forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@653 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
333721324b
commit
aaadfa57c8
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LAMMPS (22 June 2007)
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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 0.0 1.0 1.0
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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 = 8.52881 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 0.97434451 0.439712 20.499596 22.400779 4.6558589
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Loop time of 7.13438 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 2.21672 (31.0709)
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Bond time (%) = 0.614869 (8.61839)
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Neigh time (%) = 2.68187 (37.5908)
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Comm time (%) = 0.329216 (4.6145)
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Outpt time (%) = 0.001037 (0.0145353)
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Other time (%) = 1.29067 (18.0908)
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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: 9537 ave 9537 max 9537 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 155877 ave 155877 max 155877 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 155877
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Ave neighs/atom = 4.87116
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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 (22 June 2007)
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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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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/history 200000.0 50.0 0.5 0
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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 chute 26.0
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fix 2 bottom freeze
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fix 3 active nve/gran
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thermo_style granular
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thermo 100
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run 100
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Memory usage per processor = 30.935 Mbytes
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Step Atoms KinEng RotKEgrn 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 6.87253 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 4.6578 (67.7741)
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Neigh time (%) = 0.45709 (6.65097)
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Comm time (%) = 0.247749 (3.60492)
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Outpt time (%) = 0.001582 (0.0230192)
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Other time (%) = 1.50831 (21.9469)
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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 (22 June 2007)
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# bulk Cu lattice
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variable x index 20
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variable y index 20
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variable z index 20
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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 $x 0 $y 0 $z
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region box block 0 20 0 $y 0 $z
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region box block 0 20 0 20 0 $z
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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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pair_style eam
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pair_coeff 1 1 Cu_u3.eam
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velocity all create 1600.0 376847 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 5 check yes
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fix 1 all nve
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timestep 0.005
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thermo 50
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run 100
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Memory usage per processor = 15.2616 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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50 781.37184 -109870.67 0 -106638.76 52616.84
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100 792.19277 -109916.21 0 -106639.54 51739.67
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Loop time of 31.0146 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 27.1822 (87.6433)
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Neigh time (%) = 2.71986 (8.76962)
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Comm time (%) = 0.338775 (1.09231)
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Outpt time (%) = 0.002124 (0.00684839)
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Other time (%) = 0.771616 (2.48791)
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19909 ave 19909 max 19909 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20989e+06 ave 1.20989e+06 max 1.20989e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1209894
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Ave neighs/atom = 37.8092
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Neighbor list builds = 13
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Dangerous builds = 0
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LAMMPS (22 June 2007)
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# 3d Lennard-Jones melt
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variable x index 20
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variable y index 20
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variable z index 20
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 $x 0 $y 0 $z
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region box block 0 20 0 $y 0 $z
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region box block 0 20 0 20 0 $z
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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 (33.5919 33.5919 33.5919)
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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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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 100
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Memory usage per processor = 13.4306 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6134356 -5.0197073
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100 0.77196819 -5.7795465 0 -4.6216304 0.079908069
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Loop time of 13.8981 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 12.0067 (86.3907)
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Neigh time (%) = 1.07342 (7.72346)
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Comm time (%) = 0.271477 (1.95334)
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Outpt time (%) = 0.000835 (0.00600801)
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Other time (%) = 0.545714 (3.92653)
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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: 19715 ave 19715 max 19715 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20353e+06 ave 1.20353e+06 max 1.20353e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1203529
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Ave neighs/atom = 37.6103
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Neighbor list builds = 5
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Dangerous builds = 0
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LAMMPS (22 June 2007)
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# Rhodopsin model
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units real
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neigh_modify delay 5 every 1
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.rhodo
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4 = max bonds/atom
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8 = max angles/atom
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18 = max dihedrals/atom
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2 = max impropers/atom
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orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
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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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27723 bonds
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40467 angles
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56829 dihedrals
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1034 impropers
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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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24 = max # of 1-4 neighbors
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26 = max # of special neighbors
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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1617 = # of size 2 clusters
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3633 = # of size 3 clusters
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747 = # of size 4 clusters
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4233 = # of frozen angles
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fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
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special_bonds charmm
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thermo 50
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thermo_style multi
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timestep 2.0
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run 100
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PPPM initialization ...
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G vector = 0.245875
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grid = 24 32 30
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RMS precision = 8.76365e-05
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brick FFT buffer size/proc = 37555 23040 11655
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Memory usage per processor = 134.779 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46800.6567 E_bond = 2537.9940 E_angle = 10921.3742
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E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
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E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456
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Volume = 307995.0335
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---------------- Step 50 ----- CPU = 152.6104 (sec) ----------------
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TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223
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PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458
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E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669
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E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815
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Volume = 308031.8243
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---------------- Step 100 ----- CPU = 309.5271 (sec) ----------------
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TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576
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PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480
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E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511
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E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451
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Volume = 308134.7692
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Loop time of 309.527 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 231.215 (74.6994)
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Bond time (%) = 6.3242 (2.04318)
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Kspce time (%) = 19.1711 (6.19366)
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Neigh time (%) = 46.0779 (14.8865)
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Comm time (%) = 0.796922 (0.257464)
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Outpt time (%) = 0.002562 (0.000827714)
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Other time (%) = 5.93944 (1.91888)
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FFT time (% of Kspce) = 3.96566 (20.6857)
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FFT Gflps 3d 1d-only = 0.11672 0.259612
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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: 47962 ave 47962 max 47962 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.2028e+07 ave 1.2028e+07 max 1.2028e+07 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 12027978
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Ave neighs/atom = 375.874
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Ave special neighs/atom = 7.43187
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Neighbor list builds = 11
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Dangerous builds = 0
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