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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -40.721945 0.0000000) to (28.794763 40.721945 5.7022129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0814288 6.3877561 5.7022129 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.721945 0.0000000) to (28.794763 40.721945 5.7022129) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0814288 6.3877561 5.7022129 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.721945 0.0000000) to (28.794763 40.721945 5.7022129) create_atoms CPU = 0.001 seconds 410 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 = 8 22 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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 = 8 22 2 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) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2651.1302 0 -2651.1302 6531.8763 64 0 -2719.4888 0 -2719.4888 1834.7388 Loop time of 0.802677 on 1 procs for 64 steps with 812 atoms 63.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2651.13020526632 -2719.48637027837 -2719.48877658621 Force two-norm initial, final = 37.223622 0.13447610 Force max component initial, final = 8.2332803 0.035987248 Final line search alpha, max atom move = 1.0000000 0.035987248 Iterations, force evaluations = 64 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7719 | 0.7719 | 0.7719 | 0.0 | 96.17 Neigh | 0.019625 | 0.019625 | 0.019625 | 0.0 | 2.44 Comm | 0.004458 | 0.004458 | 0.004458 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006692 | | | 0.83 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4484.00 ave 4484 max 4484 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: 105668.0 ave 105668 max 105668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105668 Ave neighs/atom = 130.13300 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 = 8 22 2 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -2719.4888 0 -2719.4888 1834.7388 13372.588 71 0 -2719.6297 0 -2719.6297 27.683434 13402.192 Loop time of 0.0628737 on 1 procs for 7 steps with 812 atoms 72.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2719.48877658621 -2719.62969567167 -2719.62972409412 Force two-norm initial, final = 47.320570 0.56716271 Force max component initial, final = 45.766964 0.45088317 Final line search alpha, max atom move = 0.0012996284 0.00058598058 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061009 | 0.061009 | 0.061009 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032861 | 0.00032861 | 0.00032861 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001537 | | | 2.44 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4362.00 ave 4362 max 4362 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: 105864.0 ave 105864 max 105864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105864 Ave neighs/atom = 130.37438 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 = 8 22 2 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) = 5.077 | 5.077 | 5.077 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2719.6297 0 -2719.6297 27.683434 Loop time of 1.582e-06 on 1 procs for 0 steps with 812 atoms 126.4% 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 | | 1.582e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4348.00 ave 4348 max 4348 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: 105688.0 ave 105688 max 105688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105688 Ave neighs/atom = 130.15764 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 = 8 22 2 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) = 5.077 | 5.077 | 5.077 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 -2719.6297 -2719.6297 28.776612 81.916759 5.6854313 27.683434 27.683434 0.50570713 28.802011 53.742583 2.6158936 667.30912 Loop time of 1.949e-06 on 1 procs for 0 steps with 812 atoms 256.5% 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 | | 1.949e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4348.00 ave 4348 max 4348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52844.0 ave 52844 max 52844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105688.0 ave 105688 max 105688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105688 Ave neighs/atom = 130.15764 Neighbor list builds = 0 Dangerous builds = 0 812 -2719.62972409412 eV 2.61589360731132 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01