156 lines
6.8 KiB
Groff
156 lines
6.8 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.ang
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units real
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newton on
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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.ang
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Reading data file ...
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orthogonal box = (0 0 0) to (22.098442 22.098442 22.098442)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2000 atoms
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read_data CPU = 0.014 seconds
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#read_restart ${sname}.min.restart
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pair_style eff/cut 11.049221 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 ecoul equal c_energies[3]
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variable erres equal c_energies[4]
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thermo 100
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thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
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thermo_modify temp effTemp press effPress flush yes
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#min_style cg
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#minimize 0 1e-6 100 1000
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#write_restart ${sname}.min.restart
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timestep 0.005
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velocity all create 10.0 4928459 rot yes mom yes dist gaussian
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fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
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#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
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fix 1 all nve/eff
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run 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 = 13.049221
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ghost atom cutoff = 13.049221
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binsize = 6.5246105, 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) = 6.772 | 6.887 | 7.001 Mbytes
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Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
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0 -1934872.7 -1934932.3 59.586393 1973239.1 9338.8528 -3917510.2 0 119790.47 119790.47 40.06012
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100 -1932300.8 -1934539.4 2238.5734 1864086.1 9857.8379 -3808483.3 0 -100104.15 -105089 1505
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200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
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Loop time of 6.61662 on 4 procs for 200 steps with 2000 atoms
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Performance: 0.013 ns/day, 1837.949 hours/ns, 30.227 timesteps/s, 60.454 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 | 5.572 | 5.9389 | 6.2372 | 9.8 | 89.76
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.37051 | 0.66886 | 1.0359 | 29.2 | 10.11
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Output | 0.00076947 | 0.00078111 | 0.00081552 | 0.0 | 0.01
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Modify | 0.0035517 | 0.0038042 | 0.0040517 | 0.4 | 0.06
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Other | | 0.004249 | | | 0.06
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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: 424625 ave 448237 max 400021 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Total # of neighbors = 1698500
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Ave neighs/atom = 849.25
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix 0
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unfix 1
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fix 1 all nvt/eff temp 3000.0 3000.0 100.0
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compute 1 all property/atom spin eradius ervel
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dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
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dump 1 all custom 500 Li.ang.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
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run 500
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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) = 7.522 | 7.656 | 7.751 Mbytes
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Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
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200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
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300 -1929902.8 -1934223.4 4320.5724 2031898.3 11427.685 -3977549.4 0 268725.75 262717.84 2904.7345
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400 -1929360.3 -1935088.8 5728.4403 1850892.1 13473.172 -3799454 0 -105609.57 -118457.31 3851.2485
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500 -1929066.1 -1935648.1 6581.9291 1901305.5 14887.365 -3851840.9 0 7045.2102 -9644.887 4425.0518
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600 -1929593.6 -1934406.5 4812.986 2003446.8 16194.971 -3954048.4 0 221662.39 211620.13 3235.7857
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700 -1930061.3 -1933572.3 3510.9499 1811788.7 18436.004 -3763797 0 -182749.21 -186750.23 2360.4227
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Loop time of 16.6082 on 4 procs for 500 steps with 2000 atoms
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Performance: 0.013 ns/day, 1845.351 hours/ns, 30.106 timesteps/s, 60.211 katom-step/s
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99.7% 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 | 12.79 | 14.632 | 16.232 | 32.8 | 88.10
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.35155 | 1.9504 | 3.7924 | 89.8 | 11.74
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Output | 0.0034195 | 0.0035878 | 0.0038027 | 0.3 | 0.02
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Modify | 0.01108 | 0.011237 | 0.0114 | 0.1 | 0.07
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Other | | 0.01046 | | | 0.06
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Nlocal: 500 ave 520 max 480 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 10252 ave 10272 max 10232 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 426287 ave 457559 max 396571 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Total # of neighbors = 1705148
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Ave neighs/atom = 852.574
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:23
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