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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -36.777215 0.0000000) to (31.850002 36.777215 6.2462993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7166670 5.6580330 6.2462993 Created 620 atoms using lattice units in orthogonal box = (0.0000000 -36.777215 0.0000000) to (31.850002 36.777215 6.2462993) create_atoms CPU = 0.002 seconds 620 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7166670 5.6580330 6.2462993 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.777215 0.0000000) to (31.850002 36.777215 6.2462993) create_atoms CPU = 0.001 seconds 629 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 13 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1249 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.511 | 7.511 | 7.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4727.2235 0 -4727.2235 73050.593 69 0 -5204.5676 0 -5204.5676 11236.109 Loop time of 7.38788 on 1 procs for 69 steps with 1249 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 = -4727.22347154436 -5204.56274169004 -5204.56757999621 Force two-norm initial, final = 558.59681 0.32575161 Force max component initial, final = 178.15357 0.071947481 Final line search alpha, max atom move = 1.0000000 0.071947481 Iterations, force evaluations = 69 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1557 | 7.1557 | 7.1557 | 0.0 | 96.86 Neigh | 0.18507 | 0.18507 | 0.18507 | 0.0 | 2.51 Comm | 0.029402 | 0.029402 | 0.029402 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01774 | | | 0.24 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12435.0 ave 12435 max 12435 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: 771226.0 ave 771226 max 771226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 771226 Ave neighs/atom = 617.47478 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.513 | 7.513 | 7.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -5204.5676 0 -5204.5676 11236.109 14633.26 73 0 -5204.9352 0 -5204.9352 1.0626714 14728.686 Loop time of 0.494174 on 1 procs for 4 steps with 1249 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 = -5204.56757999625 -5204.93350032053 -5204.93522616451 Force two-norm initial, final = 182.94428 0.76232194 Force max component initial, final = 125.03106 0.52631087 Final line search alpha, max atom move = 0.00010876589 5.7244668e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48636 | 0.48636 | 0.48636 | 0.0 | 98.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014189 | 0.0014189 | 0.0014189 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006399 | | | 1.29 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12547.0 ave 12547 max 12547 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: 772308.0 ave 772308 max 772308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 772308 Ave neighs/atom = 618.34107 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.650 | 7.650 | 7.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5204.9352 0 -5204.9352 1.0626714 Loop time of 4.228e-06 on 1 procs for 0 steps with 1249 atoms 141.9% 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 | | 4.228e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12473.0 ave 12473 max 12473 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: 765178.0 ave 765178 max 765178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 765178 Ave neighs/atom = 612.63251 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 7.650 | 7.650 | 7.650 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 -5204.9352 -5204.9352 31.932623 73.779143 6.2516667 1.0626714 1.0626714 -57.400253 43.100406 17.487861 2.2563355 946.27812 Loop time of 4.331e-06 on 1 procs for 0 steps with 1249 atoms 230.9% 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 | | 4.331e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12473.0 ave 12473 max 12473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 382589.0 ave 382589 max 382589 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 765178.0 ave 765178 max 765178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 765178 Ave neighs/atom = 612.63251 Neighbor list builds = 0 Dangerous builds = 0 1249 -5204.93522616451 eV 2.25633548826807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08