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 = 4.0320827 4.0320827 4.0320827 Created orthogonal box = (0.0000000 -71.220781 0.0000000) to (41.119337 71.220781 6.9837722) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3260519 6.3916086 6.9837722 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -71.220781 0.0000000) to (41.119337 71.220781 6.9837722) create_atoms CPU = 0.007 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3260519 6.3916086 6.9837722 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.220781 0.0000000) to (41.119337 71.220781 6.9837722) create_atoms CPU = 0.008 seconds 1251 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 11 38 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 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2495 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_800509458712_002#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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.107 | 6.107 | 6.107 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8224.4189 0 -8224.4189 7514.4674 147 0 -8365.1806 0 -8365.1806 2450.7366 Loop time of 4.04812 on 1 procs for 147 steps with 2495 atoms 86.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8224.41893522033 -8365.17270291695 -8365.18061515266 Force two-norm initial, final = 59.666431 0.25093126 Force max component initial, final = 8.8281157 0.046564875 Final line search alpha, max atom move = 0.62293970 0.029007110 Iterations, force evaluations = 147 267 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8606 | 3.8606 | 3.8606 | 0.0 | 95.37 Neigh | 0.11196 | 0.11196 | 0.11196 | 0.0 | 2.77 Comm | 0.042299 | 0.042299 | 0.042299 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03327 | | | 0.82 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005.0 ave 10005 max 10005 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: 321664.0 ave 321664 max 321664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321664 Ave neighs/atom = 128.92345 Neighbor list builds = 4 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 147 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.107 | 6.107 | 6.107 Mbytes Step Temp E_pair E_mol TotEng Press Volume 147 0 -8365.1806 0 -8365.1806 2450.7366 40904.671 153 0 -8365.5258 0 -8365.5258 -74.245713 41030.673 Loop time of 0.110465 on 1 procs for 6 steps with 2495 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 = -8365.18061515266 -8365.52491319327 -8365.52579037833 Force two-norm initial, final = 144.71204 3.4364761 Force max component initial, final = 139.04414 2.3960412 Final line search alpha, max atom move = 0.00017764189 0.00042563729 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1059 | 0.1059 | 0.1059 | 0.0 | 95.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066049 | 0.00066049 | 0.00066049 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003903 | | | 3.53 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005.0 ave 10005 max 10005 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: 322180.0 ave 322180 max 322180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322180 Ave neighs/atom = 129.13026 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.245 | 6.245 | 6.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8365.5258 0 -8365.5258 -74.245713 Loop time of 2.362e-06 on 1 procs for 0 steps with 2495 atoms 211.7% 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 | | 2.362e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005.0 ave 10005 max 10005 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: 314970.0 ave 314970 max 314970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314970 Ave neighs/atom = 126.24048 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.245 | 6.245 | 6.245 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 -8365.5258 -8365.5258 41.101713 143.1934 6.9714918 -74.245713 -74.245713 -93.521148 -45.915014 -83.300976 2.5813726 1268.5387 Loop time of 2.526e-06 on 1 procs for 0 steps with 2495 atoms 237.5% 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 | | 2.526e-06 | | |100.00 Nlocal: 2495.00 ave 2495 max 2495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10005.0 ave 10005 max 10005 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157485.0 ave 157485 max 157485 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 314970.0 ave 314970 max 314970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314970 Ave neighs/atom = 126.24048 Neighbor list builds = 0 Dangerous builds = 0 2495 -8365.52579037833 eV 2.58137255869632 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04