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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -59.574428 0.0000000) to (42.125482 59.574428 5.1464468) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2873854 5.7796087 5.1464468 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.574428 0.0000000) to (42.125482 59.574428 5.1464468) create_atoms CPU = 0.009 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2873854 5.7796087 5.1464468 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.574428 0.0000000) to (42.125482 59.574428 5.1464468) create_atoms CPU = 0.008 seconds 1080 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 = 9 25 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 8 atoms, new total = 2144 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 9 25 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) = 11.15 | 11.15 | 11.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5960.9727 0 -5960.9727 110884.87 122 0 -7021.4565 0 -7021.4565 4248.854 Loop time of 18.1905 on 1 procs for 122 steps with 2144 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 = -5960.97265679898 -7021.45031008107 -7021.45651124273 Force two-norm initial, final = 1553.1958 0.20095787 Force max component initial, final = 208.91116 0.011443500 Final line search alpha, max atom move = 1.0000000 0.011443500 Iterations, force evaluations = 122 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.897 | 17.897 | 17.897 | 0.0 | 98.39 Neigh | 0.16293 | 0.16293 | 0.16293 | 0.0 | 0.90 Comm | 0.077546 | 0.077546 | 0.077546 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05304 | | | 0.29 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15049.0 ave 15049 max 15049 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: 681648.0 ave 681648 max 681648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 681648 Ave neighs/atom = 317.93284 Neighbor list builds = 2 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 = 9 25 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 : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.15 | 11.15 | 11.15 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -7021.4565 0 -7021.4565 4248.854 25831.061 126 0 -7021.6226 0 -7021.6226 -2.5038266 25906.519 Loop time of 0.631247 on 1 procs for 4 steps with 2144 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 = -7021.45651124269 -7021.62208245185 -7021.62259913833 Force two-norm initial, final = 131.26115 0.24420758 Force max component initial, final = 99.986231 0.056717573 Final line search alpha, max atom move = 0.00025051195 1.4208430e-05 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62117 | 0.62117 | 0.62117 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002467 | 0.002467 | 0.002467 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007614 | | | 1.21 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14182.0 ave 14182 max 14182 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: 680176.0 ave 680176 max 680176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 680176 Ave neighs/atom = 317.24627 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 = 9 25 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) = 10.66 | 10.66 | 10.66 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7021.6226 0 -7021.6226 -2.5038266 Loop time of 6.224e-06 on 1 procs for 0 steps with 2144 atoms 192.8% 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 | | 6.224e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14182.0 ave 14182 max 14182 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: 679840.0 ave 679840 max 679840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 679840 Ave neighs/atom = 317.08955 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 = 9 25 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) = 10.66 | 10.66 | 10.66 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 -7021.6226 -7021.6226 42.212298 119.36895 5.1413678 -2.5038266 -2.5038266 -2.1978462 -3.5141512 -1.7994823 2.4276095 1094.3535 Loop time of 7.116e-06 on 1 procs for 0 steps with 2144 atoms 267.0% 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 | | 7.116e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14182.0 ave 14182 max 14182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 339920.0 ave 339920 max 339920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 679840.0 ave 679840 max 679840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 679840 Ave neighs/atom = 317.08955 Neighbor list builds = 0 Dangerous builds = 0 2144 -7021.62259913833 eV 2.4276095244667 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20