mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@966 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
9e0c6fab7a
commit
befd8fee68
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@ -1,75 +0,0 @@
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LAMMPS (22 June 2007)
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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 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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2 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 2
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orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 50.388)
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2 by 2 by 2 processor grid
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256000 atoms
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253440 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 = 10.0921 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.97027119 0.44484087 20.494523 22.394765 4.6721833
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100 0.97424237 0.44152909 20.501694 22.404581 4.6873411
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Loop time of 5.43268 on 8 procs for 100 steps with 256000 atoms
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Pair time (%) = 1.0989 (20.2275)
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Bond time (%) = 0.542015 (9.97692)
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Neigh time (%) = 1.49201 (27.4635)
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Comm time (%) = 0.922278 (16.9765)
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Outpt time (%) = 0.00245366 (0.0451647)
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Other time (%) = 1.37503 (25.3104)
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Nlocal: 32000 ave 32058 max 31953 min
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Histogram: 1 1 0 1 2 1 1 0 0 1
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Nghost: 9505.38 ave 9533 max 9479 min
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Histogram: 2 0 0 1 0 2 1 1 0 1
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Neighs: 155776 ave 156274 max 155380 min
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Histogram: 1 0 1 1 3 1 0 0 0 1
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Total # of neighbors = 1246208
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Ave neighs/atom = 4.868
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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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@ -1,69 +0,0 @@
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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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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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read_data data.chute
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orthogonal box = (0 0 0) to (40 20 37.2886)
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2 by 2 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 4 1
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orthogonal box = (0 0 0) to (80 80 37.2887)
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2 by 4 by 1 processor grid
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256000 atoms
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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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7296 atoms in group bottom
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group active subtract all bottom
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248704 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 = 32.9126 Mbytes
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Step Atoms KinEng RotKEgrn Volume
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0 256000 6273113 12809.01 238647.04
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100 256000 6274319.9 12568.11 238654.43
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Loop time of 5.21764 on 8 procs for 100 steps with 256000 atoms
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Pair time (%) = 2.551 (48.8918)
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Neigh time (%) = 0.174133 (3.3374)
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Comm time (%) = 0.643821 (12.3393)
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Outpt time (%) = 0.00319499 (0.0612344)
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Other time (%) = 1.84549 (35.3702)
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 8 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: 8 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: 8 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 921064
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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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@ -1,60 +0,0 @@
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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 40 0 $y 0 $z
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region box block 0 40 0 40 0 $z
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region box block 0 40 0 40 0 40
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create_box 1 box
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Created orthogonal box = (0 0 0) to (144.6 144.6 144.6)
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2 by 2 by 2 processor grid
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create_atoms 1 box
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Created 256000 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 = 15.1399 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1600 -906240 0 -853295.25 18704.085
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50 799.88728 -879586.61 0 -853117.96 51535.434
