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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -60.560383 0.0000000) to (30.280192 60.560383 3.5200008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9103013 4.9103013 3.5200008 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -60.560383 0.0000000) to (30.280192 60.560383 3.5200008) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9103013 4.9103013 3.5200008 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.560383 0.0000000) to (30.280192 60.560383 3.5200008) create_atoms CPU = 0.001 seconds 594 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 32 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5191.0329 0 -5191.0329 8521.0938 65 0 -5260.8889 0 -5260.8889 9608.0769 Loop time of 1.35379 on 1 procs for 65 steps with 1186 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5191.03285172135 -5260.88452018292 -5260.88890558397 Force two-norm initial, final = 57.662046 0.34187600 Force max component initial, final = 14.642173 0.11352278 Final line search alpha, max atom move = 1.0000000 0.11352278 Iterations, force evaluations = 65 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3334 | 1.3334 | 1.3334 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011828 | 0.011828 | 0.011828 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008596 | | | 0.63 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10025.0 ave 10025 max 10025 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: 209444.0 ave 209444 max 209444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209444 Ave neighs/atom = 176.59696 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -5260.8889 0 -5260.8889 9608.0769 12909.814 71 0 -5261.3322 0 -5261.3322 103.69071 12973.018 Loop time of 0.0954866 on 1 procs for 6 steps with 1186 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 = -5260.88890558397 -5261.33184782349 -5261.33217490554 Force two-norm initial, final = 168.93718 1.7899878 Force max component initial, final = 148.49394 1.6175621 Final line search alpha, max atom move = 0.00028880694 0.00046716316 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091877 | 0.091877 | 0.091877 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061127 | 0.00061127 | 0.00061127 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002999 | | | 3.14 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9946.00 ave 9946 max 9946 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: 209812.0 ave 209812 max 209812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209812 Ave neighs/atom = 176.90725 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.609 | 5.609 | 5.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5261.3322 0 -5261.3322 103.69071 Loop time of 2.428e-06 on 1 procs for 0 steps with 1186 atoms 164.7% 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 | | 2.428e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9964.00 ave 9964 max 9964 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: 209372.0 ave 209372 max 209372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209372 Ave neighs/atom = 176.53626 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.609 | 5.609 | 5.609 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 -5261.3322 -5261.3322 30.219132 121.72674 3.5267365 103.69071 103.69071 53.56225 57.357592 200.15229 2.2500774 304.09983 Loop time of 3.107e-06 on 1 procs for 0 steps with 1186 atoms 225.3% 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 | | 3.107e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9964.00 ave 9964 max 9964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104686.0 ave 104686 max 104686 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 209372.0 ave 209372 max 209372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209372 Ave neighs/atom = 176.53626 Neighbor list builds = 0 Dangerous builds = 0 1186 -5261.33217490554 eV 2.25007737043231 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01