forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11348 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
7e5b15bb90
commit
9f6290042e
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@ -1,4 +1,4 @@
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LAMMPS (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# FENE beadspring benchmark
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units lj
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@ -6,11 +6,15 @@ atom_style bond
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special_bonds fene
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read_data data.chain
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1 = max bonds/atom
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orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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31680 bonds
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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@ -36,14 +40,14 @@ Memory usage per processor = 11.5156 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 0.992695 on 1 procs for 100 steps with 32000 atoms
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Loop time of 1.00576 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.200438 (20.1913)
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Bond time (%) = 0.0872233 (8.78652)
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Neigh time (%) = 0.450228 (45.3541)
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Comm time (%) = 0.0333259 (3.35712)
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Outpt time (%) = 9.58443e-05 (0.00965496)
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Other time (%) = 0.221384 (22.3013)
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Pair time (%) = 0.201571 (20.0416)
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Bond time (%) = 0.0877447 (8.7242)
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Neigh time (%) = 0.46259 (45.9939)
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Comm time (%) = 0.0333455 (3.31544)
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Outpt time (%) = 0.000102997 (0.0102407)
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Other time (%) = 0.22041 (21.9147)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# FENE beadspring benchmark
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units lj
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@ -6,11 +6,15 @@ atom_style bond
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special_bonds fene
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read_data data.chain
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1 = max bonds/atom
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orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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31680 bonds
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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@ -36,14 +40,14 @@ Memory usage per processor = 4.85536 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 0.272427 on 4 procs for 100 steps with 32000 atoms
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Loop time of 0.273179 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0509947 (18.7187)
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Bond time (%) = 0.0227102 (8.33625)
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Neigh time (%) = 0.116272 (42.6802)
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Comm time (%) = 0.0213055 (7.82062)
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Outpt time (%) = 7.23004e-05 (0.0265394)
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Other time (%) = 0.0610721 (22.4178)
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Pair time (%) = 0.050166 (18.3638)
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Bond time (%) = 0.0222697 (8.15205)
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Neigh time (%) = 0.119487 (43.7393)
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Comm time (%) = 0.0235835 (8.633)
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Outpt time (%) = 5.48959e-05 (0.0200952)
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Other time (%) = 0.0576181 (21.0917)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# FENE beadspring benchmark
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variable x index 1
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@ -11,11 +11,15 @@ atom_modify map hash
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special_bonds fene
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read_data data.chain
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1 = max bonds/atom
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orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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31680 bonds
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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@ -52,14 +56,14 @@ Memory usage per processor = 13.4806 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 1.188 on 4 procs for 100 steps with 128000 atoms
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Loop time of 1.22968 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 0.226131 (19.0346)
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Bond time (%) = 0.0970581 (8.16985)
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Neigh time (%) = 0.506595 (42.6426)
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Comm time (%) = 0.107507 (9.04943)