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100 784.70888 -879086.24 0 -853119.86 51937.46
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Loop time of 23.2141 on 8 procs for 100 steps with 256000 atoms
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Pair time (%) = 18.9744 (81.7368)
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Neigh time (%) = 1.94597 (8.38272)
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Comm time (%) = 1.45154 (6.25285)
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Outpt time (%) = 0.0030815 (0.0132743)
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Other time (%) = 0.839045 (3.61439)
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Nlocal: 32000 ave 32128 max 31853 min
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Histogram: 1 0 0 2 0 1 1 2 0 1
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Nghost: 19909.9 ave 20057 max 19782 min
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Histogram: 1 0 2 1 1 0 1 1 0 1
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Neighs: 1.20868e+06 ave 1.21395e+06 max 1.20304e+06 min
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Histogram: 1 2 0 0 0 0 2 2 0 1
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Total # of neighbors = 9669450
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Ave neighs/atom = 37.7713
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Neighbor list builds = 14
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Dangerous builds = 0
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@ -1,57 +0,0 @@
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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 40 0 $y 0 $z
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region box block 0 40 0 40 0 $z
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region box block 0 40 0 40 0 40
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create_box 1 box
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Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
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2 by 2 by 2 processor grid
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create_atoms 1 box
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Created 256000 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 = 13.347 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6133765 -5.019674
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100 0.7616931 -5.7642895 0 -4.6217544 0.20907141
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Loop time of 9.57871 on 8 procs for 100 steps with 256000 atoms
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Pair time (%) = 7.12462 (74.3797)
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Neigh time (%) = 0.635592 (6.63546)
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Comm time (%) = 1.05576 (11.0219)
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Outpt time (%) = 0.00168183 (0.017558)
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Other time (%) = 0.761061 (7.94533)
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Nlocal: 32000 ave 32077 max 31945 min
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Histogram: 2 2 0 1 0 0 0 1 1 1
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Nghost: 19666.1 ave 19728 max 19582 min
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Histogram: 1 0 1 1 0 1 0 2 0 2
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Neighs: 1.20362e+06 ave 1.20977e+06 max 1.19745e+06 min
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Histogram: 1 2 0 0 1 0 2 0 0 2
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Total # of neighbors = 9628940
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Ave neighs/atom = 37.613
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Neighbor list builds = 5
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Dangerous builds = 0
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@ -1,96 +0,0 @@
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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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2 by 2 by 2 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 = 7140 3072 3780
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Memory usage per processor = 30.031 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 = 10.1023 (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 = 20.8372 (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 20.8381 on 8 procs for 100 steps with 32000 atoms
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Pair time (%) = 13.4637 (64.6111)
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Bond time (%) = 0.525574 (2.52218)
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Kspce time (%) = 3.3461 (16.0576)
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Neigh time (%) = 1.63546 (7.84842)
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Comm time (%) = 0.770115 (3.69571)
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Outpt time (%) = 0.00124443 (0.00597188)
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Other time (%) = 1.09588 (5.25903)
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FFT time (% of Kspce) = 0.715048 (21.3696)
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FFT Gflps 3d 1d-only = 0.647331 7.04904
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Nlocal: 4000 ave 4083 max 3940 min
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Histogram: 2 1 0 1 2 0 0 0 1 1
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Nghost: 16028.4 ave 16084 max 15941 min
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Histogram: 1 0 0 2 0 1 0 0 2 2
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Neighs: 1.5035e+06 ave 1.55024e+06 max 1.46322e+06 min
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Histogram: 2 0 1 0 2 1 0 0 0 2
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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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@ -1,117 +0,0 @@
