.pair_python_spce.g++.1 b/examples/python/log.4May17.pair_python_spce.g++.1 new file mode 100644 index 0000000000..4e429b9cdd --- /dev/null +++ b/examples/python/log.4May17.pair_python_spce.g++.1 @@ -0,0 +1,123 @@ +LAMMPS (4 May 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay python 12.0 coul/long 12.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff * * python potentials.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair python, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair 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) = 41.05 | 41.05 | 41.05 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.369 0 -16692.369 -1289.222 + 10 120.56861 -17769.719 0 -16691.902 -4082.7098 + 20 136.08014 -17884.591 0 -16668.109 -5140.7824 + 30 136.97316 -17874.351 0 -16649.887 -5351.3571 + 40 153.37285 -18001.493 0 -16630.424 -5227.0601 + 50 167.70414 -18105.435 0 -16606.252 -4473.2089 + 60 163.08253 -18037.29 0 -16579.422 -3295.8963 + 70 169.60395 -18067.078 0 -16550.912 -2615.7026 + 80 182.94811 -18155.978 0 -16520.523 -2393.3156 + 90 191.29902 -18197.887 0 -16487.779 -2242.7104 + 100 194.70949 -18195.021 0 -16454.425 -1955.2916 +Loop time of 63.3145 on 1 procs for 100 steps with 4500 atoms + +Performance: 0.136 ns/day, 175.874 hours/ns, 1.579 timesteps/s +86.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 61.815 | 61.815 | 61.815 | 0.0 | 97.63 +Bond | 0.000132 | 0.000132 | 0.000132 | 0.0 | 0.00 +Kspace | 1.2226 | 1.2226 | 1.2226 | 0.0 | 1.93 +Neigh | 0.21684 | 0.21684 | 0.21684 | 0.0 | 0.34 +Comm | 0.015175 | 0.015175 | 0.015175 | 0.0 | 0.02 +Output | 0.000405 | 0.000405 | 0.000405 | 0.0 | 0.00 +Modify | 0.040088 | 0.040088 | 0.040088 | 0.0 | 0.06 +Other | | 0.003896 | | | 0.01 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21216 ave 21216 max 21216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.44594e+06 ave 1.44594e+06 max 1.44594e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1445935 +Ave neighs/atom = 321.319 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:01:05 diff --git a/examples/python/log.4May17.pair_python_spce.g++.4 b/examples/python/log.4May17.pair_python_spce.g++.4 new file mode 100644 index 0000000000..15c11cd376 --- /dev/null +++ b/examples/python/log.4May17.pair_python_spce.g++.4 @@ -0,0 +1,123 @@ +LAMMPS (4 May 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay python 12.0 coul/long 12.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff * * python potentials.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 34263 16000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair python, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair 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) = 14.59 | 14.59 | 14.59 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.369 0 -16692.369 -1289.222 + 10 120.56861 -17769.719 0 -16691.902 -4082.7098 + 20 136.08014 -17884.591 0 -16668.109 -5140.7824 + 30 136.97316 -17874.351 0 -16649.887 -5351.3571 + 40 153.37285 -18001.493 0 -16630.424 -5227.0601 + 50 167.70414 -18105.435 0 -16606.252 -4473.2089 + 60 163.08253 -18037.29 0 -16579.422 -3295.8963 + 70 169.60395 -18067.078 0 -16550.912 -2615.7026 + 80 182.94811 -18155.978 0 -16520.523 -2393.3156 + 90 191.29902 -18197.887 0 -16487.779 -2242.7104 + 100 194.70949 -18195.021 0 -16454.425 -1955.2916 +Loop time of 29.6024 on 4 procs for 100 steps with 4500 atoms + +Performance: 0.292 ns/day, 82.229 hours/ns, 3.378 timesteps/s +52.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 26.631 | 27.507 | 28.649 | 14.3 | 92.92 +Bond | 0.00021 | 0.00022675 | 0.000248 | 0.0 | 0.00 +Kspace | 0.72315 | 1.8708 | 2.7365 | 54.7 | 6.32 +Neigh | 0.10667 | 0.1067 | 0.10674 | 0.0 | 0.36 +Comm | 0.045357 | 0.054035 | 0.064607 | 3.6 | 0.18 +Output | 0.000424 | 0.00086625 | 0.002189 | 0.0 | 0.00 +Modify | 0.056602 | 0.056667 | 0.056763 | 0.0 | 0.19 +Other | | 0.006337 | | | 0.02 + +Nlocal: 1125 ave 1154 max 1092 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 12256.2 ave 12296 max 12213 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 361484 ave 376583 max 347969 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 1445935 +Ave neighs/atom = 321.319 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:30