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Outpt time (%) = 0.000239134 (0.0201291)
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Other time (%) = 0.250472 (21.0834)
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Pair time (%) = 0.233808 (19.0137)
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Bond time (%) = 0.102124 (8.30491)
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Neigh time (%) = 0.535992 (43.5879)
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Comm time (%) = 0.103922 (8.45112)
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Outpt time (%) = 0.000156224 (0.0127044)
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Other time (%) = 0.253678 (20.6296)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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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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@ -11,7 +11,9 @@ communicate single vel yes
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read_data data.chute
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orthogonal box = (0 0 0) to (40 20 37.2886)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
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@ -38,17 +40,17 @@ thermo_modify norm no
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thermo 100
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run 100
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Memory usage per processor = 21.0636 Mbytes
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Memory usage per processor = 21.4184 Mbytes
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Step Atoms KinEng 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 0.54007 on 1 procs for 100 steps with 32000 atoms
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Loop time of 0.532316 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.329372 (60.987)
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Neigh time (%) = 0.0422847 (7.82949)
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Comm time (%) = 0.0179758 (3.32842)
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Outpt time (%) = 0.00019002 (0.0351843)
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Other time (%) = 0.150247 (27.8199)
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Pair time (%) = 0.323012 (60.6805)
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Neigh time (%) = 0.0413709 (7.77186)
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Comm time (%) = 0.017947 (3.37149)
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Outpt time (%) = 0.000191927 (0.0360551)
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Other time (%) = 0.149794 (28.1401)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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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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@ -11,7 +11,9 @@ communicate single vel yes
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read_data data.chute
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orthogonal box = (0 0 0) to (40 20 37.2886)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
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@ -38,17 +40,17 @@ thermo_modify norm no
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thermo 100
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run 100
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Memory usage per processor = 10.5226 Mbytes
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Memory usage per processor = 10.7034 Mbytes
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Step Atoms KinEng 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 0.135566 on 4 procs for 100 steps with 32000 atoms
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Loop time of 0.13025 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0668132 (49.2847)
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Neigh time (%) = 0.0107402 (7.9225)
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Comm time (%) = 0.0142344 (10.5)
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Outpt time (%) = 0.000106156 (0.0783057)
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Other time (%) = 0.043672 (32.2145)
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Pair time (%) = 0.0655041 (50.291)
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Neigh time (%) = 0.0103548 (7.94993)
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Comm time (%) = 0.0144752 (11.1134)
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Outpt time (%) = 9.47714e-05 (0.072761)
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Other time (%) = 0.0398214 (30.573)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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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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@ -14,7 +14,9 @@ communicate single vel yes
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read_data data.chute
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orthogonal box = (0 0 0) to (40 20 37.2886)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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replicate $x $y 1
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@ -48,17 +50,17 @@ thermo_modify norm no
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thermo 100
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run 100
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Memory usage per processor = 21.8161 Mbytes
