mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7492 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
658b391e6a
commit
0bec8479f3
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@ -0,0 +1,59 @@
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LAMMPS (10 Jan 2012)
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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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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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32000 atoms
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32000 velocities
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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 = 11.3536 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 1.00598 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.200669 (19.9477)
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Bond time (%) = 0.116349 (11.5657)
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Neigh time (%) = 0.434148 (43.1567)
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Comm time (%) = 0.0310009 (3.08166)
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Outpt time (%) = 9.799e-05 (0.00974076)
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Other time (%) = 0.223714 (22.2385)
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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 +1,59 @@
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LAMMPS (10 Jan 2012)
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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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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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32000 atoms
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32000 velocities
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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 = 4.80505 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 0.277092 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0511394 (18.4557)
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Bond time (%) = 0.030314 (10.94)
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Neigh time (%) = 0.112937 (40.7578)
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Comm time (%) = 0.0222602 (8.03351)
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Outpt time (%) = 6.1214e-05 (0.0220915)
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Other time (%) = 0.0603806 (21.7908)
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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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LAMMPS (10 Jan 2012)
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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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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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32000 atoms
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32000 velocities
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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 = 13.3552 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 1.16957 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 0.227149 (19.4215)
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Bond time (%) = 0.123806 (10.5856)
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Neigh time (%) = 0.472906 (40.4341)
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Comm time (%) = 0.0951706 (8.13721)
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Outpt time (%) = 0.000224173 (0.0191671)
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Other time (%) = 0.250317 (21.4025)
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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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LAMMPS (10 Jan 2012)
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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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32000 atoms
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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 = 34.9301 Mbytes
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Step Atoms KinEng 1 Volume
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0 32000 784139.13 1601.1263 29830.88
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100 32000 784289.99 1571.0137 29831.804
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Loop time of 0.54713 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.328969 (60.1262)
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Neigh time (%) = 0.04423 (8.084)
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Comm time (%) = 0.0182245 (3.33092)
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Outpt time (%) = 0.00019002 (0.0347302)
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Other time (%) = 0.155517 (28.4242)
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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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LAMMPS (10 Jan 2012)
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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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32000 atoms
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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 = 15.2765 Mbytes
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Step Atoms KinEng 1 Volume
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0 32000 784139.13 1601.1263 29830.88
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100 32000 784289.99 1571.0137 29831.804
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Loop time of 0.146905 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0729731 (49.6735)
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Neigh time (%) = 0.0111947 (7.62035)
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Comm time (%) = 0.0153095 (10.4213)
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Outpt time (%) = 0.000119746 (0.0815122)
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Other time (%) = 0.0473083 (32.2033)
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Nlocal: 8000 ave 8010 max 7990 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 2439 ave 2452 max 2426 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 29503.5 ave 30500 max 28507 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 118014
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Ave neighs/atom = 3.68794
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Neighbor list builds = 2
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Dangerous builds = 0
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LAMMPS (10 Jan 2012)
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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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|
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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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32000 atoms
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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 37.2887)
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4 by 1 by 1 MPI processor grid
