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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -58.814712 0.0000000) to (29.405532 58.814712 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9763209 4.9763209 3.6473074 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.814712 0.0000000) to (29.405532 58.814712 3.6473074) create_atoms CPU = 0.002 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9763209 4.9763209 3.6473074 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.814712 0.0000000) to (29.405532 58.814712 3.6473074) create_atoms CPU = 0.002 seconds 522 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 1036 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4245.6757 0 -4245.6757 9738.6935 57 0 -4282.999 0 -4282.999 -655.30171 Loop time of 16.0313 on 1 procs for 57 steps with 1036 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4245.67571835821 -4282.99512808787 -4282.99902429417 Force two-norm initial, final = 42.829847 0.30127567 Force max component initial, final = 12.348470 0.057418305 Final line search alpha, max atom move = 1.0000000 0.057418305 Iterations, force evaluations = 57 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.007 | 16.007 | 16.007 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010941 | 0.010941 | 0.010941 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01335 | | | 0.08 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4338.00 ave 4338 max 4338 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: 55652.0 ave 55652 max 55652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55652 Ave neighs/atom = 53.718147 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -4282.999 0 -4282.999 -655.30171 12615.875 59 0 -4283.018 0 -4283.018 -1184.2936 12619.868 Loop time of 0.659717 on 1 procs for 2 steps with 1036 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 = -4282.99902429417 -4283.01406203631 -4283.01799772191 Force two-norm initial, final = 17.654482 7.5461119 Force max component initial, final = 14.524518 7.3956037 Final line search alpha, max atom move = 0.00010315293 0.00076287817 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65741 | 0.65741 | 0.65741 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047307 | 0.00047307 | 0.00047307 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001832 | | | 0.28 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4342.00 ave 4342 max 4342 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: 55656.0 ave 55656 max 55656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55656 Ave neighs/atom = 53.722008 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.484 | 5.484 | 5.484 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4283.018 0 -4283.018 -1184.2936 Loop time of 6.425e-06 on 1 procs for 0 steps with 1036 atoms 186.8% 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 | | 6.425e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4342.00 ave 4342 max 4342 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: 55656.0 ave 55656 max 55656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55656 Ave neighs/atom = 53.722008 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.484 | 5.484 | 5.484 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 -4283.018 -4283.018 29.371604 117.62942 3.6526762 -1184.2936 -1184.2936 -937.83794 -2428.4106 -186.63231 2.2787111 171.19739 Loop time of 6.997e-06 on 1 procs for 0 steps with 1036 atoms 271.5% 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 | | 6.997e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4342.00 ave 4342 max 4342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27828.0 ave 27828 max 27828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55656.0 ave 55656 max 55656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55656 Ave neighs/atom = 53.722008 Neighbor list builds = 0 Dangerous builds = 0 1036 -4283.01799772191 eV 2.278711086715 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17