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LAMMPS (22 June 2007)
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# Rhodopsin model
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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 real
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neigh_modify delay 5 every 1
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|
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atom_style full
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atom_modify map hash
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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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|
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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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2 by 2 by 2 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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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 2
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orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 109.088)
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2 by 2 by 2 processor grid
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256000 atoms
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221784 bonds
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323736 angles
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454632 dihedrals
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8272 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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12936 = # of size 2 clusters
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29064 = # of size 3 clusters
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5976 = # of size 4 clusters
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33864 = # 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 = 48 64 60
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RMS precision = 8.76365e-05
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brick FFT buffer size/proc = 37555 24576 11655
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Memory usage per processor = 139.074 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -202846.6035 KinEng = 171558.6503 Temp = 299.0288
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PotEng = -374405.2538 E_bond = 20303.9521 E_angle = 87370.9937
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E_dihed = 41694.2920 E_impro = 1708.0927 E_vdwl = -18462.9073
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E_coul = 1630560.5366 E_long = -2137580.2135 Press = -142.0456
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Volume = 2463960.2680
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---------------- Step 50 ----- CPU = 74.8537 (sec) ----------------
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TotEng = -202633.5610 KinEng = 172010.7811 Temp = 299.8169
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PotEng = -374644.3420 E_bond = 19774.3302 E_angle = 86693.4128
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E_dihed = 41917.7989 E_impro = 1817.0662 E_vdwl = -15943.3555
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E_coul = 1628731.3465 E_long = -2137634.9412 Press = 238.5780
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Volume = 2464254.6355
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---------------- Step 100 ----- CPU = 155.1037 (sec) ----------------
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TotEng = -202315.0204 KinEng = 172724.9944 Temp = 301.0618
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PotEng = -375040.0148 E_bond = 20545.2484 E_angle = 86257.2003
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E_dihed = 41587.6129 E_impro = 1733.5368 E_vdwl = -15186.8930
|
||||
E_coul = 1627613.3289 E_long = -2137590.0491 Press = 10.9720
|
||||
Volume = 2465078.7315
|
||||
Loop time of 155.104 on 8 procs for 100 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 102.817 (66.2892)
|
||||
Bond time (%) = 4.29529 (2.76929)
|
||||
Kspce time (%) = 22.4796 (14.4932)
|
||||
Neigh time (%) = 15.5455 (10.0226)
|
||||
Comm time (%) = 2.68199 (1.72915)
|
||||
Outpt time (%) = 0.00327626 (0.00211229)
|
||||
Other time (%) = 7.28125 (4.69442)
|
||||
|
||||
FFT time (% of Kspce) = 6.0543 (26.9324)
|
||||
FFT Gflps 3d 1d-only = 0.738243 7.05801
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 47962 ave 47962 max 47962 min
|
||||
Histogram: 8 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.2028e+07 ave 1.2057e+07 max 1.19989e+07 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 96223696
|
||||
Ave neighs/atom = 375.874
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# FENE beadspring benchmark
|
||||
|
||||
units lj
|
||||
|
|
@ -32,18 +32,18 @@ thermo 100
|
|||
timestep 0.012
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 8.52881 Mbytes
|
||||
Memory usage per processor = 8.52547 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
|
||||
100 0.97434451 0.439712 20.499596 22.400779 4.6558589
|
||||
Loop time of 7.13438 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 1.88106 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 2.21672 (31.0709)
|
||||
Bond time (%) = 0.614869 (8.61839)
|
||||
Neigh time (%) = 2.68187 (37.5908)
|
||||
Comm time (%) = 0.329216 (4.6145)
|
||||
Outpt time (%) = 0.001037 (0.0145353)
|
||||
Other time (%) = 1.29067 (18.0908)
|
||||
Pair time (%) = 0.470788 (25.0278)
|
||||
Bond time (%) = 0.240855 (12.8042)
|
||||
Neigh time (%) = 0.701759 (37.3066)
|
||||
Comm time (%) = 0.0541713 (2.87983)
|
||||
Outpt time (%) = 0.000169992 (0.00903705)
|
||||
Other time (%) = 0.413318 (21.9726)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# FENE beadspring benchmark
|
||||
|
||||
units lj
|
||||
|
|
@ -8,7 +8,7 @@ special_bonds 0.0 1.0 1.0
|
|||
read_data data.chain
