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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.104127 0.0000000) to (52.791559 43.104127 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0622043 5.3142075 5.8254140 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.104127 0.0000000) to (52.791559 43.104127 8.7381210) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0622043 5.3142075 5.8254140 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.104127 0.0000000) to (52.791559 43.104127 8.7381210) create_atoms CPU = 0.002 seconds 1756 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3468 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14101.33 0 -14101.33 22963.802 104 0 -14633.001 0 -14633.001 30099.15 Loop time of 14.6663 on 1 procs for 104 steps with 3468 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14101.3300170803 -14632.9864901113 -14633.0010677495 Force two-norm initial, final = 502.72630 0.68214351 Force max component initial, final = 95.614403 0.11479420 Final line search alpha, max atom move = 0.90849971 0.10429049 Iterations, force evaluations = 104 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.58 | 14.58 | 14.58 | 0.0 | 99.41 Neigh | 0.037457 | 0.037457 | 0.037457 | 0.0 | 0.26 Comm | 0.016333 | 0.016333 | 0.016333 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03212 | | | 0.22 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7252.00 ave 7252 max 7252 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: 199256.0 ave 199256 max 199256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199256 Ave neighs/atom = 57.455594 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.596 | 5.596 | 5.596 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -14633.001 0 -14633.001 30099.15 39767.785 109 0 -14636.499 0 -14636.499 -35.928987 40141.051 Loop time of 0.642102 on 1 procs for 5 steps with 3468 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 = -14633.0010677495 -14636.4911003581 -14636.4994599244 Force two-norm initial, final = 1295.7475 3.3996281 Force max component initial, final = 795.74698 2.1115644 Final line search alpha, max atom move = 3.7936440e-05 8.0105235e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63824 | 0.63824 | 0.63824 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045781 | 0.00045781 | 0.00045781 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003405 | | | 0.53 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7288.00 ave 7288 max 7288 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: 202592.0 ave 202592 max 202592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202592 Ave neighs/atom = 58.417532 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.734 | 5.734 | 5.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14636.499 0 -14636.499 -35.928987 Loop time of 2.216e-06 on 1 procs for 0 steps with 3468 atoms 180.5% 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 | | 2.216e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7260.00 ave 7260 max 7260 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: 197690.0 ave 197690 max 197690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197690 Ave neighs/atom = 57.004037 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.734 | 5.734 | 5.734 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 -14636.499 -14636.499 52.912589 86.494683 8.7708222 -35.928987 -35.928987 -23.448816 -84.560298 0.22215235 2.3226621 1837.6107 Loop time of 2.459e-06 on 1 procs for 0 steps with 3468 atoms 203.3% 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 | | 2.459e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7260.00 ave 7260 max 7260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98845.0 ave 98845 max 98845 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197690.0 ave 197690 max 197690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197690 Ave neighs/atom = 57.004037 Neighbor list builds = 0 Dangerous builds = 0 3468 -14636.4994599244 eV 2.32266214547117 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15