mirror of https://github.com/lammps/lammps.git
added LAST option to dump_modify thresh, more restart info printed out to screen
This commit is contained in:
Steve Plimpton
parent
e70d530c46
commit
04f5eadcf1
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# FENE beadspring benchmark
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units lj
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@ -43,25 +43,25 @@ Neighbor list info ...
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master list distance cutoff = 1.52
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ghost atom cutoff = 1.52
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binsize = 0.76 -> bins = 45 45 45
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Memory usage per processor = 11.5189 Mbytes
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Memory usage per processor = 12.0423 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
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100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
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Loop time of 0.978585 on 1 procs for 100 steps with 32000 atoms
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Loop time of 0.977647 on 1 procs for 100 steps with 32000 atoms
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Performance: 105948.895 tau/day, 102.188 timesteps/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 106050.541 tau/day, 102.286 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.19562 | 0.19562 | 0.19562 | 0.0 | 19.99
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Bond | 0.087475 | 0.087475 | 0.087475 | 0.0 | 8.94
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Neigh | 0.44861 | 0.44861 | 0.44861 | 0.0 | 45.84
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Comm | 0.032932 | 0.032932 | 0.032932 | 0.0 | 3.37
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Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.01
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Modify | 0.19413 | 0.19413 | 0.19413 | 0.0 | 19.84
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Other | | 0.01972 | | | 2.02
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Pair | 0.19421 | 0.19421 | 0.19421 | 0.0 | 19.86
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Bond | 0.08741 | 0.08741 | 0.08741 | 0.0 | 8.94
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Neigh | 0.45791 | 0.45791 | 0.45791 | 0.0 | 46.84
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Comm | 0.032649 | 0.032649 | 0.032649 | 0.0 | 3.34
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Output | 0.00012207 | 0.00012207 | 0.00012207 | 0.0 | 0.01
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Modify | 0.18071 | 0.18071 | 0.18071 | 0.0 | 18.48
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Other | | 0.02464 | | | 2.52
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# FENE beadspring benchmark
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units lj
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@ -43,25 +43,25 @@ Neighbor list info ...
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master list distance cutoff = 1.52
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ghost atom cutoff = 1.52
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binsize = 0.76 -> bins = 45 45 45
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Memory usage per processor = 3.91518 Mbytes
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Memory usage per processor = 4.14663 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
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100 0.97145835 0.43803883 20.502691 22.397872 4.626988
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Loop time of 0.271187 on 4 procs for 100 steps with 32000 atoms
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Loop time of 0.269205 on 4 procs for 100 steps with 32000 atoms
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Performance: 382319.453 tau/day, 368.749 timesteps/s
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99.6% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 385133.446 tau/day, 371.464 timesteps/s
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.048621 | 0.050076 | 0.051229 | 0.4 | 18.47
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Bond | 0.022254 | 0.022942 | 0.023567 | 0.3 | 8.46
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Neigh | 0.11873 | 0.11881 | 0.11887 | 0.0 | 43.81
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Comm | 0.019066 | 0.021357 | 0.024297 | 1.3 | 7.88
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Output | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 | 0.1 | 0.02
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Modify | 0.048737 | 0.050198 | 0.051231 | 0.4 | 18.51
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Other | | 0.007751 | | | 2.86
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Pair | 0.049383 | 0.049756 | 0.049988 | 0.1 | 18.48
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Bond | 0.022701 | 0.022813 | 0.022872 | 0.0 | 8.47
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Neigh | 0.11982 | 0.12002 | 0.12018 | 0.0 | 44.58
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Comm | 0.020274 | 0.021077 | 0.022348 | 0.5 | 7.83
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Output | 5.3167e-05 | 5.6148e-05 | 6.3181e-05 | 0.1 | 0.02
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Modify | 0.046276 | 0.046809 | 0.047016 | 0.1 | 17.39
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Other | | 0.008669 | | | 3.22
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Nlocal: 8000 ave 8030 max 7974 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# FENE beadspring benchmark
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variable x index 1
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@ -59,25 +59,25 @@ Neighbor list info ...
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master list distance cutoff = 1.52
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ghost atom cutoff = 1.52
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binsize = 0.76 -> bins = 89 89 45
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Memory usage per processor = 12.8735 Mbytes
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Memory usage per processor = 13.2993 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
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100 0.97682955 0.44239968 20.500229 22.407862 4.6527025
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Loop time of 1.20889 on 4 procs for 100 steps with 128000 atoms
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Loop time of 1.14845 on 4 procs for 100 steps with 128000 atoms
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Performance: 85764.410 tau/day, 82.720 timesteps/s
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 90277.919 tau/day, 87.074 timesteps/s
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99.9% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.21738 | 0.23306 | 0.23926 | 1.9 | 19.28
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Bond | 0.094536 | 0.10196 | 0.10534 | 1.4 | 8.43
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Neigh | 0.52311 | 0.52392 | 0.52519 | 0.1 | 43.34
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Comm | 0.090161 | 0.10022 | 0.12557 | 4.7 | 8.29
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Output | 0.00012207 | 0.00017327 | 0.00019598 | 0.2 | 0.01
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Modify | 0.19662 | 0.20262 | 0.20672 | 0.8 | 16.76
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Other | | 0.04694 | | | 3.88
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Pair | 0.2203 | 0.22207 | 0.22386 | 0.3 | 19.34
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Bond | 0.094861 | 0.095302 | 0.095988 | 0.1 | 8.30
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Neigh | 0.52127 | 0.5216 | 0.52189 | 0.0 | 45.42
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Comm | 0.079585 | 0.082159 | 0.084366 | 0.7 | 7.15
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Output | 0.00013304 | 0.00015306 | 0.00018501 | 0.2 | 0.01
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Modify | 0.18351 | 0.18419 | 0.1856 | 0.2 | 16.04
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Other | | 0.04298 | | | 3.74
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Nlocal: 32000 ave 32015 max 31983 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# LAMMPS benchmark of granular flow
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# chute flow of 32000 atoms with frozen base at 26 degrees
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@ -47,24 +47,24 @@ Neighbor list info ...
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master list distance cutoff = 1.1
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ghost atom cutoff = 1.1
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binsize = 0.55 -> bins = 73 37 68
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Memory usage per processor = 15.567 Mbytes
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Step Atoms KinEng 1 Volume
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Memory usage per processor = 16.0904 Mbytes
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Step Atoms KinEng c_1 Volume
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0 32000 784139.13 1601.1263 29833.783
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100 32000 784292.08 1571.0968 29834.707
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Loop time of 0.550482 on 1 procs for 100 steps with 32000 atoms
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Loop time of 0.534174 on 1 procs for 100 steps with 32000 atoms
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Performance: 1569.534 tau/day, 181.659 timesteps/s
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100.1% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 1617.451 tau/day, 187.205 timesteps/s
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99.8% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.33849 | 0.33849 | 0.33849 | 0.0 | 61.49
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Neigh | 0.040353 | 0.040353 | 0.040353 | 0.0 | 7.33
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Comm | 0.018023 | 0.018023 | 0.018023 | 0.0 | 3.27
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Output | 0.00020385 | 0.00020385 | 0.00020385 | 0.0 | 0.04
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Modify | 0.13155 | 0.13155 | 0.13155 | 0.0 | 23.90
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Other | | 0.02186 | | | 3.97
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Pair | 0.33346 | 0.33346 | 0.33346 | 0.0 | 62.43
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Neigh | 0.043902 | 0.043902 | 0.043902 | 0.0 | 8.22
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Comm | 0.018391 | 0.018391 | 0.018391 | 0.0 | 3.44
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Output | 0.00022411 | 0.00022411 | 0.00022411 | 0.0 | 0.04
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Modify | 0.11666 | 0.11666 | 0.11666 | 0.0 | 21.84
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Other | | 0.02153 | | | 4.03
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# LAMMPS benchmark of granular flow
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# chute flow of 32000 atoms with frozen base at 26 degrees
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@ -47,24 +47,24 @@ Neighbor list info ...
