179 lines
6.6 KiB
Groff
179 lines
6.6 KiB
Groff
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
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using 1 OpenMP thread(s) per MPI task
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variable sname index Li-dendritic
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units electron
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newton on
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boundary p p p
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atom_style electron
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read_data data.${sname}
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read_data data.Li-dendritic
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Reading data file ...
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orthogonal box = (0 0 0) to (100.224 100.224 100.224)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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3456 atoms
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read_data CPU = 0.016 seconds
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#read_restart ${sname}.min.restart
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pair_style eff/cut 50.112
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pair_coeff * *
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comm_modify vel yes
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compute effTemp all temp/eff
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compute effPress all pressure effTemp
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thermo 10
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thermo_style custom step pe temp press
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thermo_modify temp effTemp press effPress
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print "Starting minimizer"
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Starting minimizer
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min_style cg
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compute 1 all property/atom spin eradius
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#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
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#dump 2 all xyz 100 ${sname}.min.xyz
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min_modify line quadratic dmax 0.05
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minimize 0 1.0e-7 100 100
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- EFF package: doi:10.1002/jcc.21637
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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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 = 52.112
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ghost atom cutoff = 52.112
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binsize = 26.056, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eff/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/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) = 14.88 | 15.07 | 15.26 Mbytes
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Step PotEng Temp Press
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0 -5172.3316 0 -1.6720594e+09
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10 -5199.5494 0 -1.6721099e+09
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20 -5220.9343 0 -1.6720299e+09
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30 -5238.4037 0 -1.6694987e+09
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40 -5252.5928 0 -1.6515154e+09
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50 -5263.7845 0 -1.5851579e+09
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60 -5271.8051 0 -1.4304709e+09
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70 -5275.1692 0 -1.2764647e+09
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80 -5276.9804 0 -1.1135845e+09
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87 -5277.5186 0 -1.0157231e+09
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Loop time of 9.1237 on 4 procs for 87 steps with 3456 atoms
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99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = max force evaluations
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Energy initial, next-to-last, final =
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-5172.33158699748 -5277.50851484438 -5277.51857905665
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Force two-norm initial, final = 10.47944 0.61719987
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Force max component initial, final = 0.33333431 0.020508985
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Final line search alpha, max atom move = 0.48148149 0.0098746969
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Iterations, force evaluations = 87 101
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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 | 7.2296 | 8.0451 | 8.9943 | 23.5 | 88.18
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.11943 | 1.0682 | 1.8834 | 64.3 | 11.71
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Output | 0.00021247 | 0.00022521 | 0.00026234 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.01011 | | | 0.11
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Nlocal: 864 ave 864 max 864 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 17185 ave 17185 max 17185 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 890568 ave 968400 max 812736 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 3562272
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Ave neighs/atom = 1030.75
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Neighbor list builds = 0
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Dangerous builds = 0
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write_restart ${sname}.min.restart
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write_restart Li-dendritic.min.restart
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System init for write_restart ...
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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#undump 1
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#undump 2
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# NVT
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reset_timestep 0
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timestep 0.005
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print "Starting nvt"
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Starting nvt
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fix 1 all nvt/eff temp 300.0 300.0 0.1
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dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
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dump 1 all custom 100 Li-dendritic.nvt.lammpstrj id type x y z c_1[1] c_1[2]
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dump 2 all xyz 100 ${sname}.nvt.xyz
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dump 2 all xyz 100 Li-dendritic.nvt.xyz
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restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
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restart 100 Li-dendritic.nvt.restart1 ${sname}.nvt.restart2
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restart 100 Li-dendritic.nvt.restart1 Li-dendritic.nvt.restart2
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run 100
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 11.9 | 12.09 | 12.28 Mbytes
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Step PotEng Temp Press
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0 -5277.5186 0 -1.0157231e+09
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10 -5277.5187 0.028803274 -1.0157155e+09
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20 -5277.519 0.12372272 -1.0156917e+09
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30 -5277.5195 0.29618333 -1.0156507e+09
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40 -5277.5201 0.55263617 -1.0155924e+09
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50 -5277.5206 0.8932531 -1.0155176e+09
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60 -5277.521 1.3127021 -1.015428e+09
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70 -5277.5211 1.8037418 -1.0153251e+09
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80 -5277.5208 2.3644081 -1.0152094e+09
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90 -5277.52 3.0093875 -1.0150781e+09
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100 -5277.5187 3.7858675 -1.0149239e+09
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Loop time of 8.47644 on 4 procs for 100 steps with 3456 atoms
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Performance: 5096.477 fs/day, 0.005 hours/fs, 11.797 timesteps/s, 40.772 katom-step/s
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99.5% 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 | 6.8234 | 7.537 | 8.2853 | 24.1 | 88.92
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Neigh | 0.023585 | 0.024246 | 0.024867 | 0.4 | 0.29
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Comm | 0.15595 | 0.90456 | 1.6184 | 69.6 | 10.67
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Output | 0.0032476 | 0.0032612 | 0.0032984 | 0.0 | 0.04
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Modify | 0.0036078 | 0.0037554 | 0.0039448 | 0.2 | 0.04
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Other | | 0.003634 | | | 0.04
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Nlocal: 864 ave 881 max 834 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 17185 ave 17215 max 17168 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Neighs: 890568 ave 976912 max 789323 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Total # of neighbors = 3562272
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Ave neighs/atom = 1030.75
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Neighbor list builds = 1
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Dangerous builds = 0
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undump 1
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undump 2
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Total wall time: 0:00:17
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