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 = 3.1501534 3.1501534 3.1501534 Created orthogonal box = (0.0000000 -33.634434 0.0000000) to (19.418850 33.634434 5.4562257) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1102236 4.7206223 5.4562257 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -33.634434 0.0000000) to (19.418850 33.634434 5.4562257) create_atoms CPU = 0.003 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1102236 4.7206223 5.4562257 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -33.634434 0.0000000) to (19.418850 33.634434 5.4562257) create_atoms CPU = 0.002 seconds 230 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 5 17 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 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 458 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_271256517527_005#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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 5 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2964.1078 0 -2964.1078 75189.266 65 0 -3094.2327 0 -3094.2327 25988.043 Loop time of 0.890568 on 1 procs for 65 steps with 458 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2964.10783452651 -3094.2299213728 -3094.23270481334 Force two-norm initial, final = 193.97957 0.22126425 Force max component initial, final = 56.546717 0.047652752 Final line search alpha, max atom move = 1.0000000 0.047652752 Iterations, force evaluations = 65 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87204 | 0.87204 | 0.87204 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010033 | 0.010033 | 0.010033 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008493 | | | 0.95 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3670.00 ave 3670 max 3670 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: 62848.0 ave 62848 max 62848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62848 Ave neighs/atom = 137.22271 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 5 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.482 | 4.482 | 4.482 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -3094.2327 0 -3094.2327 25988.043 7127.3805 73 0 -3094.9009 0 -3094.9009 -9.4185508 7198.8698 Loop time of 0.0851592 on 1 procs for 8 steps with 458 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3094.23270481334 -3094.90004242822 -3094.90087492152 Force two-norm initial, final = 205.43271 0.54661072 Force max component initial, final = 152.49676 0.11190854 Final line search alpha, max atom move = 0.00013690060 1.5320346e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.081194 | 0.081194 | 0.081194 | 0.0 | 95.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087877 | 0.00087877 | 0.00087877 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003087 | | | 3.62 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3733.00 ave 3733 max 3733 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: 64212.0 ave 64212 max 64212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64212 Ave neighs/atom = 140.20087 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 5 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3094.9009 0 -3094.9009 -9.4185508 Loop time of 6.114e-06 on 1 procs for 0 steps with 458 atoms 0.0% 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 | | 6.114e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3733.00 ave 3733 max 3733 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: 63540.0 ave 63540 max 63540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63540 Ave neighs/atom = 138.73362 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 5 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.620 | 4.620 | 4.620 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 -3094.9009 -3094.9009 19.440654 67.715868 5.4684344 -9.4185508 -9.4185508 8.6169834 -11.910603 -24.962032 2.4792086 403.30196 Loop time of 6.364e-06 on 1 procs for 0 steps with 458 atoms 235.7% 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 | | 6.364e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3733.00 ave 3733 max 3733 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31770.0 ave 31770 max 31770 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63540.0 ave 63540 max 63540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63540 Ave neighs/atom = 138.73362 Neighbor list builds = 0 Dangerous builds = 0 458 -3094.90043813868 eV 2.47920856135536 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01