151 lines
5.1 KiB
Groff
151 lines
5.1 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 h2bulk
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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.h2bulk
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Reading data file ...
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orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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13718 atoms
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read_data CPU = 0.036 seconds
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pair_style eff/cut 30.627847
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pair_coeff * *
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neigh_modify one 10000 page 100000
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comm_modify vel yes
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compute effTemp all temp/eff
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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
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# structure minimization
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min_style cg
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minimize 0 1.0e-4 10 10
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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: 10000, page size: 100000
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master list distance cutoff = 32.627847
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ghost atom cutoff = 32.627847
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binsize = 16.313924, 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) = 86.33 | 92.54 | 98.55 Mbytes
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Step PotEng Temp Press
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0 -2871.4801 0 2.8596879e+10
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10 -2882.3401 0 2.1869586e+10
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Loop time of 11.6123 on 4 procs for 10 steps with 13718 atoms
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100.0% 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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-2871.48013813359 -2881.24844591398 -2882.34005034714
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Force two-norm initial, final = 5.4264823 1.3218657
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Force max component initial, final = 0.21424475 0.025681865
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Final line search alpha, max atom move = 0.4402147 0.011305535
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Iterations, force evaluations = 10 10
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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 | 9.2083 | 10.221 | 11.528 | 31.2 | 88.02
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.07895 | 1.3856 | 2.3982 | 84.8 | 11.93
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.005564 | | | 0.05
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Nlocal: 3429.5 ave 3800 max 3078 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Nghost: 65600.5 ave 67122 max 64060 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Total # of neighbors = 59740807
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Ave neighs/atom = 4354.9211
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Neighbor list builds = 0
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Dangerous builds = 0
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timestep 0.001
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velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
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# nve
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fix 1 all nve/eff
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#fix 2 all imd 8888 trate 1 unwrap on nowait on
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compute peatom all pe/atom
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compute keatom all ke/atom/eff
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dump 2 all xyz 1000 ${sname}.nve.xyz
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dump 2 all xyz 1000 h2bulk.nve.xyz
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compute 1 all property/atom spin eradius
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dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
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dump 3 all custom 1000 h2bulk.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
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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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Per MPI rank memory allocation (min/avg/max) = 82.52 | 87.21 | 91.69 Mbytes
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Step PotEng Temp Press
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10 -2882.3401 40002.916 1.3307606e+11
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20 -2882.2908 40001.405 1.3306905e+11
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Loop time of 9.25154 on 4 procs for 10 steps with 13718 atoms
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Performance: 93.390 fs/day, 0.257 hours/fs, 1.081 timesteps/s, 14.828 katom-step/s
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100.0% 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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Pair | 8.2948 | 8.675 | 8.9946 | 10.1 | 93.77
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.2531 | 0.57292 | 0.9531 | 39.5 | 6.19
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Output | 3.7757e-05 | 5.7819e-05 | 7.5679e-05 | 0.0 | 0.00
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Modify | 0.0005098 | 0.0005357 | 0.00055895 | 0.0 | 0.01
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Other | | 0.002988 | | | 0.03
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Nlocal: 3429.5 ave 3610 max 3249 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 65600.5 ave 66951 max 64250 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 1.49409e+07 ave 1.56765e+07 max 1.41457e+07 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 59763523
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Ave neighs/atom = 4356.577
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix 1
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#unfix 2
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undump 2
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undump 3
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Total wall time: 0:00:23
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