forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11413 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
f9e3511f2c
commit
ca3998a659
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LAMMPS (1 Feb 2014)
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# FENE beadspring benchmark
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units lj
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atom_style bond
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special_bonds fene
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read_data data.chain
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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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neighbor 0.4 bin
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neigh_modify every 1 delay 1
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bond_style fene
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bond_coeff 1 30.0 1.5 1.0 1.0
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pair_style lj/cut 1.12
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pair_modify shift yes
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pair_coeff 1 1 1.0 1.0 1.12
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fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297
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thermo 100
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timestep 0.012
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run 100
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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 1.00129 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.201344 (20.1083)
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Bond time (%) = 0.0870376 (8.69251)
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Neigh time (%) = 0.45714 (45.6549)
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Comm time (%) = 0.0338521 (3.38083)
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Outpt time (%) = 0.000102043 (0.0101911)
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Other time (%) = 0.221819 (22.1532)
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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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Nghost: 9493 ave 9493 max 9493 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 155873 ave 155873 max 155873 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 155873
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Ave neighs/atom = 4.87103
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Ave special neighs/atom = 1.98
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Neighbor list builds = 25
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Dangerous builds = 0
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@ -0,0 +1,63 @@
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LAMMPS (1 Feb 2014)
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# FENE beadspring benchmark
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units lj
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atom_style bond
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special_bonds fene
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read_data data.chain
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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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neighbor 0.4 bin
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neigh_modify every 1 delay 1
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bond_style fene
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bond_coeff 1 30.0 1.5 1.0 1.0
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pair_style lj/cut 1.12
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pair_modify shift yes
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pair_coeff 1 1 1.0 1.0 1.12
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fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297
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thermo 100
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timestep 0.012
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run 100
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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 0.274804 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0507675 (18.4741)
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Bond time (%) = 0.0225385 (8.20169)
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Neigh time (%) = 0.121537 (44.2269)
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Comm time (%) = 0.0207262 (7.54219)
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Outpt time (%) = 8.74996e-05 (0.0318408)
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Other time (%) = 0.0591468 (21.5233)
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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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Nghost: 4177 ave 4191 max 4160 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Neighs: 38995.8 ave 39169 max 38852 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Total # of neighbors = 155983
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Ave neighs/atom = 4.87447
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Ave special neighs/atom = 1.98
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Neighbor list builds = 25
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Dangerous builds = 0
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@ -0,0 +1,79 @@
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LAMMPS (1 Feb 2014)
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# FENE beadspring benchmark
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variable x index 1
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variable y index 1
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variable z index 1
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units lj
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atom_style bond
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atom_modify map hash
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special_bonds fene
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read_data data.chain
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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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replicate $x $y $z
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replicate 2 $y $z
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replicate 2 2 $z
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replicate 2 2 1
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orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
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2 by 2 by 1 MPI processor grid
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128000 atoms
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126720 bonds
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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neighbor 0.4 bin
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neigh_modify every 1 delay 1
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bond_style fene
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bond_coeff 1 30.0 1.5 1.0 1.0
