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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -38.654645 0.0000000) to (27.330402 38.654645 5.1194533) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2742880 6.1027934 5.1194533 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.654645 0.0000000) to (27.330402 38.654645 5.1194533) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2742880 6.1027934 5.1194533 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.654645 0.0000000) to (27.330402 38.654645 5.1194533) create_atoms CPU = 0.001 seconds 458 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 = 8 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 906 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 = 8 20 2 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) = 4.990 | 4.990 | 4.990 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3164.4553 0 -3164.4553 8161.778 41 0 -3194.7907 0 -3194.7907 -1852.5676 Loop time of 0.660798 on 1 procs for 41 steps with 906 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 = -3164.45529928386 -3194.78820320406 -3194.79074240123 Force two-norm initial, final = 34.198676 0.17615800 Force max component initial, final = 7.6784155 0.041314549 Final line search alpha, max atom move = 1.0000000 0.041314549 Iterations, force evaluations = 41 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64344 | 0.64344 | 0.64344 | 0.0 | 97.37 Neigh | 0.0090771 | 0.0090771 | 0.0090771 | 0.0 | 1.37 Comm | 0.0046501 | 0.0046501 | 0.0046501 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003636 | | | 0.55 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5950.00 ave 5950 max 5950 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: 156836.0 ave 156836 max 156836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156836 Ave neighs/atom = 173.10817 Neighbor list builds = 1 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 = 8 20 2 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.990 | 4.990 | 4.990 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3194.7907 0 -3194.7907 -1852.5676 10816.862 43 0 -3194.7962 0 -3194.7962 -502.3098 10806.001 Loop time of 0.0437058 on 1 procs for 2 steps with 906 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 = -3194.79074240123 -3194.79622004742 -3194.79623049181 Force two-norm initial, final = 15.308585 0.22025641 Force max component initial, final = 11.608242 0.098014297 Final line search alpha, max atom move = 0.0056842053 0.00055713338 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042377 | 0.042377 | 0.042377 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026209 | 0.00026209 | 0.00026209 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001067 | | | 2.44 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5958.00 ave 5958 max 5958 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: 157008.0 ave 157008 max 157008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157008 Ave neighs/atom = 173.29801 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 = 8 20 2 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) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3194.7962 0 -3194.7962 -502.3098 Loop time of 2.174e-06 on 1 procs for 0 steps with 906 atoms 138.0% 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 | | 2.174e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5958.00 ave 5958 max 5958 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: 157016.0 ave 157016 max 157016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157016 Ave neighs/atom = 173.30684 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 = 8 20 2 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) = 5.128 | 5.128 | 5.128 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 -3194.7962 -3194.7962 27.318809 77.309289 5.1164833 -502.3098 -502.3098 -14.52615 -1505.4696 13.066351 2.3327404 684.15743 Loop time of 1.0171e-05 on 1 procs for 0 steps with 906 atoms 137.6% 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 | | 1.017e-05 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5958.00 ave 5958 max 5958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78508.0 ave 78508 max 78508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157016.0 ave 157016 max 157016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157016 Ave neighs/atom = 173.30684 Neighbor list builds = 0 Dangerous builds = 0 906 -3194.79623049181 eV 2.33274041729669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01