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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -53.397857 0.0000000) to (18.877709 53.397857 5.1378616) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8942208 5.9326915 5.1378616 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.397857 0.0000000) to (18.877709 53.397857 5.1378616) create_atoms CPU = 0.001 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8942208 5.9326915 5.1378616 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.397857 0.0000000) to (18.877709 53.397857 5.1378616) create_atoms CPU = 0.001 seconds 434 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 856 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3610.2887 0 -3610.2887 10761.379 72 0 -3644.2615 0 -3644.2615 -6413.1175 Loop time of 0.878607 on 1 procs for 72 steps with 856 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 = -3610.2886832108 -3644.25836507129 -3644.26154596151 Force two-norm initial, final = 52.991942 0.22811850 Force max component initial, final = 17.494613 0.045846935 Final line search alpha, max atom move = 1.0000000 0.045846935 Iterations, force evaluations = 72 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85327 | 0.85327 | 0.85327 | 0.0 | 97.12 Neigh | 0.0096291 | 0.0096291 | 0.0096291 | 0.0 | 1.10 Comm | 0.009102 | 0.009102 | 0.009102 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006602 | | | 0.75 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6692.00 ave 6692 max 6692 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: 132140.0 ave 132140 max 132140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132140 Ave neighs/atom = 154.36916 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3644.2615 0 -3644.2615 -6413.1175 10358.229 78 0 -3644.4092 0 -3644.4092 -1084.8388 10321.611 Loop time of 0.0599016 on 1 procs for 6 steps with 856 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 = -3644.26154596151 -3644.40911779449 -3644.40917395348 Force two-norm initial, final = 63.413232 0.40854576 Force max component initial, final = 62.599454 0.087607203 Final line search alpha, max atom move = 0.00082401094 7.2189293e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057156 | 0.057156 | 0.057156 | 0.0 | 95.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048816 | 0.00048816 | 0.00048816 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002257 | | | 3.77 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6700.00 ave 6700 max 6700 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: 131428.0 ave 131428 max 131428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131428 Ave neighs/atom = 153.53738 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3644.4092 0 -3644.4092 -1084.8388 Loop time of 2.035e-06 on 1 procs for 0 steps with 856 atoms 147.4% 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 | | 2.035e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5812.00 ave 5812 max 5812 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: 133460.0 ave 133460 max 133460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133460 Ave neighs/atom = 155.91121 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.139 | 5.139 | 5.139 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 -3644.4092 -3644.4092 18.784288 106.79571 5.1451606 -1084.8388 -1084.8388 11.730349 -3275.0236 8.7766782 2.3216697 469.62142 Loop time of 2.548e-06 on 1 procs for 0 steps with 856 atoms 235.5% 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 | | 2.548e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5812.00 ave 5812 max 5812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66730.0 ave 66730 max 66730 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 133460.0 ave 133460 max 133460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133460 Ave neighs/atom = 155.91121 Neighbor list builds = 0 Dangerous builds = 0 856 -3644.40917395348 eV 2.32166972176783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01