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master list distance cutoff = 1.1
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ghost atom cutoff = 1.1
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binsize = 0.55 -> bins = 73 37 68
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Memory usage per processor = 6.81783 Mbytes
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Step Atoms KinEng 1 Volume
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Memory usage per processor = 7.04927 Mbytes
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Step Atoms KinEng c_1 Volume
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0 32000 784139.13 1601.1263 29833.783
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100 32000 784292.08 1571.0968 29834.707
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Loop time of 0.13141 on 4 procs for 100 steps with 32000 atoms
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Loop time of 0.171815 on 4 procs for 100 steps with 32000 atoms
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Performance: 6574.833 tau/day, 760.976 timesteps/s
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99.3% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 5028.653 tau/day, 582.020 timesteps/s
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99.7% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.062505 | 0.067 | 0.07152 | 1.5 | 50.99
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Neigh | 0.010041 | 0.0101 | 0.010178 | 0.1 | 7.69
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Comm | 0.012347 | 0.012895 | 0.013444 | 0.5 | 9.81
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Output | 6.3896e-05 | 0.00010294 | 0.00014091 | 0.3 | 0.08
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Modify | 0.031802 | 0.032348 | 0.032897 | 0.3 | 24.62
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Other | | 0.008965 | | | 6.82
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Pair | 0.093691 | 0.096898 | 0.10005 | 0.8 | 56.40
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Neigh | 0.011976 | 0.012059 | 0.012146 | 0.1 | 7.02
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Comm | 0.016384 | 0.017418 | 0.018465 | 0.8 | 10.14
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Output | 7.7963e-05 | 0.00010747 | 0.00013304 | 0.2 | 0.06
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Modify | 0.031744 | 0.031943 | 0.032167 | 0.1 | 18.59
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Other | | 0.01339 | | | 7.79
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Nlocal: 8000 ave 8008 max 7992 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# LAMMPS benchmark of granular flow
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# chute flow of 32000 atoms with frozen base at 26 degrees
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@ -57,24 +57,24 @@ Neighbor list info ...
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master list distance cutoff = 1.1
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ghost atom cutoff = 1.1
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binsize = 0.55 -> bins = 146 73 68
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Memory usage per processor = 15.7007 Mbytes
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Step Atoms KinEng 1 Volume
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Memory usage per processor = 16.1265 Mbytes
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Step Atoms KinEng c_1 Volume
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0 128000 3136556.5 6404.5051 119335.13
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100 128000 3137168.3 6284.3873 119338.83
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Loop time of 0.906913 on 4 procs for 100 steps with 128000 atoms
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Loop time of 0.832365 on 4 procs for 100 steps with 128000 atoms
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Performance: 952.683 tau/day, 110.264 timesteps/s
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99.7% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 1038.006 tau/day, 120.140 timesteps/s
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.51454 | 0.53094 | 0.55381 | 2.0 | 58.54
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Neigh | 0.042597 | 0.043726 | 0.045801 | 0.6 | 4.82
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Comm | 0.063027 | 0.064657 | 0.067367 | 0.7 | 7.13
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Output | 0.00024891 | 0.00059718 | 0.00086498 | 1.0 | 0.07
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Modify | 0.16508 | 0.17656 | 0.1925 | 2.6 | 19.47
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Other | | 0.09043 | | | 9.97
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Pair | 0.5178 | 0.52208 | 0.52793 | 0.5 | 62.72
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Neigh | 0.047003 | 0.047113 | 0.047224 | 0.0 | 5.66
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Comm | 0.05233 | 0.052988 | 0.053722 | 0.2 | 6.37
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Output | 0.00024986 | 0.00032717 | 0.00036693 | 0.3 | 0.04
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Modify | 0.15517 | 0.15627 | 0.15808 | 0.3 | 18.77
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Other | | 0.0536 | | | 6.44
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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@ -87,4 +87,4 @@ Total # of neighbors = 460532
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Ave neighs/atom = 3.59791
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:01
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Total wall time: 0:00:00
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# bulk Cu lattice
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variable x index 1
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@ -49,25 +49,25 @@ Neighbor list info ...
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master list distance cutoff = 5.95
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ghost atom cutoff = 5.95
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binsize = 2.975 -> bins = 25 25 25
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Memory usage per processor = 10.2238 Mbytes
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Memory usage per processor = 11.2238 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1600 -113280 0 -106662.09 18703.573
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50 781.69049 -109873.35 0 -106640.13 52273.088
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100 801.832 -109957.3 0 -106640.77 51322.821
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Loop time of 5.90097 on 1 procs for 100 steps with 32000 atoms
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Loop time of 5.96529 on 1 procs for 100 steps with 32000 atoms
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Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s
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Performance: 7.242 ns/day, 3.314 hours/ns, 16.764 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 5.2121 | 5.2121 | 5.2121 | 0.0 | 88.33
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Neigh | 0.58212 | 0.58212 | 0.58212 | 0.0 | 9.86
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Comm | 0.030392 | 0.030392 | 0.030392 | 0.0 | 0.52
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Output | 0.00023389 | 0.00023389 | 0.00023389 | 0.0 | 0.00
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Modify | 0.060871 | 0.060871 | 0.060871 | 0.0 | 1.03
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Other | | 0.01527 | | | 0.26
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Pair | 5.2743 | 5.2743 | 5.2743 | 0.0 | 88.42
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Neigh | 0.59212 | 0.59212 | 0.59212 | 0.0 | 9.93
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Comm | 0.030399 | 0.030399 | 0.030399 | 0.0 | 0.51
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Output | 0.00026202 | 0.00026202 | 0.00026202 | 0.0 | 0.00
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Modify | 0.050487 | 0.050487 | 0.050487 | 0.0 | 0.85
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Other | | 0.01776 | | | 0.30
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,4 +1,4 @@
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LAMMPS (15 Feb 2016)
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LAMMPS (6 Oct 2016)
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# bulk Cu lattice
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variable x index 1
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@ -49,25 +49,25 @@ Neighbor list info ...
