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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -67.341566 0.0000000) to (38.879671 67.341566 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363449 5.1518138 6.0968189 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.341566 0.0000000) to (38.879671 67.341566 6.0968189) create_atoms CPU = 0.002 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363449 5.1518138 6.0968189 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.341566 0.0000000) to (38.879671 67.341566 6.0968189) create_atoms CPU = 0.002 seconds 1466 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12592.908 0 -12592.908 45235.549 68 0 -12999.355 0 -12999.355 5595.7225 Loop time of 3.67216 on 1 procs for 68 steps with 2930 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 = -12592.9083297721 -12999.3425256326 -12999.3550483738 Force two-norm initial, final = 510.20351 0.37235519 Force max component initial, final = 84.770499 0.067322097 Final line search alpha, max atom move = 0.74060890 0.049859344 Iterations, force evaluations = 68 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4427 | 3.4427 | 3.4427 | 0.0 | 93.75 Neigh | 0.1737 | 0.1737 | 0.1737 | 0.0 | 4.73 Comm | 0.035199 | 0.035199 | 0.035199 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02051 | | | 0.56 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14475.0 ave 14475 max 14475 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: 659212.0 ave 659212 max 659212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 659212 Ave neighs/atom = 224.98703 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -12999.355 0 -12999.355 5595.7225 31925.601 71 0 -12999.579 0 -12999.579 6.5309269 32025.27 Loop time of 0.182976 on 1 procs for 3 steps with 2930 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 = -12999.3550483738 -12999.5720362087 -12999.5790247216 Force two-norm initial, final = 204.72345 3.4199127 Force max component initial, final = 160.82694 2.5935972 Final line search alpha, max atom move = 4.4335096e-05 0.00011498738 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17905 | 0.17905 | 0.17905 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069113 | 0.00069113 | 0.00069113 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003232 | | | 1.77 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14475.0 ave 14475 max 14475 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: 659180.0 ave 659180 max 659180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 659180 Ave neighs/atom = 224.97611 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.81 | 10.81 | 10.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12999.579 0 -12999.579 6.5309269 Loop time of 1.797e-06 on 1 procs for 0 steps with 2930 atoms 166.9% 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 | | 1.797e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14475.0 ave 14475 max 14475 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: 658780.0 ave 658780 max 658780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658780 Ave neighs/atom = 224.83959 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.81 | 10.81 | 10.81 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 -12999.579 -12999.579 38.914496 134.97421 6.0972021 6.5309269 6.5309269 -129.87002 53.834617 95.628186 2.2104388 993.20391 Loop time of 2.264e-06 on 1 procs for 0 steps with 2930 atoms 220.8% 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 | | 2.264e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14475.0 ave 14475 max 14475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 329390.0 ave 329390 max 329390 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 658780.0 ave 658780 max 658780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658780 Ave neighs/atom = 224.83959 Neighbor list builds = 0 Dangerous builds = 0 2930 -12919.7912676696 eV 2.21043882446856 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04