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Memory usage per processor = 22.3334 Mbytes
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Step Atoms KinEng 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 1.01235 on 4 procs for 100 steps with 128000 atoms
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Loop time of 0.981477 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 0.508497 (50.2295)
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Neigh time (%) = 0.0454835 (4.49288)
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Comm time (%) = 0.0667624 (6.59481)
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Outpt time (%) = 0.00123399 (0.121894)
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Other time (%) = 0.390371 (38.5609)
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Pair time (%) = 0.507874 (51.7459)
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Neigh time (%) = 0.0444019 (4.52399)
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Comm time (%) = 0.065434 (6.6669)
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Outpt time (%) = 0.000373006 (0.0380046)
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Other time (%) = 0.363394 (37.0252)
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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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@ -1,4 +1,4 @@
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LAMMPS (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# bulk Cu lattice
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variable x index 1
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@ -41,18 +41,18 @@ timestep 0.005
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thermo 50
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run 100
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Memory usage per processor = 15.3729 Mbytes
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Memory usage per processor = 15.3727 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 5.89581 on 1 procs for 100 steps with 32000 atoms
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Loop time of 5.88636 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 5.20005 (88.1991)
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Neigh time (%) = 0.590692 (10.0188)
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Comm time (%) = 0.0308192 (0.52273)
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Outpt time (%) = 0.000217915 (0.00369609)
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Other time (%) = 0.0740323 (1.25568)
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Pair time (%) = 5.1909 (88.1853)
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Neigh time (%) = 0.590118 (10.0252)
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Comm time (%) = 0.0310338 (0.527215)
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Outpt time (%) = 0.000212908 (0.00361697)
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Other time (%) = 0.0740924 (1.25871)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# bulk Cu lattice
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variable x index 1
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@ -41,18 +41,18 @@ timestep 0.005
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thermo 50
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run 100
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Memory usage per processor = 4.92459 Mbytes
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Memory usage per processor = 4.92441 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 1.62415 on 4 procs for 100 steps with 32000 atoms
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Loop time of 1.55795 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 1.39691 (86.0084)
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Neigh time (%) = 0.157564 (9.70131)
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Comm time (%) = 0.0479782 (2.95404)
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Outpt time (%) = 0.000121653 (0.00749025)
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Other time (%) = 0.0215805 (1.32873)
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Pair time (%) = 1.34981 (86.6403)
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Neigh time (%) = 0.153546 (9.85563)
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Comm time (%) = 0.0348434 (2.23649)
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Outpt time (%) = 9.79304e-05 (0.00628584)
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Other time (%) = 0.0196509 (1.26133)
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Nlocal: 8000 ave 8008 max 7993 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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@ -1,4 +1,4 @@
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LAMMPS (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# bulk Cu lattice
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variable x index 1
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@ -41,18 +41,18 @@ timestep 0.005
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thermo 50
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run 100
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Memory usage per processor = 15.2893 Mbytes
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Memory usage per processor = 15.2891 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1600 -453120 0 -426647.73 18704.012
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50 779.50001 -439457.02 0 -426560.06 52355.276
