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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -37.406685 0.0000000) to (17.632332 37.406685 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7120699 4.5934522 4.0451344 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.406685 0.0000000) to (17.632332 37.406685 4.0451344) create_atoms CPU = 0.001 seconds 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7120699 4.5934522 4.0451344 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.406685 0.0000000) to (17.632332 37.406685 4.0451344) create_atoms CPU = 0.000 seconds 229 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 = 5 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 451 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 = 5 20 2 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) = 4.486 | 4.486 | 4.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1913.6986 0 -1913.6986 -6679.1355 188 0 -1974.3745 0 -1974.3745 -21450.871 Loop time of 1.23031 on 1 procs for 188 steps with 451 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1913.6985629538 -1974.37254768773 -1974.37445005855 Force two-norm initial, final = 26.963191 0.25373016 Force max component initial, final = 8.6715543 0.12582509 Final line search alpha, max atom move = 1.0000000 0.12582509 Iterations, force evaluations = 188 322 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1777 | 1.1777 | 1.1777 | 0.0 | 95.72 Neigh | 0.034682 | 0.034682 | 0.034682 | 0.0 | 2.82 Comm | 0.01056 | 0.01056 | 0.01056 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007364 | | | 0.60 Nlocal: 451.000 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4110.00 ave 4110 max 4110 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: 70898.0 ave 70898 max 70898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70898 Ave neighs/atom = 157.20177 Neighbor list builds = 8 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 = 5 20 2 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 : 188 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.486 | 4.486 Mbytes Step Temp E_pair E_mol TotEng Press Volume 188 0 -1974.3745 0 -1974.3745 -21450.871 5336.0752 200 0 -1974.9669 0 -1974.9669 -5783.2285 5293.3804 Loop time of 0.0514754 on 1 procs for 12 steps with 451 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 = -1974.37445005854 -1974.96530226677 -1974.96689206222 Force two-norm initial, final = 106.55202 1.2625095 Force max component initial, final = 105.87877 0.26551929 Final line search alpha, max atom move = 0.00028007597 7.4365572e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049294 | 0.049294 | 0.049294 | 0.0 | 95.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004238 | 0.0004238 | 0.0004238 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001758 | | | 3.41 Nlocal: 451.000 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4146.00 ave 4146 max 4146 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: 70564.0 ave 70564 max 70564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70564 Ave neighs/atom = 156.46120 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 = 5 20 2 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1974.9669 0 -1974.9669 -5783.2285 Loop time of 1.724e-06 on 1 procs for 0 steps with 451 atoms 174.0% 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 | | 1.724e-06 | | |100.00 Nlocal: 451.000 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4185.00 ave 4185 max 4185 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: 71292.0 ave 71292 max 71292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71292 Ave neighs/atom = 158.07539 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 = 5 20 2 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) = 4.625 | 4.625 | 4.625 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 -1974.9669 -1974.9669 17.428789 74.813371 4.059632 -5783.2285 -5783.2285 79.438452 -17375.301 -53.822841 2.3095658 2777.9716 Loop time of 1.335e-06 on 1 procs for 0 steps with 451 atoms 224.7% 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 | | 1.335e-06 | | |100.00 Nlocal: 451.000 ave 451 max 451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4185.00 ave 4185 max 4185 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35646.0 ave 35646 max 35646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71292.0 ave 71292 max 71292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71292 Ave neighs/atom = 158.07539 Neighbor list builds = 0 Dangerous builds = 0 451 -1974.96689206222 eV 2.30956576160404 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01