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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -73.350789 0.0000000) to (42.349098 73.350789 6.3365430) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6886848 5.8388688 6.3365430 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -73.350789 0.0000000) to (42.349098 73.350789 6.3365430) create_atoms CPU = 0.004 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6886848 5.8388688 6.3365430 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -73.350789 0.0000000) to (42.349098 73.350789 6.3365430) create_atoms CPU = 0.003 seconds 1609 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3213 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.653 | 6.653 | 6.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11495.904 0 -11495.904 69108.308 761 0 -12659.047 0 -12659.047 -56932.814 Loop time of 34.7614 on 1 procs for 761 steps with 3213 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 = -11495.903632448 -12659.0366423407 -12659.0471756429 Force two-norm initial, final = 1670.2091 0.34477872 Force max component initial, final = 498.13569 0.082121597 Final line search alpha, max atom move = 0.74298771 0.061015337 Iterations, force evaluations = 761 1467 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.864 | 33.864 | 33.864 | 0.0 | 97.42 Neigh | 0.41766 | 0.41766 | 0.41766 | 0.0 | 1.20 Comm | 0.24162 | 0.24162 | 0.24162 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.238 | | | 0.68 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12456.0 ave 12456 max 12456 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: 436234.0 ave 436234 max 436234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436234 Ave neighs/atom = 135.77155 Neighbor list builds = 15 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 761 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.651 | 6.651 | 6.651 Mbytes Step Temp E_pair E_mol TotEng Press Volume 761 0 -12659.047 0 -12659.047 -56932.814 39366.911 787 0 -12694.521 0 -12694.521 -133.2454 37815.736 Loop time of 0.791166 on 1 procs for 26 steps with 3213 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 = -12659.0471756429 -12694.5161319482 -12694.5213308087 Force two-norm initial, final = 2508.6099 18.295037 Force max component initial, final = 1700.6159 14.880041 Final line search alpha, max atom move = 0.00069272352 0.010307754 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6798 | 0.6798 | 0.6798 | 0.0 | 85.92 Neigh | 0.086955 | 0.086955 | 0.086955 | 0.0 | 10.99 Comm | 0.0042642 | 0.0042642 | 0.0042642 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02015 | | | 2.55 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 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: 454258.0 ave 454258 max 454258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454258 Ave neighs/atom = 141.38126 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.789 | 6.789 | 6.789 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12694.521 0 -12694.521 -133.2454 Loop time of 2.494e-06 on 1 procs for 0 steps with 3213 atoms 160.4% 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 | | 2.494e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12555.0 ave 12555 max 12555 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: 454254.0 ave 454254 max 454254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454254 Ave neighs/atom = 141.38002 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.789 | 6.789 | 6.789 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 -12694.521 -12694.521 41.377242 143.66353 6.3615727 -133.2454 -133.2454 -121.02903 354.22043 -632.9276 2.1866368 8062.9012 Loop time of 3.329e-06 on 1 procs for 0 steps with 3213 atoms 240.3% 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 | | 3.329e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12555.0 ave 12555 max 12555 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 227127.0 ave 227127 max 227127 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 454254.0 ave 454254 max 454254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 454254 Ave neighs/atom = 141.38002 Neighbor list builds = 0 Dangerous builds = 0 3213 -12694.5213308087 eV 2.18663682477016 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:36