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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -29.942192 0.0000000) to (36.671546 29.942192 6.9929895) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6672877 4.3552279 4.6619930 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -29.942192 0.0000000) to (36.671546 29.942192 6.9929895) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6672877 4.3552279 4.6619930 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -29.942192 0.0000000) to (36.671546 29.942192 6.9929895) create_atoms CPU = 0.001 seconds 662 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1318 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2997.4171 0 -2997.4171 357186.7 77 0 -5250.6706 0 -5250.6706 5455.5138 Loop time of 1.17014 on 1 procs for 77 steps with 1318 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2997.41710192275 -5250.66583096449 -5250.67057351159 Force two-norm initial, final = 3458.9510 0.28823862 Force max component initial, final = 444.29984 0.10094154 Final line search alpha, max atom move = 1.0000000 0.10094154 Iterations, force evaluations = 77 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1324 | 1.1324 | 1.1324 | 0.0 | 96.78 Neigh | 0.022093 | 0.022093 | 0.022093 | 0.0 | 1.89 Comm | 0.0071113 | 0.0071113 | 0.0071113 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008508 | | | 0.73 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5907.00 ave 5907 max 5907 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: 180726.0 ave 180726 max 180726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180726 Ave neighs/atom = 137.12140 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -5250.6706 0 -5250.6706 5455.5138 15356.975 82 0 -5250.936 0 -5250.936 -79.629952 15407.284 Loop time of 0.0663388 on 1 procs for 5 steps with 1318 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 = -5250.67057351159 -5250.93539221896 -5250.93604979988 Force two-norm initial, final = 120.63185 2.5703294 Force max component initial, final = 97.401780 1.9253924 Final line search alpha, max atom move = 0.00015234457 0.00029332307 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06402 | 0.06402 | 0.06402 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034251 | 0.00034251 | 0.00034251 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001976 | | | 2.98 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5912.00 ave 5912 max 5912 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: 180358.0 ave 180358 max 180358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180358 Ave neighs/atom = 136.84219 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.206 | 5.206 | 5.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5250.936 0 -5250.936 -79.629952 Loop time of 1.989e-06 on 1 procs for 0 steps with 1318 atoms 150.8% 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 | | 1.989e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5909.00 ave 5909 max 5909 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: 180114.0 ave 180114 max 180114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180114 Ave neighs/atom = 136.65706 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.206 | 5.206 | 5.206 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 -5250.936 -5250.936 36.740045 60.111193 6.9763949 -79.629952 -79.629952 -140.2457 101.0989 -199.74306 2.2486692 1444.6245 Loop time of 1.803e-06 on 1 procs for 0 steps with 1318 atoms 221.9% 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 | | 1.803e-06 | | |100.00 Nlocal: 1318.00 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5909.00 ave 5909 max 5909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90057.0 ave 90057 max 90057 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180114.0 ave 180114 max 180114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180114 Ave neighs/atom = 136.65706 Neighbor list builds = 0 Dangerous builds = 0 1318 -5064.54234948223 eV 2.24866917193093 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01