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 = 3.6148132 3.6148132 3.6148132 Created orthogonal box = (0.0000000 -38.425992 0.0000000) to (38.425992 38.425992 3.6148132) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1007954 5.1007954 3.6148132 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.425992 0.0000000) to (38.425992 38.425992 3.6148132) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1007954 5.1007954 3.6148132 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.425992 0.0000000) to (38.425992 38.425992 3.6148132) create_atoms CPU = 0.001 seconds 454 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 7 14 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 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_380822813353_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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 7 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 6.231 | 6.231 | 6.231 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3068.2591 0 -3068.2591 38079.282 94 0 -3199.5206 0 -3199.5206 4336.5674 Loop time of 8.62953 on 1 procs for 94 steps with 906 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 = -3068.25914144622 -3199.51800763687 -3199.52059189531 Force two-norm initial, final = 156.62629 0.13371077 Force max component initial, final = 38.854632 0.017755909 Final line search alpha, max atom move = 1.0000000 0.017755909 Iterations, force evaluations = 94 162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3894 | 8.3894 | 8.3894 | 0.0 | 97.22 Neigh | 0.18263 | 0.18263 | 0.18263 | 0.0 | 2.12 Comm | 0.037693 | 0.037693 | 0.037693 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01982 | | | 0.23 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11939.0 ave 11939 max 11939 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: 423716.0 ave 423716 max 423716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423716 Ave neighs/atom = 467.67770 Neighbor list builds = 4 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 7 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.231 | 6.231 | 6.231 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -3199.5206 0 -3199.5206 4336.5674 10674.954 98 0 -3199.6262 0 -3199.6262 230.28757 10706.878 Loop time of 0.313457 on 1 procs for 4 steps with 906 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 = -3199.5205918953 -3199.62344836982 -3199.62618288298 Force two-norm initial, final = 59.767426 3.1724350 Force max component initial, final = 49.196294 2.9131955 Final line search alpha, max atom move = 0.00015989314 0.00046579998 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30865 | 0.30865 | 0.30865 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010119 | 0.0010119 | 0.0010119 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003793 | | | 1.21 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11946.0 ave 11946 max 11946 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: 423532.0 ave 423532 max 423532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423532 Ave neighs/atom = 467.47461 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 7 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 6.369 | 6.369 | 6.369 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3199.6262 0 -3199.6262 230.28757 Loop time of 3.335e-06 on 1 procs for 0 steps with 906 atoms 119.9% 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 | | 3.335e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11953.0 ave 11953 max 11953 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: 422296.0 ave 422296 max 422296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422296 Ave neighs/atom = 466.11038 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 7 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 6.369 | 6.369 | 6.369 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 -3199.6262 -3199.6262 38.352422 77.090234 3.6213517 230.28757 230.28757 162.31473 91.829118 436.71887 2.2775437 137.32089 Loop time of 3.524e-06 on 1 procs for 0 steps with 906 atoms 198.6% 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 | | 3.524e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11953.0 ave 11953 max 11953 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211148.0 ave 211148 max 211148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 422296.0 ave 422296 max 422296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422296 Ave neighs/atom = 466.11038 Neighbor list builds = 0 Dangerous builds = 0 906 -3199.62618288298 eV 2.27754373560624 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09