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 -62.280837 0.0000000) to (31.140419 62.280837 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0497976 5.0497976 3.6200001 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.280837 0.0000000) to (31.140419 62.280837 3.6200001) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0497976 5.0497976 3.6200001 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.280837 0.0000000) to (31.140419 62.280837 3.6200001) create_atoms CPU = 0.001 seconds 594 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 = 8 32 1 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 2 atoms, new total = 1184 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_657255834688_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 = 8 32 1 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) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3828.0407 0 -3828.0407 57573.188 81 0 -4181.6701 0 -4181.6701 3899.7159 Loop time of 1.83581 on 1 procs for 81 steps with 1184 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 = -3828.04066811633 -4181.66595765352 -4181.67012482391 Force two-norm initial, final = 673.25139 0.23559650 Force max component initial, final = 192.60918 0.053002450 Final line search alpha, max atom move = 1.0000000 0.053002450 Iterations, force evaluations = 81 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7862 | 1.7862 | 1.7862 | 0.0 | 97.30 Neigh | 0.025975 | 0.025975 | 0.025975 | 0.0 | 1.41 Comm | 0.013484 | 0.013484 | 0.013484 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01019 | | | 0.56 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8961.00 ave 8961 max 8961 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: 206472.0 ave 206472 max 206472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206472 Ave neighs/atom = 174.38514 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 = 8 32 1 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.459 | 5.459 | 5.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4181.6701 0 -4181.6701 3899.7159 14041.628 86 0 -4181.7935 0 -4181.7935 -324.85697 14085.454 Loop time of 0.0838894 on 1 procs for 5 steps with 1184 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4181.67012482392 -4181.79094012939 -4181.79349113958 Force two-norm initial, final = 70.668224 6.5919668 Force max component initial, final = 65.544119 5.5640431 Final line search alpha, max atom move = 0.00013096271 0.00072868215 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.081141 | 0.081141 | 0.081141 | 0.0 | 96.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047358 | 0.00047358 | 0.00047358 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002274 | | | 2.71 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8791.00 ave 8791 max 8791 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: 206520.0 ave 206520 max 206520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206520 Ave neighs/atom = 174.42568 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 = 8 33 1 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) = 5.597 | 5.597 | 5.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4181.7935 0 -4181.7935 -324.85697 Loop time of 2.139e-06 on 1 procs for 0 steps with 1184 atoms 140.3% 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 | | 2.139e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8791.00 ave 8791 max 8791 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: 206296.0 ave 206296 max 206296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206296 Ave neighs/atom = 174.23649 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 = 8 33 1 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) = 5.597 | 5.597 | 5.597 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 -4181.7935 -4181.7935 31.142366 125.09414 3.6156158 -324.85697 -324.85697 55.801201 -398.24607 -632.12605 2.3228203 296.30041 Loop time of 2.73e-06 on 1 procs for 0 steps with 1184 atoms 219.8% 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 | | 2.73e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8791.00 ave 8791 max 8791 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103148.0 ave 103148 max 103148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206296.0 ave 206296 max 206296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206296 Ave neighs/atom = 174.23649 Neighbor list builds = 0 Dangerous builds = 0 1184 -4181.79349113958 eV 2.32282025167879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02