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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -40.811357 0.0000000) to (28.857987 40.811357 5.7147330) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0925860 6.4017815 5.7147330 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.811357 0.0000000) to (28.857987 40.811357 5.7147330) create_atoms CPU = 0.002 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0925860 6.4017815 5.7147330 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.811357 0.0000000) to (28.857987 40.811357 5.7147330) create_atoms CPU = 0.001 seconds 410 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 17 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.379 | 5.379 | 5.379 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3004.2915 0 -3004.2915 29182.083 69 0 -3160.933 0 -3160.933 3298.6844 Loop time of 3.01127 on 1 procs for 69 steps with 812 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3004.29151122852 -3160.93002548464 -3160.9330458746 Force two-norm initial, final = 278.82156 0.13562735 Force max component initial, final = 79.039572 0.021126787 Final line search alpha, max atom move = 1.0000000 0.021126787 Iterations, force evaluations = 69 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9379 | 2.9379 | 2.9379 | 0.0 | 97.56 Neigh | 0.046202 | 0.046202 | 0.046202 | 0.0 | 1.53 Comm | 0.015742 | 0.015742 | 0.015742 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01143 | | | 0.38 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6919.00 ave 6919 max 6919 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: 199668.0 ave 199668 max 199668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199668 Ave neighs/atom = 245.89655 Neighbor list builds = 2 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.378 | 5.378 | 5.378 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -3160.933 0 -3160.933 3298.6844 13460.866 77 0 -3161.1755 0 -3161.1755 -39.595691 13514.704 Loop time of 0.257796 on 1 procs for 8 steps with 812 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 = -3160.9330458746 -3161.17389210421 -3161.17550919176 Force two-norm initial, final = 69.803331 0.98025917 Force max component initial, final = 68.827282 0.72167118 Final line search alpha, max atom move = 0.00029469403 0.00021267219 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25138 | 0.25138 | 0.25138 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012166 | 0.0012166 | 0.0012166 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005196 | | | 2.02 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6865.00 ave 6865 max 6865 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: 199560.0 ave 199560 max 199560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199560 Ave neighs/atom = 245.76355 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.516 | 5.516 | 5.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3161.1755 0 -3161.1755 -39.595691 Loop time of 3.389e-06 on 1 procs for 0 steps with 812 atoms 177.0% 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 | | 3.389e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6865.00 ave 6865 max 6865 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: 199100.0 ave 199100 max 199100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199100 Ave neighs/atom = 245.19704 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.516 | 5.516 | 5.516 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 -3161.1755 -3161.1755 28.805185 82.243255 5.7047363 -39.595691 -39.595691 -85.398023 -65.261322 31.872274 2.6010965 580.77787 Loop time of 4.068e-06 on 1 procs for 0 steps with 812 atoms 196.7% 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 | | 4.068e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6865.00 ave 6865 max 6865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99550.0 ave 99550 max 99550 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199100.0 ave 199100 max 199100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199100 Ave neighs/atom = 245.19704 Neighbor list builds = 0 Dangerous builds = 0 812 -3161.17550919176 eV 2.60109647180997 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03