190 lines
6.1 KiB
Groff
190 lines
6.1 KiB
Groff
LAMMPS (3 Aug 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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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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Reading data file ...
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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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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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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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special bonds CPU = 0.000 seconds
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read_data CPU = 0.001 seconds
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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
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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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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 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 0.334108 on 1 procs for 10 steps with 24 atoms
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Performance: 0.646 ns/day, 37.123 hours/ns, 29.930 timesteps/s
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99.2% CPU use with 1 MPI tasks x 1 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 | 3.714e-06 | 3.714e-06 | 3.714e-06 | 0.0 | 0.00
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Bond | 5.02e-07 | 5.02e-07 | 5.02e-07 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.1209e-05 | 1.1209e-05 | 1.1209e-05 | 0.0 | 0.00
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Output | 2.3638e-05 | 2.3638e-05 | 2.3638e-05 | 0.0 | 0.01
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Modify | 0.33404 | 0.33404 | 0.33404 | 0.0 | 99.98
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Other | | 2.795e-05 | | | 0.01
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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 = 1.5416667
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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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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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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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Reading data file ...
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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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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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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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special bonds CPU = 0.000 seconds
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read_data CPU = 0.007 seconds
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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
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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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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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/tri
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.902 | 5.902 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 0.0121573 on 1 procs for 10 steps with 5 atoms
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Performance: 17.767 ns/day, 1.351 hours/ns, 822.549 timesteps/s
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99.7% CPU use with 1 MPI tasks x 1 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 | 1.224e-06 | 1.224e-06 | 1.224e-06 | 0.0 | 0.01
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Bond | 2.93e-07 | 2.93e-07 | 2.93e-07 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 3.845e-06 | 3.845e-06 | 3.845e-06 | 0.0 | 0.03
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Output | 8.633e-06 | 8.633e-06 | 8.633e-06 | 0.0 | 0.07
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Modify | 0.012132 | 0.012132 | 0.012132 | 0.0 | 99.80
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Other | | 1.089e-05 | | | 0.09
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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: 0:00:00
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