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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -80.006262 0.0000000) to (48.993630 80.006262 9.8982079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6659300 5.7147330 6.5988053 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -80.006262 0.0000000) to (48.993630 80.006262 9.8982079) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6659300 5.7147330 6.5988053 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -80.006262 0.0000000) to (48.993630 80.006262 9.8982079) 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4708 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 13.63 | 13.63 | 13.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17948.028 0 -17948.028 15945.046 83 0 -18350.868 0 -18350.868 4884.6187 Loop time of 10.0147 on 1 procs for 83 steps with 4708 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -17948.0279960882 -18350.8526577596 -18350.8677561402 Force two-norm initial, final = 358.15287 0.33321750 Force max component initial, final = 58.488550 0.071885126 Final line search alpha, max atom move = 1.0000000 0.071885126 Iterations, force evaluations = 83 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7252 | 9.7252 | 9.7252 | 0.0 | 97.11 Neigh | 0.21327 | 0.21327 | 0.21327 | 0.0 | 2.13 Comm | 0.034487 | 0.034487 | 0.034487 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04172 | | | 0.42 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17642.0 ave 17642 max 17642 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: 1.16146e+06 ave 1.16146e+06 max 1.16146e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1161456 Ave neighs/atom = 246.69839 Neighbor list builds = 3 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.63 | 13.63 | 13.63 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -18350.868 0 -18350.868 4884.6187 77597.935 91 0 -18352.267 0 -18352.267 5.158148 78055.395 Loop time of 0.726919 on 1 procs for 8 steps with 4708 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 = -18350.8677561402 -18352.2648052257 -18352.2670903143 Force two-norm initial, final = 465.13376 0.87350380 Force max component initial, final = 413.01057 0.69781382 Final line search alpha, max atom move = 0.00010650402 7.4319976e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64993 | 0.64993 | 0.64993 | 0.0 | 89.41 Neigh | 0.066259 | 0.066259 | 0.066259 | 0.0 | 9.11 Comm | 0.0018158 | 0.0018158 | 0.0018158 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008916 | | | 1.23 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17600.0 ave 17600 max 17600 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: 1.16072e+06 ave 1.16072e+06 max 1.16072e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1160716 Ave neighs/atom = 246.54121 Neighbor list builds = 1 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 13.14 | 13.14 | 13.14 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18352.267 0 -18352.267 5.158148 Loop time of 2.547e-06 on 1 procs for 0 steps with 4708 atoms 196.3% 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 | | 2.547e-06 | | |100.00 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17600.0 ave 17600 max 17600 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: 1.16069e+06 ave 1.16069e+06 max 1.16069e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1160692 Ave neighs/atom = 246.53611 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 13.14 | 13.14 | 13.14 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 -18352.267 -18352.267 48.984462 161.18171 9.8861872 5.158148 5.158148 -1.2320344 2.4004444 14.306034 2.5197045 2304.1289 Loop time of 5.065e-06 on 1 procs for 0 steps with 4708 atoms 276.4% 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 | | 5.065e-06 | | |100.00 Nlocal: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17600.0 ave 17600 max 17600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 580346.0 ave 580346 max 580346 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.16069e+06 ave 1.16069e+06 max 1.16069e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1160692 Ave neighs/atom = 246.53611 Neighbor list builds = 0 Dangerous builds = 0 4708 -18352.2670903143 eV 2.51970446640862 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13