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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.401924 0.0000000) to (21.699178 43.401924 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1052500 4.1052500 3.5673230 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.401924 0.0000000) to (21.699178 43.401924 3.5673230) create_atoms CPU = 0.002 seconds 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1052500 4.1052500 3.5673230 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.401924 0.0000000) to (21.699178 43.401924 3.5673230) create_atoms CPU = 0.002 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.488 | 4.488 | 4.488 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2454.5417 0 -2454.5417 6399.7543 19 0 -2476.2394 0 -2476.2394 13906.357 Loop time of 1.44044 on 1 procs for 19 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 = -2454.54166970609 -2476.23800433129 -2476.23936948104 Force two-norm initial, final = 34.641732 1.1731491 Force max component initial, final = 9.7054955 0.46136022 Final line search alpha, max atom move = 0.48375785 0.22318663 Iterations, force evaluations = 19 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.434 | 1.434 | 1.434 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029889 | 0.0029889 | 0.0029889 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003437 | | | 0.24 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3468.00 ave 3468 max 3468 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: 31764.0 ave 31764 max 31764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31764 Ave neighs/atom = 54.020408 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.488 | 4.488 | 4.488 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -2476.2394 0 -2476.2394 13906.357 6719.3104 57 0 -2479.2581 0 -2479.2581 -8255.7686 6905.3468 Loop time of 1.49911 on 1 procs for 38 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 = -2476.23936948104 -2479.25663859841 -2479.25805182748 Force two-norm initial, final = 80.621278 4.5136916 Force max component initial, final = 80.569614 3.7856980 Final line search alpha, max atom move = 0.00048864161 0.0018498496 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4837 | 1.4837 | 1.4837 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003102 | 0.003102 | 0.003102 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01229 | | | 0.82 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3444.00 ave 3444 max 3444 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: 32948.0 ave 32948 max 32948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32948 Ave neighs/atom = 56.034014 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2479.2581 0 -2479.2581 -8255.7686 Loop time of 6.224e-06 on 1 procs for 0 steps with 588 atoms 160.7% 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 | | 6.224e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3372.00 ave 3372 max 3372 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: 34404.0 ave 34404 max 34404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34404 Ave neighs/atom = 58.510204 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.626 | 4.626 | 4.626 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 -2479.2581 -2479.2581 22.513708 86.803849 3.5334543 -8255.7686 -8255.7686 -169.38837 -25467.935 870.01728 2.2852571 218.42142 Loop time of 6.756e-06 on 1 procs for 0 steps with 588 atoms 236.8% 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 | | 6.756e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3372.00 ave 3372 max 3372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17202.0 ave 17202 max 17202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34404.0 ave 34404 max 34404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34404 Ave neighs/atom = 58.510204 Neighbor list builds = 0 Dangerous builds = 0 588 -2479.25805182748 eV 2.28525707690847 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03