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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -39.159907 0.0000000) to (13.052096 39.159907 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0200367 5.0200367 3.6200000 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.159907 0.0000000) to (13.052096 39.159907 3.6200000) create_atoms CPU = 0.002 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0200367 5.0200367 3.6200000 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.159907 0.0000000) to (13.052096 39.159907 3.6200000) 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 27 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 8 atoms, new total = 308 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_313717476091_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 27 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) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1077.1863 0 -1077.1863 209.46118 20 0 -1083.2656 0 -1083.2656 -5293.733 Loop time of 0.681801 on 1 procs for 20 steps with 308 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 = -1077.18629768376 -1083.26514046175 -1083.26561033111 Force two-norm initial, final = 19.636851 0.72588061 Force max component initial, final = 7.2619121 0.28723597 Final line search alpha, max atom move = 0.20964385 0.060217254 Iterations, force evaluations = 20 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67602 | 0.67602 | 0.67602 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0031178 | 0.0031178 | 0.0031178 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002663 | | | 0.39 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2404.00 ave 2404 max 2404 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: 23660.0 ave 23660 max 23660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23660 Ave neighs/atom = 76.818182 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 ghost atom cutoff = 6 binsize = 3, bins = 5 27 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -1083.2656 0 -1083.2656 -5293.733 3700.5004 25 0 -1083.2948 0 -1083.2948 18.265219 3685.872 Loop time of 0.130276 on 1 procs for 5 steps with 308 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 = -1083.26561033111 -1083.2943994838 -1083.29475812653 Force two-norm initial, final = 18.607470 0.92989145 Force max component initial, final = 14.891363 0.51089239 Final line search alpha, max atom move = 0.00063427893 0.00032404828 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12757 | 0.12757 | 0.12757 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053401 | 0.00053401 | 0.00053401 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002175 | | | 1.67 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2412.00 ave 2412 max 2412 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: 23708.0 ave 23708 max 23708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23708 Ave neighs/atom = 76.974026 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 27 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) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1083.2948 0 -1083.2948 18.265219 Loop time of 7.658e-06 on 1 procs for 0 steps with 308 atoms 195.9% 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 | | 7.658e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2412.00 ave 2412 max 2412 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: 23716.0 ave 23716 max 23716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23716 Ave neighs/atom = 77.000000 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 27 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) = 4.562 | 4.562 | 4.562 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 -1083.2948 -1083.2948 13.050709 78.319813 3.606073 18.265219 18.265219 -97.981909 -68.442996 221.22056 2.33437 218.08091 Loop time of 9.071e-06 on 1 procs for 0 steps with 308 atoms 242.5% 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 | | 9.071e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2412.00 ave 2412 max 2412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11858.0 ave 11858 max 11858 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23716.0 ave 23716 max 23716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23716 Ave neighs/atom = 77.000000 Neighbor list builds = 0 Dangerous builds = 0 308 -1083.29475812653 eV 2.33437000038987 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01