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master list distance cutoff = 5.95
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ghost atom cutoff = 5.95
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binsize = 2.975 -> bins = 25 25 25
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Memory usage per processor = 5.09629 Mbytes
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Memory usage per processor = 5.59629 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1600 -113280 0 -106662.09 18703.573
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50 781.69049 -109873.35 0 -106640.13 52273.088
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100 801.832 -109957.3 0 -106640.77 51322.821
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Loop time of 1.58019 on 4 procs for 100 steps with 32000 atoms
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Loop time of 1.64562 on 4 procs for 100 steps with 32000 atoms
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Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s
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Performance: 26.252 ns/day, 0.914 hours/ns, 60.767 timesteps/s
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.3617 | 1.366 | 1.3723 | 0.4 | 86.45
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Neigh | 0.15123 | 0.15232 | 0.15374 | 0.2 | 9.64
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Comm | 0.033429 | 0.041275 | 0.047066 | 2.7 | 2.61
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Output | 0.00011301 | 0.0001573 | 0.000211 | 0.3 | 0.01
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Modify | 0.014694 | 0.015085 | 0.015421 | 0.2 | 0.95
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Other | | 0.005342 | | | 0.34
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Pair | 1.408 | 1.4175 | 1.4341 | 0.9 | 86.14
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Neigh | 0.15512 | 0.15722 | 0.16112 | 0.6 | 9.55
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Comm | 0.029105 | 0.049986 | 0.061822 | 5.8 | 3.04
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Output | 0.00010991 | 0.00011539 | 0.00012302 | 0.0 | 0.01
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Modify | 0.013383 | 0.013573 | 0.013883 | 0.2 | 0.82
|
||||
Other | | 0.007264 | | | 0.44
|
||||
|
||||
Nlocal: 8000 ave 8008 max 7993 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -49,25 +49,25 @@ Neighbor list info ...
|
|||
master list distance cutoff = 5.95
|
||||
ghost atom cutoff = 5.95
|
||||
binsize = 2.975 -> bins = 49 49 25
|
||||
Memory usage per processor = 10.1402 Mbytes
|
||||
Memory usage per processor = 11.1402 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -453120 0 -426647.73 18704.012
|
||||
50 779.50001 -439457.02 0 -426560.06 52355.276
|
||||
100 797.97828 -439764.76 0 -426562.07 51474.74
|
||||
Loop time of 6.46849 on 4 procs for 100 steps with 128000 atoms
|
||||
Loop time of 6.60121 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s
|
||||
Performance: 6.544 ns/day, 3.667 hours/ns, 15.149 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.581 | 5.5997 | 5.6265 | 0.8 | 86.57
|
||||
Neigh | 0.65287 | 0.658 | 0.66374 | 0.5 | 10.17
|
||||
Comm | 0.075706 | 0.11015 | 0.13655 | 7.2 | 1.70
|
||||
Output | 0.00026488 | 0.00028312 | 0.00029302 | 0.1 | 0.00
|
||||
Modify | 0.069607 | 0.072407 | 0.074555 | 0.7 | 1.12
|
||||
Other | | 0.02794 | | | 0.43
|
||||
Pair | 5.6676 | 5.7011 | 5.7469 | 1.3 | 86.36
|
||||
Neigh | 0.66423 | 0.67119 | 0.68082 | 0.7 | 10.17
|
||||
Comm | 0.079367 | 0.13668 | 0.1791 | 10.5 | 2.07
|
||||
Output | 0.00026989 | 0.00028622 | 0.00031209 | 0.1 | 0.00
|
||||
Modify | 0.060046 | 0.062203 | 0.065009 | 0.9 | 0.94
|
||||
Other | | 0.02974 | | | 0.45
|
||||
|
||||
Nlocal: 32000 ave 32092 max 31914 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -50,20 +50,20 @@ Memory usage per processor = 8.21387 Mbytes
|
|||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 2.26309 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 2.26185 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 19088.920 tau/day, 44.187 timesteps/s
|
||||
Performance: 19099.377 tau/day, 44.212 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9341 | 1.9341 | 1.9341 | 0.0 | 85.46
|
||||
Neigh | 0.2442 | 0.2442 | 0.2442 | 0.0 | 10.79
|
||||
Comm | 0.024158 | 0.024158 | 0.024158 | 0.0 | 1.07
|
||||
Output | 0.00011611 | 0.00011611 | 0.00011611 | 0.0 | 0.01
|
||||
Modify | 0.053222 | 0.053222 | 0.053222 | 0.0 | 2.35
|
||||
Other | | 0.007258 | | | 0.32
|
||||
Pair | 1.9328 | 1.9328 | 1.9328 | 0.0 | 85.45
|
||||
Neigh | 0.2558 | 0.2558 | 0.2558 | 0.0 | 11.31
|
||||
Comm | 0.024061 | 0.024061 | 0.024061 | 0.0 | 1.06
|
||||
Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.01
|
||||
Modify | 0.040887 | 0.040887 | 0.040887 | 0.0 | 1.81
|
||||
Other | | 0.008214 | | | 0.36
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -50,20 +50,20 @@ Memory usage per processor = 4.09506 Mbytes
|
|||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 0.640733 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.635957 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 67422.779 tau/day, 156.071 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 67929.172 tau/day, 157.243 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.49487 | 0.51733 | 0.5322 | 1.9 | 80.74
|
||||
Neigh | 0.061131 | 0.063685 | 0.065433 | 0.6 | 9.94
|
||||
Comm | 0.02457 | 0.042349 | 0.069598 | 8.1 | 6.61
|
||||
Output | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 | 0.0 | 0.01
|
||||
Modify | 0.012961 | 0.013863 | 0.014491 | 0.5 | 2.16
|
||||
Other | | 0.003448 | | | 0.54
|
||||
Pair | 0.51335 | 0.51822 | 0.52569 | 0.7 | 81.49
|
||||
Neigh | 0.063695 | 0.064309 | 0.065397 | 0.3 | 10.11
|
||||
Comm | 0.027525 | 0.03629 | 0.041959 | 3.1 | 5.71
|
||||
Output | 6.3896e-05 | 6.6698e-05 | 7.081e-05 | 0.0 | 0.01
|
||||
Modify | 0.012472 | 0.01254 | 0.012618 | 0.1 | 1.97
|
||||
Other | | 0.004529 | | | 0.71
|
||||
|
||||
Nlocal: 8000 ave 8037 max 7964 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -50,20 +50,20 @@ Memory usage per processor = 8.13678 Mbytes
|
|||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6133849 -5.0196788
|
||||
100 0.75841891 -5.759957 0 -4.6223375 0.20008866
|
||||
Loop time of 2.57914 on 4 procs for 100 steps with 128000 atoms
|
||||
Loop time of 2.55762 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Performance: 16749.768 tau/day, 38.773 timesteps/s
|
||||
Performance: 16890.677 tau/day, 39.099 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.042 | 2.1092 | 2.1668 | 3.1 | 81.78
|
||||
Neigh | 0.23982 | 0.24551 | 0.25233 | 1.0 | 9.52
|
||||
Comm | 0.067088 | 0.13887 | 0.22681 | 15.7 | 5.38
|
||||
Output | 0.00013185 | 0.00021666 | 0.00027108 | 0.4 | 0.01
|
||||
Modify | 0.060348 | 0.071269 | 0.077063 | 2.5 | 2.76
|
||||
Other | | 0.01403 | | | 0.54
|
||||
Pair | 2.0583 | 2.0988 | 2.1594 | 2.6 | 82.06
|
||||
Neigh | 0.24411 | 0.24838 | 0.25585 | 0.9 | 9.71
|
||||
Comm | 0.066397 | 0.13872 | 0.1863 | 11.9 | 5.42
|
||||
Output | 0.00012994 | 0.00021023 | 0.00025702 | 0.3 | 0.01
|
||||
Modify | 0.055533 | 0.058343 | 0.061791 | 1.2 | 2.28
|
||||
Other | | 0.0132 | | | 0.52
|
||||
|
||||
Nlocal: 32000 ave 32060 max 31939 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
|
|
@ -56,6 +56,7 @@ timestep 2.0
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.248835
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
|
|
@ -70,41 +71,41 @@ Neighbor list info ...
