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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -49.775709 0.0000000) to (13.546247 49.775709 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8055343 5.5302320 5.9120667 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -49.775709 0.0000000) to (13.546247 49.775709 8.8681001) create_atoms CPU = 0.001 seconds 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8055343 5.5302320 5.9120667 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -49.775709 0.0000000) to (13.546247 49.775709 8.8681001) create_atoms CPU = 0.001 seconds 508 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 34 3 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 16 atoms, new total = 1000 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_390178379548_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 34 3 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) = 4.566 | 4.566 | 4.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3494.2893 0 -3494.2893 8936.8011 60 0 -3527.7556 0 -3527.7556 -4984.1579 Loop time of 1.76589 on 1 procs for 60 steps with 1000 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 = -3494.28926909602 -3527.75302829528 -3527.75561313595 Force two-norm initial, final = 51.349950 0.13259871 Force max component initial, final = 11.792002 0.020370203 Final line search alpha, max atom move = 1.0000000 0.020370203 Iterations, force evaluations = 60 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7566 | 1.7566 | 1.7566 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043363 | 0.0043363 | 0.0043363 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004935 | | | 0.28 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4128.00 ave 4128 max 4128 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: 77256.0 ave 77256 max 77256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77256 Ave neighs/atom = 77.256000 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 34 3 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3527.7556 0 -3527.7556 -4984.1579 11959.059 63 0 -3527.8129 0 -3527.8129 -809.96731 11923.772 Loop time of 0.0912912 on 1 procs for 3 steps with 1000 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 = -3527.75561313594 -3527.8120469354 -3527.81291688428 Force two-norm initial, final = 51.036543 0.15337905 Force max component initial, final = 42.546497 0.025466450 Final line search alpha, max atom move = 0.00027474949 6.9968942e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09018 | 0.09018 | 0.09018 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019376 | 0.00019376 | 0.00019376 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009171 | | | 1.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3866.00 ave 3866 max 3866 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: 77272.0 ave 77272 max 77272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77272 Ave neighs/atom = 77.272000 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 34 3 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) = 4.702 | 4.702 | 4.702 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3527.8129 0 -3527.8129 -809.96731 Loop time of 1.937e-06 on 1 procs for 0 steps with 1000 atoms 154.9% 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 | | 1.937e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3874.00 ave 3874 max 3874 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: 77280.0 ave 77280 max 77280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77280 Ave neighs/atom = 77.280000 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 34 3 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) = 4.702 | 4.702 | 4.702 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 -3527.8129 -3527.8129 13.535607 99.551417 8.8488836 -809.96731 -809.96731 -0.68471032 -2430.2558 1.0386136 2.3338134 445.53687 Loop time of 1.662e-06 on 1 procs for 0 steps with 1000 atoms 180.5% 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 | | 1.662e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3874.00 ave 3874 max 3874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38640.0 ave 38640 max 38640 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77280.0 ave 77280 max 77280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77280 Ave neighs/atom = 77.280000 Neighbor list builds = 0 Dangerous builds = 0 1000 -3527.81291688428 eV 2.3338133737822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02