|
||||
1 = max bonds/atom
|
||||
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
||||
2 by 2 by 2 processor grid
|
||||
1 by 2 by 2 processor grid
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
31680 bonds
|
||||
|
|
@ -32,28 +32,28 @@ thermo 100
|
|||
timestep 0.012
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.62762 Mbytes
|
||||
Memory usage per processor = 3.53032 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
|
||||
100 0.97000691 0.44751221 20.498199 22.400676 4.7159344
|
||||
Loop time of 0.559036 on 8 procs for 100 steps with 32000 atoms
|
||||
100 0.96717514 0.4422441 20.503712 22.396674 4.6686541
|
||||
Loop time of 0.550458 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 0.0874849 (15.6492)
|
||||
Bond time (%) = 0.0473607 (8.47185)
|
||||
Neigh time (%) = 0.138014 (24.6879)
|
||||
Comm time (%) = 0.167274 (29.9218)
|
||||
Outpt time (%) = 0.000471383 (0.0843207)
|
||||
Other time (%) = 0.118431 (21.1848)
|
||||
Pair time (%) = 0.092812 (16.8609)
|
||||
Bond time (%) = 0.06107 (11.0944)
|
||||
Neigh time (%) = 0.169702 (30.8293)
|
||||
Comm time (%) = 0.113217 (20.5678)
|
||||
Outpt time (%) = 0.000525832 (0.0955263)
|
||||
Other time (%) = 0.113131 (20.5521)
|
||||
|
||||
Nlocal: 4000 ave 4029 max 3985 min
|
||||
Histogram: 2 0 2 1 2 0 0 0 0 1
|
||||
Nghost: 2592.25 ave 2602 max 2566 min
|
||||
Histogram: 1 0 0 0 0 1 1 1 0 4
|
||||
Neighs: 19477.4 ave 19776 max 19279 min
|
||||
Histogram: 1 2 2 0 0 0 1 1 0 1
|
||||
Nlocal: 8000 ave 8024 max 7973 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 4169 ave 4212 max 4141 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 38936.2 ave 39212 max 38690 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 155819
|
||||
Ave neighs/atom = 4.86934
|
||||
Total # of neighbors = 155745
|
||||
Ave neighs/atom = 4.86703
|
||||
Ave special neighs/atom = 1.98
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
LAMMPS (5 Oct 2007)
|
||||
# FENE beadspring benchmark
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units lj
|
||||
atom_style bond
|
||||
atom_modify map hash
|
||||
special_bonds 0.0 1.0 1.0
|
||||
|
||||
read_data data.chain
|
||||
1 = max bonds/atom
|
||||
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 processor grid
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
31680 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 1
|
||||
orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796)
|
||||
2 by 2 by 1 processor grid
|
||||
128000 atoms
|
||||
126720 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all langevin 1.0 1.0 10.0 904297
|
||||
|
||||
thermo 100
|
||||
timestep 0.012
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 9.56386 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
|
||||
100 0.97400897 0.44134715 20.501052 22.403401 4.6879813
|
||||
Loop time of 2.98639 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 0.56241 (18.8325)
|
||||
Bond time (%) = 0.284682 (9.53266)
|
||||
Neigh time (%) = 0.780229 (26.1262)
|
||||
Comm time (%) = 0.48756 (16.3261)
|
||||
Outpt time (%) = 0.00329143 (0.110214)
|
||||
Other time (%) = 0.868214 (29.0724)
|
||||
|
||||
Nlocal: 32000 ave 32015 max 31986 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 9499 ave 9524 max 9446 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Neighs: 155798 ave 156103 max 155422 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 623193
|
||||
Ave neighs/atom = 4.8687
|
||||
Ave special neighs/atom = 1.98
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# LAMMPS benchmark of granular flow
|
||||
# chute flow of 32000 atoms with frozen base at 26 degrees
|
||||
|
||||
|
|
@ -26,7 +26,7 @@ group active subtract all bottom
|
|||
31088 atoms in group active
|
||||
neigh_modify exclude group bottom bottom
|
||||
|
||||
fix 1 all gravity chute 26.0
|
||||
fix 1 all gravity 1.0 chute 26.0
|
||||
fix 2 bottom freeze
|
||||
fix 3 active nve/gran
|
||||
|
||||
|
|
@ -34,17 +34,17 @@ thermo_style granular
|
|||
thermo 100
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 30.935 Mbytes
|
||||
Memory usage per processor = 32.9693 Mbytes
|
||||
Step Atoms KinEng RotKEgrn Volume
|
||||
0 32000 784139.13 1601.1263 29830.88
|
||||
100 32000 784289.99 1571.0137 29831.804
|
||||
Loop time of 6.87253 on 1 procs for 100 steps with 32000 atoms
|
||||
Loop time of 1.91739 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 4.6578 (67.7741)
|
||||
Neigh time (%) = 0.45709 (6.65097)
|
||||
Comm time (%) = 0.247749 (3.60492)
|
||||
Outpt time (%) = 0.001582 (0.0230192)
|
||||
Other time (%) = 1.50831 (21.9469)
|
||||
Pair time (%) = 1.09812 (57.2715)
|
||||
Neigh time (%) = 0.0856261 (4.46577)
|
||||
Comm time (%) = 0.0961592 (5.01512)
|
||||
Outpt time (%) = 0.000524998 (0.0273809)
|
||||
Other time (%) = 0.63696 (33.2202)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# LAMMPS benchmark of granular flow
|
||||
# chute flow of 32000 atoms with frozen base at 26 degrees
|
||||
|
||||
|
|
@ -9,7 +9,7 @@ newton off
|
|||
|
||||
read_data data.chute
|
||||
orthogonal box = (0 0 0) to (40 20 37.2886)
|
||||
2 by 2 by 2 processor grid
|
||||
2 by 1 by 2 processor grid
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
|
||||
|
|
@ -26,7 +26,7 @@ group active subtract all bottom
|
|||
31088 atoms in group active
|
||||
neigh_modify exclude group bottom bottom
|
||||
|
||||
fix 1 all gravity chute 26.0
|
||||
fix 1 all gravity 1.0 chute 26.0
|
||||
fix 2 bottom freeze
|
||||
fix 3 active nve/gran
|
||||
|
||||
|
|
@ -34,26 +34,26 @@ thermo_style granular
|
|||
thermo 100
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 9.4635 Mbytes
|
||||
Memory usage per processor = 13.5416 Mbytes
|
||||
Step Atoms KinEng RotKEgrn Volume
|
||||
0 32000 784139.13 1601.1263 29830.88
|
||||
100 32000 784289.99 1571.0137 29831.804
|
||||
Loop time of 0.672613 on 8 procs for 100 steps with 32000 atoms
|
||||
Loop time of 0.562479 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 0.302915 (45.0355)
|
||||
