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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -47.978107 0.0000000) to (33.925645 47.978107 5.1736123) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3117478 6.1367346 5.1736123 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -47.978107 0.0000000) to (33.925645 47.978107 5.1736123) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3117478 6.1367346 5.1736123 Created 696 atoms using lattice units in orthogonal box = (0.0000000 -47.978107 0.0000000) to (33.925645 47.978107 5.1736123) create_atoms CPU = 0.002 seconds 696 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1376 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_942420706858_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4794.6604 0 -4794.6604 90169.235 369 0 -5589.9428 0 -5589.9428 -71083.04 Loop time of 9.02934 on 1 procs for 369 steps with 1376 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 = -4794.66043170338 -5589.93790856122 -5589.94281654963 Force two-norm initial, final = 673.21077 0.24558095 Force max component initial, final = 107.76321 0.021373273 Final line search alpha, max atom move = 1.0000000 0.021373273 Iterations, force evaluations = 369 685 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7579 | 8.7579 | 8.7579 | 0.0 | 96.99 Neigh | 0.14891 | 0.14891 | 0.14891 | 0.0 | 1.65 Comm | 0.068523 | 0.068523 | 0.068523 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05405 | | | 0.60 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8273.00 ave 8273 max 8273 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: 235704.0 ave 235704 max 235704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235704 Ave neighs/atom = 171.29651 Neighbor list builds = 10 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 369 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 369 0 -5589.9428 0 -5589.9428 -71083.04 16842.055 394 0 -5609.6315 0 -5609.6315 53.282437 16076.71 Loop time of 0.337941 on 1 procs for 25 steps with 1376 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 = -5589.94281654962 -5609.63078272281 -5609.63149870671 Force two-norm initial, final = 1317.0597 4.5479868 Force max component initial, final = 871.49508 2.5495066 Final line search alpha, max atom move = 0.00090722807 0.0023129839 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31348 | 0.31348 | 0.31348 | 0.0 | 92.76 Neigh | 0.013895 | 0.013895 | 0.013895 | 0.0 | 4.11 Comm | 0.0019151 | 0.0019151 | 0.0019151 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008647 | | | 2.56 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8442.00 ave 8442 max 8442 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: 239888.0 ave 239888 max 239888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239888 Ave neighs/atom = 174.33721 Neighbor list builds = 1 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.634 | 5.634 | 5.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5609.6315 0 -5609.6315 53.282437 Loop time of 1.771e-06 on 1 procs for 0 steps with 1376 atoms 169.4% 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 | | 1.771e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8554.00 ave 8554 max 8554 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: 242176.0 ave 242176 max 242176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242176 Ave neighs/atom = 176.00000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.634 | 5.634 | 5.634 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 -5609.6315 -5609.6315 33.849975 93.994306 5.05286 53.282437 53.282437 -243.93124 155.62945 248.14911 2.3366539 2026.1024 Loop time of 2.08e-06 on 1 procs for 0 steps with 1376 atoms 240.4% 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 | | 2.08e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8554.00 ave 8554 max 8554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 121088.0 ave 121088 max 121088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 242176.0 ave 242176 max 242176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242176 Ave neighs/atom = 176.00000 Neighbor list builds = 0 Dangerous builds = 0 1376 -5609.63149870671 eV 2.33665387041714 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09