133 lines
5.2 KiB
Groff
133 lines
5.2 KiB
Groff
LAMMPS (30 Apr 2019)
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using 1 OpenMP thread(s) per MPI task
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units metal
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kim_style init ex_sim_model_Si_mod_tersoff
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units metal
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newton on
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atom_style atomic
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atom_modify map array
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boundary p p p
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# temperatures
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variable tlo equal 1800.0
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variable thi equal 2400.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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# diamond unit cell
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variable a equal 5.431
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lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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Lattice spacing in x,y,z = 5.431 5.431 5.431
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region myreg block 0 4 0 4 0 4
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create_box 1 myreg
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Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 region myreg
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Created 512 atoms
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create_atoms CPU = 0.102434 secs
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mass 1 28.06
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group Si type 1
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512 atoms in group Si
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velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
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velocity all create 2400 5287286 mom yes rot yes dist gaussian
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# make a vacancy
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group del id 300
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1 atoms in group del
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delete_atoms group del
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Deleted 1 atoms, new total = 511
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kim_style define Si
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Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff
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For Simulator : LAMMPS 12-Dec-2018
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Running on : LAMMPS 30 Apr 2019
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pair_style tersoff/mod
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pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL Si
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Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL with DATE: 2013-07-26
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thermo 10
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fix 1 all nve
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fix 2 all langevin ${thi} ${thi} 0.1 48278
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fix 2 all langevin 2400 ${thi} 0.1 48278
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fix 2 all langevin 2400 2400 0.1 48278
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4.3
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ghost atom cutoff = 4.3
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binsize = 2.15, bins = 11 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff/mod, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 2397.5824 -2363.0694 0 -2205.0143 15087.562
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10 1298.5003 -2292.5456 0 -2206.945 28361.893
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20 1114.7065 -2260.7006 0 -2187.2161 30574.077
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30 1504.9472 -2271.8639 0 -2172.6537 20395.651
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40 1357.5949 -2248.6066 0 -2159.1103 21779.773
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50 1351.7212 -2235.0803 0 -2145.9713 23404.844
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60 1582.4191 -2238.3233 0 -2134.006 21711.26
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70 1654.3988 -2230.0965 0 -2121.0341 24276.504
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80 1654.9629 -2218.6654 0 -2109.5658 27571.472
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90 1815.7206 -2219.2065 0 -2099.5093 28475.757
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100 1901.1544 -2216.5428 0 -2091.2137 28962.04
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Loop time of 4.36959 on 4 procs for 100 steps with 511 atoms
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Performance: 1.977 ns/day, 12.138 hours/ns, 22.885 timesteps/s
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47.8% CPU use with 4 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 | 0.051784 | 0.056551 | 0.064825 | 2.1 | 1.29
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Neigh | 0.00093389 | 0.001028 | 0.0011392 | 0.3 | 0.02
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Comm | 2.8964 | 2.9342 | 3.016 | 2.8 | 67.15
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Output | 0.673 | 0.68159 | 0.69707 | 1.1 | 15.60
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Modify | 0.0011303 | 0.0029655 | 0.0081694 | 5.5 | 0.07
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Other | | 0.6933 | | | 15.87
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Nlocal: 127.75 ave 134 max 123 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Nghost: 495 ave 498 max 489 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 2302 ave 2443 max 2194 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Total # of neighbors = 9208
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Ave neighs/atom = 18.0196
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Neighbor list builds = 4
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Dangerous builds = 0
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Total wall time: 0:00:05
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