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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -37.914442 0.0000000) to (46.435518 37.914442 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9099750 5.5148279 5.9032705 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -37.914442 0.0000000) to (46.435518 37.914442 8.8549058) create_atoms CPU = 0.008 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9099750 5.5148279 5.9032705 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.914442 0.0000000) to (46.435518 37.914442 8.8549058) create_atoms CPU = 0.007 seconds 1323 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2616 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.456 | 6.456 | 6.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8991.5916 0 -8991.5916 5677.4926 66 0 -9219.945 0 -9219.945 -6501.7534 Loop time of 4.52135 on 1 procs for 66 steps with 2616 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 = -8991.59164800798 -9219.93670637205 -9219.94499873747 Force two-norm initial, final = 85.661957 0.26949945 Force max component initial, final = 9.8995609 0.035693253 Final line search alpha, max atom move = 1.0000000 0.035693253 Iterations, force evaluations = 66 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3454 | 4.3454 | 4.3454 | 0.0 | 96.11 Neigh | 0.11938 | 0.11938 | 0.11938 | 0.0 | 2.64 Comm | 0.02428 | 0.02428 | 0.02428 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03232 | | | 0.71 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8827.00 ave 8827 max 8827 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: 428156.0 ave 428156 max 428156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428156 Ave neighs/atom = 163.66820 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.456 | 6.456 | 6.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -9219.945 0 -9219.945 -6501.7534 31179.482 71 0 -9220.4304 0 -9220.4304 248.6164 31023.894 Loop time of 0.26812 on 1 procs for 5 steps with 2616 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 = -9219.94499873745 -9220.42705915933 -9220.43037138735 Force two-norm initial, final = 238.80346 10.319763 Force max component initial, final = 186.06306 9.7610467 Final line search alpha, max atom move = 8.3174939e-05 0.00081187446 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26095 | 0.26095 | 0.26095 | 0.0 | 97.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013555 | 0.0013555 | 0.0013555 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005814 | | | 2.17 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8863.00 ave 8863 max 8863 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: 424708.0 ave 424708 max 424708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 424708 Ave neighs/atom = 162.35015 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.594 | 6.594 | 6.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9220.4304 0 -9220.4304 248.6164 Loop time of 6.535e-06 on 1 procs for 0 steps with 2616 atoms 198.9% 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 | | 6.535e-06 | | |100.00 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8869.00 ave 8869 max 8869 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: 432838.0 ave 432838 max 432838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432838 Ave neighs/atom = 165.45795 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.594 | 6.594 | 6.594 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 -9220.4304 -9220.4304 46.259835 75.651468 8.864921 248.6164 248.6164 134.30671 106.8796 504.66288 2.3577224 2023.301 Loop time of 6.475e-06 on 1 procs for 0 steps with 2616 atoms 293.4% 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 | | 6.475e-06 | | |100.00 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8869.00 ave 8869 max 8869 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 216419.0 ave 216419 max 216419 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 432838.0 ave 432838 max 432838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432838 Ave neighs/atom = 165.45795 Neighbor list builds = 0 Dangerous builds = 0 2616 -9220.43037138735 eV 2.35772241198834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05