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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -38.242677 0.0000000) to (13.520828 38.242677 4.0766831) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9166648 4.3457588 4.0766831 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -38.242677 0.0000000) to (13.520828 38.242677 4.0766831) create_atoms CPU = 0.002 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9166648 4.3457588 4.0766831 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -38.242677 0.0000000) to (13.520828 38.242677 4.0766831) create_atoms CPU = 0.001 seconds 178 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 18 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 354 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -978.24067 0 -978.24067 145791.26 75 0 -1362.9509 0 -1362.9509 19275.285 Loop time of 1.47243 on 1 procs for 75 steps with 354 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 = -978.240669327543 -1362.94980181489 -1362.95093806918 Force two-norm initial, final = 724.07937 0.15284208 Force max component initial, final = 207.10605 0.022608558 Final line search alpha, max atom move = 1.0000000 0.022608558 Iterations, force evaluations = 75 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4254 | 1.4254 | 1.4254 | 0.0 | 96.80 Neigh | 0.020462 | 0.020462 | 0.020462 | 0.0 | 1.39 Comm | 0.016688 | 0.016688 | 0.016688 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009922 | | | 0.67 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4709.00 ave 4709 max 4709 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: 86184.0 ave 86184 max 86184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86184 Ave neighs/atom = 243.45763 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.488 | 4.488 | 4.488 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -1362.9509 0 -1362.9509 19275.285 4215.8828 92 0 -1363.7861 0 -1363.7861 289.36182 4262.9732 Loop time of 0.209051 on 1 procs for 17 steps with 354 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 = -1362.95093806918 -1363.78594800452 -1363.78606134728 Force two-norm initial, final = 113.74370 1.5351928 Force max component initial, final = 108.10337 0.97604252 Final line search alpha, max atom move = 0.0037430385 0.0036533647 Iterations, force evaluations = 17 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20071 | 0.20071 | 0.20071 | 0.0 | 96.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019844 | 0.0019844 | 0.0019844 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006352 | | | 3.04 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4695.00 ave 4695 max 4695 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: 86752.0 ave 86752 max 86752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86752 Ave neighs/atom = 245.06215 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1363.7861 0 -1363.7861 289.36182 Loop time of 6.545e-06 on 1 procs for 0 steps with 354 atoms 168.1% 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 | | 6.545e-06 | | |100.00 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4650.00 ave 4650 max 4650 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: 82612.0 ave 82612 max 82612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82612 Ave neighs/atom = 233.36723 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 4 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.625 | 4.625 | 4.625 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 -1363.7861 -1363.7861 13.569167 75.921863 4.1380198 289.36182 289.36182 289.97289 364.12883 213.98374 2.2691223 324.84237 Loop time of 7.016e-06 on 1 procs for 0 steps with 354 atoms 270.8% 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 | | 7.016e-06 | | |100.00 Nlocal: 354.000 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4650.00 ave 4650 max 4650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41306.0 ave 41306 max 41306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82612.0 ave 82612 max 82612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82612 Ave neighs/atom = 233.36723 Neighbor list builds = 0 Dangerous builds = 0 354 -1363.78606134728 eV 2.26912231448922 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02