162 lines
6.3 KiB
Groff
162 lines
6.3 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 = 0.048 seconds
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pair_style eff/cut 30.627847
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pair_coeff * *
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neigh_modify one 20000 page 200000
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comm_modify vel yes
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compute effTemp all temp/eff
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thermo 100
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thermo_style custom step pe temp press vol
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thermo_modify temp effTemp
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# structure minimization
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dump 1 all xyz 1 ${sname}.min.xyz
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dump 1 all xyz 1 h2bulk.min.xyz
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min_style cg
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minimize 0 1.0e-4 1 10000
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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: 20000, page size: 200000
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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) = 87.11 | 93.61 | 100.1 Mbytes
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Step PotEng Temp Press Volume
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0 -2871.4801 0 2.8596879e+10 229847.29
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1 -2872.8077 0 2.8046824e+10 229847.29
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Loop time of 1.02378 on 4 procs for 1 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 iterations
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Energy initial, next-to-last, final =
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-2871.48013813359 -2871.48013813359 -2872.8076730722
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Force two-norm initial, final = 5.4264823 5.0563616
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Force max component initial, final = 0.21424475 0.19518835
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Final line search alpha, max atom move = 0.046675588 0.0091105311
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Iterations, force evaluations = 1 1
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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 | 0.7704 | 0.89228 | 1.0165 | 11.0 | 87.16
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0028288 | 0.12705 | 0.24891 | 29.2 | 12.41
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Output | 0.0037898 | 0.0038794 | 0.0039584 | 0.1 | 0.38
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0005774 | | | 0.06
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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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undump 1
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# create initial velocities according to temp, w/out e radial dof
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velocity all create 20000.0 4928459 rot yes dist gaussian
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# npt
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fix 1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
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variable density equal 11.2058851*mass(all)
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thermo_style custom step pe temp press vol v_density
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
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thermo_modify temp effTemp
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dump 2 all xyz 10000 ${sname}.npt.xyz
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dump 2 all xyz 10000 h2bulk.npt.xyz
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compute 1 all property/atom spin eradius
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dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
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dump 3 all custom 10000 h2bulk.npt.lammpstrj id type x y z c_1[1] c_1[2]
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thermo 1
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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) = 79.61 | 86.11 | 92.6 Mbytes
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Step PotEng Temp Press Volume v_density
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1 -2872.8077 40002.916 1.392533e+11 229847.29 154332.61
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2 -2872.8075 40002.808 1.3925254e+11 229847.72 154332.61
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3 -2872.8072 40002.493 1.3925022e+11 229849.01 154332.61
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4 -2872.8068 40001.97 1.3924633e+11 229851.15 154332.61
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5 -2872.8064 40001.241 1.3924088e+11 229854.15 154332.61
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6 -2872.8058 40000.304 1.3923386e+11 229858.01 154332.61
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7 -2872.8052 39999.161 1.3922528e+11 229862.72 154332.61
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8 -2872.8045 39997.81 1.3921514e+11 229868.29 154332.61
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9 -2872.8037 39996.253 1.3920343e+11 229874.72 154332.61
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10 -2872.8028 39994.488 1.3919016e+11 229882.01 154332.61
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11 -2872.8018 39992.517 1.3917533e+11 229890.15 154332.61
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Loop time of 10.5538 on 4 procs for 10 steps with 13718 atoms
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Performance: 81.866 fs/day, 0.293 hours/fs, 0.948 timesteps/s, 12.998 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 | 8.6596 | 9.2995 | 10.519 | 24.8 | 88.12
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.029706 | 1.2492 | 1.8893 | 67.7 | 11.84
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Output | 0.00056676 | 0.00059312 | 0.00063847 | 0.0 | 0.01
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Modify | 0.0017284 | 0.0019179 | 0.0020891 | 0.4 | 0.02
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Other | | 0.002503 | | | 0.02
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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: 1.49356e+07 ave 1.64691e+07 max 1.33702e+07 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Total # of neighbors = 59742327
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Ave neighs/atom = 4355.0319
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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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undump 2
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undump 3
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Total wall time: 0:00:14
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