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128000 atoms
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|
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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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|
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neighbor 0.1 bin
|
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neigh_modify every 1 delay 0
|
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|
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timestep 0.0001
|
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|
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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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|
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run 100
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Memory usage per processor = 37.0464 Mbytes
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Step Atoms KinEng 1 Volume
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0 128000 3136556.5 6404.5051 119323.52
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100 128000 3137160 6284.0549 119327.22
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Loop time of 0.893496 on 4 procs for 100 steps with 128000 atoms
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|
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Pair time (%) = 0.524706 (58.7251)
|
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Neigh time (%) = 0.0462004 (5.17075)
|
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Comm time (%) = 0.0590464 (6.60847)
|
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Outpt time (%) = 0.00043273 (0.0484311)
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Other time (%) = 0.26311 (29.4473)
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|
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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: 5456 ave 5456 max 5456 min
|
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Histogram: 4 0 0 0 0 0 0 0 0 0
|
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Neighs: 115135 ave 115135 max 115135 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
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|
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Total # of neighbors = 460540
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Ave neighs/atom = 3.59797
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Neighbor list builds = 2
|
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Dangerous builds = 0
|
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|
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LAMMPS (10 Jan 2012)
|
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# bulk Cu lattice
|
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|
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variable x index 1
|
||||
variable y index 1
|
||||
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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|
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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}
|
||||
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
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
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velocity all create 1600.0 376847 loop geom
|
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|
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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
|
||||
|
||||
timestep 0.005
|
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thermo 50
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|
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run 100
|
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Memory usage per processor = 15.3728 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 5.8924 on 1 procs for 100 steps with 32000 atoms
|
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|
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Pair time (%) = 5.20714 (88.3704)
|
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Neigh time (%) = 0.579568 (9.83586)
|
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Comm time (%) = 0.0308812 (0.524085)
|
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Outpt time (%) = 0.000219822 (0.0037306)
|
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Other time (%) = 0.0745952 (1.26596)
|
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|
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Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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Nghost: 19909 ave 19909 max 19909 min
|
||||
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
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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|
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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 (10 Jan 2012)
|
||||
# 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*$y
|
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variable yy equal 20*1
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variable zz equal 20*$z
|
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variable zz equal 20*1
|
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|
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units metal
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atom_style atomic
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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 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 0.005
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.92442 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
50 781.69049 -109873.35 0 -106640.13 52273.088
|
||||
100 801.832 -109957.3 0 -106640.77 51322.821
|
||||
Loop time of 1.58434 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 1.37178 (86.5835)
|
||||
Neigh time (%) = 0.151559 (9.56606)
|
||||
Comm time (%) = 0.0399128 (2.5192)
|
||||
Outpt time (%) = 0.000169277 (0.0106844)
|
||||
Other time (%) = 0.0209216 (1.32052)
|
||||
|
||||
Nlocal: 8000 ave 8008 max 7993 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9130.25 ave 9138 max 9122 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 301946 ave 302392 max 301360 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1207784
|
||||
Ave neighs/atom = 37.7433
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 ${zz}
|
||||
region box block 0 40 0 40 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 0.005
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 15.2892 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -453120 0 -426647.73 18704.012
|
||||
50 779.50001 -439457.02 0 -426560.06 52355.276
|
||||
100 797.97828 -439764.76 0 -426562.07 51474.74
|
||||
Loop time of 6.64398 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 5.7169 (86.0464)
|
||||
Neigh time (%) = 0.659102 (9.92029)
|
||||
Comm time (%) = 0.164221 (2.47173)
|
||||
Outpt time (%) = 0.000294626 (0.00443448)
|
||||
Other time (%) = 0.103457 (1.55716)
|
||||
|
||||
Nlocal: 32000 ave 32092 max 31914 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 19910 ave 19997 max 19818 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4829126
|
||||
Ave neighs/atom = 37.7275
