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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -63.821525 0.0000000) to (22.564316 63.821525 4.9836238) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0538410 5.4481789 4.9836238 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.821525 0.0000000) to (22.564316 63.821525 4.9836238) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0538410 5.4481789 4.9836238 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.821525 0.0000000) to (22.564316 63.821525 4.9836238) create_atoms CPU = 0.002 seconds 658 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 34 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1308 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5712.659 0 -5712.659 11215.176 40 0 -5786.3035 0 -5786.3035 -761.6262 Loop time of 0.707101 on 1 procs for 40 steps with 1308 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 = -5712.65904120837 -5786.29847409978 -5786.30353334651 Force two-norm initial, final = 123.52053 0.23147125 Force max component initial, final = 40.356251 0.033255882 Final line search alpha, max atom move = 1.0000000 0.033255882 Iterations, force evaluations = 40 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6711 | 0.6711 | 0.6711 | 0.0 | 94.91 Neigh | 0.027551 | 0.027551 | 0.027551 | 0.0 | 3.90 Comm | 0.0045958 | 0.0045958 | 0.0045958 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003859 | | | 0.55 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9175.00 ave 9175 max 9175 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: 229412.0 ave 229412 max 229412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229412 Ave neighs/atom = 175.39144 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -5786.3035 0 -5786.3035 -761.6262 14353.724 41 0 -5786.3079 0 -5786.3079 300.64105 14345.326 Loop time of 0.0351633 on 1 procs for 1 steps with 1308 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 = -5786.30353334651 -5786.30353334651 -5786.30786553025 Force two-norm initial, final = 17.391903 6.3851128 Force max component initial, final = 14.428374 6.1264293 Final line search alpha, max atom move = 6.9307880e-05 0.00042460983 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034296 | 0.034296 | 0.034296 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019891 | 0.00019891 | 0.00019891 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006687 | | | 1.90 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9175.00 ave 9175 max 9175 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: 229364.0 ave 229364 max 229364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229364 Ave neighs/atom = 175.35474 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.659 | 5.659 | 5.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5786.3079 0 -5786.3079 300.64105 Loop time of 1.733e-06 on 1 procs for 0 steps with 1308 atoms 115.4% 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 | | 1.733e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9175.00 ave 9175 max 9175 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: 229392.0 ave 229392 max 229392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229392 Ave neighs/atom = 175.37615 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.659 | 5.659 | 5.659 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 -5786.3079 -5786.3079 22.566344 127.60953 4.9815683 300.64105 300.64105 684.29976 198.24154 19.381851 2.2437034 296.53057 Loop time of 8.918e-06 on 1 procs for 0 steps with 1308 atoms 145.8% 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 | | 8.918e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9175.00 ave 9175 max 9175 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114696.0 ave 114696 max 114696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229392.0 ave 229392 max 229392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229392 Ave neighs/atom = 175.37615 Neighbor list builds = 0 Dangerous builds = 0 1308 -5786.30786553025 eV 2.2437034466957 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01