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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -66.943992 0.0000000) to (33.470037 66.943992 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0434303 5.0434303 3.9173716 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -66.943992 0.0000000) to (33.470037 66.943992 3.9173716) create_atoms CPU = 0.004 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0434303 5.0434303 3.9173716 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -66.943992 0.0000000) to (33.470037 66.943992 3.9173716) create_atoms CPU = 0.003 seconds 586 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1156 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_020840179467_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6621.0027 0 -6621.0027 4.9161133 25 0 -6641.3437 0 -6641.3437 -6130.3254 Loop time of 2.35607 on 1 procs for 25 steps with 1156 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 = -6621.00265286547 -6641.33775797713 -6641.3436607903 Force two-norm initial, final = 42.006375 0.27089249 Force max component initial, final = 15.545907 0.055680514 Final line search alpha, max atom move = 1.0000000 0.055680514 Iterations, force evaluations = 25 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.341 | 2.341 | 2.341 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0078681 | 0.0078681 | 0.0078681 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007241 | | | 0.31 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6752.00 ave 6752 max 6752 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: 89220.0 ave 89220 max 89220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89220 Ave neighs/atom = 77.179931 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -6641.3437 0 -6641.3437 -6130.3254 17554.666 28 0 -6641.4756 0 -6641.4756 -114.33168 17493.617 Loop time of 0.324367 on 1 procs for 3 steps with 1156 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6641.34366079029 -6641.47378814457 -6641.4756305494 Force two-norm initial, final = 105.41574 0.33498804 Force max component initial, final = 78.223990 0.086658004 Final line search alpha, max atom move = 0.00020273692 1.7568777e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32039 | 0.32039 | 0.32039 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091079 | 0.00091079 | 0.00091079 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00307 | | | 0.95 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6747.00 ave 6747 max 6747 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: 89440.0 ave 89440 max 89440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89440 Ave neighs/atom = 77.370242 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.779 | 4.779 | 4.779 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6641.4756 0 -6641.4756 -114.33168 Loop time of 6.596e-06 on 1 procs for 0 steps with 1156 atoms 212.2% 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 | | 6.596e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6752.00 ave 6752 max 6752 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: 89440.0 ave 89440 max 89440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89440 Ave neighs/atom = 77.370242 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.779 | 4.779 | 4.779 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 -6641.4756 -6641.4756 33.430021 133.88798 3.9084212 -114.33168 -114.33168 -3.0469507 -340.85983 0.91172701 2.4990652 652.76586 Loop time of 6.866e-06 on 1 procs for 0 steps with 1156 atoms 276.7% 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 | | 6.866e-06 | | |100.00 Nlocal: 1156.00 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6752.00 ave 6752 max 6752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44720.0 ave 44720 max 44720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 89440.0 ave 89440 max 89440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89440 Ave neighs/atom = 77.370242 Neighbor list builds = 0 Dangerous builds = 0 1156 -6641.4756305494 eV 2.49906523808618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03