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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -37.944781 0.0000000) to (23.236338 37.944781 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2247887 4.3119069 4.6706796 Created 523 atoms using lattice units in orthogonal box = (0.0000000 -37.944781 0.0000000) to (23.236338 37.944781 7.0060194) create_atoms CPU = 0.001 seconds 523 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2247887 4.3119069 4.6706796 Created 529 atoms using lattice units in orthogonal box = (0.0000000 -37.944781 0.0000000) to (23.236338 37.944781 7.0060194) create_atoms CPU = 0.001 seconds 529 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 = 9 29 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 0 atoms, new total = 1052 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 = 9 29 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) = 5.286 | 5.286 | 5.286 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4363.5357 0 -4363.5357 24651.728 96 0 -4476.5158 0 -4476.5158 1658.1903 Loop time of 12.1412 on 1 procs for 96 steps with 1052 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 = -4363.53572610368 -4476.51241478052 -4476.51581796588 Force two-norm initial, final = 141.56480 0.24627538 Force max component initial, final = 39.699906 0.077353533 Final line search alpha, max atom move = 1.0000000 0.077353533 Iterations, force evaluations = 96 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.125 | 12.125 | 12.125 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064676 | 0.0064676 | 0.0064676 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009665 | | | 0.08 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3316.00 ave 3316 max 3316 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: 60518.0 ave 60518 max 60518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60518 Ave neighs/atom = 57.526616 Neighbor list builds = 0 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 = 9 29 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 : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.286 | 5.286 | 5.286 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -4476.5158 0 -4476.5158 1658.1903 12354.383 101 0 -4476.6733 0 -4476.6733 -93.497556 12365.323 Loop time of 0.454132 on 1 procs for 5 steps with 1052 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 = -4476.51581796587 -4476.67306369185 -4476.67329315161 Force two-norm initial, final = 68.024571 1.3831074 Force max component initial, final = 65.242190 0.83346990 Final line search alpha, max atom move = 0.00046616182 0.00038853185 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45283 | 0.45283 | 0.45283 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020492 | 0.00020492 | 0.00020492 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001093 | | | 0.24 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3390.00 ave 3390 max 3390 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: 60546.0 ave 60546 max 60546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60546 Ave neighs/atom = 57.553232 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 = 9 29 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) = 5.424 | 5.424 | 5.424 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4476.6733 0 -4476.6733 -93.497556 Loop time of 1.801e-06 on 1 procs for 0 steps with 1052 atoms 222.1% 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 | | 1.801e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3394.00 ave 3394 max 3394 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: 60498.0 ave 60498 max 60498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60498 Ave neighs/atom = 57.507605 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 = 9 29 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) = 5.424 | 5.424 | 5.424 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 -4476.6733 -4476.6733 23.190451 76.204307 6.9970785 -93.497556 -93.497556 -107.77954 -69.158003 -103.55512 2.1859096 840.25254 Loop time of 1.752e-06 on 1 procs for 0 steps with 1052 atoms 171.2% 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 | | 1.752e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3394.00 ave 3394 max 3394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30249.0 ave 30249 max 30249 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60498.0 ave 60498 max 60498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60498 Ave neighs/atom = 57.507605 Neighbor list builds = 0 Dangerous builds = 0 1052 -4476.67329315161 eV 2.18590956054274 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13