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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -54.563483 0.0000000) to (38.579654 54.563483 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0915243 5.2645489 5.1100000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.563483 0.0000000) to (38.579654 54.563483 5.1100000) create_atoms CPU = 0.006 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0915243 5.2645489 5.1100000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.563483 0.0000000) to (38.579654 54.563483 5.1100000) create_atoms CPU = 0.005 seconds 916 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1808 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_353393547686_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6354.9976 0 -6354.9976 1925.7682 27 0 -6384.2885 0 -6384.2885 -8102.6951 Loop time of 5.32498 on 1 procs for 27 steps with 1808 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6354.99756194115 -6384.28300446829 -6384.28851856275 Force two-norm initial, final = 35.509728 0.21138346 Force max component initial, final = 8.5237751 0.024639250 Final line search alpha, max atom move = 1.0000000 0.024639250 Iterations, force evaluations = 27 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3059 | 5.3059 | 5.3059 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0094336 | 0.0094336 | 0.0094336 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009619 | | | 0.18 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8305.00 ave 8305 max 8305 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: 155224.0 ave 155224 max 155224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155224 Ave neighs/atom = 85.853982 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -6384.2885 0 -6384.2885 -8102.6951 21513.512 31 0 -6384.4905 0 -6384.4905 -2105.023 21420.852 Loop time of 0.783023 on 1 procs for 4 steps with 1808 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 = -6384.28851856275 -6384.4899240213 -6384.49049564995 Force two-norm initial, final = 128.09917 0.25869058 Force max component initial, final = 101.95555 0.034038188 Final line search alpha, max atom move = 0.00022772623 7.7513880e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77712 | 0.77712 | 0.77712 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012958 | 0.0012958 | 0.0012958 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004603 | | | 0.59 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8329.00 ave 8329 max 8329 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: 155816.0 ave 155816 max 155816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155816 Ave neighs/atom = 86.181416 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.311 | 5.311 | 5.311 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6384.4905 0 -6384.4905 -2105.023 Loop time of 6.455e-06 on 1 procs for 0 steps with 1808 atoms 185.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8329.00 ave 8329 max 8329 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: 155912.0 ave 155912 max 155912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155912 Ave neighs/atom = 86.234513 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.311 | 5.311 | 5.311 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 -6384.4905 -6384.4905 38.520451 109.12697 5.0958108 -2105.023 -2105.023 -2.5419856 -6310.9823 -1.5445838 2.3701953 594.62818 Loop time of 6.947e-06 on 1 procs for 0 steps with 1808 atoms 259.1% 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 | | 6.947e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8329.00 ave 8329 max 8329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77956.0 ave 77956 max 77956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 155912.0 ave 155912 max 155912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155912 Ave neighs/atom = 86.234513 Neighbor list builds = 0 Dangerous builds = 0 1808 -6384.49049564995 eV 2.37019526010676 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07