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 13.2267 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 2.24442 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 1.92371 (85.7108)
|
||||
Neigh time (%) = 0.23672 (10.547)
|
||||
Comm time (%) = 0.0241742 (1.07708)
|
||||
Outpt time (%) = 0.000104189 (0.00464212)
|
||||
Other time (%) = 0.059711 (2.66042)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19657 ave 19657 max 19657 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.5885
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.31284 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 0.62139 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 0.502622 (80.8866)
|
||||
Neigh time (%) = 0.0616071 (9.9144)
|
||||
Comm time (%) = 0.0411073 (6.61538)
|
||||
Outpt time (%) = 5.79953e-05 (0.00933316)
|
||||
Other time (%) = 0.0159961 (2.57424)
|
||||
|
||||
Nlocal: 8000 ave 8037 max 7964 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9007.5 ave 9050 max 8968 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 300708 ave 305113 max 297203 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.5885
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 2.43423 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 2.04092 (83.8422)
|
||||
Neigh time (%) = 0.238374 (9.79258)
|
||||
Comm time (%) = 0.0766696 (3.14964)
|
||||
Outpt time (%) = 0.000154495 (0.00634677)
|
||||
Other time (%) = 0.0781193 (3.20919)
|
||||
|
||||
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 +1,98 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# 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
|
||||
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
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
27723 bonds
|
||||
40467 angles
|
||||
56829 dihedrals
|
||||
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 = 0.248831
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
RMS precision = 7.57143e-05
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 41070 25600 12321
|
||||
Memory usage per processor = 138.965 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 17.8190 (sec) ----------------
|
||||
TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230
|
||||
PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977
|
||||
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753
|
||||
E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744
|
||||
Volume = 308031.5641
|
||||
---------------- Step 100 ----- CPU = 36.2635 (sec) ----------------
|
||||
TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
|
||||
PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
|
||||
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
|
||||
E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875
|
||||
Volume = 308133.9900
|
||||
Loop time of 36.2636 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 25.8498 (71.283)
|
||||
Bond time (%) = 1.49598 (4.1253)
|
||||
Kspce time (%) = 3.27236 (9.02382)
|
||||
Neigh time (%) = 4.27552 (11.7901)
|
||||
Comm time (%) = 0.0665278 (0.183456)
|
||||
Outpt time (%) = 0.000251055 (0.000692305)
|
||||
Other time (%) = 1.30319 (3.59366)
|
||||
|
||||
FFT time (% of Kspce) = 0.279837 (8.55152)
|
||||
FFT Gflps 3d (1d only) = 1.85715 3.22108
|
||||
|
||||
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 +1,98 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# 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
|
||||
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
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
27723 bonds
|
||||
40467 angles
|
||||
56829 dihedrals
|
||||
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 = 0.248831
|
||||
grid = 25 32 32
|
||||
stencil order = 5
|
||||
RMS precision = 7.57143e-05
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 13230 6400 5670
|
||||
Memory usage per processor = 54.4744 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 4.7389 (sec) ----------------
|
||||
TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230
|
||||
PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977
|
||||
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753
|
||||
E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744
|
||||
Volume = 308031.5641
|
||||
---------------- Step 100 ----- CPU = 9.6394 (sec) ----------------
|
||||
TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
|
||||
PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
|
||||
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
|
||||
E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875
|
||||
Volume = 308133.9900
|
||||
Loop time of 9.63943 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 6.60502 (68.5208)
|
||||
Bond time (%) = 0.375643 (3.89695)
|
||||
Kspce time (%) = 1.09311 (11.3399)
|
||||
Neigh time (%) = 1.08158 (11.2203)
|
||||
Comm time (%) = 0.0815379 (0.845879)
|
||||
Outpt time (%) = 0.000157952 (0.00163861)
|
||||
Other time (%) = 0.402393 (4.17445)
|
||||
|
||||
FFT time (% of Kspce) = 0.0966156 (8.83863)
|
||||
FFT Gflps 3d (1d only) = 5.37903 12.4303
|
||||
|
||||
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 +1,119 @@
|
|||
LAMMPS (10 Jan 2012)
|
||||
# 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
|
||||
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
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
27723 bonds
|
||||
40467 angles
|
||||
56829 dihedrals
|
||||
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 = 0.248586
|
||||
grid = 48 60 36
|
||||
stencil order = 5
|
||||
RMS precision = 7.66425e-05
|
||||
using double precision FFTs
|
||||
brick FFT buffer size/proc = 41615 25920 12915
|
||||
Memory usage per processor = 146.135 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -101425.4826 KinEng = 85779.3251 Temp = 299.0304
|
||||
PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968
|
||||
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
|
||||
E_coul = 827025.3556 E_long = -1080537.3749 Press = -142.3084
|
||||
Volume = 1231980.1340
|
||||
---------------- Step 50 ----- CPU = 19.1088 (sec) ----------------
|
||||
TotEng = -101320.2612 KinEng = 86003.4849 Temp = 299.8118
|
||||
PotEng = -187323.7461 E_bond = 9887.1072 E_angle = 43346.7920
|
||||
E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456
|
||||
E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165
|
||||
Volume = 1232126.1854
|
||||
---------------- Step 100 ----- CPU = 39.1056 (sec) ----------------
|
||||
TotEng = -101158.1517 KinEng = 86355.6231 Temp = 301.0394
|
||||
PotEng = -187513.7747 E_bond = 10272.0700 E_angle = 43128.6453
|
||||
E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196
|
||||
E_coul = 825555.5009 E_long = -1080544.3307 Press = 15.2192
|
||||
Volume = 1232535.8453
|
||||
Loop time of 39.1057 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 27.0353 (69.1339)
|
||||
Bond time (%) = 1.5462 (3.9539)
|
||||
Kspce time (%) = 4.17715 (10.6817)
|
||||
Neigh time (%) = 4.37974 (11.1997)
|
||||
Comm time (%) = 0.208052 (0.532026)
|
||||
Outpt time (%) = 0.000296533 (0.000758287)
|
||||
Other time (%) = 1.75896 (4.49797)
|
||||
|
||||
FFT time (% of Kspce) = 0.535835 (12.8278)
|
||||
FFT Gflps 3d (1d only) = 4.46931 11.0706
|
||||
|
||||
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 = 48112468
|
||||
Ave neighs/atom = 375.879
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Loading…
Reference in New Issue