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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -42.235043 0.0000000) to (14.931098 42.235043 4.9770328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9770328 5.8654894 4.9770328 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -42.235043 0.0000000) to (14.931098 42.235043 4.9770328) create_atoms CPU = 0.003 seconds 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9770328 5.8654894 4.9770328 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -42.235043 0.0000000) to (14.931098 42.235043 4.9770328) create_atoms CPU = 0.002 seconds 292 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 568 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.928 | 4.928 | 4.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2514.7308 0 -2514.7308 -2605.4244 25 0 -2516.4198 0 -2516.4198 -9079.5191 Loop time of 0.566656 on 1 procs for 25 steps with 568 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2514.73075469812 -2516.41867280668 -2516.41982844544 Force two-norm initial, final = 2.2480225 0.10871109 Force max component initial, final = 0.41666835 0.010066268 Final line search alpha, max atom move = 1.0000000 0.010066268 Iterations, force evaluations = 25 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55645 | 0.55645 | 0.55645 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058053 | 0.0058053 | 0.0058053 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004401 | | | 0.78 Nlocal: 568.000 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5165.00 ave 5165 max 5165 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: 98224.0 ave 98224 max 98224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98224 Ave neighs/atom = 172.92958 Neighbor list builds = 0 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -2516.4198 0 -2516.4198 -9079.5191 6277.1889 30 0 -2516.5019 0 -2516.5019 -2959.1828 6255.2912 Loop time of 0.0784678 on 1 procs for 5 steps with 568 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2516.41982844544 -2516.50161228546 -2516.50188489445 Force two-norm initial, final = 43.403435 0.53031849 Force max component initial, final = 41.160758 0.37373256 Final line search alpha, max atom move = 0.00070590315 0.00026381900 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075349 | 0.075349 | 0.075349 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076978 | 0.00076978 | 0.00076978 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002349 | | | 2.99 Nlocal: 568.000 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5229.00 ave 5229 max 5229 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: 98528.0 ave 98528 max 98528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98528 Ave neighs/atom = 173.46479 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.067 | 5.067 | 5.067 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2516.5019 0 -2516.5019 -2959.1828 Loop time of 5.994e-06 on 1 procs for 0 steps with 568 atoms 0.0% 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 | | 5.994e-06 | | |100.00 Nlocal: 568.000 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5229.00 ave 5229 max 5229 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: 98544.0 ave 98544 max 98544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98544 Ave neighs/atom = 173.49296 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.067 | 5.067 | 5.067 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 -2516.5019 -2516.5019 14.868557 84.470086 4.9805324 -2959.1828 -2959.1828 -95.323688 -8695.5283 -86.696338 2.3404074 322.60406 Loop time of 7.106e-06 on 1 procs for 0 steps with 568 atoms 225.2% 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 | | 7.106e-06 | | |100.00 Nlocal: 568.000 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5229.00 ave 5229 max 5229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49272.0 ave 49272 max 49272 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98544.0 ave 98544 max 98544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98544 Ave neighs/atom = 173.49296 Neighbor list builds = 0 Dangerous builds = 0 568 -2516.50188489445 eV 2.34040744039646 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01