Neigh time (%) = 0.0175665 (2.61168)
|
||||
Comm time (%) = 0.158755 (23.6026)
|
||||
Outpt time (%) = 0.000497788 (0.0740081)
|
||||
Other time (%) = 0.19288 (28.6762)
|
||||
Pair time (%) = 0.227851 (40.5084)
|
||||
Neigh time (%) = 0.0203491 (3.61776)
|
||||
Comm time (%) = 0.102512 (18.225)
|
||||
Outpt time (%) = 0.000804424 (0.143014)
|
||||
Other time (%) = 0.210963 (37.5058)
|
||||
|
||||
Nlocal: 4000 ave 4005 max 3995 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 4
|
||||
Nghost: 1736.5 ave 1739 max 1734 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 4
|
||||
Neighs: 15093 ave 15610 max 14576 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 4
|
||||
Nlocal: 8000 ave 8010 max 7990 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 2439 ave 2452 max 2426 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 29503.5 ave 30500 max 28507 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 120744
|
||||
Ave neighs/atom = 3.77325
|
||||
Total # of neighbors = 118014
|
||||
Ave neighs/atom = 3.68794
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
LAMMPS (5 Oct 2007)
|
||||
# LAMMPS benchmark of granular flow
|
||||
# chute flow of 32000 atoms with frozen base at 26 degrees
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
|
||||
units lj
|
||||
atom_style granular
|
||||
boundary p p fs
|
||||
newton off
|
||||
|
||||
read_data data.chute
|
||||
orthogonal box = (0 0 0) to (40 20 37.2886)
|
||||
2 by 1 by 2 processor grid
|
||||
32000 atoms
|
||||
32000 velocities
|
||||
|
||||
replicate $x $y 1
|
||||
replicate 2 $y 1
|
||||
replicate 2 2 1
|
||||
orthogonal box = (0 0 0) to (80 40 37.2887)
|
||||
4 by 1 by 1 processor grid
|
||||
128000 atoms
|
||||
|
||||
pair_style gran/history 200000.0 50.0 0.5 0
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
group bottom type 2
|
||||
3648 atoms in group bottom
|
||||
group active subtract all bottom
|
||||
124352 atoms in group active
|
||||
neigh_modify exclude group bottom bottom
|
||||
|
||||
fix 1 all gravity 1.0 chute 26.0
|
||||
fix 2 bottom freeze
|
||||
fix 3 active nve/gran
|
||||
|
||||
thermo_style granular
|
||||
thermo 100
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 35.0123 Mbytes
|
||||
Step Atoms KinEng RotKEgrn Volume
|
||||
0 128000 3136556.5 6404.5051 119323.52
|
||||
100 128000 3137160 6284.0549 119327.22
|
||||
Loop time of 3.77144 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 1.685 (44.6779)
|
||||
Neigh time (%) = 0.0923538 (2.44877)
|
||||
Comm time (%) = 0.346049 (9.17553)
|
||||
Outpt time (%) = 0.00418776 (0.111039)
|
||||
Other time (%) = 1.64385 (43.5867)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5456 ave 5456 max 5456 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 115135 ave 115135 max 115135 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 460540
|
||||
Ave neighs/atom = 3.59797
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 20
|
||||
|
|
@ -34,27 +34,27 @@ timestep 0.005
|
|||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 15.2616 Mbytes
|
||||
Memory usage per processor = 14.6785 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
50 781.37184 -109870.67 0 -106638.76 52616.84
|
||||
100 792.19277 -109916.21 0 -106639.54 51739.67
|
||||
Loop time of 31.0146 on 1 procs for 100 steps with 32000 atoms
|
||||
50 781.55267 -109870.85 0 -106638.19 52764.534
|
||||
100 805.29574 -109970.16 0 -106639.3 51178.427
|
||||
Loop time of 11.2999 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 27.1822 (87.6433)
|
||||
Neigh time (%) = 2.71986 (8.76962)
|
||||
Comm time (%) = 0.338775 (1.09231)
|
||||
Outpt time (%) = 0.002124 (0.00684839)
|
||||
Other time (%) = 0.771616 (2.48791)
|
||||
Pair time (%) = 10.1502 (89.8261)
|
||||
Neigh time (%) = 0.871946 (7.71642)
|
||||
Comm time (%) = 0.0720956 (0.638021)
|
||||
Outpt time (%) = 0.000406027 (0.00359319)
|
||||
Other time (%) = 0.205194 (1.81589)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19909 ave 19909 max 19909 min
|
||||
Nghost: 19910 ave 19910 max 19910 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20989e+06 ave 1.20989e+06 max 1.20989e+06 min
|
||||
Neighs: 1.20857e+06 ave 1.20857e+06 max 1.20857e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1209894
|
||||
Ave neighs/atom = 37.8092
|
||||
Total # of neighbors = 1208570
|
||||
Ave neighs/atom = 37.7678
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 20
|
||||
|
|
@ -16,7 +16,7 @@ region box block 0 20 0 20 0 $z
|
|||
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)
|
||||
2 by 2 by 2 processor grid
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
|
||||
|
|
@ -34,27 +34,27 @@ timestep 0.005
|
|||
thermo 50
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.51765 Mbytes
|
||||
Memory usage per processor = 4.42085 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -113280 0 -106662.09 18703.573
|
||||
50 781.37184 -109870.67 0 -106638.76 52616.84
|
||||
100 792.19277 -109916.21 0 -106639.54 51739.67
|
||||
Loop time of 2.7327 on 8 procs for 100 steps with 32000 atoms
|
||||
50 781.55267 -109870.85 0 -106638.19 52764.534
|
||||
100 805.29574 -109970.16 0 -106639.3 51178.427
|
||||
Loop time of 3.11047 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 2.16792 (79.3324)
|
||||
Neigh time (%) = 0.187726 (6.86961)
|
||||
Comm time (%) = 0.306913 (11.2311)
|
||||
Outpt time (%) = 0.000829369 (0.0303498)
|
||||
Other time (%) = 0.0693147 (2.53649)
|
||||
Pair time (%) = 2.61131 (83.9521)
|
||||
Neigh time (%) = 0.222731 (7.1607)
|
||||
Comm time (%) = 0.20405 (6.56012)
|
||||
Outpt time (%) = 0.000865459 (0.0278241)
|
||||
Other time (%) = 0.0715173 (2.29925)
|
||||
|
||||
Nlocal: 4000 ave 4026 max 3981 min
|
||||
Histogram: 1 1 0 2 1 2 0 0 0 1
|
||||
Nghost: 5840.62 ave 5860 max 5815 min
|
||||
Histogram: 1 0 0 0 3 0 2 0 1 1
|
||||
Neighs: 151237 ave 152083 max 150648 min
|
||||
Histogram: 2 1 0 0 3 1 0 0 0 1
|
||||
