git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14617 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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70
examples/reax/AB/log.15Feb16.AB.g++.1
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70
examples/reax/AB/log.15Feb16.AB.g++.1
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LAMMPS (15 Feb 2016)
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# REAX potential for Nitroamines system
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# .....
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units real
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atom_style charge
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read_data data.AB
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orthogonal box = (0 0 0) to (25 25 25)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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104 atoms
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pair_style reax/c lmp_control
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pair_coeff * * ffield.reax.AB H B N
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Reading potential file ffield.reax.AB with DATE: 2011-02-18
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neighbor 2 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
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fix 3 all temp/berendsen 500.0 500.0 100.0
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timestep 0.25
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#dump 1 all atom 30 dump.reax.ab
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run 3000
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Neighbor list info ...
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2 neighbor list requests
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update every 10 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6 -> bins = 5 5 5
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Memory usage per processor = 18.4119 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -8505.1816 0 -8505.1816 -673.36566
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3000 499.30579 -8405.1387 0 -8251.8401 -94.844317
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Loop time of 13.0873 on 1 procs for 3000 steps with 104 atoms
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Performance: 4.951 ns/day, 4.847 hours/ns, 229.230 timesteps/s
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99.1% 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 | 11.677 | 11.677 | 11.677 | 0.0 | 89.22
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Neigh | 0.30209 | 0.30209 | 0.30209 | 0.0 | 2.31
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Comm | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.16
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Output | 1.3113e-05 | 1.3113e-05 | 1.3113e-05 | 0.0 | 0.00
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Modify | 1.0816 | 1.0816 | 1.0816 | 0.0 | 8.26
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Other | | 0.005851 | | | 0.04
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Nlocal: 104 ave 104 max 104 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 694 ave 694 max 694 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2927 ave 2927 max 2927 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2927
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Ave neighs/atom = 28.1442
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Neighbor list builds = 300
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Dangerous builds not checked
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:13
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70
examples/reax/AB/log.15Feb16.AB.g++.4
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70
examples/reax/AB/log.15Feb16.AB.g++.4
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LAMMPS (15 Feb 2016)
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# REAX potential for Nitroamines system
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# .....
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units real
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atom_style charge
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read_data data.AB
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orthogonal box = (0 0 0) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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104 atoms
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pair_style reax/c lmp_control
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pair_coeff * * ffield.reax.AB H B N
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Reading potential file ffield.reax.AB with DATE: 2011-02-18
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neighbor 2 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
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fix 3 all temp/berendsen 500.0 500.0 100.0
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timestep 0.25
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#dump 1 all atom 30 dump.reax.ab
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run 3000
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Neighbor list info ...
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2 neighbor list requests
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update every 10 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6 -> bins = 5 5 5
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Memory usage per processor = 12.622 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -8505.1816 0 -8505.1816 -673.36566
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3000 496.56561 -8405.3755 0 -8252.9182 472.58916
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Loop time of 7.75039 on 4 procs for 3000 steps with 104 atoms
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Performance: 8.361 ns/day, 2.871 hours/ns, 387.077 timesteps/s
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99.1% CPU use with 4 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 | 6.2104 | 6.2314 | 6.2572 | 0.7 | 80.40
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Neigh | 0.14908 | 0.16363 | 0.17274 | 2.3 | 2.11
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Comm | 0.061391 | 0.089224 | 0.11185 | 6.1 | 1.15
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Output | 1.8835e-05 | 2.1577e-05 | 2.7895e-05 | 0.1 | 0.00
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Modify | 1.2535 | 1.2609 | 1.2736 | 0.7 | 16.27
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Other | | 0.005226 | | | 0.07
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Nlocal: 26 ave 35 max 13 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Nghost: 421 ave 450 max 377 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 847.25 ave 1149 max 444 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 3389
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Ave neighs/atom = 32.5865
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Neighbor list builds = 300
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Dangerous builds not checked
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:07
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26
examples/reax/AB/log.cite
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26
examples/reax/AB/log.cite
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This LAMMPS simulation made specific use of work described in the
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following references. See http://lammps.sandia.gov/cite.html
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for details.
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pair reax/c command:
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@Article{Aktulga12,
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author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
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title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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pages = {245--259}
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}
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fix qeq/reax command:
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@Article{Aktulga12,
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author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
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title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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pages = {245--259}
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}
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54
examples/reax/AB/log.lammps
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54
examples/reax/AB/log.lammps
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LAMMPS (12 Apr 2014)
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# REAX potential for Nitroamines system
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# .....
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units real
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atom_style charge
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read_data data.AB
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orthogonal box = (0 0 0) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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104 atoms
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pair_style reax/c lmp_control
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pair_coeff * * ffield.reax.AB H B N
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neighbor 2 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
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fix 3 all temp/berendsen 500.0 500.0 100.0
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timestep 0.25
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#dump 1 all atom 30 dump.reax.ab
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run 3000
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Memory usage per processor = 10.8036 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -8505.1816 0 -8505.1816 -673.36566
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3000 505.80651 -8408.2747 0 -8252.9802 851.95508
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Loop time of 5.75922 on 4 procs for 3000 steps with 104 atoms
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Pair time (%) = 4.25008 (73.7961)
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Neigh time (%) = 0.158397 (2.75033)
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Comm time (%) = 0.086283 (1.49817)
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Outpt time (%) = 3.58224e-05 (0.000622001)
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Other time (%) = 1.26442 (21.9547)
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Nlocal: 26 ave 35 max 13 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Nghost: 422.5 ave 452 max 377 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Neighs: 868 ave 1168 max 440 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 3472
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Ave neighs/atom = 33.3846
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Neighbor list builds = 300
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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