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 -69.692460 0.0000000) to (42.677741 69.692460 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355211 4.9780328 5.7481372 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -69.692460 0.0000000) to (42.677741 69.692460 8.6222058) create_atoms CPU = 0.004 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355211 4.9780328 5.7481372 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.692460 0.0000000) to (42.677741 69.692460 8.6222058) create_atoms CPU = 0.003 seconds 2357 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 = 11 36 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 4692 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 = 11 36 3 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) = 12.34 | 12.34 | 12.34 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20394.428 0 -20394.428 16387.554 113 0 -20805.388 0 -20805.388 3332.6854 Loop time of 8.31631 on 1 procs for 113 steps with 4692 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 = -20394.4278599076 -20805.3685390543 -20805.3879388025 Force two-norm initial, final = 473.63397 0.58475533 Force max component initial, final = 63.729380 0.065499199 Final line search alpha, max atom move = 1.0000000 0.065499199 Iterations, force evaluations = 113 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.1164 | 8.1164 | 8.1164 | 0.0 | 97.60 Neigh | 0.11595 | 0.11595 | 0.11595 | 0.0 | 1.39 Comm | 0.035212 | 0.035212 | 0.035212 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04877 | | | 0.59 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15382.0 ave 15382 max 15382 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: 827108.0 ave 827108 max 827108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 827108 Ave neighs/atom = 176.28048 Neighbor list builds = 2 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 = 11 36 3 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 : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.34 | 12.34 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -20805.388 0 -20805.388 3332.6854 51290.342 116 0 -20805.646 0 -20805.646 451.06724 51370.647 Loop time of 0.194026 on 1 procs for 3 steps with 4692 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 = -20805.3879388027 -20805.6332253279 -20805.6455778528 Force two-norm initial, final = 232.24799 29.766251 Force max component initial, final = 214.48396 27.144011 Final line search alpha, max atom move = 3.2426886e-05 0.00088019575 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19001 | 0.19001 | 0.19001 | 0.0 | 97.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059488 | 0.00059488 | 0.00059488 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003421 | | | 1.76 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15148.0 ave 15148 max 15148 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: 826308.0 ave 826308 max 826308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 826308 Ave neighs/atom = 176.10997 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 = 11 36 3 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) = 11.85 | 11.85 | 11.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20805.646 0 -20805.646 451.06724 Loop time of 2.122e-06 on 1 procs for 0 steps with 4692 atoms 188.5% 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 | | 2.122e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15169.0 ave 15169 max 15169 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: 825840.0 ave 825840 max 825840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825840 Ave neighs/atom = 176.01023 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 = 11 36 3 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) = 11.85 | 11.85 | 11.85 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 -20805.646 -20805.646 42.679643 139.692 8.6163382 451.06724 451.06724 159.63937 848.4477 345.11465 2.2375203 1737.7668 Loop time of 2.505e-06 on 1 procs for 0 steps with 4692 atoms 279.4% 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 | | 2.505e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15169.0 ave 15169 max 15169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 412920.0 ave 412920 max 412920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 825840.0 ave 825840 max 825840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825840 Ave neighs/atom = 176.01023 Neighbor list builds = 0 Dangerous builds = 0 4692 -20805.6455778528 eV 2.23752025418738 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09