LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -44.607499 0.0000000) to (21.028177 44.607499 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1847579 6.1225980 5.1000820 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -44.607499 0.0000000) to (21.028177 44.607499 5.1000820) create_atoms CPU = 0.002 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1847579 6.1225980 5.1000820 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.607499 0.0000000) to (21.028177 44.607499 5.1000820) create_atoms CPU = 0.001 seconds 412 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 820 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_147603128437_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.642 | 6.642 | 6.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3220.2205 0 -3220.2205 60996.944 99 0 -3432.4434 0 -3432.4434 13323.933 Loop time of 4.58382 on 1 procs for 99 steps with 820 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3220.22053200065 -3432.44029233596 -3432.44343100885 Force two-norm initial, final = 244.36905 0.25127041 Force max component initial, final = 48.275763 0.021699007 Final line search alpha, max atom move = 1.0000000 0.021699007 Iterations, force evaluations = 99 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5195 | 4.5195 | 4.5195 | 0.0 | 98.60 Neigh | 0.026247 | 0.026247 | 0.026247 | 0.0 | 0.57 Comm | 0.026277 | 0.026277 | 0.026277 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01179 | | | 0.26 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11933.0 ave 11933 max 11933 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 507416.0 ave 507416 max 507416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507416 Ave neighs/atom = 618.80000 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.642 | 6.642 | 6.642 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -3432.4434 0 -3432.4434 13323.933 9567.9007 105 0 -3432.8498 0 -3432.8498 153.06021 9640.1653 Loop time of 0.198989 on 1 procs for 6 steps with 820 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3432.44343100884 -3432.84848490631 -3432.849789797 Force two-norm initial, final = 151.14737 1.7895279 Force max component initial, final = 128.48414 1.5257660 Final line search alpha, max atom move = 0.00019801950 0.00030213141 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19445 | 0.19445 | 0.19445 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008793 | 0.0008793 | 0.0008793 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003662 | | | 1.84 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11937.0 ave 11937 max 11937 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 509288.0 ave 509288 max 509288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509288 Ave neighs/atom = 621.08293 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.780 | 6.780 | 6.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3432.8498 0 -3432.8498 153.06021 Loop time of 2.246e-06 on 1 procs for 0 steps with 820 atoms 133.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.246e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11865.0 ave 11865 max 11865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 502048.0 ave 502048 max 502048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502048 Ave neighs/atom = 612.25366 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.780 | 6.780 | 6.780 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3432.8498 -3432.8498 21.137147 89.270252 5.1089464 153.06021 153.06021 254.89338 122.129 82.158255 2.4074839 882.29882 Loop time of 2.901e-06 on 1 procs for 0 steps with 820 atoms 206.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.901e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11865.0 ave 11865 max 11865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251024.0 ave 251024 max 251024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 502048.0 ave 502048 max 502048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502048 Ave neighs/atom = 612.25366 Neighbor list builds = 0 Dangerous builds = 0 820 -3432.849789797 eV 2.40748392681143 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05