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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -30.036297 0.0000000) to (36.786800 30.036297 7.0149676) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6819564 4.3689159 4.6766450 Created 657 atoms using lattice units in orthogonal box = (0.0000000 -30.036297 0.0000000) to (36.786800 30.036297 7.0149676) create_atoms CPU = 0.001 seconds 657 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6819564 4.3689159 4.6766450 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -30.036297 0.0000000) to (36.786800 30.036297 7.0149676) create_atoms CPU = 0.001 seconds 663 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 = 7 11 2 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 9 atoms, new total = 1311 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 = 7 11 2 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) = 7.901 | 7.901 | 7.901 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4845.0645 0 -4845.0645 66663.231 159 0 -5431.9621 0 -5431.9621 -1398.4549 Loop time of 9.88023 on 1 procs for 159 steps with 1311 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4845.06448214951 -5431.95698448658 -5431.96212838785 Force two-norm initial, final = 637.17323 0.32170643 Force max component initial, final = 125.86516 0.060780462 Final line search alpha, max atom move = 1.0000000 0.060780462 Iterations, force evaluations = 159 297 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.5879 | 9.5879 | 9.5879 | 0.0 | 97.04 Neigh | 0.23075 | 0.23075 | 0.23075 | 0.0 | 2.34 Comm | 0.037416 | 0.037416 | 0.037416 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02419 | | | 0.24 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11880.0 ave 11880 max 11880 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: 789982.0 ave 789982 max 789982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 789982 Ave neighs/atom = 602.57971 Neighbor list builds = 6 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 = 7 11 2 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 : 159 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.902 | 7.902 | 7.902 Mbytes Step Temp E_pair E_mol TotEng Press Volume 159 0 -5431.9621 0 -5431.9621 -1398.4549 15502.226 164 0 -5432.1748 0 -5432.1748 39.112136 15488.778 Loop time of 0.250102 on 1 procs for 5 steps with 1311 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 = -5431.96212838777 -5432.17462544021 -5432.17477153409 Force two-norm initial, final = 100.80522 0.82492535 Force max component initial, final = 93.026561 0.41598676 Final line search alpha, max atom move = 0.00045723760 0.00019020479 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24645 | 0.24645 | 0.24645 | 0.0 | 98.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071457 | 0.00071457 | 0.00071457 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00294 | | | 1.18 Nlocal: 1311.00 ave 1311 max 1311 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: 790074.0 ave 790074 max 790074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 790074 Ave neighs/atom = 602.64989 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 = 7 11 2 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) = 8.040 | 8.040 | 8.040 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5432.1748 0 -5432.1748 39.112136 Loop time of 2.061e-06 on 1 procs for 0 steps with 1311 atoms 194.1% 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 | | 2.061e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11868.0 ave 11868 max 11868 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: 790388.0 ave 790388 max 790388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 790388 Ave neighs/atom = 602.88940 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 = 7 11 2 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) = 8.040 | 8.040 | 8.040 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 -5432.1748 -5432.1748 36.839129 60.160687 6.9886778 39.112136 39.112136 32.764044 43.093237 41.479126 2.2986637 2370.1236 Loop time of 2.433e-06 on 1 procs for 0 steps with 1311 atoms 246.6% 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 | | 2.433e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11868.0 ave 11868 max 11868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 395194.0 ave 395194 max 395194 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 790388.0 ave 790388 max 790388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 790388 Ave neighs/atom = 602.88940 Neighbor list builds = 0 Dangerous builds = 0 1311 -5432.17477153409 eV 2.29866366217442 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11