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 = 2.8510002 2.8510002 2.8510002 Created orthogonal box = (0.0000000 -37.822791 0.0000000) to (13.372376 37.822791 4.0319231) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8626822 4.2980444 4.0319231 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -37.822791 0.0000000) to (13.372376 37.822791 4.0319231) create_atoms CPU = 0.002 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8626822 4.2980444 4.0319231 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.822791 0.0000000) to (13.372376 37.822791 4.0319231) create_atoms CPU = 0.001 seconds 178 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 350 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.434 | 4.434 | 4.434 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1431.2189 0 -1431.2189 62747.063 62 0 -1494.1111 0 -1494.1111 -1776.7353 Loop time of 2.98044 on 1 procs for 62 steps with 350 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 = -1431.21887979794 -1494.10979475024 -1494.11113784927 Force two-norm initial, final = 250.86203 0.12016747 Force max component initial, final = 84.306737 0.035502530 Final line search alpha, max atom move = 1.0000000 0.035502530 Iterations, force evaluations = 62 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9634 | 2.9634 | 2.9634 | 0.0 | 99.43 Neigh | 0.0040362 | 0.0040362 | 0.0040362 | 0.0 | 0.14 Comm | 0.0070242 | 0.0070242 | 0.0070242 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006012 | | | 0.20 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2363.00 ave 2363 max 2363 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: 22548.0 ave 22548 max 22548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22548 Ave neighs/atom = 64.422857 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.434 | 4.434 | 4.434 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1494.1111 0 -1494.1111 -1776.7353 4078.5368 67 0 -1494.1612 0 -1494.1612 -9.5137313 4074.1395 Loop time of 0.208324 on 1 procs for 5 steps with 350 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 = -1494.11113784927 -1494.16122581256 -1494.16124334374 Force two-norm initial, final = 20.926315 0.39936907 Force max component initial, final = 12.646517 0.29048136 Final line search alpha, max atom move = 0.013831546 0.0040178063 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20646 | 0.20646 | 0.20646 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041589 | 0.00041589 | 0.00041589 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001449 | | | 0.70 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2295.00 ave 2295 max 2295 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: 22488.0 ave 22488 max 22488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22488 Ave neighs/atom = 64.251429 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.572 | 4.572 | 4.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1494.1612 0 -1494.1612 -9.5137313 Loop time of 6.064e-06 on 1 procs for 0 steps with 350 atoms 181.4% 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 | | 6.064e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2295.00 ave 2295 max 2295 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: 22480.0 ave 22480 max 22480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22480 Ave neighs/atom = 64.228571 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 ghost atom cutoff = 6 binsize = 3, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.572 | 4.572 | 4.572 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 -1494.1612 -1494.1612 13.343803 75.922301 4.0214892 -9.5137313 -9.5137313 -113.98922 4.6145323 80.833491 2.2600783 272.18562 Loop time of 7.968e-06 on 1 procs for 0 steps with 350 atoms 225.9% 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 | | 7.968e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2295.00 ave 2295 max 2295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11240.0 ave 11240 max 11240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22480.0 ave 22480 max 22480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22480 Ave neighs/atom = 64.228571 Neighbor list builds = 0 Dangerous builds = 0 350 -1494.16124334374 eV 2.26007834896872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03