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 = 3.6284422 3.6284422 3.6284422 Created orthogonal box = (0.0000000 -69.416186 0.0000000) to (40.077454 69.416186 6.2846462) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9130669 5.3105279 6.2846462 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.416186 0.0000000) to (40.077454 69.416186 6.2846462) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9130669 5.3105279 6.2846462 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.416186 0.0000000) to (40.077454 69.416186 6.2846462) create_atoms CPU = 0.003 seconds 1465 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 11 37 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2924 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.604 | 6.604 | 6.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11126.854 0 -11126.854 82268.029 758 0 -12397.425 0 -12397.425 -17697.421 Loop time of 32.8062 on 1 procs for 758 steps with 2924 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 = -11126.8539494179 -12397.413831376 -12397.4248018545 Force two-norm initial, final = 1849.2185 0.38507686 Force max component initial, final = 421.40053 0.11739069 Final line search alpha, max atom move = 1.0000000 0.11739069 Iterations, force evaluations = 758 1461 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.766 | 31.766 | 31.766 | 0.0 | 96.83 Neigh | 0.58433 | 0.58433 | 0.58433 | 0.0 | 1.78 Comm | 0.23489 | 0.23489 | 0.23489 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2209 | | | 0.67 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12255.0 ave 12255 max 12255 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: 456748.0 ave 456748 max 456748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 456748 Ave neighs/atom = 156.20657 Neighbor list builds = 19 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 758 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.606 | 6.606 | 6.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 758 0 -12397.425 0 -12397.425 -17697.421 34968.073 775 0 -12406.044 0 -12406.044 -2.6276276 34576.985 Loop time of 0.465631 on 1 procs for 17 steps with 2924 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 = -12397.4248018542 -12406.0437385419 -12406.0441110828 Force two-norm initial, final = 937.73086 3.0717075 Force max component initial, final = 742.81843 1.5484353 Final line search alpha, max atom move = 0.00036574018 0.00056632500 Iterations, force evaluations = 17 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42007 | 0.42007 | 0.42007 | 0.0 | 90.22 Neigh | 0.030241 | 0.030241 | 0.030241 | 0.0 | 6.49 Comm | 0.0024197 | 0.0024197 | 0.0024197 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0129 | | | 2.77 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12237.0 ave 12237 max 12237 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: 461720.0 ave 461720 max 461720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461720 Ave neighs/atom = 157.90698 Neighbor list builds = 1 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.743 | 6.743 | 6.743 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12406.044 0 -12406.044 -2.6276276 Loop time of 2.464e-06 on 1 procs for 0 steps with 2924 atoms 162.3% 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 | | 2.464e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 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: 463436.0 ave 463436 max 463436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463436 Ave neighs/atom = 158.49384 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 6.743 | 6.743 | 6.743 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 -12406.044 -12406.044 39.731185 136.87099 6.3583467 -2.6276276 -2.6276276 31.510101 33.197497 -72.59048 2.2670615 8466.0359 Loop time of 2.705e-06 on 1 procs for 0 steps with 2924 atoms 295.7% 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 | | 2.705e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 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: 231718.0 ave 231718 max 231718 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463436.0 ave 463436 max 463436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463436 Ave neighs/atom = 158.49384 Neighbor list builds = 0 Dangerous builds = 0 2924 -12406.0441110828 eV 2.26706145111999 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33