forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5842 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
803fd6a64e
commit
a1978f660a
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LAMMPS (27 Mar 2011)
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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 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 1.87328 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.438668 (23.4171)
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Bond time (%) = 0.289005 (15.4277)
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Neigh time (%) = 0.679554 (36.2761)
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Comm time (%) = 0.0552287 (2.94823)
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Outpt time (%) = 0.00018096 (0.00966003)
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Other time (%) = 0.410646 (21.9212)
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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 (27 Mar 2011)
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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 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 0.436674 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.0835696 (19.1378)
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Bond time (%) = 0.0588097 (13.4677)
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Neigh time (%) = 0.157872 (36.1532)
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Comm time (%) = 0.047663 (10.915)
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Outpt time (%) = 9.69768e-05 (0.0222081)
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Other time (%) = 0.0886627 (20.3041)
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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 +1,75 @@
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LAMMPS (27 Mar 2011)
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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 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 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 2.4188 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 0.507936 (20.9995)
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Bond time (%) = 0.340843 (14.0914)
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Neigh time (%) = 0.735922 (30.425)
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Comm time (%) = 0.228828 (9.46038)
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Outpt time (%) = 0.000289202 (0.0119564)
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Other time (%) = 0.604987 (25.0118)
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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 +1,63 @@
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LAMMPS (27 Mar 2011)
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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 granular
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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 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 = 35.2505 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 1.58777 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.887784 (55.9139)
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Neigh time (%) = 0.070847 (4.46205)
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Comm time (%) = 0.0669501 (4.21661)
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Outpt time (%) = 0.000550032 (0.0346418)
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Other time (%) = 0.561639 (35.3728)
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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 (27 Mar 2011)
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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 granular
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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 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 = 15.4199 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 0.270323 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 0.135713 (50.2038)
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Neigh time (%) = 0.0173983 (6.43611)
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Comm time (%) = 0.0378563 (14.0041)
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Outpt time (%) = 0.000246227 (0.091086)
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Other time (%) = 0.0791097 (29.2649)
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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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@ -0,0 +1,73 @@
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LAMMPS (27 Mar 2011)
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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 granular
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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 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 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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|
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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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|
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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 = 37.3912 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 2.79202 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 1.13366 (40.6034)
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Neigh time (%) = 0.0699974 (2.50705)
|
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Comm time (%) = 0.24415 (8.74457)
|
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Outpt time (%) = 0.00162953 (0.0583639)
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Other time (%) = 1.34259 (48.0866)
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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
|
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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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@ -0,0 +1,67 @@
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LAMMPS (27 Mar 2011)
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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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|
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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 processor grid
|
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create_atoms 1 box
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Created 32000 atoms
|
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|
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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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|
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neighbor 1.0 bin
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neigh_modify every 1 delay 5 check yes
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|
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fix 1 all nve
|
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|
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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 = 15.3728 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 11.4086 on 1 procs for 100 steps with 32000 atoms
|
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Pair time (%) = 10.2465 (89.814)
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Neigh time (%) = 0.893404 (7.83096)
|
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Comm time (%) = 0.0694258 (0.608539)
|
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Outpt time (%) = 0.000409126 (0.00358612)
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Other time (%) = 0.198848 (1.74296)
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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
|
