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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -38.054298 0.0000000) to (12.684766 38.054298 3.5181211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8787562 4.8787562 3.5181211 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -38.054298 0.0000000) to (12.684766 38.054298 3.5181211) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8787562 4.8787562 3.5181211 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.054298 0.0000000) to (12.684766 38.054298 3.5181211) create_atoms CPU = 0.001 seconds 158 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 16 1 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_306032198193_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 4.878 | 4.878 | 4.878 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1308.1655 0 -1308.1655 75935.184 48 0 -1361.9033 0 -1361.9033 9563.9459 Loop time of 1.36168 on 1 procs for 48 steps with 312 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 = -1308.16553474654 -1361.90231983852 -1361.9032739193 Force two-norm initial, final = 163.27975 0.084728571 Force max component initial, final = 50.184565 0.013974556 Final line search alpha, max atom move = 1.0000000 0.013974556 Iterations, force evaluations = 48 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3424 | 1.3424 | 1.3424 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012422 | 0.012422 | 0.012422 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006909 | | | 0.51 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6025.00 ave 6025 max 6025 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: 100652.0 ave 100652 max 100652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100652 Ave neighs/atom = 322.60256 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.878 | 4.878 | 4.878 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -1361.9033 0 -1361.9033 9563.9459 3396.4636 55 0 -1362.0056 0 -1362.0056 -244.31593 3415.9375 Loop time of 0.153876 on 1 procs for 7 steps with 312 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 = -1361.9032739193 -1362.00527012063 -1362.00563043604 Force two-norm initial, final = 40.195961 1.2517631 Force max component initial, final = 35.921525 0.86782907 Final line search alpha, max atom move = 0.00056191364 0.00048764500 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14908 | 0.14908 | 0.14908 | 0.0 | 96.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012628 | 0.0012628 | 0.0012628 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003535 | | | 2.30 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6123.00 ave 6123 max 6123 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: 102920.0 ave 102920 max 102920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102920 Ave neighs/atom = 329.87179 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1362.0056 0 -1362.0056 -244.31593 Loop time of 6.415e-06 on 1 procs for 0 steps with 312 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6123.00 ave 6123 max 6123 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: 101176.0 ave 101176 max 101176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101176 Ave neighs/atom = 324.28205 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.016 | 5.016 | 5.016 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 -1362.0056 -1362.0056 12.686505 76.566658 3.5166425 -244.31593 -244.31593 82.872702 -409.48748 -406.33303 2.196509 142.06113 Loop time of 7.457e-06 on 1 procs for 0 steps with 312 atoms 201.2% 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 | | 7.457e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6123.00 ave 6123 max 6123 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50588.0 ave 50588 max 50588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101176.0 ave 101176 max 101176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101176 Ave neighs/atom = 324.28205 Neighbor list builds = 0 Dangerous builds = 0 312 -1362.00563043604 eV 2.19650904625822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02