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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -40.445521 0.0000000) to (28.596813 40.445521 4.9780662) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0659906 5.5148183 4.9780662 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445521 0.0000000) to (28.596813 40.445521 4.9780662) create_atoms CPU = 0.001 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0659906 5.5148183 4.9780662 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445521 0.0000000) to (28.596813 40.445521 4.9780662) create_atoms CPU = 0.001 seconds 532 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.430 | 5.430 | 5.430 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4605.2796 0 -4605.2796 15039.562 32 0 -4647.1698 0 -4647.1698 -6613.5571 Loop time of 0.592251 on 1 procs for 32 steps with 1048 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 = -4605.27963147071 -4647.16699224906 -4647.16984247513 Force two-norm initial, final = 54.843504 0.16433566 Force max component initial, final = 14.404941 0.013147033 Final line search alpha, max atom move = 1.0000000 0.013147033 Iterations, force evaluations = 32 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5734 | 0.5734 | 0.5734 | 0.0 | 96.82 Neigh | 0.013083 | 0.013083 | 0.013083 | 0.0 | 2.21 Comm | 0.0031608 | 0.0031608 | 0.0031608 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002604 | | | 0.44 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7506.00 ave 7506 max 7506 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: 233368.0 ave 233368 max 233368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233368 Ave neighs/atom = 222.67939 Neighbor list builds = 1 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.430 | 5.430 | 5.430 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -4647.1698 0 -4647.1698 -6613.5571 11515.392 35 0 -4647.207 0 -4647.207 -3943.9742 11497.827 Loop time of 0.0661154 on 1 procs for 3 steps with 1048 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 = -4647.16984247514 -4647.20661745403 -4647.20699124249 Force two-norm initial, final = 40.596682 0.18651181 Force max component initial, final = 40.455477 0.020832224 Final line search alpha, max atom move = 0.00021985028 4.5799703e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064482 | 0.064482 | 0.064482 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032058 | 0.00032058 | 0.00032058 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001313 | | | 1.99 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7517.00 ave 7517 max 7517 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: 233568.0 ave 233568 max 233568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233568 Ave neighs/atom = 222.87023 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4647.207 0 -4647.207 -3943.9742 Loop time of 1.655e-06 on 1 procs for 0 steps with 1048 atoms 181.3% 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 | | 1.655e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7517.00 ave 7517 max 7517 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: 233608.0 ave 233608 max 233608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233608 Ave neighs/atom = 222.90840 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.568 | 5.568 | 5.568 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 -4647.207 -4647.207 28.606371 80.891042 4.9688121 -3943.9742 -3943.9742 -2.9038579 -11826.762 -2.2566366 2.3246357 554.03298 Loop time of 2.049e-06 on 1 procs for 0 steps with 1048 atoms 195.2% 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 | | 2.049e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7517.00 ave 7517 max 7517 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116804.0 ave 116804 max 116804 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233608.0 ave 233608 max 233608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233608 Ave neighs/atom = 222.90840 Neighbor list builds = 0 Dangerous builds = 0 1048 -4618.63704215609 eV 2.3246356600531 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01