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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -35.820261 0.0000000) to (17.908901 35.820261 2.4599767) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.0411341 3.0411341 2.4599767 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -35.820261 0.0000000) to (17.908901 35.820261 2.4599767) create_atoms CPU = 0.001 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.0411341 3.0411341 2.4599767 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -35.820261 0.0000000) to (17.908901 35.820261 2.4599767) create_atoms CPU = 0.000 seconds 213 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 418 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_677328661525_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.888 | 4.888 | 4.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5204.7381 0 -5204.7381 46613.545 109 0 -5277.7185 0 -5277.7185 -24907.184 Loop time of 5.60771 on 1 procs for 109 steps with 418 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 = -5204.73811102119 -5277.71377776126 -5277.71848153489 Force two-norm initial, final = 141.99356 0.57074944 Force max component initial, final = 57.059873 0.057452630 Final line search alpha, max atom move = 0.65804922 0.037806658 Iterations, force evaluations = 109 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5881 | 5.5881 | 5.5881 | 0.0 | 99.65 Neigh | 0.0054458 | 0.0054458 | 0.0054458 | 0.0 | 0.10 Comm | 0.0090356 | 0.0090356 | 0.0090356 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005144 | | | 0.09 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6084.00 ave 6084 max 6084 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: 104352.0 ave 104352 max 104352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104352 Ave neighs/atom = 249.64593 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.891 | 4.891 | 4.891 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -5277.7185 0 -5277.7185 -24907.184 3156.1575 125 0 -5278.9344 0 -5278.9344 34559.598 3130.3471 Loop time of 0.485759 on 1 procs for 16 steps with 418 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 = -5277.71848153486 -5278.92971121923 -5278.9343906029 Force two-norm initial, final = 178.45974 2.0209528 Force max component initial, final = 171.79252 0.37352653 Final line search alpha, max atom move = 0.00019964940 7.4574347e-05 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48164 | 0.48164 | 0.48164 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083694 | 0.00083694 | 0.00083694 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003285 | | | 0.68 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6560.00 ave 6560 max 6560 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: 105258.0 ave 105258 max 105258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105258 Ave neighs/atom = 251.81340 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5278.9344 0 -5278.9344 34559.598 Loop time of 1.637e-06 on 1 procs for 0 steps with 418 atoms 183.3% 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 | | 1.637e-06 | | |100.00 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6560.00 ave 6560 max 6560 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: 105340.0 ave 105340 max 105340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105340 Ave neighs/atom = 252.00957 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.029 | 5.029 | 5.029 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 -5278.9344 -5278.9344 18.049556 71.640522 2.4208464 34559.598 34559.598 -187.2627 103677.92 188.13758 2.0126223 228.01906 Loop time of 1.481e-06 on 1 procs for 0 steps with 418 atoms 135.0% 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 | | 1.481e-06 | | |100.00 Nlocal: 418.000 ave 418 max 418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6560.00 ave 6560 max 6560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52670.0 ave 52670 max 52670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105340.0 ave 105340 max 105340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105340 Ave neighs/atom = 252.00957 Neighbor list builds = 0 Dangerous builds = 0 418 -5278.9343906029 eV 2.01262229125307 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06