|
|||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6 -> bins = 10 13 13
|
||||
Memory usage per processor = 91.7487 Mbytes
|
||||
Memory usage per processor = 93.2721 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
|
||||
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 17.6362 (sec) ----------------
|
||||
TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
|
||||
PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
|
||||
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
|
||||
E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
|
||||
Volume = 308031.5639
|
||||
---------------- Step 100 ----- CPU = 35.9089 (sec) ----------------
|
||||
TotEng = -25290.7593 KinEng = 21592.0117 Temp = 301.0920
|
||||
PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408
|
||||
E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
|
||||
E_coul = 206659.2326 E_long = -270404.9733 Press = 6.9960
|
||||
Volume = 308133.9888
|
||||
Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms
|
||||
---------------- Step 50 ----- CPU = 17.2007 (sec) ----------------
|
||||
TotEng = -25330.0321 KinEng = 21501.0036 Temp = 299.8230
|
||||
PotEng = -46831.0357 E_bond = 2471.7033 E_angle = 10836.5108
|
||||
E_dihed = 5239.6316 E_impro = 227.1219 E_vdwl = -1993.2763
|
||||
E_coul = 206797.6655 E_long = -270410.3927 Press = 237.6866
|
||||
Volume = 308031.5640
|
||||
---------------- Step 100 ----- CPU = 35.0315 (sec) ----------------
|
||||
TotEng = -25290.7387 KinEng = 21591.9096 Temp = 301.0906
|
||||
PotEng = -46882.6484 E_bond = 2567.9789 E_angle = 10781.9556
|
||||
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
|
||||
E_coul = 206659.5006 E_long = -270404.9733 Press = 6.7898
|
||||
Volume = 308133.9933
|
||||
Loop time of 35.0316 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s
|
||||
Performance: 0.493 ns/day, 48.655 hours/ns, 2.855 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 25.731 | 25.731 | 25.731 | 0.0 | 71.66
|
||||
Bond | 1.2771 | 1.2771 | 1.2771 | 0.0 | 3.56
|
||||
Kspace | 3.2094 | 3.2094 | 3.2094 | 0.0 | 8.94
|
||||
Neigh | 4.4538 | 4.4538 | 4.4538 | 0.0 | 12.40
|
||||
Comm | 0.068507 | 0.068507 | 0.068507 | 0.0 | 0.19
|
||||
Output | 0.00025916 | 0.00025916 | 0.00025916 | 0.0 | 0.00
|
||||
Modify | 1.1417 | 1.1417 | 1.1417 | 0.0 | 3.18
|
||||
Other | | 0.027 | | | 0.08
|
||||
Pair | 25.021 | 25.021 | 25.021 | 0.0 | 71.42
|
||||
Bond | 1.2834 | 1.2834 | 1.2834 | 0.0 | 3.66
|
||||
Kspace | 3.2116 | 3.2116 | 3.2116 | 0.0 | 9.17
|
||||
Neigh | 4.2767 | 4.2767 | 4.2767 | 0.0 | 12.21
|
||||
Comm | 0.069283 | 0.069283 | 0.069283 | 0.0 | 0.20
|
||||
Output | 0.00028205 | 0.00028205 | 0.00028205 | 0.0 | 0.00
|
||||
Modify | 1.14 | 1.14 | 1.14 | 0.0 | 3.25
|
||||
Other | | 0.02938 | | | 0.08
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -113,9 +114,9 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
|
|||
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12028107
|
||||
Total # of neighbors = 12028098
|
||||
Ave neighs/atom = 375.878
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:37
|
||||
Total wall time: 0:00:36
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
|
|
@ -56,6 +56,7 @@ timestep 2.0
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.248835
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
|
|
@ -70,52 +71,52 @@ Neighbor list info ...
|
|||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6 -> bins = 10 13 13
|
||||
Memory usage per processor = 36.629 Mbytes
|
||||
Memory usage per processor = 37.3604 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
|
||||
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 4.7461 (sec) ----------------
|
||||
TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
|
||||
PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
|
||||
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
|
||||
E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
|
||||
Volume = 308031.5639
|
||||
---------------- Step 100 ----- CPU = 9.6332 (sec) ----------------
|
||||
TotEng = -25290.7591 KinEng = 21592.0117 Temp = 301.0920
|
||||
PotEng = -46882.7708 E_bond = 2567.9807 E_angle = 10781.9408
|
||||
E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
|
||||
E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960
|
||||
Volume = 308133.9888
|
||||
Loop time of 9.63322 on 4 procs for 100 steps with 32000 atoms
|
||||
---------------- Step 50 ----- CPU = 4.6056 (sec) ----------------
|
||||
TotEng = -25330.0321 KinEng = 21501.0036 Temp = 299.8230
|
||||
PotEng = -46831.0357 E_bond = 2471.7033 E_angle = 10836.5108
|
||||
E_dihed = 5239.6316 E_impro = 227.1219 E_vdwl = -1993.2763
|
||||
E_coul = 206797.6655 E_long = -270410.3927 Press = 237.6866
|
||||
Volume = 308031.5640
|
||||
---------------- Step 100 ----- CPU = 9.3910 (sec) ----------------
|
||||
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
|
||||
PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
|
||||
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
|
||||
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
|
||||
Volume = 308133.9933
|
||||
Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.4364 | 6.5993 | 6.7208 | 4.7 | 68.51
|
||||
Bond | 0.30755 | 0.32435 | 0.35704 | 3.4 | 3.37
|
||||
Kspace | 0.92248 | 1.0782 | 1.2597 | 13.0 | 11.19
|
||||
Neigh | 1.1669 | 1.1672 | 1.1675 | 0.0 | 12.12
|
||||
Comm | 0.094674 | 0.098065 | 0.10543 | 1.4 | 1.02
|
||||
Output | 0.00015521 | 0.00016224 | 0.00018215 | 0.1 | 0.00
|
||||
Modify | 0.32982 | 0.34654 | 0.35365 | 1.6 | 3.60
|
||||
Other | | 0.01943 | | | 0.20
|
||||
Pair | 6.2189 | 6.3266 | 6.6072 | 6.5 | 67.37
|
||||
Bond | 0.30793 | 0.32122 | 0.3414 | 2.4 | 3.42
|
||||
Kspace | 0.87994 | 1.1644 | 1.2855 | 15.3 | 12.40
|
||||
Neigh | 1.1358 | 1.136 | 1.1362 | 0.0 | 12.10
|
||||
Comm | 0.08292 | 0.084935 | 0.087077 | 0.5 | 0.90
|
||||
Output | 0.00015712 | 0.00016558 | 0.00018501 | 0.1 | 0.00
|
||||
Modify | 0.33717 | 0.34246 | 0.34794 | 0.7 | 3.65
|
||||
Other | | 0.01526 | | | 0.16
|
||||
|
||||
Nlocal: 8000 ave 8143 max 7933 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 22733.5 ave 22769 max 22693 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
|
||||
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 12028107
|
||||
Total # of neighbors = 12028098
|
||||
Ave neighs/atom = 375.878
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:10
|
||||
Total wall time: 0:00:09
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (15 Feb 2016)
|
||||
LAMMPS (6 Oct 2016)
|
||||
# Rhodopsin model
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -77,6 +77,7 @@ timestep 2.0
|
|||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
|
||||
G vector (1/distance) = 0.248593
|
||||
grid = 48 60 36
|
||||
stencil order = 5
|
||||
|
|
@ -91,52 +92,52 @@ Neighbor list info ...
