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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -43.998540 0.0000000) to (21.999270 43.998540 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7929776 3.7929776 2.8886457 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -43.998540 0.0000000) to (21.999270 43.998540 2.8886457) create_atoms CPU = 0.002 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7929776 3.7929776 2.8886457 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.998540 0.0000000) to (21.999270 43.998540 2.8886457) create_atoms CPU = 0.001 seconds 233 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 464 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.827 | 4.827 | 4.827 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1765.6647 0 -1765.6647 77486.992 65 0 -1928.2145 0 -1928.2145 6795.9985 Loop time of 10.1033 on 1 procs for 65 steps with 464 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 = -1765.66473764076 -1928.21260652613 -1928.21452098488 Force two-norm initial, final = 414.39777 0.18453004 Force max component initial, final = 95.275007 0.034448889 Final line search alpha, max atom move = 1.0000000 0.034448889 Iterations, force evaluations = 65 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.062 | 10.062 | 10.062 | 0.0 | 99.59 Neigh | 0.024045 | 0.024045 | 0.024045 | 0.0 | 0.24 Comm | 0.0085463 | 0.0085463 | 0.0085463 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008345 | | | 0.08 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3006.00 ave 3006 max 3006 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: 26692.0 ave 26692 max 26692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26692 Ave neighs/atom = 57.525862 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.827 | 4.827 | 4.827 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1928.2145 0 -1928.2145 6795.9985 5592.0469 74 0 -1928.4047 0 -1928.4047 -20.493624 5611.5871 Loop time of 0.892631 on 1 procs for 9 steps with 464 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 = -1928.21452098489 -1928.40391635033 -1928.40468234952 Force two-norm initial, final = 53.359420 0.62374003 Force max component initial, final = 49.490115 0.22339573 Final line search alpha, max atom move = 0.00061045908 0.00013637395 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88917 | 0.88917 | 0.88917 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073226 | 0.00073226 | 0.00073226 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002725 | | | 0.31 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3006.00 ave 3006 max 3006 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: 26688.0 ave 26688 max 26688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26688 Ave neighs/atom = 57.517241 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1928.4047 0 -1928.4047 -20.493624 Loop time of 6.575e-06 on 1 procs for 0 steps with 464 atoms 167.3% 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 | | 6.575e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2992.00 ave 2992 max 2992 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: 26674.0 ave 26674 max 26674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26674 Ave neighs/atom = 57.487069 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.965 | 4.965 | 4.965 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 -1928.4047 -1928.4047 22.053104 88.608812 2.8717 -20.493624 -20.493624 -63.938284 -13.145278 15.602689 2.3767487 358.60899 Loop time of 6.815e-06 on 1 procs for 0 steps with 464 atoms 220.1% 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 | | 6.815e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2992.00 ave 2992 max 2992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13337.0 ave 13337 max 13337 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26674.0 ave 26674 max 26674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26674 Ave neighs/atom = 57.487069 Neighbor list builds = 0 Dangerous builds = 0 464 -1928.40468234952 eV 2.376748658954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11