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pair_style lj/cut 1.12
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pair_modify shift yes
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pair_coeff 1 1 1.0 1.0 1.12
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fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297
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thermo 100
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timestep 0.012
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run 100
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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 1.16627 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 0.224354 (19.2369)
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Bond time (%) = 0.0961447 (8.24378)
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Neigh time (%) = 0.510646 (43.7846)
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Comm time (%) = 0.0876382 (7.5144)
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Outpt time (%) = 0.000156462 (0.0134156)
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Other time (%) = 0.24733 (21.207)
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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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Nghost: 9492 ave 9522 max 9432 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Neighs: 155837 ave 156079 max 155506 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Total # of neighbors = 623349
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Ave neighs/atom = 4.86991
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Ave special neighs/atom = 1.98
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Neighbor list builds = 25
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Dangerous builds = 0
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@ -0,0 +1,65 @@
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LAMMPS (1 Feb 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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units lj
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atom_style sphere
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boundary p p fs
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newton off
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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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pair_coeff * *
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neighbor 0.1 bin
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neigh_modify every 1 delay 0
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timestep 0.0001
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group bottom type 2
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912 atoms in group bottom
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group active subtract all bottom
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31088 atoms in group active
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neigh_modify exclude group bottom bottom
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fix 1 all gravity 1.0 chute 26.0
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fix 2 bottom freeze
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fix 3 active nve/sphere
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compute 1 all erotate/sphere
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thermo_style custom step atoms ke c_1 vol
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thermo_modify norm no
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thermo 100
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run 100
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Memory usage per processor = 21.4184 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 0.540977 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.330571 (61.1064)
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Neigh time (%) = 0.0416589 (7.70067)
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Comm time (%) = 0.018239 (3.3715)
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Outpt time (%) = 0.000189066 (0.034949)
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Other time (%) = 0.150319 (27.7865)
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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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Nghost: 5463 ave 5463 max 5463 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 115133 ave 115133 max 115133 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 115133
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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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@ -0,0 +1,65 @@
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LAMMPS (1 Feb 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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units lj
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atom_style sphere
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boundary p p fs
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newton off
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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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pair_coeff * *
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neighbor 0.1 bin
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neigh_modify every 1 delay 0
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timestep 0.0001
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group bottom type 2
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912 atoms in group bottom
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group active subtract all bottom
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31088 atoms in group active
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neigh_modify exclude group bottom bottom
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fix 1 all gravity 1.0 chute 26.0
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fix 2 bottom freeze
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fix 3 active nve/sphere
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compute 1 all erotate/sphere
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thermo_style custom step atoms ke c_1 vol
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thermo_modify norm no
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thermo 100
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run 100
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Memory usage per processor = 10.7034 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 0.133553 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0669281 (50.1135)
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Neigh time (%) = 0.01061 (7.9444)
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Comm time (%) = 0.0142241 (10.6505)
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Outpt time (%) = 9.28044e-05 (0.0694888)
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Other time (%) = 0.041698 (31.2221)
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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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Nghost: 2439 ave 2450 max 2428 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 29500.5 ave 30488 max 28513 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 118002
