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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -80.130550 0.0000000) to (49.067262 80.130550 9.9130839) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6744453 5.7233217 6.6087226 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.130550 0.0000000) to (49.067262 80.130550 9.9130839) create_atoms CPU = 0.003 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6744453 5.7233217 6.6087226 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.130550 0.0000000) to (49.067262 80.130550 9.9130839) create_atoms CPU = 0.002 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 14 46 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 60 atoms, new total = 4656 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_958395190627_001#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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 6.671 | 6.671 | 6.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15559.95 0 -15559.95 -488.83919 33 0 -15605.913 0 -15605.913 -5136.4471 Loop time of 10.6026 on 1 procs for 33 steps with 4656 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 = -15559.9499939777 -15605.9006195477 -15605.9128392033 Force two-norm initial, final = 30.632129 0.33957721 Force max component initial, final = 5.8435778 0.042873868 Final line search alpha, max atom move = 1.0000000 0.042873868 Iterations, force evaluations = 33 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.583 | 10.583 | 10.583 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0070831 | 0.0070831 | 0.0070831 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01245 | | | 0.12 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11105.0 ave 11105 max 11105 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: 397320.0 ave 397320 max 397320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 397320 Ave neighs/atom = 85.335052 Neighbor list builds = 0 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.671 | 6.671 | 6.671 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -15605.913 0 -15605.913 -5136.4471 77952.263 37 0 -15606.495 0 -15606.495 -1118.4494 77548.551 Loop time of 1.26499 on 1 procs for 4 steps with 4656 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 = -15605.9128392033 -15606.4918538835 -15606.4945074659 Force two-norm initial, final = 311.40332 0.45645891 Force max component initial, final = 235.77127 0.064108665 Final line search alpha, max atom move = 0.00010765878 6.9018603e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2601 | 1.2601 | 1.2601 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063628 | 0.00063628 | 0.00063628 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004284 | | | 0.34 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11145.0 ave 11145 max 11145 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: 398640.0 ave 398640 max 398640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398640 Ave neighs/atom = 85.618557 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 6.809 | 6.809 | 6.809 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15606.495 0 -15606.495 -1118.4494 Loop time of 1.847e-06 on 1 procs for 0 steps with 4656 atoms 216.6% 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 | | 1.847e-06 | | |100.00 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11145.0 ave 11145 max 11145 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: 398688.0 ave 398688 max 398688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398688 Ave neighs/atom = 85.628866 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 6.809 | 6.809 | 6.809 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 -15606.495 -15606.495 48.970445 160.2611 9.8812415 -1118.4494 -1118.4494 -0.66357181 -3355.487 0.80238295 2.4098569 2188.7735 Loop time of 1.983e-06 on 1 procs for 0 steps with 4656 atoms 201.7% 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 | | 1.983e-06 | | |100.00 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11145.0 ave 11145 max 11145 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 199344.0 ave 199344 max 199344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 398688.0 ave 398688 max 398688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398688 Ave neighs/atom = 85.628866 Neighbor list builds = 0 Dangerous builds = 0 4656 -15606.4945074659 eV 2.4098569049722 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13