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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -41.830000 0.0000000) to (24.148300 41.830000 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3548158 5.8703274 6.7850866 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -41.830000 0.0000000) to (24.148300 41.830000 6.7850866) create_atoms CPU = 0.003 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3548158 5.8703274 6.7850866 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -41.830000 0.0000000) to (24.148300 41.830000 6.7850866) create_atoms CPU = 0.003 seconds 458 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 26 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 896 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5098.9781 0 -5098.9781 3642.3582 96 0 -5131.6464 0 -5131.6464 -13334.361 Loop time of 6.62823 on 1 procs for 96 steps with 896 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 = -5098.97808493645 -5131.64213453352 -5131.6464275478 Force two-norm initial, final = 43.687162 0.25564498 Force max component initial, final = 11.597473 0.038853916 Final line search alpha, max atom move = 1.0000000 0.038853916 Iterations, force evaluations = 96 184 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5895 | 6.5895 | 6.5895 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017345 | 0.017345 | 0.017345 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02137 | | | 0.32 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3817.00 ave 3817 max 3817 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: 68524.0 ave 68524 max 68524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68524 Ave neighs/atom = 76.477679 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -5131.6464 0 -5131.6464 -13334.361 13707.549 100 0 -5131.8147 0 -5131.8147 -6003.6292 13648.512 Loop time of 0.240322 on 1 procs for 4 steps with 896 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 = -5131.64642754778 -5131.81429158095 -5131.81474195178 Force two-norm initial, final = 107.21956 0.31169528 Force max component initial, final = 84.409235 0.051688537 Final line search alpha, max atom move = 0.00026804762 1.3854989e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23733 | 0.23733 | 0.23733 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056244 | 0.00056244 | 0.00056244 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00243 | | | 1.01 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3853.00 ave 3853 max 3853 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: 68836.0 ave 68836 max 68836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68836 Ave neighs/atom = 76.825893 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.709 | 4.709 | 4.709 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5131.8147 0 -5131.8147 -6003.6292 Loop time of 6.836e-06 on 1 procs for 0 steps with 896 atoms 175.5% 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 | | 6.836e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3859.00 ave 3859 max 3859 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: 68868.0 ave 68868 max 68868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68868 Ave neighs/atom = 76.861607 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.709 | 4.709 | 4.709 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 -5131.8147 -5131.8147 24.081915 83.66 6.7744871 -6003.6292 -6003.6292 -1.2552348 -18005.599 -4.0328724 2.482334 712.44883 Loop time of 6.976e-06 on 1 procs for 0 steps with 896 atoms 272.4% 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 | | 6.976e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3859.00 ave 3859 max 3859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34434.0 ave 34434 max 34434 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68868.0 ave 68868 max 68868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68868 Ave neighs/atom = 76.861607 Neighbor list builds = 0 Dangerous builds = 0 896 -5131.81474195178 eV 2.48233399258058 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07