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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -48.411133 0.0000000) to (13.175841 48.411133 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6467892 5.3790147 5.7504086 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -48.411133 0.0000000) to (13.175841 48.411133 8.6256130) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6467892 5.3790147 5.7504086 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -48.411133 0.0000000) to (13.175841 48.411133 8.6256130) create_atoms CPU = 0.001 seconds 507 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 31 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3667.6368 0 -3667.6368 227936.86 83 0 -4467.6684 0 -4467.6684 10139.268 Loop time of 5.95124 on 1 procs for 83 steps with 1008 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 = -3667.63681892855 -4467.66491973329 -4467.66842368862 Force two-norm initial, final = 1979.1993 0.22859344 Force max component initial, final = 338.06636 0.044990346 Final line search alpha, max atom move = 1.0000000 0.044990346 Iterations, force evaluations = 83 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9194 | 5.9194 | 5.9194 | 0.0 | 99.47 Neigh | 0.01475 | 0.01475 | 0.01475 | 0.0 | 0.25 Comm | 0.0075717 | 0.0075717 | 0.0075717 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009483 | | | 0.16 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4487.00 ave 4487 max 4487 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: 86682.0 ave 86682 max 86682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86682 Ave neighs/atom = 85.994048 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4467.6684 0 -4467.6684 10139.268 11003.822 90 0 -4468.0904 0 -4468.0904 -1.5398873 11063.528 Loop time of 0.353259 on 1 procs for 7 steps with 1008 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 = -4467.66842368861 -4468.08692332637 -4468.09037827961 Force two-norm initial, final = 144.89548 0.42492854 Force max component initial, final = 134.51659 0.086313076 Final line search alpha, max atom move = 0.00012706014 1.0966951e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35057 | 0.35057 | 0.35057 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040779 | 0.00040779 | 0.00040779 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002279 | | | 0.65 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4386.00 ave 4386 max 4386 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: 86388.0 ave 86388 max 86388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86388 Ave neighs/atom = 85.702381 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.717 | 4.717 | 4.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4468.0904 0 -4468.0904 -1.5398873 Loop time of 2.662e-06 on 1 procs for 0 steps with 1008 atoms 150.3% 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 | | 2.662e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 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: 86330.0 ave 86330 max 86330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86330 Ave neighs/atom = 85.644841 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.717 | 4.717 | 4.717 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 -4468.0904 -4468.0904 13.174841 97.460467 8.6162796 -1.5398873 -1.5398873 -10.74477 -3.7531465 9.8782547 2.2590692 447.00972 Loop time of 2.959e-06 on 1 procs for 0 steps with 1008 atoms 169.0% 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 | | 2.959e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43165.0 ave 43165 max 43165 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86330.0 ave 86330 max 86330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86330 Ave neighs/atom = 85.644841 Neighbor list builds = 0 Dangerous builds = 0 1008 -4468.09037827961 eV 2.25906923171973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06