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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -40.859139 0.0000000) to (17.690963 40.859139 6.2546998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8969875 5.1069410 6.2546998 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.859139 0.0000000) to (17.690963 40.859139 6.2546998) create_atoms CPU = 0.001 seconds 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8969875 5.1069410 6.2546998 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.859139 0.0000000) to (17.690963 40.859139 6.2546998) create_atoms CPU = 0.001 seconds 396 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 31 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 26 atoms, new total = 766 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.888 | 4.888 | 4.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3136.4056 0 -3136.4056 37398.266 113 0 -3237.2884 0 -3237.2884 1835.5261 Loop time of 8.84325 on 1 procs for 113 steps with 766 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 = -3136.40564371876 -3237.28638207907 -3237.28837938012 Force two-norm initial, final = 87.751523 0.17114914 Force max component initial, final = 14.510287 0.041949488 Final line search alpha, max atom move = 1.0000000 0.041949488 Iterations, force evaluations = 113 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7989 | 8.7989 | 8.7989 | 0.0 | 99.50 Neigh | 0.031117 | 0.031117 | 0.031117 | 0.0 | 0.35 Comm | 0.0057458 | 0.0057458 | 0.0057458 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007479 | | | 0.08 Nlocal: 766.000 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2997.00 ave 2997 max 2997 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: 41268.0 ave 41268 max 41268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41268 Ave neighs/atom = 53.874674 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.887 | 4.887 | 4.887 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -3237.2884 0 -3237.2884 1835.5261 9042.2633 115 0 -3237.2991 0 -3237.2991 733.81214 9048.1382 Loop time of 0.164827 on 1 procs for 2 steps with 766 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 = -3237.28837938012 -3237.29780752937 -3237.29907567596 Force two-norm initial, final = 17.770878 1.2173539 Force max component initial, final = 17.752059 1.1582207 Final line search alpha, max atom move = 0.00017368457 0.00020116506 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1642 | 0.1642 | 0.1642 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011297 | 0.00011297 | 0.00011297 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005134 | | | 0.31 Nlocal: 766.000 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2949.00 ave 2949 max 2949 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: 41328.0 ave 41328 max 41328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41328 Ave neighs/atom = 53.953003 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.025 | 5.025 | 5.025 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3237.2991 0 -3237.2991 733.81214 Loop time of 1.895e-06 on 1 procs for 0 steps with 766 atoms 158.3% 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 | | 1.895e-06 | | |100.00 Nlocal: 766.000 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2948.00 ave 2948 max 2948 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: 41324.0 ave 41324 max 41324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41324 Ave neighs/atom = 53.947781 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.025 | 5.025 | 5.025 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 -3237.2991 -3237.2991 17.682658 81.718279 6.2617029 733.81214 733.81214 56.731009 1939.3868 205.31867 2.2732375 419.89873 Loop time of 1.967e-06 on 1 procs for 0 steps with 766 atoms 152.5% 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 | | 1.967e-06 | | |100.00 Nlocal: 766.000 ave 766 max 766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2948.00 ave 2948 max 2948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20662.0 ave 20662 max 20662 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41324.0 ave 41324 max 41324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41324 Ave neighs/atom = 53.947781 Neighbor list builds = 0 Dangerous builds = 0 766 -3237.29907567596 eV 2.27323753681053 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09