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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -51.976532 0.0000000) to (36.752958 51.976532 5.1464435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7651699 4.5861645 5.1464435 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -51.976532 0.0000000) to (36.752958 51.976532 5.1464435) create_atoms CPU = 0.004 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7651699 4.5861645 5.1464435 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -51.976532 0.0000000) to (36.752958 51.976532 5.1464435) create_atoms CPU = 0.004 seconds 821 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 22 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1632 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_600021860456_005#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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.759 | 6.759 | 6.759 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4583.0294 0 -4583.0294 117732.12 141 0 -5338.1763 0 -5338.1763 5822.6776 Loop time of 14.9283 on 1 procs for 141 steps with 1632 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4583.02943863252 -5338.17108163488 -5338.17627053385 Force two-norm initial, final = 1152.2275 0.18610198 Force max component initial, final = 167.94832 0.017088913 Final line search alpha, max atom move = 1.0000000 0.017088913 Iterations, force evaluations = 141 237 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.623 | 14.623 | 14.623 | 0.0 | 97.96 Neigh | 0.18853 | 0.18853 | 0.18853 | 0.0 | 1.26 Comm | 0.068344 | 0.068344 | 0.068344 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04831 | | | 0.32 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12315.0 ave 12315 max 12315 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: 518280.0 ave 518280 max 518280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518280 Ave neighs/atom = 317.57353 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 141 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.763 | 6.763 | 6.763 Mbytes Step Temp E_pair E_mol TotEng Press Volume 141 0 -5338.1763 0 -5338.1763 5822.6776 19662.412 147 0 -5338.4207 0 -5338.4207 -5.4262334 19740.863 Loop time of 0.505929 on 1 procs for 6 steps with 1632 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5338.17627053386 -5338.41924115987 -5338.42068572376 Force two-norm initial, final = 132.07481 0.88038506 Force max component initial, final = 104.00072 0.59019918 Final line search alpha, max atom move = 0.00013001905 7.6737135e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49701 | 0.49701 | 0.49701 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022188 | 0.0022188 | 0.0022188 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006697 | | | 1.32 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12299.0 ave 12299 max 12299 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: 518060.0 ave 518060 max 518060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518060 Ave neighs/atom = 317.43873 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.901 | 6.901 | 6.901 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5338.4207 0 -5338.4207 -5.4262334 Loop time of 6.315e-06 on 1 procs for 0 steps with 1632 atoms 190.0% 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 | | 6.315e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 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: 517568.0 ave 517568 max 517568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517568 Ave neighs/atom = 317.13725 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.901 | 6.901 | 6.901 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 -5338.4207 -5338.4207 36.7031 104.48605 5.1476035 -5.4262334 -5.4262334 46.374164 -14.74126 -47.911604 2.3783221 1001.2064 Loop time of 6.805e-06 on 1 procs for 0 steps with 1632 atoms 249.8% 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 | | 6.805e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 258784.0 ave 258784 max 258784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 517568.0 ave 517568 max 517568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517568 Ave neighs/atom = 317.13725 Neighbor list builds = 0 Dangerous builds = 0 1632 -5338.42068572376 eV 2.37832209686943 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16