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100 797.97828 -439764.76 0 -426562.07 51474.74
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Loop time of 6.63538 on 4 procs for 100 steps with 128000 atoms
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Loop time of 6.49873 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 5.70315 (85.9507)
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Neigh time (%) = 0.671065 (10.1134)
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Comm time (%) = 0.154897 (2.33441)
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Outpt time (%) = 0.0003497 (0.00527024)
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Other time (%) = 0.105914 (1.5962)
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Pair time (%) = 5.61886 (86.4609)
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Neigh time (%) = 0.667741 (10.2749)
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Comm time (%) = 0.110698 (1.70337)
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Outpt time (%) = 0.000267088 (0.00410985)
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Other time (%) = 0.101163 (1.55666)
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Nlocal: 32000 ave 32092 max 31914 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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# 3d Lennard-Jones melt
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variable x index 1
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@ -39,17 +39,17 @@ neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 13.2267 Mbytes
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Memory usage per processor = 13.2266 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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Loop time of 2.24794 on 1 procs for 100 steps with 32000 atoms
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Loop time of 2.25121 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 1.92284 (85.5376)
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Neigh time (%) = 0.241012 (10.7215)
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Comm time (%) = 0.0244191 (1.08629)
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Outpt time (%) = 0.000105858 (0.0047091)
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Other time (%) = 0.0595703 (2.64999)
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Pair time (%) = 1.92625 (85.5648)
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Neigh time (%) = 0.241071 (10.7085)
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Comm time (%) = 0.0242682 (1.078)
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Outpt time (%) = 0.000102997 (0.00457517)
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Other time (%) = 0.0595243 (2.6441)
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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 (14 Aug 2013)
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LAMMPS (30 Jan 2014)
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# 3d Lennard-Jones melt
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variable x index 1
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@ -39,17 +39,17 @@ neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 4.31295 Mbytes
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Memory usage per processor = 4.31282 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
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Loop time of 0.621459 on 4 procs for 100 steps with 32000 atoms
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Loop time of 0.632266 on 4 procs for 100 steps with 32000 atoms
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|
||||
Pair time (%) = 0.50556 (81.3506)
|
||||
Neigh time (%) = 0.0630878 (10.1516)
|
||||
Comm time (%) = 0.036548 (5.88099)
|
||||
Outpt time (%) = 5.19753e-05 (0.00836343)
|
||||
Other time (%) = 0.0162107 (2.60849)
|
||||
Pair time (%) = 0.509912 (80.6484)
|
||||
Neigh time (%) = 0.0636757 (10.071)
|
||||
Comm time (%) = 0.0426416 (6.74425)
|
||||
Outpt time (%) = 5.04255e-05 (0.00797537)
|
||||
Other time (%) = 0.015986 (2.52837)
|
||||
|
||||
Nlocal: 8000 ave 8037 max 7964 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (14 Aug 2013)
|
||||
LAMMPS (30 Jan 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -39,17 +39,17 @@ neigh_modify delay 0 every 20 check no
|
|||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 13.1496 Mbytes
|
||||
Memory usage per processor = 13.1495 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 2.51513 on 4 procs for 100 steps with 128000 atoms
|
||||
Loop time of 2.53652 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 2.06373 (82.0527)
|
||||
Neigh time (%) = 0.246449 (9.79865)
|
||||
Comm time (%) = 0.122232 (4.85986)
|
||||
Outpt time (%) = 0.000143051 (0.00568762)
|
||||
Other time (%) = 0.0825751 (3.28313)
|
||||
Pair time (%) = 2.08358 (82.1432)
|
||||
Neigh time (%) = 0.246569 (9.72079)
|
||||
Comm time (%) = 0.121166 (4.77688)
|
||||
Outpt time (%) = 0.000156581 (0.00617309)
|
||||
Other time (%) = 0.0850482 (3.35295)
|
||||
|
||||
Nlocal: 32000 ave 32060 max 31939 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (14 Aug 2013)
|
||||
LAMMPS (30 Jan 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
|
|
@ -14,17 +14,27 @@ pair_modify mix arithmetic
|
|||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
8 = max angles/atom
|
||||
18 = max dihedrals/atom
|
||||
2 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
8 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
|
|
@ -60,30 +70,30 @@ 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
