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 = 3.5927866 3.5927866 3.5927866 Created orthogonal box = (0.0000000 -51.315256 0.0000000) to (36.285366 51.315256 5.0809675) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6918220 4.5278167 5.0809675 Created 811 atoms using lattice units in orthogonal box = (0.0000000 -51.315256 0.0000000) to (36.285366 51.315256 5.0809675) create_atoms CPU = 0.005 seconds 811 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6918220 4.5278167 5.0809675 Created 819 atoms using lattice units in orthogonal box = (0.0000000 -51.315256 0.0000000) to (36.285366 51.315256 5.0809675) create_atoms CPU = 0.004 seconds 819 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 11 30 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 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1630 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_396616545191_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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 5.520 | 5.520 | 5.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5379.0991 0 -5379.0991 50649.706 97 0 -5705.4335 0 -5705.4335 4088.8423 Loop time of 7.15758 on 1 procs for 97 steps with 1630 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 = -5379.09909736968 -5705.42840984534 -5705.43349601516 Force two-norm initial, final = 357.86160 0.23155643 Force max component initial, final = 118.23590 0.031338237 Final line search alpha, max atom move = 0.85702102 0.026857528 Iterations, force evaluations = 97 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0055 | 7.0055 | 7.0055 | 0.0 | 97.87 Neigh | 0.087463 | 0.087463 | 0.087463 | 0.0 | 1.22 Comm | 0.032107 | 0.032107 | 0.032107 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03254 | | | 0.45 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7928.00 ave 7928 max 7928 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: 216058.0 ave 216058 max 216058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216058 Ave neighs/atom = 132.55092 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.522 | 5.522 | 5.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -5705.4335 0 -5705.4335 4088.8423 18921.45 101 0 -5705.5367 0 -5705.5367 -1.3643656 18979.128 Loop time of 0.34034 on 1 procs for 4 steps with 1630 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 = -5705.43349601516 -5705.53578594542 -5705.53674111222 Force two-norm initial, final = 87.206425 0.27438914 Force max component initial, final = 65.632486 0.033796276 Final line search alpha, max atom move = 0.00020194732 6.8250671e-06 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33414 | 0.33414 | 0.33414 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014582 | 0.0014582 | 0.0014582 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004738 | | | 1.39 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7926.00 ave 7926 max 7926 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: 216304.0 ave 216304 max 216304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216304 Ave neighs/atom = 132.70184 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 5.659 | 5.659 | 5.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5705.5367 0 -5705.5367 -1.3643656 Loop time of 7.067e-06 on 1 procs for 0 steps with 1630 atoms 198.1% 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 | | 7.067e-06 | | |100.00 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7868.00 ave 7868 max 7868 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: 216252.0 ave 216252 max 216252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216252 Ave neighs/atom = 132.66994 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 5.659 | 5.659 | 5.659 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 -5705.5367 -5705.5367 36.270513 102.94322 5.083055 -1.3643656 -1.3643656 -0.14651496 -1.6083693 -2.3382124 2.3705279 889.64626 Loop time of 6.585e-06 on 1 procs for 0 steps with 1630 atoms 288.5% 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 | | 6.585e-06 | | |100.00 Nlocal: 1630.00 ave 1630 max 1630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7868.00 ave 7868 max 7868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108126.0 ave 108126 max 108126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216252.0 ave 216252 max 216252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216252 Ave neighs/atom = 132.66994 Neighbor list builds = 0 Dangerous builds = 0 1630 -5705.53674111222 eV 2.37052793283797 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08