|
|||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6 -> bins = 19 26 13
|
||||
Memory usage per processor = 95.5339 Mbytes
|
||||
Memory usage per processor = 96.9597 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304
|
||||
PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968
|
||||
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
|
||||
E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092
|
||||
E_coul = 827053.5824 E_long = -1080565.6077 Press = -149.0358
|
||||
Volume = 1231980.1340
|
||||
---------------- Step 50 ----- CPU = 18.7806 (sec) ----------------
|
||||
TotEng = -101320.2677 KinEng = 86003.4837 Temp = 299.8118
|
||||
PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922
|
||||
E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457
|
||||
E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161
|
||||
Volume = 1232126.1855
|
||||
---------------- Step 100 ----- CPU = 38.3684 (sec) ----------------
|
||||
TotEng = -101158.1849 KinEng = 86355.6149 Temp = 301.0393
|
||||
PotEng = -187513.7998 E_bond = 10272.0693 E_angle = 43128.6454
|
||||
E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186
|
||||
E_coul = 825583.7122 E_long = -1080572.5667 Press = 15.2151
|
||||
Volume = 1232535.8423
|
||||
Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
|
||||
---------------- Step 50 ----- CPU = 18.1689 (sec) ----------------
|
||||
TotEng = -101320.0211 KinEng = 86003.4933 Temp = 299.8118
|
||||
PotEng = -187323.5144 E_bond = 9887.1189 E_angle = 43346.8448
|
||||
E_dihed = 20958.7108 E_impro = 908.4721 E_vdwl = -7973.4486
|
||||
E_coul = 826141.5493 E_long = -1080592.7617 Press = 238.0404
|
||||
Volume = 1232126.1814
|
||||
---------------- Step 100 ----- CPU = 37.2027 (sec) ----------------
|
||||
TotEng = -101157.9546 KinEng = 86355.7413 Temp = 301.0398
|
||||
PotEng = -187513.6959 E_bond = 10272.0456 E_angle = 43128.7018
|
||||
E_dihed = 20794.0107 E_impro = 867.0928 E_vdwl = -7587.2409
|
||||
E_coul = 825584.2416 E_long = -1080572.5474 Press = 15.1729
|
||||
Volume = 1232535.8440
|
||||
Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
|
||||
Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 26.205 | 26.538 | 26.911 | 5.0 | 69.17
|
||||
Bond | 1.298 | 1.3125 | 1.3277 | 1.0 | 3.42
|
||||
Kspace | 3.7099 | 4.0992 | 4.4422 | 13.3 | 10.68
|
||||
Neigh | 4.6137 | 4.6144 | 4.615 | 0.0 | 12.03
|
||||
Comm | 0.21398 | 0.21992 | 0.22886 | 1.2 | 0.57
|
||||
Output | 0.00030518 | 0.00031543 | 0.00033307 | 0.1 | 0.00
|
||||
Modify | 1.5066 | 1.5232 | 1.5388 | 1.0 | 3.97
|
||||
Other | | 0.06051 | | | 0.16
|
||||
Pair | 25.431 | 25.738 | 25.984 | 4.0 | 69.18
|
||||
Bond | 1.2966 | 1.3131 | 1.3226 | 0.9 | 3.53
|
||||
Kspace | 3.7563 | 4.0123 | 4.3127 | 10.0 | 10.79
|
||||
Neigh | 4.3778 | 4.378 | 4.3782 | 0.0 | 11.77
|
||||
Comm | 0.1903 | 0.19549 | 0.20485 | 1.3 | 0.53
|
||||
Output | 0.00031805 | 0.00037521 | 0.00039601 | 0.2 | 0.00
|
||||
Modify | 1.4861 | 1.5051 | 1.5122 | 0.9 | 4.05
|
||||
Other | | 0.05992 | | | 0.16
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 47957 ave 47957 max 47957 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
|
||||
Neighs: 1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 48112472
|
||||
Total # of neighbors = 48112540
|
||||
Ave neighs/atom = 375.879
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:39
|
||||
Total wall time: 0:00:38
|
||||
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="6 Oct 2016 version">
|
||||
<META NAME="docnumber" CONTENT="11 Oct 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h3
|
||||
6 Oct 2016 version :c,h4
|
||||
11 Oct 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
|
|
|||
|
|
@ -475,9 +475,6 @@ be generated by variable formulas that use comparison or Boolean math
|
|||
operators or special functions like gmask() and rmask() and grmask().
|
||||
See the "variable"_variable.html command doc page for details.
|
||||
|
||||
NOTE: The LAST option, discussed below, is not yet implemented. It
|
||||
will be soon.
|
||||
|
||||
The specified value must be a simple numeric value or the word LAST.
|
||||
If LAST is used, it refers to the value of the attribute the last time
|
||||
the dump command was invoked to produce a snapshot. This is a way to
|
||||
|
|
|
|||
|
|
@ -191,13 +191,18 @@ input script should specify all fixes it will use. However, note that
|
|||
some fixes store an internal "state" which is written to the restart
|
||||
file. This allows the fix to continue on with its calculations in a
|
||||
restarted simulation. To re-enable such a fix, the fix command in the
|
||||
new input script must use the same fix-ID and group-ID as was used in
|
||||
the input script that wrote the restart file. If a match is found,
|
||||
LAMMPS prints a message indicating that the fix is being re-enabled.
|
||||
If no match is found before the first run or minimization is performed
|
||||
by the new script, the "state" information for the saved fix is
|
||||
discarded. See the doc pages for individual fixes for info on which
|
||||
ones can be restarted in this manner.
|
||||
new input script must be of the same style and use the same fix-ID as
|
||||
was used in the input script that wrote the restart file.
|
||||
|
||||
If a match is found, LAMMPS prints a message indicating that the fix
|
||||
is being re-enabled. If no match is found before the first run or
|
||||
minimization is performed by the new script, the "state" information
|
||||
for the saved fix is discarded. LAMMPS will also print a list of
|
||||
fixes for which the information is being discarded. See the doc pages
|
||||
for individual fixes for info on which ones can be restarted in this
|
||||
manner. Note that fixes which are created internally by other LAMMPS
|
||||
commands (computes, fixes, etc) will have style names which are
|
||||
all-capitalized, and IDs which are generated internally.
|
||||
|
||||
Likewise, the "computes"_fix.html used for a simulation are not stored
|
||||
in the restart file. This means the new input script should specify
|
||||
|
|
@ -213,6 +218,14 @@ re-created fix will be re-enabled with the stored state information as
|
|||
described in the previous paragraph, so that the compute can continue
|
||||
its calculations in a consistent manner.
