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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -59.930036 0.0000000) to (48.932670 59.930036 9.9196902) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0327949 5.7467158 6.6131268 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -59.930036 0.0000000) to (48.932670 59.930036 9.9196902) create_atoms CPU = 0.006 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0327949 5.7467158 6.6131268 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -59.930036 0.0000000) to (48.932670 59.930036 9.9196902) create_atoms CPU = 0.006 seconds 1759 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 32 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 3488 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_284963179498_005#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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10605.368 0 -10605.368 40174.45 130 0 -11727.158 0 -11727.158 964.55429 Loop time of 9.73846 on 1 procs for 130 steps with 3488 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10605.3679245982 -11727.1477566294 -11727.1578445759 Force two-norm initial, final = 1002.1271 0.26374576 Force max component initial, final = 160.38688 0.051828889 Final line search alpha, max atom move = 1.0000000 0.051828889 Iterations, force evaluations = 130 245 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4086 | 9.4086 | 9.4086 | 0.0 | 96.61 Neigh | 0.19282 | 0.19282 | 0.19282 | 0.0 | 1.98 Comm | 0.056291 | 0.056291 | 0.056291 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08077 | | | 0.83 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9364.00 ave 9364 max 9364 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: 446136.0 ave 446136 max 446136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446136 Ave neighs/atom = 127.90596 Neighbor list builds = 3 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 130 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 130 0 -11727.158 0 -11727.158 964.55429 58179.711 135 0 -11727.371 0 -11727.371 30.067773 58258.05 Loop time of 0.272093 on 1 procs for 5 steps with 3488 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 = -11727.1578445759 -11727.3688591476 -11727.3708626319 Force two-norm initial, final = 104.70117 2.2992115 Force max component initial, final = 104.43362 1.6474051 Final line search alpha, max atom move = 6.0833249e-05 0.00010021700 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26372 | 0.26372 | 0.26372 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013983 | 0.0013983 | 0.0013983 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006974 | | | 2.56 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9366.00 ave 9366 max 9366 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: 450900.0 ave 450900 max 450900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450900 Ave neighs/atom = 129.27179 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.638 | 6.638 | 6.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11727.371 0 -11727.371 30.067773 Loop time of 6.384e-06 on 1 procs for 0 steps with 3488 atoms 203.6% 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 | | 6.384e-06 | | |100.00 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9366.00 ave 9366 max 9366 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: 448588.0 ave 448588 max 448588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448588 Ave neighs/atom = 128.60894 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.638 | 6.638 | 6.638 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 -11727.371 -11727.371 48.844267 120.34543 9.9108918 30.067773 30.067773 1.9221083 43.015489 45.26572 2.5982826 2221.0943 Loop time of 6.967e-06 on 1 procs for 0 steps with 3488 atoms 258.4% 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 | | 6.967e-06 | | |100.00 Nlocal: 3488.00 ave 3488 max 3488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9366.00 ave 9366 max 9366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224294.0 ave 224294 max 224294 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 448588.0 ave 448588 max 448588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448588 Ave neighs/atom = 128.60894 Neighbor list builds = 0 Dangerous builds = 0 3488 -11727.3708626319 eV 2.59828257804601 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11