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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -43.573833 0.0000000) to (21.784894 43.573833 4.0453532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2584227 5.2584227 4.0453532 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.573833 0.0000000) to (21.784894 43.573833 4.0453532) create_atoms CPU = 0.001 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2584227 5.2584227 4.0453532 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.573833 0.0000000) to (21.784894 43.573833 4.0453532) create_atoms CPU = 0.000 seconds 233 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 28 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 456 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1519.5179 0 -1519.5179 -1353.9499 60 0 -1525.4498 0 -1525.4498 -7350.9209 Loop time of 1.65684 on 1 procs for 60 steps with 456 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1519.51786002302 -1525.44829795045 -1525.44979559695 Force two-norm initial, final = 7.4200473 0.087631583 Force max component initial, final = 2.1173868 0.0095686830 Final line search alpha, max atom move = 1.0000000 0.0095686830 Iterations, force evaluations = 60 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6475 | 1.6475 | 1.6475 | 0.0 | 99.44 Neigh | 0.0024912 | 0.0024912 | 0.0024912 | 0.0 | 0.15 Comm | 0.0033503 | 0.0033503 | 0.0033503 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00345 | | | 0.21 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2844.00 ave 2844 max 2844 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: 24660.0 ave 24660 max 24660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24660 Ave neighs/atom = 54.078947 Neighbor list builds = 1 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1525.4498 0 -1525.4498 -7350.9209 7680.1139 67 0 -1525.6093 0 -1525.6093 -1048.1534 7611.6237 Loop time of 0.153782 on 1 procs for 7 steps with 456 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 = -1525.44979559695 -1525.60857500101 -1525.60934133632 Force two-norm initial, final = 48.002093 0.16120189 Force max component initial, final = 37.644836 0.032392123 Final line search alpha, max atom move = 0.00042314671 1.3706620e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1522 | 0.1522 | 0.1522 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026611 | 0.00026611 | 0.00026611 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001315 | | | 0.86 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2836.00 ave 2836 max 2836 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: 24656.0 ave 24656 max 24656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24656 Ave neighs/atom = 54.070175 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1525.6093 0 -1525.6093 -1048.1534 Loop time of 2.733e-06 on 1 procs for 0 steps with 456 atoms 146.4% 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 | | 2.733e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2836.00 ave 2836 max 2836 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: 24698.0 ave 24698 max 24698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24698 Ave neighs/atom = 54.162281 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.588 | 4.588 | 4.588 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 -1525.6093 -1525.6093 21.726013 87.147666 4.0201431 -1048.1534 -1048.1534 -2.2894848 -3144.7293 2.558696 2.5429192 368.98362 Loop time of 2.537e-06 on 1 procs for 0 steps with 456 atoms 197.1% 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 | | 2.537e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2836.00 ave 2836 max 2836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12349.0 ave 12349 max 12349 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24698.0 ave 24698 max 24698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24698 Ave neighs/atom = 54.162281 Neighbor list builds = 0 Dangerous builds = 0 456 -1525.60934133632 eV 2.54291922802885 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02