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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -67.328052 0.0000000) to (38.871869 67.328052 6.0955954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7351938 5.1507799 6.0955954 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -67.328052 0.0000000) to (38.871869 67.328052 6.0955954) create_atoms CPU = 0.009 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7351938 5.1507799 6.0955954 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -67.328052 0.0000000) to (38.871869 67.328052 6.0955954) create_atoms CPU = 0.009 seconds 1465 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2924 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.993 | 6.993 | 6.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12375.329 0 -12375.329 54794.067 119 0 -12966.689 0 -12966.689 5924.4554 Loop time of 12.3222 on 1 procs for 119 steps with 2924 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 = -12375.3289317838 -12966.6788550428 -12966.6892197797 Force two-norm initial, final = 1578.3872 0.35173226 Force max component initial, final = 559.95432 0.030580952 Final line search alpha, max atom move = 1.0000000 0.030580952 Iterations, force evaluations = 119 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.061 | 12.061 | 12.061 | 0.0 | 97.88 Neigh | 0.12967 | 0.12967 | 0.12967 | 0.0 | 1.05 Comm | 0.067612 | 0.067612 | 0.067612 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06405 | | | 0.52 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12120.0 ave 12120 max 12120 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: 510384.0 ave 510384 max 510384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510384 Ave neighs/atom = 174.54993 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -12966.689 0 -12966.689 5924.4554 31906.385 124 0 -12967.079 0 -12967.079 -5.537674 32013.403 Loop time of 0.444763 on 1 procs for 5 steps with 2924 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 = -12966.6892197797 -12967.0775937464 -12967.0789274947 Force two-norm initial, final = 239.11571 1.4924502 Force max component initial, final = 219.30217 0.99181925 Final line search alpha, max atom move = 6.3598648e-05 6.3078363e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43441 | 0.43441 | 0.43441 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022589 | 0.0022589 | 0.0022589 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008098 | | | 1.82 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12153.0 ave 12153 max 12153 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: 510384.0 ave 510384 max 510384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510384 Ave neighs/atom = 174.54993 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.131 | 7.131 | 7.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12967.079 0 -12967.079 -5.537674 Loop time of 9.963e-06 on 1 procs for 0 steps with 2924 atoms 562.1% 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 | | 9.963e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12153.0 ave 12153 max 12153 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: 510122.0 ave 510122 max 510122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510122 Ave neighs/atom = 174.46033 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.131 | 7.131 | 7.131 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 -12967.079 -12967.079 38.857154 135.14532 6.0962088 -5.537674 -5.537674 -46.277776 -19.977871 49.642625 2.2001889 1035.8593 Loop time of 6.966e-06 on 1 procs for 0 steps with 2924 atoms 287.1% 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 | | 6.966e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12153.0 ave 12153 max 12153 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 255061.0 ave 255061 max 255061 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 510122.0 ave 510122 max 510122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510122 Ave neighs/atom = 174.46033 Neighbor list builds = 0 Dangerous builds = 0 2924 -12967.0789274947 eV 2.20018891129092 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14