|
||||
|
||||
NOTE: There are a handful of commands which can be used before or
|
||||
between runs which require a system initialization. Examples include
|
||||
the "balance", "displace_atoms", and "delete_atoms" commands. This is
|
||||
because they may migrate atoms to new processors. Thus they will also
|
||||
discard unused "state" information from fixes. This means that, if
|
||||
desired, you must re-specify the relevant fixes and computes (which
|
||||
create fixes) before those commands are used.
|
||||
|
||||
Some pair styles, like the "granular pair styles"_pair_gran.html, also
|
||||
use a fix to store "state" information that persists from timestep to
|
||||
timestep. In the case of granular potentials, it is contact
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@
|
|||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
#include "fix.h"
|
||||
#include "fix_store.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
|
|
@ -82,10 +83,17 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
|
|||
buffer_flag = 1;
|
||||
iregion = -1;
|
||||
idregion = NULL;
|
||||
|
||||
nthresh = 0;
|
||||
thresh_array = NULL;
|
||||
thresh_op = NULL;
|
||||
thresh_value = NULL;
|
||||
thresh_last = NULL;
|
||||
|
||||
nthreshlast = 0;
|
||||
thresh_fix = NULL;
|
||||
thresh_fixID = NULL;
|
||||
thresh_first = NULL;
|
||||
|
||||
// computes, fixes, variables which the dump accesses
|
||||
|
||||
|
|
@ -193,6 +201,17 @@ DumpCustom::~DumpCustom()
|
|||
memory->destroy(thresh_array);
|
||||
memory->destroy(thresh_op);
|
||||
memory->destroy(thresh_value);
|
||||
memory->destroy(thresh_last);
|
||||
|
||||
// check nfix in case all fixes have already been deleted
|
||||
|
||||
for (int i = 0; i < nthreshlast; i++) {
|
||||
if (modify->nfix) modify->delete_fix(thresh_fixID[i]);
|
||||
delete [] thresh_fixID[i];
|
||||
}
|
||||
memory->sfree(thresh_fix);
|
||||
memory->sfree(thresh_fixID);
|
||||
memory->destroy(thresh_first);
|
||||
|
||||
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
|
||||
memory->sfree(id_compute);
|
||||
|
|
@ -498,9 +517,10 @@ int DumpCustom::count()
|
|||
// un-choose if any threshold criterion isn't met
|
||||
|
||||
if (nthresh) {
|
||||
double *ptr;
|
||||
double *ptr,*ptrhold;
|
||||
double *values;
|
||||
double value;
|
||||
int nstride;
|
||||
int nstride,lastflag;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int ithresh = 0; ithresh < nthresh; ithresh++) {
|
||||
|
|
@ -926,32 +946,91 @@ int DumpCustom::count()
|
|||
}
|
||||
|
||||
// unselect atoms that don't meet threshold criterion
|
||||
// compare to single value or values stored in threshfix
|
||||
// copy ptr attribute into thresh_fix if this is first comparison
|
||||
|
||||
value = thresh_value[ithresh];
|
||||
if (thresh_last[ithresh] < 0) {
|
||||
lastflag = 0;
|
||||
value = thresh_value[ithresh];
|
||||
} else {
|
||||
lastflag = 1;
|
||||
int ilast = thresh_last[ithresh];
|
||||
values = thresh_fix[ilast]->vstore;
|
||||
ptrhold = ptr;
|
||||
if (thresh_first[ilast]) {
|
||||
thresh_first[ilast] = 0;
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
|
||||
ptr = ptrhold;
|
||||
}
|
||||
}
|
||||
|
||||
if (thresh_op[ithresh] == LT) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr >= value) choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr >= values[i]) choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr >= value) choose[i] = 0;
|
||||
}
|
||||
} else if (thresh_op[ithresh] == LE) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr > value) choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr > values[i]) choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr > value) choose[i] = 0;
|
||||
}
|
||||
} else if (thresh_op[ithresh] == GT) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr <= value) choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr <= values[i]) choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr <= value) choose[i] = 0;
|
||||
}
|
||||
} else if (thresh_op[ithresh] == GE) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr < value) choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr < values[i]) choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr < value) choose[i] = 0;
|
||||
}
|
||||
} else if (thresh_op[ithresh] == EQ) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr != value) choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr != values[i]) choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr != value) choose[i] = 0;
|
||||
}
|
||||
} else if (thresh_op[ithresh] == NEQ) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr == value) choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr == values[i]) choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && *ptr == value) choose[i] = 0;
|
||||
}
|
||||
} else if (thresh_op[ithresh] == XOR) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
|
||||
(*ptr != 0.0 && value != 0.0))
|
||||
choose[i] = 0;
|
||||
if (lastflag) {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
|
||||
(*ptr != 0.0 && values[i] != 0.0))
|
||||
choose[i] = 0;
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride)
|
||||
if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
|
||||
(*ptr != 0.0 && value != 0.0))
|
||||
choose[i] = 0;
|
||||
}
|
||||
}
|
||||
|
||||
// update values stored in threshfix
|
||||
|
||||
if (lastflag) {
|
||||
ptr = ptrhold;
|
||||
for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -1594,8 +1673,16 @@ int DumpCustom::modify_param(int narg, char **arg)
|
|||
thresh_array = NULL;
|
||||
thresh_op = NULL;
|
||||
thresh_value = NULL;
|
||||
thresh_last = NULL;
|
||||
for (int i = 0; i < nthreshlast; i++) {
|
||||
modify->delete_fix(thresh_fixID[i]);
|
||||
delete [] thresh_fixID[i];
|
||||
}
|
||||
thresh_fix = NULL;
|
||||
thresh_fixID = NULL;
|
||||
thresh_first = NULL;
|
||||
}
|
||||
nthresh = 0;
|
||||
nthresh = nthreshlast = 0;
|
||||
return 2;
|
||||
}
|
||||
|
||||
|
|
@ -1606,7 +1693,8 @@ int DumpCustom::modify_param(int narg, char **arg)
|
|||
memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
|
||||
memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
|
||||
memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
|
||||
|
||||
memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
|
||||
|
||||
// set attribute type of threshold
|
||||
// customize by adding to if statement
|
||||
|
||||
|
|
@ -1830,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
|
|||
field2index[nfield+nthresh] = add_custom(suffix,0);
|
||||
delete [] suffix;
|
||||
|
||||
} else error->all(FLERR,"Invalid dump_modify threshhold operator");
|
||||
} else error->all(FLERR,"Invalid dump_modify threshold operator");
|
||||
|
||||
// set operation type of threshold
|
||||
|
||||
|
|
@ -1843,9 +1931,43 @@ int DumpCustom::modify_param(int narg, char **arg)
|
|||
else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
|
||||
else error->all(FLERR,"Invalid dump_modify threshold operator");
