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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -41.305963 0.0000000) to (20.650957 41.305963 4.0499858) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7656054 4.7656054 4.0499858 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.305963 0.0000000) to (20.650957 41.305963 4.0499858) create_atoms CPU = 0.002 seconds 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7656054 4.7656054 4.0499858 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.305963 0.0000000) to (20.650957 41.305963 4.0499858) create_atoms CPU = 0.001 seconds 209 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 = 7 28 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 10 atoms, new total = 408 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_022920256108_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 = 7 28 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) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1355.2767 0 -1355.2767 752.33437 17 0 -1361.9434 0 -1361.9434 -6731.7767 Loop time of 0.535339 on 1 procs for 17 steps with 408 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 = -1355.27673334883 -1361.94214269008 -1361.9434061395 Force two-norm initial, final = 8.3798659 0.77102516 Force max component initial, final = 1.7726814 0.26770936 Final line search alpha, max atom move = 0.22428140 0.060042229 Iterations, force evaluations = 17 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53092 | 0.53092 | 0.53092 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002066 | 0.002066 | 0.002066 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00235 | | | 0.44 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572.00 ave 2572 max 2572 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: 21604.0 ave 21604 max 21604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21604 Ave neighs/atom = 52.950980 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 = 7 28 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1361.9434 0 -1361.9434 -6731.7767 6909.3379 27 0 -1362.1219 0 -1362.1219 -81.756669 6836.8076 Loop time of 0.228719 on 1 procs for 10 steps with 408 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1361.9434061395 -1362.12149704008 -1362.12185920142 Force two-norm initial, final = 43.460114 1.4806787 Force max component initial, final = 35.484689 1.0433855 Final line search alpha, max atom move = 0.0010274209 0.0010719961 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22364 | 0.22364 | 0.22364 | 0.0 | 97.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009623 | 0.0009623 | 0.0009623 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004115 | | | 1.80 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2560.00 ave 2560 max 2560 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: 21770.0 ave 21770 max 21770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21770 Ave neighs/atom = 53.357843 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 = 7 28 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1362.1219 0 -1362.1219 -81.756669 Loop time of 7.046e-06 on 1 procs for 0 steps with 408 atoms 170.3% 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 | | 7.046e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2560.00 ave 2560 max 2560 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: 21786.0 ave 21786 max 21786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21786 Ave neighs/atom = 53.397059 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 = 7 28 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) = 4.575 | 4.575 | 4.575 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 -1362.1219 -1362.1219 20.625381 82.611927 4.0124407 -81.756669 -81.756669 244.21009 -639.80554 150.32544 2.6165526 210.24695 Loop time of 9.272e-06 on 1 procs for 0 steps with 408 atoms 226.5% 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 | | 9.272e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2560.00 ave 2560 max 2560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10893.0 ave 10893 max 10893 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21786.0 ave 21786 max 21786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21786 Ave neighs/atom = 53.397059 Neighbor list builds = 0 Dangerous builds = 0 408 -1362.12185920142 eV 2.61655260402271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01