Nlocal: 8000 ave 8023 max 7981 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 9130 ave 9150 max 9105 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 302142 ave 303202 max 300766 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1209894
|
||||
Ave neighs/atom = 37.8092
|
||||
Total # of neighbors = 1208570
|
||||
Ave neighs/atom = 37.7678
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
LAMMPS (5 Oct 2007)
|
||||
# bulk Cu lattice
|
||||
|
||||
variable x index 20
|
||||
variable y index 20
|
||||
variable z index 20
|
||||
|
||||
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 $x 0 $y 0 $z
|
||||
region box block 0 40 0 $y 0 $z
|
||||
region box block 0 40 0 40 0 $z
|
||||
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 = 14.5948 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1600 -453120 0 -426647.73 18704.012
|
||||
50 772.46776 -439343 0 -426562.39 52646.044
|
||||
100 798.31788 -439771.6 0 -426563.3 51493.923
|
||||
Loop time of 13.0599 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 10.8899 (83.3838)
|
||||
Neigh time (%) = 0.99729 (7.63627)
|
||||
Comm time (%) = 0.631329 (4.8341)
|
||||
Outpt time (%) = 0.00184333 (0.0141144)
|
||||
Other time (%) = 0.539597 (4.13171)
|
||||
|
||||
Nlocal: 32000 ave 32087 max 31920 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 19909.8 ave 19989 max 19824 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1.20802e+06 ave 1.21174e+06 max 1.20443e+06 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4832066
|
||||
Ave neighs/atom = 37.7505
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 20
|
||||
|
|
@ -32,26 +32,26 @@ neigh_modify delay 0 every 20 check no
|
|||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 13.4306 Mbytes
|
||||
Memory usage per processor = 12.8375 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.77196819 -5.7795465 0 -4.6216304 0.079908069
|
||||
Loop time of 13.8981 on 1 procs for 100 steps with 32000 atoms
|
||||
100 0.77218928 -5.7804197 0 -4.6221719 0.072558996
|
||||
Loop time of 4.11023 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 12.0067 (86.3907)
|
||||
Neigh time (%) = 1.07342 (7.72346)
|
||||
Comm time (%) = 0.271477 (1.95334)
|
||||
Outpt time (%) = 0.000835 (0.00600801)
|
||||
Other time (%) = 0.545714 (3.92653)
|
||||
Pair time (%) = 3.54178 (86.1699)
|
||||
Neigh time (%) = 0.351553 (8.55311)
|
||||
Comm time (%) = 0.0573781 (1.39598)
|
||||
Outpt time (%) = 0.000291109 (0.00708254)
|
||||
Other time (%) = 0.159229 (3.87395)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19715 ave 19715 max 19715 min
|
||||
Nghost: 19665 ave 19665 max 19665 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.20353e+06 ave 1.20353e+06 max 1.20353e+06 min
|
||||
Neighs: 1.20232e+06 ave 1.20232e+06 max 1.20232e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1203529
|
||||
Ave neighs/atom = 37.6103
|
||||
Total # of neighbors = 1202315
|
||||
Ave neighs/atom = 37.5723
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 20
|
||||
|
|
@ -16,7 +16,7 @@ region box block 0 20 0 20 0 $z
|
|||
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)
|
||||
2 by 2 by 2 processor grid
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
|
@ -32,26 +32,26 @@ neigh_modify delay 0 every 20 check no
|
|||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.13618 Mbytes
|
||||
Memory usage per processor = 3.88556 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
|
||||
100 0.77196819 -5.7795465 0 -4.6216304 0.079908069
|
||||
Loop time of 1.25475 on 8 procs for 100 steps with 32000 atoms
|
||||
100 0.77218928 -5.7804197 0 -4.6221719 0.072558996
|
||||
Loop time of 1.12636 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 0.816538 (65.0759)
|
||||
Neigh time (%) = 0.0738717 (5.88738)
|
||||
Comm time (%) = 0.30246 (24.1053)
|
||||
Outpt time (%) = 0.000414073 (0.0330006)
|
||||
Other time (%) = 0.061462 (4.89836)
|
||||
Pair time (%) = 0.867727 (77.0383)
|
||||
Neigh time (%) = 0.0890129 (7.90273)
|
||||
Comm time (%) = 0.138108 (12.2615)
|
||||
Outpt time (%) = 0.00042218 (0.0374819)
|
||||
Other time (%) = 0.0310873 (2.75999)
|
||||
|
||||
Nlocal: 4000 ave 4038 max 3962 min
|
||||
Histogram: 2 1 0 1 0 0 2 0 0 2
|
||||
Nghost: 5778.12 ave 5820 max 5742 min
|
||||
Histogram: 2 0 2 0 0 1 0 2 0 1
|
||||
Neighs: 150441 ave 152219 max 147904 min
|
||||
Histogram: 1 0 0 2 0 1 0 2 0 2
|
||||
Nlocal: 8000 ave 8049 max 7971 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Nghost: 9015.5 ave 9051 max 8966 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 300579 ave 304810 max 298185 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1203529
|
||||
Ave neighs/atom = 37.6103
|
||||
Total # of neighbors = 1202315
|
||||
Ave neighs/atom = 37.5723
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
LAMMPS (5 Oct 2007)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 20
|
||||
variable y index 20
|
||||
variable z index 20
|
||||
|
||||
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 $x 0 $y 0 $z
|
||||
region box block 0 40 0 $y 0 $z
|
||||
region box block 0 40 0 40 0 $z
|
||||
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 = 12.7603 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6133849 -5.0196788
|
||||
100 0.75341035 -5.7518267 0 -4.62172 0.2612672
|
||||
Loop time of 5.14761 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 3.82234 (74.2548)
|
||||
Neigh time (%) = 0.361516 (7.02299)
|
||||
Comm time (%) = 0.496529 (9.64583)
|
||||
Outpt time (%) = 0.000954211 (0.018537)
|
||||
Other time (%) = 0.466263 (9.05786)
|
||||
|
||||
Nlocal: 32000 ave 32038 max 31942 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 19629.8 ave 19675 max 19594 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 1.20282e+06 ave 1.20573e+06 max 1.20081e+06 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4811274
|
||||
Ave neighs/atom = 37.5881
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (22 June 2007)
|
||||
LAMMPS (5 Oct 2007)
|
||||
# Rhodopsin model
|
||||
|
||||
units real
|
||||
|
|
@ -50,37 +50,37 @@ PPPM initialization ...