|
||||
|
||||
// set threshold value
|
||||
// set threshold value as number or special LAST keyword
|
||||
// create FixStore to hold LAST values, should work with restart
|
||||
// id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
|
||||
|
||||
thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
|
||||
if (strcmp(arg[3],"LAST") != 0) {
|
||||
thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
|
||||
thresh_last[nthresh] = -1;
|
||||
} else {
|
||||
thresh_fix = (FixStore **)
|
||||
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
|
||||
"dump:thresh_fix");
|
||||
thresh_fixID = (char **)
|
||||
memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),
|
||||
"dump:thresh_fixID");
|
||||
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
|
||||
|
||||
int n = strlen(id) + strlen("_DUMP_STORE") + 8;
|
||||
thresh_fixID[nthreshlast] = new char[n];
|
||||
strcpy(thresh_fixID[nthreshlast],id);
|
||||
sprintf(&thresh_fixID[nthreshlast][strlen(id)],"%d",nthreshlast);
|
||||
strcat(thresh_fixID[nthreshlast],"_DUMP_STORE");
|
||||
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = thresh_fixID[nthreshlast];
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "1";
|
||||
modify->add_fix(6,newarg);
|
||||
thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
|
||||
thresh_last[nthreshlast] = nthreshlast;
|
||||
thresh_first[nthreshlast] = 1;
|
||||
nthreshlast++;
|
||||
}
|
||||
|
||||
nthresh++;
|
||||
return 4;
|
||||
|
|
|
|||
|
|
@ -33,10 +33,20 @@ class DumpCustom : public Dump {
|
|||
int nevery; // dump frequency for output
|
||||
int iregion; // -1 if no region, else which region
|
||||
char *idregion; // region ID
|
||||
int nthresh; // # of defined threshholds
|
||||
int *thresh_array; // array to threshhhold on for each nthresh
|
||||
int *thresh_op; // threshhold operation for each nthresh
|
||||
double *thresh_value; // threshhold value for each nthresh
|
||||
|
||||
int nthresh; // # of defined thresholds
|
||||
int nthreshlast; // # of defined thresholds with value = LAST
|
||||
|
||||
int *thresh_array; // array to threshold on for each nthresh
|
||||
int *thresh_op; // threshold operation for each nthresh
|
||||
double *thresh_value; // threshold value for each nthresh
|
||||
int *thresh_last; // for threshold value = LAST,
|
||||
// index into thresh_fix
|
||||
// -1 if not LAST, value is numeric
|
||||
|
||||
class FixStore **thresh_fix; // stores values for each threshold LAST
|
||||
char **thresh_fixID; // IDs of thresh_fixes
|
||||
int *thresh_first; // 1 the first time a FixStore values accessed
|
||||
|
||||
int expand; // flag for whether field args were expanded
|
||||
char **earg; // field names with wildcard expansion
|
||||
|
|
@ -50,7 +60,7 @@ class DumpCustom : public Dump {
|
|||
int nchoose; // # of selected atoms
|
||||
int maxlocal; // size of atom selection and variable arrays
|
||||
int *choose; // local indices of selected atoms
|
||||
double *dchoose; // value for each atom to threshhold against
|
||||
double *dchoose; // value for each atom to threshold against
|
||||
int *clist; // compressed list of indices of selected atoms
|
||||
|
||||
int nfield; // # of keywords listed by user
|
||||
|
|
@ -233,9 +243,9 @@ E: Compute used in dump between runs is not current
|
|||
The compute was not invoked on the current timestep, therefore it
|
||||
cannot be used in a dump between runs.
|
||||
|
||||
E: Threshhold for an atom property that isn't allocated
|
||||
E: Threshold for an atom property that isn't allocated
|
||||
|
||||
A dump threshhold has been requested on a quantity that is
|
||||
A dump threshold has been requested on a quantity that is
|
||||
not defined by the atom style used in this simulation.
|
||||
|
||||
E: Dumping an atom property that isn't allocated
|
||||
|
|
@ -362,7 +372,7 @@ E: Could not find dump modify custom atom integer property ID
|
|||
|
||||
Self-explanatory.
|
||||
|
||||
E: Invalid dump_modify threshhold operator
|
||||
E: Invalid dump_modify threshold operator
|
||||
|
||||
Operator keyword used for threshold specification in not recognized.
|
||||
|
||||
|
|
|
|||
|
|
@ -154,6 +154,9 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
|
|||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
|
||||
|
||||
printf("AAA HOW GET HERE\n");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -68,10 +68,12 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
|
|||
list_timeflag = NULL;
|
||||
|
||||
nfix_restart_global = 0;
|
||||
id_restart_global = style_restart_global = state_restart_global = NULL;
|
||||
id_restart_global = style_restart_global = NULL;
|
||||
state_restart_global = NULL;
|
||||
used_restart_global = NULL;
|
||||
nfix_restart_peratom = 0;
|
||||
id_restart_peratom = style_restart_peratom = NULL;
|
||||
index_restart_peratom = NULL;
|
||||
index_restart_peratom = used_restart_peratom = NULL;
|
||||
|
||||
ncompute = maxcompute = 0;
|
||||
compute = NULL;
|
||||
|
|
@ -140,7 +142,7 @@ Modify::~Modify()
|
|||
delete [] end_of_step_every;
|
||||
delete [] list_timeflag;
|
||||
|
||||
restart_deallocate();
|
||||
restart_deallocate(0);
|
||||
|
||||
delete compute_map;
|
||||
delete fix_map;
|
||||
|
|
@ -156,7 +158,7 @@ void Modify::init()
|
|||
|
||||
// delete storage of restart info since it is not valid after 1st run
|
||||
|
||||
restart_deallocate();
|
||||
restart_deallocate(1);
|
||||
|
||||
// create lists of fixes to call at each stage of run
|
||||
|
||||
|
|
@ -819,11 +821,16 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
|
|||
if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
|
||||
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
|
||||
fix[ifix]->restart(state_restart_global[i]);
|
||||
used_restart_global[i] = 1;
|
||||
if (comm->me == 0) {
|
||||
const char *str = (const char *) ("Resetting global state of Fix %s "
|
||||
"Style %s from restart file info\n");
|
||||
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
|
||||
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
|
||||
if (screen)
|
||||
fprintf(screen,"Resetting global fix info from restart file:\n");
|
||||
if (logfile)
|
||||
fprintf(logfile,"Resetting global fix info from restart file:\n");
|
||||
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
|
||||
fix[ifix]->style,fix[ifix]->id);
|
||||
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
|
||||
fix[ifix]->style,fix[ifix]->id);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -833,14 +840,19 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
|
|||
for (int i = 0; i < nfix_restart_peratom; i++)
|
||||
if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
|
||||
strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
|
||||
used_restart_peratom[i] = 1;
|
||||
for (int j = 0; j < atom->nlocal; j++)
|
||||
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
|
||||
fix[ifix]->restart_reset = 1;
|
||||
if (comm->me == 0) {
|
||||
