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 = 3.6056636 3.6056636 3.6056636 Created orthogonal box = (0.0000000 -68.980406 0.0000000) to (39.825856 68.980406 6.2451925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8759459 5.2771895 6.2451925 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -68.980406 0.0000000) to (39.825856 68.980406 6.2451925) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8759459 5.2771895 6.2451925 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -68.980406 0.0000000) to (39.825856 68.980406 6.2451925) create_atoms CPU = 0.003 seconds 1466 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 11 36 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2928 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 6.989 | 6.989 | 6.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 368821.43 0 368821.43 55786761 778 0 -12396.589 0 -12396.589 16153.844 Loop time of 34.2543 on 1 procs for 778 steps with 2928 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 368821.430652712 -12396.5777679356 -12396.5891773652 Force two-norm initial, final = 2158181.7 0.58491307 Force max component initial, final = 627544.88 0.099234983 Final line search alpha, max atom move = 0.67398454 0.066882844 Iterations, force evaluations = 778 1529 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.093 | 33.093 | 33.093 | 0.0 | 96.61 Neigh | 0.73939 | 0.73939 | 0.73939 | 0.0 | 2.16 Comm | 0.21779 | 0.21779 | 0.21779 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2039 | | | 0.60 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12626.0 ave 12626 max 12626 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: 479684.0 ave 479684 max 479684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479684 Ave neighs/atom = 163.82650 Neighbor list builds = 25 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 778 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.616 | 6.616 | 6.616 Mbytes Step Temp E_pair E_mol TotEng Press Volume 778 0 -12396.589 0 -12396.589 16153.844 34313.632 790 0 -12400.022 0 -12400.022 67.558533 34639.132 Loop time of 0.325777 on 1 procs for 12 steps with 2928 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 = -12396.589177365 -12400.0222405174 -12400.0223675107 Force two-norm initial, final = 686.26868 3.1347764 Force max component initial, final = 584.17864 1.6227206 Final line search alpha, max atom move = 0.00056437252 0.00091581894 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31626 | 0.31626 | 0.31626 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015067 | 0.0015067 | 0.0015067 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008014 | | | 2.46 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12759.0 ave 12759 max 12759 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: 479784.0 ave 479784 max 479784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479784 Ave neighs/atom = 163.86066 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 6.753 | 6.753 | 6.753 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12400.022 0 -12400.022 67.558533 Loop time of 1.919e-06 on 1 procs for 0 steps with 2928 atoms 156.3% 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 | | 1.919e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12633.0 ave 12633 max 12633 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: 478746.0 ave 478746 max 478746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478746 Ave neighs/atom = 163.50615 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 6.753 | 6.753 | 6.753 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 -12400.022 -12400.022 39.982177 137.29029 6.3104562 67.558533 67.558533 63.16282 74.691501 64.821277 2.3039744 9958.4814 Loop time of 2.222e-06 on 1 procs for 0 steps with 2928 atoms 270.0% 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 | | 2.222e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12633.0 ave 12633 max 12633 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239373.0 ave 239373 max 239373 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 478746.0 ave 478746 max 478746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478746 Ave neighs/atom = 163.50615 Neighbor list builds = 0 Dangerous builds = 0 2928 -12400.0223675107 eV 2.30397443284806 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35