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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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|
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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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|
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@ -0,0 +1,67 @@
|
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LAMMPS (27 Mar 2011)
|
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# bulk Cu lattice
|
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|
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variable x index 1
|
||||
variable y index 1
|
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variable z index 1
|
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|
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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
|
||||
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 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 0.005
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.92442 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
50 781.69049 -109873.35 0 -106640.13 52273.088
|
||||
100 801.832 -109957.3 0 -106640.77 51322.821
|
||||
Loop time of 2.84421 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 2.47554 (87.0379)
|
||||
Neigh time (%) = 0.216563 (7.61418)
|
||||
Comm time (%) = 0.104262 (3.66577)
|
||||
Outpt time (%) = 0.000251591 (0.00884573)
|
||||
Other time (%) = 0.0475937 (1.67335)
|
||||
|
||||
Nlocal: 8000 ave 8008 max 7993 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9130.25 ave 9138 max 9122 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 301946 ave 302392 max 301360 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1207784
|
||||
Ave neighs/atom = 37.7433
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 ${zz}
|
||||
region box block 0 40 0 40 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1 box
|
||||
Created 128000 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff 1 1 Cu_u3.eam
|
||||
|
||||
velocity all create 1600.0 376847 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 5 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 0.005
|
||||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 15.2892 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -453120 0 -426647.73 18704.012
|
||||
50 779.50001 -439457.02 0 -426560.06 52355.276
|
||||
100 797.97828 -439764.76 0 -426562.07 51474.74
|
||||
Loop time of 12.0882 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 10.3589 (85.6942)
|
||||
Neigh time (%) = 0.963713 (7.97234)
|
||||
Comm time (%) = 0.316817 (2.62088)
|
||||
Outpt time (%) = 0.000717819 (0.00593818)
|
||||
Other time (%) = 0.448062 (3.70661)
|
||||
|
||||
Nlocal: 32000 ave 32092 max 31914 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 19910 ave 19997 max 19818 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4829126
|
||||
Ave neighs/atom = 37.7275
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 13.2267 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 4.24155 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 3.6555 (86.1832)
|
||||
Neigh time (%) = 0.359136 (8.4671)
|
||||
Comm time (%) = 0.0590658 (1.39255)
|
||||
Outpt time (%) = 0.000212193 (0.00500272)
|
||||
Other time (%) = 0.167634 (3.95218)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19657 ave 19657 max 19657 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.5885
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.31284 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
|
||||
Loop time of 1.08102 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 0.86205 (79.7443)
|
||||
Neigh time (%) = 0.0897413 (8.30156)
|
||||
Comm time (%) = 0.0998399 (9.23573)
|
||||
Outpt time (%) = 0.000194311 (0.0179748)
|
||||
Other time (%) = 0.0291918 (2.7004)
|
||||
|
||||
Nlocal: 8000 ave 8037 max 7964 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9007.5 ave 9050 max 8968 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 300708 ave 305113 max 297203 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1202833
|
||||
Ave neighs/atom = 37.5885
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$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 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 4.71885 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 3.70177 (78.4464)
|
||||
Neigh time (%) = 0.350671 (7.43129)
|
||||
Comm time (%) = 0.278878 (5.90987)
|
||||
Outpt time (%) = 0.000279307 (0.00591897)
|
||||
Other time (%) = 0.387254 (8.20654)
|
||||
|
||||
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 +1,97 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# 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 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
|
||||
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 = 32.2123 (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 = 65.3867 (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 = -270400.7389 Press = 6.9875
|
||||
Volume = 308133.9900
|
||||
Loop time of 65.3868 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 46.2231 (70.6918)
|
||||
Bond time (%) = 2.88711 (4.41543)
|
||||
Kspce time (%) = 7.06667 (10.8075)
|
||||
Neigh time (%) = 6.61535 (10.1173)
|
||||
Comm time (%) = 0.185745 (0.28407)
|
||||
Outpt time (%) = 0.000392199 (0.000599813)
|
||||
Other time (%) = 2.4084 (3.68331)
|
||||
|
||||
FFT time (% of Kspce) = 0.430403 (6.0906)
|
||||
FFT Gflps 3d (1d only) = 1.20747 1.74267
|
||||
|
||||
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 +1,97 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# 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 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
|
||||
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 = 8.2683 (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 = 16.8728 (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 = -270400.7389 Press = 6.9875
|
||||
Volume = 308133.9900
|
||||
Loop time of 16.8729 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 11.2248 (66.5258)
|
||||
Bond time (%) = 0.687313 (4.07347)
|
||||
Kspce time (%) = 2.07329 (12.2877)
|
||||
Neigh time (%) = 1.59928 (9.47838)
|
||||
Comm time (%) = 0.410708 (2.43412)
|
||||
Outpt time (%) = 0.000243425 (0.0014427)
|
||||
Other time (%) = 0.877245 (5.19914)
|
||||
|
||||
FFT time (% of Kspce) = 0.223284 (10.7696)
|
||||
FFT Gflps 3d (1d only) = 2.32752 6.8543
|
||||
|
||||
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 +1,118 @@
|
|||
LAMMPS (27 Mar 2011)
|
||||
# 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 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 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
|
||||
brick FFT buffer size/proc = 41615 25920 12915
|
||||
Memory usage per processor = 146.135 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -101425.4825 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 = -1080537.3748 Press = -142.3084
|
||||
Volume = 1231980.1340
|
||||
---------------- Step 50 ----- CPU = 32.8194 (sec) ----------------
|
||||
TotEng = -101320.2611 KinEng = 86003.4849 Temp = 299.8118
|
||||
PotEng = -187323.7460 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 = 66.9547 (sec) ----------------
|
||||
TotEng = -101158.1519 KinEng = 86355.6231 Temp = 301.0394
|
||||
PotEng = -187513.7749 E_bond = 10272.0700 E_angle = 43128.6453
|
||||
E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196
|
||||
E_coul = 825555.5006 E_long = -1080544.3306 Press = 15.2192
|
||||
Volume = 1232535.8453
|
||||
Loop time of 66.9548 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 45.779 (68.373)
|
||||
Bond time (%) = 2.87439 (4.29303)
|
||||
Kspce time (%) = 7.5089 (11.2149)
|
||||
Neigh time (%) = 6.52016 (9.73816)
|
||||
Comm time (%) = 0.765243 (1.14293)
|
||||
Outpt time (%) = 0.000411808 (0.000615055)
|
||||
Other time (%) = 3.50669 (5.2374)
|
||||
|
||||
FFT time (% of Kspce) = 1.17001 (15.5816)
|
||||
FFT Gflps 3d (1d only) = 2.04683 6.15771
|
||||
|
||||
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