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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -44.677681 0.0000000) to (22.338841 44.677681 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0283155 4.0283155 2.8601955 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -44.677681 0.0000000) to (22.338841 44.677681 2.8601955) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0283155 4.0283155 2.8601955 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.677681 0.0000000) to (22.338841 44.677681 2.8601955) create_atoms CPU = 0.001 seconds 245 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 489 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.834 | 4.834 | 4.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2000.4737 0 -2000.4737 41189.526 99 0 -2085.0797 0 -2085.0797 7079.5469 Loop time of 16.2414 on 1 procs for 99 steps with 489 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 = -2000.47370466373 -2085.07759956898 -2085.07966357887 Force two-norm initial, final = 155.95381 0.17598211 Force max component initial, final = 46.661041 0.036972522 Final line search alpha, max atom move = 1.0000000 0.036972522 Iterations, force evaluations = 99 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.214 | 16.214 | 16.214 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.013814 | 0.013814 | 0.013814 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01363 | | | 0.08 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3172.00 ave 3172 max 3172 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: 28330.0 ave 28330 max 28330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28330 Ave neighs/atom = 57.934560 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.837 | 4.837 | 4.837 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -2085.0797 0 -2085.0797 7079.5469 5709.2224 106 0 -2085.2274 0 -2085.2274 500.68459 5728.938 Loop time of 0.878343 on 1 procs for 7 steps with 489 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 = -2085.07966357887 -2085.22610384045 -2085.22744991404 Force two-norm initial, final = 55.953399 3.2762039 Force max component initial, final = 53.706459 2.3382413 Final line search alpha, max atom move = 0.00030128850 0.00070448522 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87458 | 0.87458 | 0.87458 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076837 | 0.00076837 | 0.00076837 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002991 | | | 0.34 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3555.00 ave 3555 max 3555 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: 28284.0 ave 28284 max 28284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28284 Ave neighs/atom = 57.840491 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2085.2274 0 -2085.2274 500.68459 Loop time of 7.889e-06 on 1 procs for 0 steps with 489 atoms 164.8% 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 | | 7.889e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3560.00 ave 3560 max 3560 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: 28268.0 ave 28268 max 28268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28268 Ave neighs/atom = 57.807771 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.975 | 4.975 | 4.975 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 -2085.2274 -2085.2274 22.362662 89.854686 2.8510832 500.68459 500.68459 573.43885 657.57557 271.03934 2.2796018 121.79413 Loop time of 9.081e-06 on 1 procs for 0 steps with 489 atoms 209.2% 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 | | 9.081e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3560.00 ave 3560 max 3560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14134.0 ave 14134 max 14134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28268.0 ave 28268 max 28268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28268 Ave neighs/atom = 57.807771 Neighbor list builds = 0 Dangerous builds = 0 489 -2085.22744991404 eV 2.27960177445659 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17