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 = 2.8147787 2.8147787 2.8147787 Created orthogonal box = (0.0000000 -40.983797 0.0000000) to (20.491898 40.983797 2.8147787) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.4797563 3.4797563 2.8147787 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -40.983797 0.0000000) to (20.491898 40.983797 2.8147787) create_atoms CPU = 0.001 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.4797563 3.4797563 2.8147787 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -40.983797 0.0000000) to (20.491898 40.983797 2.8147787) create_atoms CPU = 0.001 seconds 213 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1628.2245 0 -1628.2245 89394.39 37 0 -1743.7562 0 -1743.7562 9076.8964 Loop time of 0.247733 on 1 procs for 37 steps with 425 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1628.22446382496 -1743.754429923 -1743.75616931322 Force two-norm initial, final = 267.79981 0.18957282 Force max component initial, final = 118.27913 0.064593931 Final line search alpha, max atom move = 1.0000000 0.064593931 Iterations, force evaluations = 37 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24294 | 0.24294 | 0.24294 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028095 | 0.0028095 | 0.0028095 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001986 | | | 0.80 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4801.00 ave 4801 max 4801 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: 71198.0 ave 71198 max 71198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71198 Ave neighs/atom = 167.52471 Neighbor list builds = 0 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -1743.7562 0 -1743.7562 9076.8964 4727.9039 43 0 -1743.8557 0 -1743.8557 27.992146 4751.4976 Loop time of 0.0327387 on 1 procs for 6 steps with 425 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1743.75616931322 -1743.85516246038 -1743.85568603445 Force two-norm initial, final = 48.655785 0.74268759 Force max component initial, final = 38.228144 0.51526678 Final line search alpha, max atom move = 0.00023183425 0.00011945649 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031203 | 0.031203 | 0.031203 | 0.0 | 95.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031546 | 0.00031546 | 0.00031546 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00122 | | | 3.73 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4789.00 ave 4789 max 4789 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: 70704.0 ave 70704 max 70704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70704 Ave neighs/atom = 166.36235 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1743.8557 0 -1743.8557 27.992146 Loop time of 1.636e-06 on 1 procs for 0 steps with 425 atoms 122.2% 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 | | 1.636e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4789.00 ave 4789 max 4789 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: 70654.0 ave 70654 max 70654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70654 Ave neighs/atom = 166.24471 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.615 | 4.615 | 4.615 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 -1743.8557 -1743.8557 20.516934 82.377745 2.8113061 27.992146 27.992146 173.95714 -64.229266 -25.751439 2.2445762 271.31202 Loop time of 1.743e-06 on 1 procs for 0 steps with 425 atoms 114.7% 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 | | 1.743e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4789.00 ave 4789 max 4789 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35327.0 ave 35327 max 35327 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70654.0 ave 70654 max 70654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70654 Ave neighs/atom = 166.24471 Neighbor list builds = 0 Dangerous builds = 0 425 -1743.85568603445 eV 2.24457622443984 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01