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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -69.254680 0.0000000) to (39.984208 69.254680 6.2700241) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8993094 5.2981723 6.2700241 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.254680 0.0000000) to (39.984208 69.254680 6.2700241) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8993094 5.2981723 6.2700241 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.254680 0.0000000) to (39.984208 69.254680 6.2700241) create_atoms CPU = 0.008 seconds 1466 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 = 11 36 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 4 atoms, new total = 2926 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 = 11 36 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) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9657.1446 0 -9657.1446 45104.788 184 0 -10333.126 0 -10333.126 3644.8084 Loop time of 19.6341 on 1 procs for 184 steps with 2926 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 = -9657.14460936579 -10333.116102937 -10333.1257312307 Force two-norm initial, final = 1017.9378 0.37352303 Force max component initial, final = 330.21660 0.090510837 Final line search alpha, max atom move = 1.0000000 0.090510837 Iterations, force evaluations = 184 345 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.02 | 19.02 | 19.02 | 0.0 | 96.87 Neigh | 0.39938 | 0.39938 | 0.39938 | 0.0 | 2.03 Comm | 0.11114 | 0.11114 | 0.11114 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1032 | | | 0.53 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12175.0 ave 12175 max 12175 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: 510152.0 ave 510152 max 510152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510152 Ave neighs/atom = 174.35133 Neighbor list builds = 6 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 = 11 36 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 : 184 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 184 0 -10333.126 0 -10333.126 3644.8084 34724.567 188 0 -10333.32 0 -10333.32 -8.4557007 34818.283 Loop time of 0.389218 on 1 procs for 4 steps with 2926 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 = -10333.1257312305 -10333.3174363389 -10333.3200746807 Force two-norm initial, final = 153.32739 2.2595237 Force max component initial, final = 135.48608 1.5755470 Final line search alpha, max atom move = 4.6640710e-05 7.3484633e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38052 | 0.38052 | 0.38052 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019331 | 0.0019331 | 0.0019331 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006769 | | | 1.74 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12174.0 ave 12174 max 12174 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: 510500.0 ave 510500 max 510500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510500 Ave neighs/atom = 174.47027 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 = 11 36 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) = 7.132 | 7.132 | 7.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10333.32 0 -10333.32 -8.4557007 Loop time of 6.334e-06 on 1 procs for 0 steps with 2926 atoms 189.5% 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 | | 6.334e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12156.0 ave 12156 max 12156 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: 510236.0 ave 510236 max 510236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510236 Ave neighs/atom = 174.38004 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 = 11 36 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) = 7.132 | 7.132 | 7.132 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 -10333.32 -10333.32 39.972148 138.92208 6.2701594 -8.4557007 -8.4557007 -72.477526 -21.640069 68.750492 2.3312527 1078.053 Loop time of 7.047e-06 on 1 procs for 0 steps with 2926 atoms 241.2% 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 | | 7.047e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12156.0 ave 12156 max 12156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 255118.0 ave 255118 max 255118 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 510236.0 ave 510236 max 510236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510236 Ave neighs/atom = 174.38004 Neighbor list builds = 0 Dangerous builds = 0 2926 -10333.3200746807 eV 2.33125273434312 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21