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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -39.001407 0.0000000) to (7.9604023 39.001407 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7762414 5.1997130 5.8134559 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.001407 0.0000000) to (7.9604023 39.001407 8.7201838) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7762414 5.1997130 5.8134559 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.001407 0.0000000) to (7.9604023 39.001407 8.7201838) create_atoms CPU = 0.001 seconds 242 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 = 3 20 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 12 atoms, new total = 472 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 = 3 20 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) = 4.557 | 4.557 | 4.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2051.9082 0 -2051.9082 -13903.715 59 0 -2065.251 0 -2065.251 -15814.599 Loop time of 0.481503 on 1 procs for 59 steps with 472 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 = -2051.908186338 -2065.24900276173 -2065.25096096867 Force two-norm initial, final = 18.313401 0.21506953 Force max component initial, final = 5.7765279 0.057368033 Final line search alpha, max atom move = 1.0000000 0.057368033 Iterations, force evaluations = 59 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47579 | 0.47579 | 0.47579 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033581 | 0.0033581 | 0.0033581 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002354 | | | 0.49 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4196.00 ave 4196 max 4196 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: 81648.0 ave 81648 max 81648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81648 Ave neighs/atom = 172.98305 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 = 3 20 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -2065.251 0 -2065.251 -15814.599 5414.6567 64 0 -2065.5295 0 -2065.5295 793.92411 5368.3493 Loop time of 0.0304279 on 1 procs for 5 steps with 472 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 = -2065.25096096867 -2065.52792857371 -2065.52950007095 Force two-norm initial, final = 88.797616 0.60010879 Force max component initial, final = 63.231825 0.24847790 Final line search alpha, max atom move = 0.00019315939 4.7995840e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029404 | 0.029404 | 0.029404 | 0.0 | 96.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020276 | 0.00020276 | 0.00020276 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008206 | | | 2.70 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4055.00 ave 4055 max 4055 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: 82204.0 ave 82204 max 82204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82204 Ave neighs/atom = 174.16102 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 = 3 20 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) = 4.694 | 4.694 | 4.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2065.5295 0 -2065.5295 793.92411 Loop time of 1.469e-06 on 1 procs for 0 steps with 472 atoms 136.1% 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 | | 1.469e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4064.00 ave 4064 max 4064 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: 82360.0 ave 82360 max 82360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82360 Ave neighs/atom = 174.49153 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 = 3 20 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) = 4.694 | 4.694 | 4.694 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 -2065.5295 -2065.5295 7.9262024 78.002815 8.6829107 793.92411 793.92411 49.997051 2405.6162 -73.840913 2.2833263 275.18211 Loop time of 1.564e-06 on 1 procs for 0 steps with 472 atoms 127.9% 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 | | 1.564e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4064.00 ave 4064 max 4064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41180.0 ave 41180 max 41180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82360.0 ave 82360 max 82360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82360 Ave neighs/atom = 174.49153 Neighbor list builds = 0 Dangerous builds = 0 472 -2065.52950007095 eV 2.28332634102989 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00