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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -42.179746 0.0000000) to (34.439618 42.179746 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2459803 4.0446331 4.6544275 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -42.179746 0.0000000) to (34.439618 42.179746 6.9816412) create_atoms CPU = 0.001 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2459803 4.0446331 4.6544275 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.179746 0.0000000) to (34.439618 42.179746 6.9816412) create_atoms CPU = 0.001 seconds 877 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1744 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5531.7958 0 -5531.7958 218751.89 82 0 -7446.825 0 -7446.825 -260.84273 Loop time of 13.6141 on 1 procs for 82 steps with 1744 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5531.79583045474 -7446.81801243492 -7446.82501247854 Force two-norm initial, final = 3493.9547 0.25008266 Force max component initial, final = 748.77891 0.042501047 Final line search alpha, max atom move = 1.0000000 0.042501047 Iterations, force evaluations = 82 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.549 | 13.549 | 13.549 | 0.0 | 99.52 Neigh | 0.04241 | 0.04241 | 0.04241 | 0.0 | 0.31 Comm | 0.0090925 | 0.0090925 | 0.0090925 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01363 | | | 0.10 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5432.00 ave 5432 max 5432 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: 114168.0 ave 114168 max 114168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114168 Ave neighs/atom = 65.463303 Neighbor list builds = 4 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -7446.825 0 -7446.825 -260.84273 20283.823 87 0 -7447.0537 0 -7447.0537 -10.463975 20280.646 Loop time of 0.821191 on 1 procs for 5 steps with 1744 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7446.82501247853 -7447.053553509 -7447.05368808987 Force two-norm initial, final = 95.077206 0.43276089 Force max component initial, final = 74.153839 0.16860505 Final line search alpha, max atom move = 0.00051824200 8.7378220e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81844 | 0.81844 | 0.81844 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038132 | 0.00038132 | 0.00038132 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002372 | | | 0.29 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5448.00 ave 5448 max 5448 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: 114306.0 ave 114306 max 114306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114306 Ave neighs/atom = 65.542431 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7447.0537 0 -7447.0537 -10.463975 Loop time of 2.382e-06 on 1 procs for 0 steps with 1744 atoms 167.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5448.00 ave 5448 max 5448 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: 114240.0 ave 114240 max 114240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114240 Ave neighs/atom = 65.504587 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.203 | 5.203 | 5.203 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 -7447.0537 -7447.0537 34.356756 84.68831 6.9702151 -10.463975 -10.463975 -7.9657783 -10.128102 -13.298045 2.2548038 1138.2765 Loop time of 2.482e-06 on 1 procs for 0 steps with 1744 atoms 241.7% 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 | | 2.482e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5448.00 ave 5448 max 5448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57120.0 ave 57120 max 57120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114240.0 ave 114240 max 114240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114240 Ave neighs/atom = 65.504587 Neighbor list builds = 0 Dangerous builds = 0 1744 -7447.05368808987 eV 2.25480383597512 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15