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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -38.133706 0.0000000) to (17.976401 38.133706 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2871768 5.2340380 4.3599177 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -38.133706 0.0000000) to (17.976401 38.133706 4.3599177) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2871768 5.2340380 4.3599177 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -38.133706 0.0000000) to (17.976401 38.133706 4.3599177) create_atoms CPU = 0.001 seconds 206 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 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 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 406 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.831 | 4.831 | 4.831 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2437.3992 0 -2437.3992 103401.94 188 0 -2630.5538 0 -2630.5538 -3281.8032 Loop time of 44.8426 on 1 procs for 188 steps with 406 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 = -2437.39915950788 -2630.55124174922 -2630.55376733215 Force two-norm initial, final = 515.67051 0.24660354 Force max component initial, final = 181.49647 0.079786664 Final line search alpha, max atom move = 0.78872715 0.062929908 Iterations, force evaluations = 188 369 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.76 | 44.76 | 44.76 | 0.0 | 99.82 Neigh | 0.060842 | 0.060842 | 0.060842 | 0.0 | 0.14 Comm | 0.012038 | 0.012038 | 0.012038 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009631 | | | 0.02 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3107.00 ave 3107 max 3107 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: 29946.0 ave 29946 max 29946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29946 Ave neighs/atom = 73.758621 Neighbor list builds = 3 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 188 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.212 | 5.212 | 5.212 Mbytes Step Temp E_pair E_mol TotEng Press Volume 188 0 -2630.5538 0 -2630.5538 -3281.8032 5977.5064 192 0 -2630.6735 0 -2630.6735 -3.5417668 5968.3198 Loop time of 0.730929 on 1 procs for 4 steps with 406 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 = -2630.55376733215 -2630.67280584484 -2630.67347311214 Force two-norm initial, final = 55.440938 0.89167967 Force max component initial, final = 38.425063 0.47962824 Final line search alpha, max atom move = 0.00035185807 0.00016876107 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72998 | 0.72998 | 0.72998 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016908 | 0.00016908 | 0.00016908 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000776 | | | 0.11 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3230.00 ave 3230 max 3230 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: 30258.0 ave 30258 max 30258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30258 Ave neighs/atom = 74.527094 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.350 | 5.350 | 5.350 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2630.6735 0 -2630.6735 -3.5417668 Loop time of 1.866e-06 on 1 procs for 0 steps with 406 atoms 160.8% 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 | | 1.866e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3259.00 ave 3259 max 3259 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: 30314.0 ave 30314 max 30314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30314 Ave neighs/atom = 74.665025 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.350 | 5.350 | 5.350 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 -2630.6735 -2630.6735 18.031022 76.074642 4.3510274 -3.5417668 -3.5417668 -71.70696 128.42924 -67.347586 2.4819204 993.30263 Loop time of 1.924e-06 on 1 procs for 0 steps with 406 atoms 155.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 406.000 ave 406 max 406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3259.00 ave 3259 max 3259 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15157.0 ave 15157 max 15157 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30314.0 ave 30314 max 30314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30314 Ave neighs/atom = 74.665025 Neighbor list builds = 0 Dangerous builds = 0 406 -2630.67347311214 eV 2.48192035825516 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:46