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 = 2.8553247 2.8553247 2.8553247 Created orthogonal box = (0.0000000 -37.338215 0.0000000) to (17.601403 37.338215 4.0380389) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7055586 4.5853948 4.0380389 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -37.338215 0.0000000) to (17.601403 37.338215 4.0380389) create_atoms CPU = 0.002 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7055586 4.5853948 4.0380389 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.338215 0.0000000) to (17.601403 37.338215 4.0380389) create_atoms CPU = 0.002 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 452 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_769582363439_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1757.1921 0 -1757.1921 59283.141 61 0 -1851.7843 0 -1851.7843 -5639.8887 Loop time of 0.953024 on 1 procs for 61 steps with 452 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 = -1757.19213433202 -1851.78268096897 -1851.78432477232 Force two-norm initial, final = 327.09034 0.14244452 Force max component initial, final = 113.42699 0.034050884 Final line search alpha, max atom move = 1.0000000 0.034050884 Iterations, force evaluations = 61 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92099 | 0.92099 | 0.92099 | 0.0 | 96.64 Neigh | 0.010261 | 0.010261 | 0.010261 | 0.0 | 1.08 Comm | 0.012634 | 0.012634 | 0.012634 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009143 | | | 0.96 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4493.00 ave 4493 max 4493 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: 61750.0 ave 61750 max 61750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61750 Ave neighs/atom = 136.61504 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -1851.7843 0 -1851.7843 -5639.8887 5307.6385 64 0 -1851.8167 0 -1851.8167 -7.9227534 5290.1606 Loop time of 0.0482852 on 1 procs for 3 steps with 452 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 = -1851.78432477232 -1851.81623673731 -1851.8167391333 Force two-norm initial, final = 32.588633 0.74570625 Force max component initial, final = 21.649816 0.61881144 Final line search alpha, max atom move = 0.00053160568 0.00032896368 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04601 | 0.04601 | 0.04601 | 0.0 | 95.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056756 | 0.00056756 | 0.00056756 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001707 | | | 3.54 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4483.00 ave 4483 max 4483 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: 61680.0 ave 61680 max 61680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61680 Ave neighs/atom = 136.46018 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1851.8167 0 -1851.8167 -7.9227534 Loop time of 6.455e-06 on 1 procs for 0 steps with 452 atoms 154.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4498.00 ave 4498 max 4498 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: 61738.0 ave 61738 max 61738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61738 Ave neighs/atom = 136.58850 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.619 | 4.619 | 4.619 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 -1851.8167 -1851.8167 17.59191 74.548893 4.0338029 -7.9227534 -7.9227534 80.768836 82.679358 -187.21645 2.2457809 343.93322 Loop time of 6.666e-06 on 1 procs for 0 steps with 452 atoms 240.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4498.00 ave 4498 max 4498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30869.0 ave 30869 max 30869 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61738.0 ave 61738 max 61738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61738 Ave neighs/atom = 136.58850 Neighbor list builds = 0 Dangerous builds = 0 452 -1851.8167391333 eV 2.24578086817994 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01