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 = 3.1599882 3.1599882 3.1599882 Created orthogonal box = (0.0000000 -34.034115 0.0000000) to (17.017057 34.034115 3.1599882) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1075656 4.1075656 3.1599882 Created 116 atoms using lattice units in orthogonal box = (0.0000000 -34.034115 0.0000000) to (17.017057 34.034115 3.1599882) create_atoms CPU = 0.001 seconds 116 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1075656 4.1075656 3.1599882 Created 117 atoms using lattice units in orthogonal box = (0.0000000 -34.034115 0.0000000) to (17.017057 34.034115 3.1599882) create_atoms CPU = 0.000 seconds 117 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 6 21 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 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 233 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_698578166685_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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.404 | 4.404 | 4.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5101.1873 0 -5101.1873 85044.758 26 0 -5204.8056 0 -5204.8056 42008.465 Loop time of 4.41127 on 1 procs for 26 steps with 233 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 = -5101.18732140295 -5204.80097751234 -5204.8055660989 Force two-norm initial, final = 147.44937 0.21998622 Force max component initial, final = 48.353082 0.034324371 Final line search alpha, max atom move = 1.0000000 0.034324371 Iterations, force evaluations = 26 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4069 | 4.4069 | 4.4069 | 0.0 | 99.90 Neigh | 0.001315 | 0.001315 | 0.001315 | 0.0 | 0.03 Comm | 0.0013943 | 0.0013943 | 0.0013943 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001622 | | | 0.04 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2248.00 ave 2248 max 2248 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: 15114.0 ave 15114 max 15114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15114 Ave neighs/atom = 64.866953 Neighbor list builds = 1 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.404 | 4.404 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -5204.8056 0 -5204.8056 42008.465 3660.2806 43 0 -5206.1345 0 -5206.1345 -38.582553 3717.5333 Loop time of 1.47469 on 1 procs for 17 steps with 233 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 = -5204.8055660989 -5206.13235889695 -5206.13454197984 Force two-norm initial, final = 187.68153 0.78730850 Force max component initial, final = 165.80045 0.24636110 Final line search alpha, max atom move = 0.00024652965 6.0735317e-05 Iterations, force evaluations = 17 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4711 | 1.4711 | 1.4711 | 0.0 | 99.76 Neigh | 0.0012284 | 0.0012284 | 0.0012284 | 0.0 | 0.08 Comm | 0.00047229 | 0.00047229 | 0.00047229 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001894 | | | 0.13 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2234.00 ave 2234 max 2234 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: 14996.0 ave 14996 max 14996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14996 Ave neighs/atom = 64.360515 Neighbor list builds = 1 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5206.1345 0 -5206.1345 -38.582553 Loop time of 1.735e-06 on 1 procs for 0 steps with 233 atoms 172.9% 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 | | 1.735e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2234.00 ave 2234 max 2234 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: 14992.0 ave 14992 max 14992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14992 Ave neighs/atom = 64.343348 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.542 | 4.542 | 4.542 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 -5206.1345 -5206.1345 17.029467 69.20763 3.1542771 -38.582553 -38.582553 -106.25374 -83.477039 73.983116 2.4941108 237.88734 Loop time of 1.376e-06 on 1 procs for 0 steps with 233 atoms 218.0% 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 | | 1.376e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2234.00 ave 2234 max 2234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7496.00 ave 7496 max 7496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 14992.0 ave 14992 max 14992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14992 Ave neighs/atom = 64.343348 Neighbor list builds = 0 Dangerous builds = 0 233 -1180.87411116664 eV 2.4941107851694 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06