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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.247506 0.0000000) to (35.721388 41.247506 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4115312 6.3457702 7.0055406 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -41.247506 0.0000000) to (35.721388 41.247506 7.0055406) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4115312 6.3457702 7.0055406 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.247506 0.0000000) to (35.721388 41.247506 7.0055406) create_atoms CPU = 0.001 seconds 629 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 26 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1250 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_353977746962_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3959.2503 0 -3959.2503 31834.202 152 0 -4179.7511 0 -4179.7511 7004.4405 Loop time of 12.9312 on 1 procs for 152 steps with 1250 atoms 95.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3959.25028226069 -4179.7470898847 -4179.75106530449 Force two-norm initial, final = 244.15498 0.15747196 Force max component initial, final = 63.849903 0.055522631 Final line search alpha, max atom move = 0.87806547 0.048752505 Iterations, force evaluations = 152 279 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.847 | 12.847 | 12.847 | 0.0 | 99.35 Neigh | 0.044986 | 0.044986 | 0.044986 | 0.0 | 0.35 Comm | 0.016928 | 0.016928 | 0.016928 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02203 | | | 0.17 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4681.00 ave 4681 max 4681 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: 95276.0 ave 95276 max 95276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95276 Ave neighs/atom = 76.220800 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 152 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press Volume 152 0 -4179.7511 0 -4179.7511 7004.4405 20644.182 163 0 -4180.4894 0 -4180.4894 23.866693 20824.698 Loop time of 0.5514 on 1 procs for 11 steps with 1250 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4179.7510653045 -4180.4880356753 -4180.48944040725 Force two-norm initial, final = 173.71694 0.69020224 Force max component initial, final = 151.24154 0.41021749 Final line search alpha, max atom move = 0.00027026391 0.00011086698 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54744 | 0.54744 | 0.54744 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054584 | 0.00054584 | 0.00054584 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003415 | | | 0.62 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4684.00 ave 4684 max 4684 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: 95344.0 ave 95344 max 95344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95344 Ave neighs/atom = 76.275200 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.770 | 4.770 | 4.770 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4180.4894 0 -4180.4894 23.866693 Loop time of 2.288e-06 on 1 procs for 0 steps with 1250 atoms 174.8% 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 | | 2.288e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4657.00 ave 4657 max 4657 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: 95120.0 ave 95120 max 95120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95120 Ave neighs/atom = 76.096000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.770 | 4.770 | 4.770 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 -4180.4894 -4180.4894 35.723606 83.359763 6.9930551 23.866693 23.866693 17.303677 22.792008 31.504393 2.5069114 1048.5947 Loop time of 2.174e-06 on 1 procs for 0 steps with 1250 atoms 276.0% 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 | | 2.174e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4657.00 ave 4657 max 4657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47560.0 ave 47560 max 47560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95120.0 ave 95120 max 95120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95120 Ave neighs/atom = 76.096000 Neighbor list builds = 0 Dangerous builds = 0 1250 -4180.48944040725 eV 2.50691136942934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14