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Ave neighs/atom = 3.68756
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Neighbor list builds = 2
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Dangerous builds = 0
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@ -0,0 +1,75 @@
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LAMMPS (1 Feb 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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variable x index 1
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variable y index 1
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units lj
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atom_style sphere
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boundary p p fs
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newton off
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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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replicate 2 $y 1
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replicate 2 2 1
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orthogonal box = (0 0 0) to (80 40 37.2923)
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2 by 2 by 1 MPI processor grid
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128000 atoms
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pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
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pair_coeff * *
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neighbor 0.1 bin
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neigh_modify every 1 delay 0
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timestep 0.0001
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group bottom type 2
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3648 atoms in group bottom
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group active subtract all bottom
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124352 atoms in group active
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neigh_modify exclude group bottom bottom
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fix 1 all gravity 1.0 chute 26.0
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fix 2 bottom freeze
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fix 3 active nve/sphere
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compute 1 all erotate/sphere
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thermo_style custom step atoms ke c_1 vol
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thermo_modify norm no
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thermo 100
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run 100
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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 0.862817 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 0.518524 (60.0966)
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Neigh time (%) = 0.0441293 (5.11455)
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Comm time (%) = 0.057479 (6.66178)
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Outpt time (%) = 0.000286222 (0.0331729)
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Other time (%) = 0.242399 (28.0939)
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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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Nghost: 5463 ave 5463 max 5463 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 115133 ave 115133 max 115133 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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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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@ -0,0 +1,67 @@
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LAMMPS (1 Feb 2014)
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# bulk Cu lattice
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units metal
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atom_style atomic
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lattice fcc 3.615
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Lattice spacing in x,y,z = 3.615 3.615 3.615
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 32000 atoms
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pair_style eam
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pair_coeff 1 1 Cu_u3.eam
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velocity all create 1600.0 376847 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 5 check yes
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fix 1 all nve
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timestep 0.005
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thermo 50
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run 100
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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 5.93175 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 5.20741 (87.7887)
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Neigh time (%) = 0.618579 (10.4283)
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Comm time (%) = 0.0310862 (0.524064)
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Outpt time (%) = 0.000214815 (0.00362144)
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Other time (%) = 0.0744634 (1.25533)
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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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Nghost: 19909 ave 19909 max 19909 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1207784
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Ave neighs/atom = 37.7433
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Neighbor list builds = 13
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Dangerous builds = 0
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@ -0,0 +1,67 @@
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LAMMPS (1 Feb 2014)
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# bulk Cu lattice
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.615
|
||||
Lattice spacing in x,y,z = 3.615 3.615 3.615
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 0.005
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.92441 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
50 781.69049 -109873.35 0 -106640.13 52273.088
|
||||
100 801.832 -109957.3 0 -106640.77 51322.821
|
||||
Loop time of 1.57335 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 1.35199 (85.9304)
|
||||
Neigh time (%) = 0.160176 (10.1806)
|
||||
Comm time (%) = 0.0413526 (2.62832)
|
||||
Outpt time (%) = 0.000119448 (0.00759193)
|
||||
Other time (%) = 0.0197157 (1.2531)
|
||||
|
||||
Nlocal: 8000 ave 8008 max 7993 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9130.25 ave 9138 max 9122 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 301946 ave 302392 max 301360 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1207784
|
||||
Ave neighs/atom = 37.7433
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 3.615
|
||||
Lattice spacing in x,y,z = 3.615 3.615 3.615
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 0.005
