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 -43.397484 0.0000000) to (15.343328 43.397484 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6528049 4.5681562 4.9780328 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.397484 0.0000000) to (15.343328 43.397484 4.9780328) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6528049 4.5681562 4.9780328 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.397484 0.0000000) to (15.343328 43.397484 4.9780328) create_atoms CPU = 0.001 seconds 306 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 = 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 608 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_657255834688_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 = 4 23 2 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) = 4.938 | 4.938 | 4.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2477.4195 0 -2477.4195 73508.613 78 0 -2693.4182 0 -2693.4182 8965.0473 Loop time of 0.887908 on 1 procs for 78 steps with 608 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 = -2477.41953796641 -2693.41584304917 -2693.41824703062 Force two-norm initial, final = 514.06496 0.21074835 Force max component initial, final = 147.37759 0.044419761 Final line search alpha, max atom move = 0.79275608 0.035214036 Iterations, force evaluations = 78 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86712 | 0.86712 | 0.86712 | 0.0 | 97.66 Neigh | 0.0076714 | 0.0076714 | 0.0076714 | 0.0 | 0.86 Comm | 0.0076424 | 0.0076424 | 0.0076424 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005475 | | | 0.62 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5650.00 ave 5650 max 5650 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: 107804.0 ave 107804 max 107804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107804 Ave neighs/atom = 177.30921 Neighbor list builds = 1 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 = 4 23 2 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -2693.4182 0 -2693.4182 8965.0473 6629.3639 83 0 -2693.5258 0 -2693.5258 17.081271 6660.9679 Loop time of 0.0505596 on 1 procs for 5 steps with 608 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2693.41824703061 -2693.52517860516 -2693.52577734653 Force two-norm initial, final = 65.816850 0.69357380 Force max component initial, final = 48.002158 0.56184746 Final line search alpha, max atom move = 0.00019623301 0.00011025302 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048325 | 0.048325 | 0.048325 | 0.0 | 95.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040015 | 0.00040015 | 0.00040015 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001834 | | | 3.63 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636.00 ave 5636 max 5636 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: 107692.0 ave 107692 max 107692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107692 Ave neighs/atom = 177.12500 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 = 4 23 2 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) = 5.079 | 5.079 | 5.079 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2693.5258 0 -2693.5258 17.081271 Loop time of 2.028e-06 on 1 procs for 0 steps with 608 atoms 147.9% 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 | | 2.028e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5618.00 ave 5618 max 5618 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: 107388.0 ave 107388 max 107388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107388 Ave neighs/atom = 176.62500 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 = 4 23 2 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) = 5.079 | 5.079 | 5.079 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 -2693.5258 -2693.5258 15.345235 87.126443 4.9821156 17.081271 17.081271 135.15915 -16.492937 -67.422395 2.3622502 281.15836 Loop time of 2.384e-06 on 1 procs for 0 steps with 608 atoms 209.7% 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 | | 2.384e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5618.00 ave 5618 max 5618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53694.0 ave 53694 max 53694 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107388.0 ave 107388 max 107388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107388 Ave neighs/atom = 176.62500 Neighbor list builds = 0 Dangerous builds = 0 608 -2693.52577734653 eV 2.36225015715106 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01