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 17.7652 (sec) ----------------
|
||||
---------------- Step 50 ----- CPU = 17.7678 (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 = 36.1527 (sec) ----------------
|
||||
---------------- Step 100 ----- CPU = 36.1938 (sec) ----------------
|
||||
TotEng = -25290.7592 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 = 206659.2327 E_long = -270404.9733 Press = 6.9960
|
||||
Volume = 308133.9888
|
||||
Loop time of 36.1528 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 36.1938 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 26.1216 (72.2533)
|
||||
Bond time (%) = 1.27574 (3.52875)
|
||||
Kspce time (%) = 3.25689 (9.00869)
|
||||
Neigh time (%) = 4.3025 (11.9009)
|
||||
Comm time (%) = 0.0688474 (0.190435)
|
||||
Outpt time (%) = 0.000230074 (0.000636394)
|
||||
Other time (%) = 1.127 (3.11732)
|
||||
Pair time (%) = 25.9243 (71.6264)
|
||||
Bond time (%) = 1.26808 (3.50358)
|
||||
Kspce time (%) = 3.25738 (8.99982)
|
||||
Neigh time (%) = 4.54843 (12.5669)
|
||||
Comm time (%) = 0.0694413 (0.19186)
|
||||
Outpt time (%) = 0.000235081 (0.000649505)
|
||||
Other time (%) = 1.12593 (3.11082)
|
||||
|
||||
FFT time (% of Kspce) = 0.277417 (8.51784)
|
||||
FFT Gflps 3d (1d only) = 1.87335 3.23863
|
||||
FFT time (% of Kspce) = 0.27522 (8.44911)
|
||||
FFT Gflps 3d (1d only) = 1.8883 3.24026
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (14 Aug 2013)
|
||||
LAMMPS (30 Jan 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
|
|
@ -14,17 +14,27 @@ pair_modify mix arithmetic
|
|||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
8 = max angles/atom
|
||||
18 = max dihedrals/atom
|
||||
2 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
8 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
|
|
@ -60,30 +70,30 @@ 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
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 4.6553 (sec) ----------------
|
||||
---------------- Step 50 ----- CPU = 4.8445 (sec) ----------------
|
||||
TotEng = -25330.0829 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 = 9.5123 (sec) ----------------
|
||||
---------------- Step 100 ----- CPU = 9.9262 (sec) ----------------
|
||||
TotEng = -25290.7592 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 = 206659.2327 E_long = -270404.9733 Press = 6.9960
|
||||
Volume = 308133.9888
|
||||
Loop time of 9.51235 on 4 procs for 100 steps with 32000 atoms
|
||||
Loop time of 9.92624 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 6.58797 (69.2571)
|
||||
Bond time (%) = 0.319462 (3.35839)
|
||||
Kspce time (%) = 1.08263 (11.3813)
|
||||
Neigh time (%) = 1.08542 (11.4107)
|
||||
Comm time (%) = 0.0859144 (0.903188)
|
||||
Outpt time (%) = 0.000161052 (0.00169308)
|
||||
Other time (%) = 0.350788 (3.68772)
|
||||
Pair time (%) = 6.65637 (67.0583)
|
||||
Bond time (%) = 0.320161 (3.2254)
|
||||
Kspce time (%) = 1.26452 (12.7392)
|
||||
Neigh time (%) = 1.21993 (12.2899)
|
||||
Comm time (%) = 0.0982867 (0.99017)
|
||||
Outpt time (%) = 0.000156939 (0.00158105)
|
||||
Other time (%) = 0.366824 (3.69549)
|
||||
|
||||
FFT time (% of Kspce) = 0.0982845 (9.07835)
|
||||
FFT Gflps 3d (1d only) = 5.28769 12.8216
|
||||
FFT time (% of Kspce) = 0.0959004 (7.58393)
|
||||
FFT Gflps 3d (1d only) = 5.41914 12.8168
|
||||
|
||||
Nlocal: 8000 ave 8143 max 7933 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (14 Aug 2013)
|
||||
LAMMPS (30 Jan 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
variable x index 1
|
||||
|
|
@ -19,17 +19,27 @@ pair_modify mix arithmetic
|
|||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
4 = max bonds/atom
|
||||
8 = max angles/atom
|
||||
18 = max dihedrals/atom
|
||||
2 = max impropers/atom
|
||||
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
8 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
|
|
@ -81,30 +91,30 @@ 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
|
||||
Volume = 1231980.1340
|
||||
---------------- Step 50 ----- CPU = 19.2151 (sec) ----------------
|
||||
---------------- Step 50 ----- CPU = 19.1272 (sec) ----------------
|
||||
TotEng = -101320.2676 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 = 39.0436 (sec) ----------------
|
||||
---------------- Step 100 ----- CPU = 39.2968 (sec) ----------------
|
||||
TotEng = -101158.1853 KinEng = 86355.6148 Temp = 301.0393
|
||||
PotEng = -187513.8001 E_bond = 10272.0693 E_angle = 43128.6453
|
||||
E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186
|
||||
E_coul = 825583.7120 E_long = -1080572.5667 Press = 15.2151
|
||||
Volume = 1232535.8423
|
||||
Loop time of 39.0437 on 4 procs for 100 steps with 128000 atoms
|
||||
Loop time of 39.2969 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 27.1533 (69.546)
|
||||
Bond time (%) = 1.31501 (3.36805)
|
||||
Kspce time (%) = 4.35908 (11.1646)
|
||||
Neigh time (%) = 4.42268 (11.3275)
|
||||
Comm time (%) = 0.229435 (0.587637)
|
||||
Outpt time (%) = 0.000313759 (0.00080361)
|
||||
Other time (%) = 1.56382 (4.00532)
|
||||
Pair time (%) = 27.1236 (69.0224)
|
||||
Bond time (%) = 1.30692 (3.32576)
|
||||
Kspce time (%) = 4.30137 (10.9458)
|
||||
Neigh time (%) = 4.78495 (12.1764)
|
||||
Comm time (%) = 0.217593 (0.553716)
|
||||
Outpt time (%) = 0.000282824 (0.000719711)
|
||||
Other time (%) = 1.56213 (3.9752)
|
||||
|
||||
FFT time (% of Kspce) = 0.466478 (10.7013)
|
||||
FFT Gflps 3d (1d only) = 5.13382 11.4048
|
||||
FFT time (% of Kspce) = 0.505049 (11.7416)
|
||||
FFT Gflps 3d (1d only) = 4.74174 11.1028
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Loading…
Reference in New Issue