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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -71.675964 0.0000000) to (43.890168 71.675964 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0757337 5.1194532 5.9114353 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.675964 0.0000000) to (43.890168 71.675964 8.8671530) create_atoms CPU = 0.003 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0757337 5.1194532 5.9114353 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.675964 0.0000000) to (43.890168 71.675964 8.8671530) create_atoms CPU = 0.003 seconds 2358 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 37 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 54 atoms, new total = 4662 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_803527979660_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 12.31 | 12.31 | 12.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16392.53 0 -16392.53 -685.51884 80 0 -16462.615 0 -16462.615 -7049.713 Loop time of 6.2536 on 1 procs for 80 steps with 4662 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 = -16392.5303316524 -16462.5985932415 -16462.6149922691 Force two-norm initial, final = 37.543992 0.50733689 Force max component initial, final = 4.7289627 0.062848781 Final line search alpha, max atom move = 1.0000000 0.062848781 Iterations, force evaluations = 80 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0973 | 6.0973 | 6.0973 | 0.0 | 97.50 Neigh | 0.096517 | 0.096517 | 0.096517 | 0.0 | 1.54 Comm | 0.024916 | 0.024916 | 0.024916 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03484 | | | 0.56 Nlocal: 4662.00 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14605.0 ave 14605 max 14605 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: 812028.0 ave 812028 max 812028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 812028 Ave neighs/atom = 174.18018 Neighbor list builds = 2 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.31 | 12.31 | 12.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -16462.615 0 -16462.615 -7049.713 55789.823 84 0 -16463.204 0 -16463.204 -688.49775 55524.71 Loop time of 0.256556 on 1 procs for 4 steps with 4662 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 = -16462.6149922691 -16463.2014509497 -16463.2039539732 Force two-norm initial, final = 347.08080 0.56966665 Force max component initial, final = 256.14867 0.079023458 Final line search alpha, max atom move = 9.0412470e-05 7.1447061e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25155 | 0.25155 | 0.25155 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074068 | 0.00074068 | 0.00074068 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004262 | | | 1.66 Nlocal: 4662.00 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14563.0 ave 14563 max 14563 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: 812232.0 ave 812232 max 812232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 812232 Ave neighs/atom = 174.22394 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 11.83 | 11.83 | 11.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16463.204 0 -16463.204 -688.49775 Loop time of 1.943e-06 on 1 procs for 0 steps with 4662 atoms 154.4% 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 | | 1.943e-06 | | |100.00 Nlocal: 4662.00 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14565.0 ave 14565 max 14565 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: 812628.0 ave 812628 max 812628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 812628 Ave neighs/atom = 174.30888 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 11.83 | 11.83 | 11.83 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 -16463.204 -16463.204 43.763476 143.35193 8.8505641 -688.49775 -688.49775 2.2736555 -2069.2025 1.4355507 2.3089162 1710.5328 Loop time of 2.276e-06 on 1 procs for 0 steps with 4662 atoms 219.7% 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 | | 2.276e-06 | | |100.00 Nlocal: 4662.00 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14565.0 ave 14565 max 14565 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 406314.0 ave 406314 max 406314 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 812628.0 ave 812628 max 812628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 812628 Ave neighs/atom = 174.30888 Neighbor list builds = 0 Dangerous builds = 0 4662 -16463.2039539732 eV 2.30891621130771 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07