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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.269880 0.0000000) to (29.179987 41.269880 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499063 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.269880 0.0000000) to (29.179987 41.269880 4.4499063) create_atoms CPU = 0.003 seconds 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499063 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.269880 0.0000000) to (29.179987 41.269880 4.4499063) create_atoms CPU = 0.003 seconds 345 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 29 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 687 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4620.2326 0 -4620.2326 20255.468 23 0 -4656.1804 0 -4656.1804 3997.6886 Loop time of 1.46761 on 1 procs for 23 steps with 687 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 = -4620.23259980413 -4656.17635451273 -4656.18038996817 Force two-norm initial, final = 31.678591 0.20724707 Force max component initial, final = 7.2294494 0.031247972 Final line search alpha, max atom move = 1.0000000 0.031247972 Iterations, force evaluations = 23 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4609 | 1.4609 | 1.4609 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028642 | 0.0028642 | 0.0028642 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003828 | | | 0.26 Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3177.00 ave 3177 max 3177 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: 39536.0 ave 39536 max 39536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39536 Ave neighs/atom = 57.548763 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -4656.1804 0 -4656.1804 3997.6886 10717.64 25 0 -4656.2067 0 -4656.2067 48.342928 10733.568 Loop time of 0.193589 on 1 procs for 2 steps with 687 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 = -4656.18038996817 -4656.20500780943 -4656.20674784272 Force two-norm initial, final = 43.653401 0.20731477 Force max component initial, final = 37.645033 0.034502060 Final line search alpha, max atom move = 0.00017538446 6.0511251e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19194 | 0.19194 | 0.19194 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033632 | 0.00033632 | 0.00033632 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001315 | | | 0.68 Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3167.00 ave 3167 max 3167 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: 39570.0 ave 39570 max 39570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39570 Ave neighs/atom = 57.598253 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4656.2067 0 -4656.2067 48.342928 Loop time of 6.204e-06 on 1 procs for 0 steps with 687 atoms 177.3% 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 | | 6.204e-06 | | |100.00 Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3167.00 ave 3167 max 3167 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: 39570.0 ave 39570 max 39570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39570 Ave neighs/atom = 57.598253 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.637 | 4.637 | 4.637 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 -4656.2067 -4656.2067 29.217401 82.539761 4.4508128 48.342928 48.342928 0.3970822 144.75293 -0.12122437 2.4493625 473.27937 Loop time of 6.475e-06 on 1 procs for 0 steps with 687 atoms 278.0% 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 | | 6.475e-06 | | |100.00 Nlocal: 687.000 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3167.00 ave 3167 max 3167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19785.0 ave 19785 max 19785 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39570.0 ave 39570 max 39570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39570 Ave neighs/atom = 57.598253 Neighbor list builds = 0 Dangerous builds = 0 687 -4656.20674784272 eV 2.44936249576016 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02