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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -43.680212 0.0000000) to (53.497116 43.680212 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1298604 5.3852316 5.9032704 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.680212 0.0000000) to (53.497116 43.680212 8.8549056) create_atoms CPU = 0.010 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1298604 5.3852316 5.9032704 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.680212 0.0000000) to (53.497116 43.680212 8.8549056) create_atoms CPU = 0.009 seconds 1756 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 15 24 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3480 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_346334655118_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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.607 | 6.607 | 6.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9797.4439 0 -9797.4439 151158.26 90 0 -12280.023 0 -12280.023 -4666.5449 Loop time of 7.57014 on 1 procs for 90 steps with 3480 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 = -9797.44392030983 -12280.0124067997 -12280.0231728392 Force two-norm initial, final = 3836.1608 0.32556651 Force max component initial, final = 744.15223 0.031516571 Final line search alpha, max atom move = 1.0000000 0.031516571 Iterations, force evaluations = 90 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2302 | 7.2302 | 7.2302 | 0.0 | 95.51 Neigh | 0.24362 | 0.24362 | 0.24362 | 0.0 | 3.22 Comm | 0.039868 | 0.039868 | 0.039868 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05647 | | | 0.75 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10668.0 ave 10668 max 10668 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: 490998.0 ave 490998 max 490998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490998 Ave neighs/atom = 141.09138 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.604 | 6.604 | 6.604 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -12280.023 0 -12280.023 -4666.5449 41383.674 94 0 -12280.307 0 -12280.307 70.548136 41241.78 Loop time of 0.342336 on 1 procs for 4 steps with 3480 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 = -12280.0231728392 -12280.3059393376 -12280.3066220523 Force two-norm initial, final = 219.17822 5.0330770 Force max component initial, final = 167.71867 4.8810810 Final line search alpha, max atom move = 0.00010082158 0.00049211832 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3336 | 0.3336 | 0.3336 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017091 | 0.0017091 | 0.0017091 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007022 | | | 2.05 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10480.0 ave 10480 max 10480 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: 489612.0 ave 489612 max 489612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489612 Ave neighs/atom = 140.69310 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.742 | 6.742 | 6.742 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12280.307 0 -12280.307 70.548136 Loop time of 6.465e-06 on 1 procs for 0 steps with 3480 atoms 185.6% 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 | | 6.465e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 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: 489984.0 ave 489984 max 489984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489984 Ave neighs/atom = 140.80000 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.742 | 6.742 | 6.742 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 -12280.307 -12280.307 53.446282 87.104017 8.8589392 70.548136 70.548136 189.44193 41.348372 -19.14589 2.3741747 1408.0456 Loop time of 6.445e-06 on 1 procs for 0 steps with 3480 atoms 279.3% 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 | | 6.445e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244992.0 ave 244992 max 244992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 489984.0 ave 489984 max 489984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489984 Ave neighs/atom = 140.80000 Neighbor list builds = 0 Dangerous builds = 0 3480 -12280.3059228899 eV 2.37417470698991 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09