|
|||
grid = 24 32 30
|
||||
RMS precision = 8.76365e-05
|
||||
brick FFT buffer size/proc = 37555 23040 11655
|
||||
Memory usage per processor = 134.779 Mbytes
|
||||
Memory usage per processor = 133.859 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46800.6567 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
TotEng = -25355.8260 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46800.6573 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456
|
||||
E_coul = 203820.0665 E_long = -267197.5267 Press = -142.0485
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 152.6104 (sec) ----------------
|
||||
TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223
|
||||
PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458
|
||||
E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669
|
||||
E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815
|
||||
Volume = 308031.8243
|
||||
---------------- Step 100 ----- CPU = 309.5271 (sec) ----------------
|
||||
TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576
|
||||
PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480
|
||||
E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511
|
||||
E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451
|
||||
Volume = 308134.7692
|
||||
Loop time of 309.527 on 1 procs for 100 steps with 32000 atoms
|
||||
---------------- Step 50 ----- CPU = 37.2652 (sec) ----------------
|
||||
TotEng = -25329.9165 KinEng = 21500.9587 Temp = 299.8223
|
||||
PotEng = -46830.8751 E_bond = 2471.7583 E_angle = 10836.5458
|
||||
E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9667
|
||||
E_coul = 203591.3235 E_long = -267204.3691 Press = 238.4820
|
||||
Volume = 308031.8242
|
||||
---------------- Step 100 ----- CPU = 75.6253 (sec) ----------------
|
||||
TotEng = -25291.5444 KinEng = 21589.5406 Temp = 301.0576
|
||||
PotEng = -46881.0850 E_bond = 2568.0538 E_angle = 10781.7478
|
||||
E_dihed = 5198.3743 E_impro = 216.6829 E_vdwl = -1898.4506
|
||||
E_coul = 203451.2690 E_long = -267198.7621 Press = 10.7475
|
||||
Volume = 308134.7686
|
||||
Loop time of 75.6254 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 231.215 (74.6994)
|
||||
Bond time (%) = 6.3242 (2.04318)
|
||||
Kspce time (%) = 19.1711 (6.19366)
|
||||
Neigh time (%) = 46.0779 (14.8865)
|
||||
Comm time (%) = 0.796922 (0.257464)
|
||||
Outpt time (%) = 0.002562 (0.000827714)
|
||||
Other time (%) = 5.93944 (1.91888)
|
||||
Pair time (%) = 56.2927 (74.4362)
|
||||
Bond time (%) = 2.58034 (3.41201)
|
||||
Kspce time (%) = 6.11111 (8.08076)
|
||||
Neigh time (%) = 8.38886 (11.0927)
|
||||
Comm time (%) = 0.208683 (0.275943)
|
||||
Outpt time (%) = 0.000406027 (0.000536892)
|
||||
Other time (%) = 2.0433 (2.70186)
|
||||
|
||||
FFT time (% of Kspce) = 3.96566 (20.6857)
|
||||
FFT Gflps 3d 1d-only = 0.11672 0.259612
|
||||
FFT time (% of Kspce) = 0.42448 (6.94605)
|
||||
FFT Gflps 3d 1d-only = 1.09045 1.58681
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -89,7 +89,7 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
|
|||
Neighs: 1.2028e+07 ave 1.2028e+07 max 1.2028e+07 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 12027978
|
||||
Total # of neighbors = 12027976
|
||||
Ave neighs/atom = 375.874
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
|
|
@ -0,0 +1,96 @@
|
|||
LAMMPS (5 Oct 2007)
|
||||
# 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 50
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector = 0.245875
|
||||
grid = 24 32 30
|
||||
RMS precision = 8.76365e-05
|
||||
brick FFT buffer size/proc = 12180 6144 5481
|
||||
Memory usage per processor = 50.2175 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -25355.8260 KinEng = 21444.8313 Temp = 299.0397
|
||||
PotEng = -46800.6573 E_bond = 2537.9940 E_angle = 10921.3742
|
||||
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
|
||||
E_coul = 203820.0665 E_long = -267197.5267 Press = -142.0485
