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 -69.258299 0.0000000) to (39.984207 69.258299 6.2700240) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8993093 5.2981722 6.2700240 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.258299 0.0000000) to (39.984207 69.258299 6.2700240) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8993093 5.2981722 6.2700240 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.258299 0.0000000) to (39.984207 69.258299 6.2700240) create_atoms CPU = 0.002 seconds 1466 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 = 11 36 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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_803527979660_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 = 11 36 2 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) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10215.464 0 -10215.464 -425.53704 83 0 -10255.213 0 -10255.213 -6875.3612 Loop time of 4.17266 on 1 procs for 83 steps with 2904 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 = -10215.4640291631 -10255.2032764579 -10255.2133327637 Force two-norm initial, final = 28.938472 0.38585280 Force max component initial, final = 4.5904815 0.11115990 Final line search alpha, max atom move = 1.0000000 0.11115990 Iterations, force evaluations = 83 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0572 | 4.0572 | 4.0572 | 0.0 | 97.23 Neigh | 0.063771 | 0.063771 | 0.063771 | 0.0 | 1.53 Comm | 0.027383 | 0.027383 | 0.027383 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02431 | | | 0.58 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13531.0 ave 13531 max 13531 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: 505864.0 ave 505864 max 505864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505864 Ave neighs/atom = 174.19559 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 = 11 36 2 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -10255.213 0 -10255.213 -6875.3612 34726.38 86 0 -10255.437 0 -10255.437 -1946.2717 34599.466 Loop time of 0.132881 on 1 procs for 3 steps with 2904 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 = -10255.2133327636 -10255.4296316995 -10255.4371525662 Force two-norm initial, final = 167.76368 10.304168 Force max component initial, final = 140.33188 10.194987 Final line search alpha, max atom move = 4.0095492e-05 0.00040877303 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12945 | 0.12945 | 0.12945 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005812 | 0.0005812 | 0.0005812 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002851 | | | 2.15 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13393.0 ave 13393 max 13393 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: 505640.0 ave 505640 max 505640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505640 Ave neighs/atom = 174.11846 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 = 11 36 2 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) = 10.40 | 10.40 | 10.40 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10255.437 0 -10255.437 -1946.2717 Loop time of 2.236e-06 on 1 procs for 0 steps with 2904 atoms 178.9% 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 | | 2.236e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13415.0 ave 13415 max 13415 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: 505884.0 ave 505884 max 505884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505884 Ave neighs/atom = 174.20248 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 = 11 36 2 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) = 10.40 | 10.40 | 10.40 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 -10255.437 -10255.437 39.880618 138.5166 6.2633358 -1946.2717 -1946.2717 66.209223 -6376.6139 471.58953 2.3349083 1253.4154 Loop time of 2.686e-06 on 1 procs for 0 steps with 2904 atoms 260.6% 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 | | 2.686e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13415.0 ave 13415 max 13415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 252942.0 ave 252942 max 252942 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 505884.0 ave 505884 max 505884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505884 Ave neighs/atom = 174.20248 Neighbor list builds = 0 Dangerous builds = 0 2904 -10255.4371525662 eV 2.33490828315839 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04