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 = 2.6534432 2.6534432 2.6534432 Created orthogonal box = (0.0000000 -26.798463 0.0000000) to (18.949375 26.798463 3.7525354) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3440073 4.2036804 3.7525354 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -26.798463 0.0000000) to (18.949375 26.798463 3.7525354) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3440073 4.2036804 3.7525354 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -26.798463 0.0000000) to (18.949375 26.798463 3.7525354) create_atoms CPU = 0.000 seconds 206 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 15 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_201919462778_001#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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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 -2476.8191 0 -2476.8191 712806.89 66 0 -3377.2437 0 -3377.2437 84388.219 Loop time of 1.79921 on 1 procs for 66 steps with 408 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 = -2476.81912214673 -3377.24047185513 -3377.24368619845 Force two-norm initial, final = 3033.8574 0.37461263 Force max component initial, final = 870.52106 0.050182147 Final line search alpha, max atom move = 1.0000000 0.050182147 Iterations, force evaluations = 66 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7868 | 1.7868 | 1.7868 | 0.0 | 99.31 Neigh | 0.0041794 | 0.0041794 | 0.0041794 | 0.0 | 0.23 Comm | 0.0049145 | 0.0049145 | 0.0049145 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003328 | | | 0.18 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4289.00 ave 4289 max 4289 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: 73112.0 ave 73112 max 73112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73112 Ave neighs/atom = 179.19608 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -3377.2437 0 -3377.2437 84388.219 3811.1809 78 0 -3379.3743 0 -3379.3743 -653.22156 3859.5677 Loop time of 0.209709 on 1 procs for 12 steps with 408 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 = -3377.24368619846 -3379.3740032392 -3379.37429593115 Force two-norm initial, final = 405.89193 3.3524665 Force max component initial, final = 352.96212 2.0835416 Final line search alpha, max atom move = 0.00051679609 0.0010767661 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20691 | 0.20691 | 0.20691 | 0.0 | 98.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056657 | 0.00056657 | 0.00056657 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002232 | | | 1.06 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4741.00 ave 4741 max 4741 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: 73108.0 ave 73108 max 73108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73108 Ave neighs/atom = 179.18627 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3379.3743 0 -3379.3743 -653.22156 Loop time of 1.632e-06 on 1 procs for 0 steps with 408 atoms 122.5% 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 | | 1.632e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4741.00 ave 4741 max 4741 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: 72548.0 ave 72548 max 72548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72548 Ave neighs/atom = 177.81373 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.622 | 4.622 | 4.622 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 -3379.3743 -3379.3743 19.016341 54.169536 3.7467661 -653.22156 -653.22156 -867.97245 -675.42266 -416.26959 2.1309348 334.17393 Loop time of 1.584e-06 on 1 procs for 0 steps with 408 atoms 189.4% 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 | | 1.584e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4741.00 ave 4741 max 4741 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36274.0 ave 36274 max 36274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72548.0 ave 72548 max 72548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72548 Ave neighs/atom = 177.81373 Neighbor list builds = 0 Dangerous builds = 0 408 -3379.37429593115 eV 2.13093477633717 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02