167 lines
8.9 KiB
Groff
167 lines
8.9 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.bohr
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units electron
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newton off
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boundary p p p
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dielectric 1.0
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atom_style electron
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read_data data.${sname}
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read_data data.Li.bohr
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Reading data file ...
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orthogonal box = (0 0 0) to (41.76 41.76 41.76)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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2000 atoms
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read_data CPU = 0.006 seconds
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pair_style eff/cut 20.88 limit/eradius pressure/evirials
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pair_coeff * *
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comm_modify vel yes
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neigh_modify one 2000 page 20000
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compute peratom all stress/atom NULL
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compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
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variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
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compute effTemp all temp/eff
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compute effPress all pressure effTemp
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compute energies all pair eff/cut
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variable eke equal c_energies[1]
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variable epauli equal c_energies[2]
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variable estatics equal c_energies[3]
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variable errestrain equal c_energies[4]
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thermo 10
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thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain press v_press temp
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thermo_modify temp effTemp press effPress
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min_style cg
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minimize 0 1e-6 100 200
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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: 20000
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master list distance cutoff = 22.88
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ghost atom cutoff = 22.88
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binsize = 11.44, 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 off
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pair build: half/bin/atomonly/newtoff
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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) = 9.51 | 9.51 | 9.51 Mbytes
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Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
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0 -3083.509 -3083.509 0 3144.5578 14.882406 -6242.9492 0 1.2112606e+10 1.2112606e+10 0
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10 -3085.4657 -3085.4657 0 3062.6201 21.113244 -6169.199 0 1.797769e+09 1.797769e+09 0
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20 -3085.9152 -3085.9152 0 3063.3218 21.843788 -6171.0808 0 1.9306772e+09 1.9306772e+09 0
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30 -3086.103 -3086.103 0 3065.4937 21.7953 -6173.392 0 2.1693045e+09 2.1693045e+09 0
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40 -3086.2065 -3086.2065 0 3062.3955 22.002457 -6170.6045 0 1.7527596e+09 1.7527596e+09 0
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50 -3086.2558 -3086.2558 0 3059.7162 22.165243 -6168.1372 0 1.4005967e+09 1.4005967e+09 0
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60 -3086.2823 -3086.2823 0 3061.7509 22.016476 -6170.0497 0 1.6419693e+09 1.6419693e+09 0
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70 -3086.3068 -3086.3068 0 3063.1496 22.125331 -6171.5817 0 1.8371954e+09 1.8371954e+09 0
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80 -3086.3286 -3086.3286 0 3063.4058 22.112083 -6171.8465 0 1.8595352e+09 1.8595352e+09 0
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90 -3086.342 -3086.342 0 3062.6876 22.145517 -6171.1752 0 1.761838e+09 1.761838e+09 0
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100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
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Loop time of 9.51021 on 4 procs for 100 steps with 2000 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 iterations
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Energy initial, next-to-last, final =
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-3083.5089570212 -3086.34842671529 -3086.34926128553
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Force two-norm initial, final = 3.4238461 0.15353209
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Force max component initial, final = 0.15119069 0.017560878
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Final line search alpha, max atom move = 0.75419179 0.01324427
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Iterations, force evaluations = 100 191
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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 | 8.8842 | 9.0722 | 9.2808 | 5.4 | 95.39
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.04463 | 0.04473 | 0.04481 | 0.0 | 0.47
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Output | 0.00071317 | 0.00073223 | 0.0007793 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.3926 | | | 4.13
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Nlocal: 500 ave 500 max 500 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 10252 ave 10252 max 10252 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 648158 ave 648158 max 648158 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2592632
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Ave neighs/atom = 1296.316
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Neighbor list builds = 0
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Dangerous builds = 0
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fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
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fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
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compute 1 all property/atom spin eradius
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dump 1 all custom 100 ${sname}.spe.lammpstrj id type q c_1[1] c_1[2] x y z
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dump 1 all custom 100 Li.bohr.spe.lammpstrj id type q c_1[1] c_1[2] x y z
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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) = 8.76 | 8.76 | 8.76 Mbytes
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Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
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100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
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110 -3085.709 -3086.35 0.64098668 3062.5195 22.168933 -6171.0384 0 1.9130428e+09 1.8610249e+09 270.41729
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120 -3084.995 -3086.3497 1.3546418 3064.69 22.151949 -6173.1916 0 2.3968054e+09 2.2869572e+09 571.49172
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130 -3084.2774 -3086.3449 2.0675114 3067.5683 22.125927 -6176.0391 0 2.9762332e+09 2.8088108e+09 872.23471
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140 -3083.5543 -3086.3327 2.7783319 3071.0091 22.090343 -6179.4321 0 3.6318905e+09 3.4073653e+09 1172.1133
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150 -3082.8209 -3086.3101 3.4891918 3074.9323 22.044189 -6183.2866 0 4.3538347e+09 4.0726292e+09 1472.0085
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160 -3082.0735 -3086.274 4.2005492 3079.2855 21.986186 -6187.5458 0 5.1353281e+09 4.7979569e+09 1772.1135
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170 -3081.3099 -3086.2215 4.911672 3084.0302 21.914874 -6192.1667 0 5.9710184e+09 5.5781934e+09 2072.1196
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180 -3080.5276 -3086.1495 5.6218934 3089.1358 21.828679 -6197.1139 0 6.8564778e+09 6.4091119e+09 2371.7454
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190 -3079.7237 -3086.0546 6.330928 3094.5768 21.725972 -6202.3574 0 7.787914e+09 7.2871001e+09 2670.8705
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200 -3078.895 -3085.9337 7.0387107 3100.3318 21.605131 -6207.8707 0 8.7619059e+09 8.2089091e+09 2969.4675
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Loop time of 5.34836 on 4 procs for 100 steps with 2000 atoms
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Performance: 1615.450 fs/day, 0.015 hours/fs, 18.697 timesteps/s, 37.395 katom-step/s
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99.9% 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 | 4.8621 | 5.065 | 5.2272 | 5.9 | 94.70
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.02486 | 0.025085 | 0.025316 | 0.1 | 0.47
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Output | 0.0016755 | 0.0018282 | 0.0019368 | 0.2 | 0.03
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Modify | 0.092978 | 0.25534 | 0.4584 | 26.2 | 4.77
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Other | | 0.00111 | | | 0.02
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Nlocal: 500 ave 518 max 484 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 10252 ave 10268 max 10234 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Neighs: 621113 ave 642857 max 604509 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Total # of neighbors = 2484453
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Ave neighs/atom = 1242.2265
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:15
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