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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -54.721564 0.0000000) to (31.593510 54.721564 4.9542577) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6613375 4.1863492 4.9542577 Created 732 atoms using lattice units in orthogonal box = (0.0000000 -54.721564 0.0000000) to (31.593510 54.721564 4.9542577) create_atoms CPU = 0.002 seconds 732 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6613375 4.1863492 4.9542577 Created 734 atoms using lattice units in orthogonal box = (0.0000000 -54.721564 0.0000000) to (31.593510 54.721564 4.9542577) create_atoms CPU = 0.002 seconds 734 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1466 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6106.6978 0 -6106.6978 27391.849 208 0 -6411.0647 0 -6411.0647 -6627.5192 Loop time of 4.11898 on 1 procs for 208 steps with 1466 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6106.69780955351 -6411.05888123001 -6411.06469029239 Force two-norm initial, final = 299.51888 0.33685710 Force max component initial, final = 116.64542 0.046410088 Final line search alpha, max atom move = 1.0000000 0.046410088 Iterations, force evaluations = 208 340 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9801 | 3.9801 | 3.9801 | 0.0 | 96.63 Neigh | 0.083865 | 0.083865 | 0.083865 | 0.0 | 2.04 Comm | 0.029679 | 0.029679 | 0.029679 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02529 | | | 0.61 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8654.00 ave 8654 max 8654 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: 238204.0 ave 238204 max 238204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238204 Ave neighs/atom = 162.48568 Neighbor list builds = 6 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 208 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.518 | 5.518 | 5.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 208 0 -6411.0647 0 -6411.0647 -6627.5192 17130.3 222 0 -6413.8493 0 -6413.8493 -5.9726513 17060.312 Loop time of 0.202607 on 1 procs for 14 steps with 1466 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 = -6411.06469029239 -6413.84696839195 -6413.8493250807 Force two-norm initial, final = 374.86983 2.9524531 Force max component initial, final = 329.04213 0.67822160 Final line search alpha, max atom move = 0.00013506283 9.1602531e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18255 | 0.18255 | 0.18255 | 0.0 | 90.10 Neigh | 0.013707 | 0.013707 | 0.013707 | 0.0 | 6.77 Comm | 0.0012096 | 0.0012096 | 0.0012096 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005142 | | | 2.54 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8528.00 ave 8528 max 8528 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: 237864.0 ave 237864 max 237864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237864 Ave neighs/atom = 162.25375 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.655 | 5.655 | 5.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6413.8493 0 -6413.8493 -5.9726513 Loop time of 2.039e-06 on 1 procs for 0 steps with 1466 atoms 147.1% 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 | | 2.039e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8520.00 ave 8520 max 8520 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: 237256.0 ave 237256 max 237256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237256 Ave neighs/atom = 161.83902 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.655 | 5.655 | 5.655 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 -6413.8493 -6413.8493 31.641422 107.97637 4.9934678 -5.9726513 -5.9726513 -27.436708 62.839862 -53.321108 2.3469675 8103.9349 Loop time of 2.416e-06 on 1 procs for 0 steps with 1466 atoms 248.3% 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 | | 2.416e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8520.00 ave 8520 max 8520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118628.0 ave 118628 max 118628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237256.0 ave 237256 max 237256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237256 Ave neighs/atom = 161.83902 Neighbor list builds = 0 Dangerous builds = 0 1466 -6413.8493250807 eV 2.34696747152848 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04