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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -38.651023 0.0000000) to (22.315179 38.651023 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8724154 5.4247050 6.2700239 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.651023 0.0000000) to (22.315179 38.651023 6.2700239) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8724154 5.4247050 6.2700239 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.651023 0.0000000) to (22.315179 38.651023 6.2700239) create_atoms CPU = 0.001 seconds 458 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 26 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_313717476091_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2914.8177 0 -2914.8177 108951.83 23 0 -3209.2181 0 -3209.2181 6214.5497 Loop time of 0.78887 on 1 procs for 23 steps with 912 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2914.8177494628 -3209.21662031599 -3209.21812524901 Force two-norm initial, final = 849.71914 1.7711254 Force max component initial, final = 237.75667 0.45843383 Final line search alpha, max atom move = 0.35312444 0.16188419 Iterations, force evaluations = 23 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78494 | 0.78494 | 0.78494 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016589 | 0.0016589 | 0.0016589 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002268 | | | 0.29 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3417.00 ave 3417 max 3417 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: 70928.0 ave 70928 max 70928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70928 Ave neighs/atom = 77.771930 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -3209.2181 0 -3209.2181 6214.5497 10815.847 29 0 -3209.4612 0 -3209.4612 107.9375 10865.25 Loop time of 0.141916 on 1 procs for 6 steps with 912 atoms 95.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3209.21812524903 -3209.45843094563 -3209.46115839341 Force two-norm initial, final = 92.293368 2.0357517 Force max component initial, final = 84.620355 1.2769087 Final line search alpha, max atom move = 0.00017823976 0.00022759591 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13957 | 0.13957 | 0.13957 | 0.0 | 98.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033627 | 0.00033627 | 0.00033627 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002006 | | | 1.41 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3417.00 ave 3417 max 3417 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: 70516.0 ave 70516 max 70516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70516 Ave neighs/atom = 77.320175 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.681 | 4.681 | 4.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3209.4612 0 -3209.4612 107.9375 Loop time of 2.147e-06 on 1 procs for 0 steps with 912 atoms 139.7% 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 | | 2.147e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3417.00 ave 3417 max 3417 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: 70476.0 ave 70476 max 70476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70476 Ave neighs/atom = 77.276316 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.681 | 4.681 | 4.681 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 -3209.4612 -3209.4612 22.331604 77.730535 6.2593339 107.9375 107.9375 37.040273 98.801832 187.97039 2.2378411 554.85614 Loop time of 2.489e-06 on 1 procs for 0 steps with 912 atoms 241.1% 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 | | 2.489e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3417.00 ave 3417 max 3417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35238.0 ave 35238 max 35238 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70476.0 ave 70476 max 70476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70476 Ave neighs/atom = 77.276316 Neighbor list builds = 0 Dangerous builds = 0 912 -3209.46115839341 eV 2.23784110733545 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01