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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -56.062938 0.0000000) to (34.331398 56.062938 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5373222 5.4254456 5.8134559 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -56.062938 0.0000000) to (34.331398 56.062938 8.7201838) create_atoms CPU = 0.003 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5373222 5.4254456 5.8134559 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -56.062938 0.0000000) to (34.331398 56.062938 8.7201838) create_atoms CPU = 0.002 seconds 1494 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2964 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.974 | 6.974 | 6.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12668.43 0 -12668.43 23554.502 130 0 -13003.466 0 -13003.466 5505.0694 Loop time of 6.79712 on 1 procs for 130 steps with 2964 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12668.4298394074 -13003.4540423212 -13003.4655744794 Force two-norm initial, final = 446.25860 0.56428624 Force max component initial, final = 81.844004 0.067242146 Final line search alpha, max atom move = 0.98089361 0.065957391 Iterations, force evaluations = 130 249 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6167 | 6.6167 | 6.6167 | 0.0 | 97.35 Neigh | 0.10636 | 0.10636 | 0.10636 | 0.0 | 1.56 Comm | 0.032797 | 0.032797 | 0.032797 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04129 | | | 0.61 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10922.0 ave 10922 max 10922 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: 519048.0 ave 519048 max 519048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519048 Ave neighs/atom = 175.11741 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 130 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.973 | 6.973 | 6.973 Mbytes Step Temp E_pair E_mol TotEng Press Volume 130 0 -13003.466 0 -13003.466 5505.0694 33567.807 135 0 -13003.978 0 -13003.978 -5.8241482 33655.015 Loop time of 0.216497 on 1 procs for 5 steps with 2964 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 = -13003.4655744793 -13003.9722561259 -13003.9779314663 Force two-norm initial, final = 250.33331 3.3889452 Force max component initial, final = 179.95685 2.5812192 Final line search alpha, max atom move = 2.5339108e-05 6.5405791e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21107 | 0.21107 | 0.21107 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076766 | 0.00076766 | 0.00076766 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00466 | | | 2.15 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10901.0 ave 10901 max 10901 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: 519240.0 ave 519240 max 519240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519240 Ave neighs/atom = 175.18219 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.111 | 7.111 | 7.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13003.978 0 -13003.978 -5.8241482 Loop time of 2.628e-06 on 1 procs for 0 steps with 2964 atoms 152.2% 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 | | 2.628e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10896.0 ave 10896 max 10896 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: 518832.0 ave 518832 max 518832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518832 Ave neighs/atom = 175.04453 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.111 | 7.111 | 7.111 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 -13003.978 -13003.978 34.428735 112.45237 8.6928089 -5.8241482 -5.8241482 -123.2296 97.736573 8.0205778 2.3164777 941.04101 Loop time of 2.918e-06 on 1 procs for 0 steps with 2964 atoms 308.4% 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 | | 2.918e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10896.0 ave 10896 max 10896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259416.0 ave 259416 max 259416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 518832.0 ave 518832 max 518832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518832 Ave neighs/atom = 175.04453 Neighbor list builds = 0 Dangerous builds = 0 2964 -13003.9779314663 eV 2.31647766460939 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07