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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -44.731577 0.0000000) to (22.365788 44.731577 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0331750 4.0331750 2.8636458 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -44.731577 0.0000000) to (22.365788 44.731577 2.8636458) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0331750 4.0331750 2.8636458 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.731577 0.0000000) to (22.365788 44.731577 2.8636458) create_atoms CPU = 0.001 seconds 245 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 1 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 489 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.483 | 4.483 | 4.483 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1994.9475 0 -1994.9475 51363.901 30 0 -2091.0958 0 -2091.0958 8066.1703 Loop time of 7.32236 on 1 procs for 30 steps with 489 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 = -1994.94749970082 -2091.09381770776 -2091.0957838285 Force two-norm initial, final = 205.90846 0.15410149 Force max component initial, final = 82.333508 0.027604821 Final line search alpha, max atom move = 1.0000000 0.027604821 Iterations, force evaluations = 30 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3115 | 7.3115 | 7.3115 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0060811 | 0.0060811 | 0.0060811 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004763 | | | 0.07 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4489.00 ave 4489 max 4489 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: 54826.0 ave 54826 max 54826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54826 Ave neighs/atom = 112.11861 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -2091.0958 0 -2091.0958 8066.1703 5729.9088 39 0 -2091.327 0 -2091.327 159.1936 5755.6778 Loop time of 1.43673 on 1 procs for 9 steps with 489 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2091.0957838285 -2091.32668584244 -2091.32702988312 Force two-norm initial, final = 65.913825 1.0213240 Force max component initial, final = 63.566202 0.67423723 Final line search alpha, max atom move = 0.00066562395 0.00044878845 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4318 | 1.4318 | 1.4318 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011231 | 0.0011231 | 0.0011231 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003789 | | | 0.26 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4731.00 ave 4731 max 4731 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: 54898.0 ave 54898 max 54898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54898 Ave neighs/atom = 112.26585 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2091.327 0 -2091.327 159.1936 Loop time of 6.725e-06 on 1 procs for 0 steps with 489 atoms 148.7% 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 | | 6.725e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4860.00 ave 4860 max 4860 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: 54832.0 ave 54832 max 54832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54832 Ave neighs/atom = 112.13088 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.624 | 4.624 | 4.624 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 -2091.327 -2091.327 22.402948 90.117026 2.8509162 159.1936 159.1936 164.15716 189.05547 124.36816 2.3177869 126.16856 Loop time of 7.026e-06 on 1 procs for 0 steps with 489 atoms 270.4% 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 | | 7.026e-06 | | |100.00 Nlocal: 489.000 ave 489 max 489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4860.00 ave 4860 max 4860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27416.0 ave 27416 max 27416 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54832.0 ave 54832 max 54832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54832 Ave neighs/atom = 112.13088 Neighbor list builds = 0 Dangerous builds = 0 489 -2091.32702988312 eV 2.3177869006167 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09