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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -42.871438 0.0000000) to (21.435719 42.871438 3.5240105) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0554063 4.0554063 3.5240105 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -42.871438 0.0000000) to (21.435719 42.871438 3.5240105) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0554063 4.0554063 3.5240105 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.871438 0.0000000) to (21.435719 42.871438 3.5240105) create_atoms CPU = 0.000 seconds 298 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 1 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 588 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2614.7338 0 -2614.7338 4467.4928 49 0 -2651.3629 0 -2651.3629 -334.17483 Loop time of 0.538611 on 1 procs for 49 steps with 588 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 = -2614.73384928268 -2651.3607489476 -2651.36292718777 Force two-norm initial, final = 32.042504 0.15026504 Force max component initial, final = 9.0808136 0.020518016 Final line search alpha, max atom move = 1.0000000 0.020518016 Iterations, force evaluations = 49 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52368 | 0.52368 | 0.52368 | 0.0 | 97.23 Neigh | 0.0065855 | 0.0065855 | 0.0065855 | 0.0 | 1.22 Comm | 0.0050546 | 0.0050546 | 0.0050546 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003291 | | | 0.61 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5954.00 ave 5954 max 5954 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: 102244.0 ave 102244 max 102244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102244 Ave neighs/atom = 173.88435 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -2651.3629 0 -2651.3629 -334.17483 6476.9911 50 0 -2651.3636 0 -2651.3636 331.71698 6474.5782 Loop time of 0.0167867 on 1 procs for 1 steps with 588 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 = -2651.36292718778 -2651.36292718778 -2651.36361363143 Force two-norm initial, final = 3.8598853 2.9267139 Force max component initial, final = 3.7202410 2.4012832 Final line search alpha, max atom move = 0.00026879979 0.00064546441 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016188 | 0.016188 | 0.016188 | 0.0 | 96.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013007 | 0.00013007 | 0.00013007 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004683 | | | 2.79 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5895.00 ave 5895 max 5895 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: 102264.0 ave 102264 max 102264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102264 Ave neighs/atom = 173.91837 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.058 | 5.058 | 5.058 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2651.3636 0 -2651.3636 331.71698 Loop time of 1.849e-06 on 1 procs for 0 steps with 588 atoms 162.2% 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 | | 1.849e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5895.00 ave 5895 max 5895 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: 102256.0 ave 102256 max 102256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102256 Ave neighs/atom = 173.90476 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.058 | 5.058 | 5.058 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 -2651.3636 -2651.3636 21.436771 85.713554 3.5237298 331.71698 331.71698 594.24231 -11.229844 412.13848 2.2822236 188.0736 Loop time of 3.357e-06 on 1 procs for 0 steps with 588 atoms 148.9% 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 | | 3.357e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5895.00 ave 5895 max 5895 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51128.0 ave 51128 max 51128 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102256.0 ave 102256 max 102256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102256 Ave neighs/atom = 173.90476 Neighbor list builds = 0 Dangerous builds = 0 588 -2651.36361363143 eV 2.28222358162872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00