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 15.2891 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -453120 0 -426647.73 18704.012
|
||||
50 779.50001 -439457.02 0 -426560.06 52355.276
|
||||
100 797.97828 -439764.76 0 -426562.07 51474.74
|
||||
Loop time of 6.55459 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 5.63064 (85.9037)
|
||||
Neigh time (%) = 0.698691 (10.6596)
|
||||
Comm time (%) = 0.123277 (1.88077)
|
||||
Outpt time (%) = 0.000314116 (0.00479231)
|
||||
Other time (%) = 0.101672 (1.55115)
|
||||
|
||||
Nlocal: 32000 ave 32092 max 31914 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 19910 ave 19997 max 19818 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4829126
|
||||
Ave neighs/atom = 37.7275
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 13.2266 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 2.26599 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 1.92891 (85.1244)
|
||||
Neigh time (%) = 0.252641 (11.1493)
|
||||
Comm time (%) = 0.0243704 (1.07549)
|
||||
Outpt time (%) = 0.000110865 (0.00489256)
|
||||
Other time (%) = 0.059957 (2.64596)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19657 ave 19657 max 19657 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.5885
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.31282 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 0.628341 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 0.505093 (80.3851)
|
||||
Neigh time (%) = 0.0659957 (10.5032)
|
||||
Comm time (%) = 0.0406293 (6.46611)
|
||||
Outpt time (%) = 8.43406e-05 (0.0134227)
|
||||
Other time (%) = 0.016539 (2.63216)
|
||||
|
||||
Nlocal: 8000 ave 8037 max 7964 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9007.5 ave 9050 max 8968 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 300708 ave 305113 max 297203 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.5885
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
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 2.54147 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 2.08305 (81.9623)
|
||||
Neigh time (%) = 0.258072 (10.1545)
|
||||
Comm time (%) = 0.116279 (4.57528)
|
||||
Outpt time (%) = 0.000139415 (0.00548562)
|
||||
Other time (%) = 0.0839326 (3.30252)
|
||||
|
||||
Nlocal: 32000 ave 32060 max 31939 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 19630.8 ave 19681 max 19562 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
|
||||
Total # of neighbors = 4807797
|
||||
Ave neighs/atom = 37.5609
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,109 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
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
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
1617 = # of size 2 clusters
|
||||
3633 = # of size 3 clusters
|
||||
747 = # of size 4 clusters
|
||||
4233 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 50
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.248835
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0355478
|
||||
estimated relative force accuracy = 0.000107051
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 41070 25600
|
||||
Memory usage per processor = 139.238 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
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 17.8100 (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 = 36.2348 (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 36.2348 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 26.0418 (71.8696)
|
||||
Bond time (%) = 1.26644 (3.4951)
|
||||
Kspce time (%) = 3.24933 (8.96742)
|
||||
Neigh time (%) = 4.47968 (12.3629)
|
||||
Comm time (%) = 0.0700378 (0.193289)
|
||||
Outpt time (%) = 0.000230074 (0.000634953)
|
||||
Other time (%) = 1.12729 (3.11108)
|
||||
|
||||
FFT time (% of Kspce) = 0.276809 (8.51896)
|
||||
FFT Gflps 3d (1d only) = 1.87746 3.23903
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 47958 ave 47958 max 47958 min
|
||||
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
|
||||
Ave neighs/atom = 375.878
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,109 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
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
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
1617 = # of size 2 clusters
|
||||
3633 = # of size 3 clusters
|
||||
747 = # of size 4 clusters
|
||||
4233 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 50
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.248835
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0355478
|
||||
estimated relative force accuracy = 0.000107051
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 13230 6400
|
||||
Memory usage per processor = 54.595 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
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 4.7061 (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 = 9.5889 (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 9.58898 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 6.62576 (69.0976)
|
||||
Bond time (%) = 0.317414 (3.31019)
|
||||
Kspce time (%) = 1.04771 (10.9262)
|
||||
Neigh time (%) = 1.15891 (12.0859)
|
||||
Comm time (%) = 0.0844751 (0.88096)
|
||||
Outpt time (%) = 0.00015074 (0.00157201)
|
||||
Other time (%) = 0.354558 (3.69756)
|
||||
|
||||
FFT time (% of Kspce) = 0.0967343 (9.23289)
|
||||
FFT Gflps 3d (1d only) = 5.37243 12.7459
|
||||
|
||||
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
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 12028107
|
||||
Ave neighs/atom = 375.878
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,130 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
atom_modify map hash
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
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
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 1
|
||||
orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
128000 atoms
|
||||
110892 bonds
|
||||
161868 angles
|
||||
227316 dihedrals
|
||||
4136 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
6468 = # of size 2 clusters
|
||||
14532 = # of size 3 clusters
|
||||
2988 = # of size 4 clusters
|
||||
16932 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 50
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.248593
|
||||
grid = 48 60 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0359793
|
||||
estimated relative force accuracy = 0.00010835
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 41615 25920
|
||||
Memory usage per processor = 146.358 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
|
||||
Volume = 1231980.1340
|
||||
---------------- Step 50 ----- CPU = 18.9852 (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 = 38.9161 (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 38.9162 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 27.1908 (69.8701)
|
||||
Bond time (%) = 1.30758 (3.35999)
|
||||
Kspce time (%) = 3.99359 (10.262)
|
||||
Neigh time (%) = 4.65272 (11.9557)
|
||||
Comm time (%) = 0.216829 (0.557168)
|
||||
Outpt time (%) = 0.000280738 (0.000721391)
|
||||
Other time (%) = 1.55441 (3.99426)
|
||||
|
||||
FFT time (% of Kspce) = 0.448314 (11.2258)
|
||||
FFT Gflps 3d (1d only) = 5.34183 11.5795
|
||||
|
||||
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
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 48112472
|
||||
Ave neighs/atom = 375.879
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Loading…
Reference in New Issue