char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
|
||||
"from restart file info\n");
|
||||
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
|
||||
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
|
||||
if (screen)
|
||||
fprintf(screen,"Resetting peratom fix info from restart file:\n");
|
||||
if (logfile)
|
||||
fprintf(logfile,"Resetting peratom fix info from restart file:\n");
|
||||
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
|
||||
fix[ifix]->style,fix[ifix]->id);
|
||||
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
|
||||
fix[ifix]->style,fix[ifix]->id);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1158,6 +1170,7 @@ int Modify::read_restart(FILE *fp)
|
|||
id_restart_global = new char*[nfix_restart_global];
|
||||
style_restart_global = new char*[nfix_restart_global];
|
||||
state_restart_global = new char*[nfix_restart_global];
|
||||
used_restart_global = new int[nfix_restart_global];
|
||||
}
|
||||
|
||||
// read each entry and Bcast to all procs
|
||||
|
|
@ -1182,6 +1195,8 @@ int Modify::read_restart(FILE *fp)
|
|||
state_restart_global[i] = new char[n];
|
||||
if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
|
||||
MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);
|
||||
|
||||
used_restart_global[i] = 0;
|
||||
}
|
||||
|
||||
// nfix_restart_peratom = # of restart entries with peratom info
|
||||
|
|
@ -1197,6 +1212,7 @@ int Modify::read_restart(FILE *fp)
|
|||
id_restart_peratom = new char*[nfix_restart_peratom];
|
||||
style_restart_peratom = new char*[nfix_restart_peratom];
|
||||
index_restart_peratom = new int[nfix_restart_peratom];
|
||||
used_restart_peratom = new int[nfix_restart_peratom];
|
||||
}
|
||||
|
||||
// read each entry and Bcast to all procs
|
||||
|
|
@ -1221,6 +1237,7 @@ int Modify::read_restart(FILE *fp)
|
|||
maxsize += n;
|
||||
|
||||
index_restart_peratom[i] = i;
|
||||
used_restart_peratom[i] = 0;
|
||||
}
|
||||
|
||||
return maxsize;
|
||||
|
|
@ -1228,11 +1245,36 @@ int Modify::read_restart(FILE *fp)
|
|||
|
||||
/* ----------------------------------------------------------------------
|
||||
delete all lists of restart file Fix info
|
||||
if flag set, print list of restart file info not assigned to new fixes
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Modify::restart_deallocate()
|
||||
void Modify::restart_deallocate(int flag)
|
||||
{
|
||||
if (nfix_restart_global) {
|
||||
if (flag && comm->me == 0) {
|
||||
int i;
|
||||
for (i = 0; i < nfix_restart_global; i++)
|
||||
if (used_restart_global[i] == 0) break;
|
||||
if (i == nfix_restart_global) {
|
||||
if (screen)
|
||||
fprintf(screen,"All restart file global fix info "
|
||||
"was re-assigned\n");
|
||||
if (logfile)
|
||||
fprintf(logfile,"All restart file global fix info "
|
||||
"was re-assigned\n");
|
||||
} else {
|
||||
if (screen) fprintf(screen,"Unused restart file global fix info:\n");
|
||||
if (logfile) fprintf(logfile,"Unused restart file global fix info:\n");
|
||||
for (i = 0; i < nfix_restart_global; i++) {
|
||||
if (used_restart_global[i]) continue;
|
||||
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
|
||||
style_restart_global[i],id_restart_global[i]);
|
||||
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
|
||||
style_restart_global[i],id_restart_global[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 0; i < nfix_restart_global; i++) {
|
||||
delete [] id_restart_global[i];
|
||||
delete [] style_restart_global[i];
|
||||
|
|
@ -1241,9 +1283,34 @@ void Modify::restart_deallocate()
|
|||
delete [] id_restart_global;
|
||||
delete [] style_restart_global;
|
||||
delete [] state_restart_global;
|
||||
delete [] used_restart_global;
|
||||
}
|
||||
|
||||
if (nfix_restart_peratom) {
|
||||
if (flag && comm->me == 0) {
|
||||
int i;
|
||||
for (i = 0; i < nfix_restart_peratom; i++)
|
||||
if (used_restart_peratom[i] == 0) break;
|
||||
if (i == nfix_restart_peratom) {
|
||||
if (screen)
|
||||
fprintf(screen,"All restart file peratom fix info "
|
||||
"was re-assigned\n");
|
||||
if (logfile)
|
||||
fprintf(logfile,"All restart file peratom fix info "
|
||||
"was re-assigned\n");
|
||||
} else {
|
||||
if (screen) fprintf(screen,"Unused restart file peratom fix info:\n");
|
||||
if (logfile) fprintf(logfile,"Unused restart file peratom fix info:\n");
|
||||
for (i = 0; i < nfix_restart_peratom; i++) {
|
||||
if (used_restart_peratom[i]) continue;
|
||||
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
|
||||
style_restart_peratom[i],id_restart_peratom[i]);
|
||||
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
|
||||
style_restart_peratom[i],id_restart_peratom[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 0; i < nfix_restart_peratom; i++) {
|
||||
delete [] id_restart_peratom[i];
|
||||
delete [] style_restart_peratom[i];
|
||||
|
|
@ -1251,6 +1318,7 @@ void Modify::restart_deallocate()
|
|||
delete [] id_restart_peratom;
|
||||
delete [] style_restart_peratom;
|
||||
delete [] index_restart_peratom;
|
||||
delete [] used_restart_peratom;
|
||||
}
|
||||
|
||||
nfix_restart_global = nfix_restart_peratom = 0;
|
||||
|
|
|
|||
|
|
@ -107,7 +107,7 @@ class Modify : protected Pointers {
|
|||
|
||||
void write_restart(FILE *);
|
||||
int read_restart(FILE *);
|
||||
void restart_deallocate();
|
||||
void restart_deallocate(int);
|
||||
|
||||
bigint memory_usage();
|
||||
|
||||
|
|
@ -135,10 +135,12 @@ class Modify : protected Pointers {
|
|||
char **id_restart_global; // stored fix global info
|
||||
char **style_restart_global; // from read-in restart file
|
||||
char **state_restart_global;
|
||||
int *used_restart_global;
|
||||
|
||||
char **id_restart_peratom; // stored fix peratom info
|
||||
char **style_restart_peratom; // from read-in restart file
|
||||
int *index_restart_peratom;
|
||||
int *used_restart_peratom;
|
||||
|
||||
int index_permanent; // fix/compute index returned to library call
|
||||
|
||||
|
|
|
|||
|
|
@ -106,11 +106,12 @@ class Region : protected Pointers {
|
|||
void options(int, char **);
|
||||
void point_on_line_segment(double *, double *, double *, double *);
|
||||
void forward_transform(double &, double &, double &);
|
||||
double point[3],runit[3];
|
||||
|
||||
private:
|
||||
char *xstr,*ystr,*zstr,*tstr;
|
||||
int xvar,yvar,zvar,tvar;
|
||||
double axis[3],point[3],runit[3];
|
||||
double axis[3];
|
||||
|
||||
void inverse_transform(double &, double &, double &);
|
||||
void rotate(double &, double &, double &, double);
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
#define LAMMPS_VERSION "6 Oct 2016"
|
||||
#define LAMMPS_VERSION "11 Oct 2016"
|
||||
|
|
|
|||
|
|
@ -32,7 +32,6 @@ using namespace LAMMPS_NS;
|
|||
|
||||
void WriteDump::command(int narg, char **arg)
|
||||
{
|
||||
|
||||
if (narg < 3) error->all(FLERR,"Illegal write_dump command");
|
||||
|
||||
// modindex = index in args of "modify" keyword
|
||||
|
|
|
|||
Loading…
Reference in New Issue