|
||||
Volume = 307995.0335
|
||||
---------------- Step 50 ----- CPU = 9.6422 (sec) ----------------
|
||||
TotEng = -25329.9165 KinEng = 21500.9586 Temp = 299.8223
|
||||
PotEng = -46830.8752 E_bond = 2471.7583 E_angle = 10836.5458
|
||||
E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9667
|
||||
E_coul = 203591.3235 E_long = -267204.3691 Press = 238.4820
|
||||
Volume = 308031.8242
|
||||
---------------- Step 100 ----- CPU = 19.4814 (sec) ----------------
|
||||
TotEng = -25291.5443 KinEng = 21589.5406 Temp = 301.0576
|
||||
PotEng = -46881.0849 E_bond = 2568.0538 E_angle = 10781.7478
|
||||
E_dihed = 5198.3743 E_impro = 216.6829 E_vdwl = -1898.4506
|
||||
E_coul = 203451.2690 E_long = -267198.7621 Press = 10.7475
|
||||
Volume = 308134.7686
|
||||
Loop time of 19.4821 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 12.9977 (66.7161)
|
||||
Bond time (%) = 0.64311 (3.30104)
|
||||
Kspce time (%) = 2.5143 (12.9057)
|
||||
Neigh time (%) = 1.95058 (10.0122)
|
||||
Comm time (%) = 0.480013 (2.46387)
|
||||
Outpt time (%) = 0.0015353 (0.00788057)
|
||||
Other time (%) = 0.894842 (4.59316)
|
||||
|
||||
FFT time (% of Kspce) = 0.315807 (12.5604)
|
||||
FFT Gflps 3d 1d-only = 1.46568 6.19563
|
||||
|
||||
Nlocal: 8000 ave 8143 max 7933 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 22735.5 ave 22770 max 22697 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 3.00699e+06 ave 3.0975e+06 max 2.96494e+06 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 12027976
|
||||
Ave neighs/atom = 375.874
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,117 @@
|
|||
LAMMPS (5 Oct 2007)
|
||||
# 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 50
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
G vector = 0.246338
|
||||
grid = 45 60 36
|
||||
RMS precision = 8.56639e-05
|
||||
brick FFT buffer size/proc = 40180 24840 17220
|
||||
Memory usage per processor = 137.911 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -101423.5112 KinEng = 85779.3251 Temp = 299.0304
|
||||
PotEng = -187202.8364 E_bond = 10151.9760 E_angle = 43685.4968
|
||||
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538
|
||||
E_coul = 817284.2513 E_long = -1070794.2991 Press = -141.9925
|
||||
Volume = 1231980.1340
|
||||
---------------- Step 50 ----- CPU = 38.9431 (sec) ----------------
|
||||
TotEng = -101316.6996 KinEng = 86004.2667 Temp = 299.8145
|
||||
PotEng = -187320.9663 E_bond = 9887.1225 E_angle = 43346.5775
|
||||
E_dihed = 20958.7139 E_impro = 908.4248 E_vdwl = -7973.9399
|
||||
E_coul = 816372.0088 E_long = -1070819.8739 Press = 238.0995
|
||||
Volume = 1232127.0570
|
||||
---------------- Step 100 ----- CPU = 79.6546 (sec) ----------------
|
||||
TotEng = -101158.1182 KinEng = 86360.5576 Temp = 301.0566
|
||||
PotEng = -187518.6758 E_bond = 10272.2506 E_angle = 43128.8182
|
||||
E_dihed = 20794.4833 E_impro = 867.0824 E_vdwl = -7591.0566
|
||||
E_coul = 815810.2886 E_long = -1070800.5424 Press = 13.1624
|
||||
Volume = 1232538.4006
|
||||
Loop time of 79.6554 on 4 procs for 100 steps with 128000 atoms
|
||||
|
||||
Pair time (%) = 54.0019 (67.7944)
|
||||
Bond time (%) = 2.60068 (3.26491)
|
||||
Kspce time (%) = 9.92803 (12.4637)
|
||||
Neigh time (%) = 8.09826 (10.1666)
|
||||
Comm time (%) = 1.17806 (1.47895)
|
||||
Outpt time (%) = 0.00191575 (0.00240505)
|
||||
Other time (%) = 3.84657 (4.82902)
|
||||
|
||||
FFT time (% of Kspce) = 1.57698 (15.8841)
|
||||
FFT Gflps 3d 1d-only = 1.41574 5.85277
|
||||
|
||||
Nlocal: 32000 ave 32001 max 31999 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 47957.5 ave 47959 max 47956 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1.2028e+07 ave 1.20576e+07 max 1.19984e+07 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 48112030
|
||||
Ave neighs/atom = 375.875
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 11
|
||||
Dangerous builds = 0
|
||||
Loading…
Reference in New Issue