forked from lijiext/lammps
172 lines
5.0 KiB
Groff
172 lines
5.0 KiB
Groff
LAMMPS (22 Jun 2018)
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units metal
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atom_style full
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atom_modify sort 0 0.0 # turn off sorting of the coordinates
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read_data data.water
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orthogonal box = (0 0 0) to (6.267 6.267 6.267)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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24 atoms
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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# initialize system
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velocity all create 0.0 87287 loop geom
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pair_style zero 1.0
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pair_coeff * *
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.00025
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fix 1 all nve
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fix 2 all latte NULL
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fix_modify 2 energy yes
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thermo_style custom step temp pe etotal press
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# dynamics
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thermo 10
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run 10
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2
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ghost atom cutoff = 2
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binsize = 1, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -104.95596 -104.95596 48235.442
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10 336.53107 -105.96027 -104.95977 97996.851
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Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms
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Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s
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6614.5% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00
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Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04
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Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01
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Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90
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Other | | 0.0003812 | | | 0.04
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Nlocal: 24 ave 24 max 24 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 71 ave 71 max 71 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 37 ave 37 max 37 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 37
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Ave neighs/atom = 1.54167
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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# Clear up previus calculation
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clear
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# simple CH4 molecule with LATTE
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units metal
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atom_style full
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atom_modify sort 0 0.0 # turn off sorting of the coordinates
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read_data data.ch4
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triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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5 atoms
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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# initialize system
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velocity all create 0.0 87287 loop geom
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pair_style zero 1.0
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pair_coeff * *
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.00025
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fix 1 all nve
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fix 2 all latte NULL
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fix_modify 2 energy yes
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thermo_style custom step temp pe etotal press
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# dynamics
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thermo 10
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run 10
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2
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ghost atom cutoff = 2
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binsize = 1, bins = 20 13 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton/tri
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stencil: half/bin/3d/newton/tri
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -23.980353 -23.980353 348.02716
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10 19.123149 -23.990297 -23.98041 18.774332
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Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms
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Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s
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6674.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01
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Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04
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Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05
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Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65
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Other | | 9.322e-05 | | | 0.22
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Nlocal: 5 ave 5 max 5 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 7 ave 7 max 7 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 10 ave 10 max 10 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 10
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Ave neighs/atom = 2
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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