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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -44.354486 0.0000000) to (36.215286 44.354486 8.9609594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1736123 5.1294304 5.9739729 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.354486 0.0000000) to (36.215286 44.354486 8.9609594) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1736123 5.1294304 5.9739729 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.354486 0.0000000) to (36.215286 44.354486 8.9609594) create_atoms CPU = 0.001 seconds 1184 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 ghost atom cutoff = 8 binsize = 4, bins = 10 23 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2360 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.452 | 6.452 | 6.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6552.0121 0 -6552.0121 226947.45 636 0 -9558.8527 0 -9558.8527 -45662.23 Loop time of 24.2892 on 1 procs for 636 steps with 2360 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6552.01206892765 -9558.84332456203 -9558.85273666004 Force two-norm initial, final = 2729.1593 0.33178146 Force max component initial, final = 577.26037 0.067842533 Final line search alpha, max atom move = 1.0000000 0.067842533 Iterations, force evaluations = 636 1241 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.765 | 23.765 | 23.765 | 0.0 | 97.84 Neigh | 0.30061 | 0.30061 | 0.30061 | 0.0 | 1.24 Comm | 0.096504 | 0.096504 | 0.096504 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1269 | | | 0.52 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8718.00 ave 8718 max 8718 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: 397828.0 ave 397828 max 397828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 397828 Ave neighs/atom = 168.57119 Neighbor list builds = 12 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 ghost atom cutoff = 8 binsize = 4, bins = 10 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 636 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.450 | 6.450 | 6.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 636 0 -9558.8527 0 -9558.8527 -45662.23 28788.165 687 0 -9611.8406 0 -9611.8406 -9.5824718 28018.356 Loop time of 1.04656 on 1 procs for 51 steps with 2360 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 = -9558.85273666017 -9611.83258970136 -9611.84062442226 Force two-norm initial, final = 2024.3861 6.3941008 Force max component initial, final = 1782.5084 1.6460624 Final line search alpha, max atom move = 7.0527550e-05 0.00011609275 Iterations, force evaluations = 51 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94335 | 0.94335 | 0.94335 | 0.0 | 90.14 Neigh | 0.077072 | 0.077072 | 0.077072 | 0.0 | 7.36 Comm | 0.0040114 | 0.0040114 | 0.0040114 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02213 | | | 2.11 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8704.00 ave 8704 max 8704 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: 400404.0 ave 400404 max 400404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400404 Ave neighs/atom = 169.66271 Neighbor list builds = 3 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 ghost atom cutoff = 8 binsize = 4, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.586 | 6.586 | 6.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9611.8406 0 -9611.8406 -9.5824718 Loop time of 2.202e-06 on 1 procs for 0 steps with 2360 atoms 136.2% 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 | | 2.202e-06 | | |100.00 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8624.00 ave 8624 max 8624 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: 399700.0 ave 399700 max 399700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 399700 Ave neighs/atom = 169.36441 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 ghost atom cutoff = 8 binsize = 4, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.586 | 6.586 | 6.586 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 -9611.8406 -9611.8406 35.696263 84.590651 9.278922 -9.5824718 -9.5824718 -5.7165974 74.436054 -97.466872 2.2358425 3923.3443 Loop time of 2.107e-06 on 1 procs for 0 steps with 2360 atoms 237.3% 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 | | 2.107e-06 | | |100.00 Nlocal: 2360.00 ave 2360 max 2360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8624.00 ave 8624 max 8624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 199850.0 ave 199850 max 199850 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 399700.0 ave 399700 max 399700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 399700 Ave neighs/atom = 169.36441 Neighbor list builds = 0 Dangerous builds = 0 2360 -9611.84062442225 eV 2.23584252566676 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:25