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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -39.358467 0.0000000) to (19.279908 39.358467 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1413088 4.7225937 5.7481580 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.358467 0.0000000) to (19.279908 39.358467 8.6222370) create_atoms CPU = 0.001 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1413088 4.7225937 5.7481580 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.358467 0.0000000) to (19.279908 39.358467 8.6222370) create_atoms CPU = 0.001 seconds 612 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 19 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 1188 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5235.0353 0 -5235.0353 3045.4988 86 0 -5257.2378 0 -5257.2378 -858.5982 Loop time of 1.96894 on 1 procs for 86 steps with 1188 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 = -5235.03529289696 -5257.23397868618 -5257.2377643523 Force two-norm initial, final = 16.210184 0.18576787 Force max component initial, final = 2.8900672 0.011889527 Final line search alpha, max atom move = 1.0000000 0.011889527 Iterations, force evaluations = 86 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.937 | 1.937 | 1.937 | 0.0 | 98.38 Neigh | 0.015215 | 0.015215 | 0.015215 | 0.0 | 0.77 Comm | 0.0086071 | 0.0086071 | 0.0086071 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008094 | | | 0.41 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6885.00 ave 6885 max 6885 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: 266136.0 ave 266136 max 266136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266136 Ave neighs/atom = 224.02020 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.523 | 5.523 | 5.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -5257.2378 0 -5257.2378 -858.5982 13085.583 88 0 -5257.2564 0 -5257.2564 1791.296 13066.06 Loop time of 0.057528 on 1 procs for 2 steps with 1188 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 = -5257.2377643523 -5257.25633074446 -5257.2564037753 Force two-norm initial, final = 35.262919 0.20007790 Force max component initial, final = 25.031438 0.043406863 Final line search alpha, max atom move = 0.00091909966 3.9895233e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.056257 | 0.056257 | 0.056257 | 0.0 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024506 | 0.00024506 | 0.00024506 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001026 | | | 1.78 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6888.00 ave 6888 max 6888 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: 264576.0 ave 264576 max 264576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264576 Ave neighs/atom = 222.70707 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.661 | 5.661 | 5.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5257.2564 0 -5257.2564 1791.296 Loop time of 1.504e-06 on 1 procs for 0 steps with 1188 atoms 133.0% 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 | | 1.504e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6895.00 ave 6895 max 6895 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: 264576.0 ave 264576 max 264576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264576 Ave neighs/atom = 222.70707 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.661 | 5.661 | 5.661 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 -5257.2564 -5257.2564 19.264248 78.716935 8.6163711 1791.296 1791.296 -0.6655219 5379.8726 -5.3189825 2.2371483 901.34786 Loop time of 1.68e-06 on 1 procs for 0 steps with 1188 atoms 178.6% 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 | | 1.68e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6895.00 ave 6895 max 6895 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 132288.0 ave 132288 max 132288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 264576.0 ave 264576 max 264576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264576 Ave neighs/atom = 222.70707 Neighbor list builds = 0 Dangerous builds = 0 1188 -5224.86985849395 eV 2.23714834218007 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02