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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2390280 5.7351567 5.1068645 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068645) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2390280 5.7351567 5.1068645 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.116231 0.0000000) to (41.801488 59.116231 5.1068645) create_atoms CPU = 0.003 seconds 1080 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 35 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2128 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8952.3976 0 -8952.3976 2804.1841 425 0 -9046.3391 0 -9046.3391 -7895.9361 Loop time of 135.596 on 1 procs for 425 steps with 2128 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8952.39759560081 -9046.33009247908 -9046.3390645545 Force two-norm initial, final = 67.002791 0.32310895 Force max component initial, final = 12.027468 0.073761562 Final line search alpha, max atom move = 0.78409188 0.057835842 Iterations, force evaluations = 425 815 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 135.16 | 135.16 | 135.16 | 0.0 | 99.68 Neigh | 0.22992 | 0.22992 | 0.22992 | 0.0 | 0.17 Comm | 0.11098 | 0.11098 | 0.11098 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09792 | | | 0.07 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9366.00 ave 9366 max 9366 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: 240860.0 ave 240860 max 240860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240860 Ave neighs/atom = 113.18609 Neighbor list builds = 12 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 425 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press Volume 425 0 -9046.3391 0 -9046.3391 -7895.9361 25239.62 457 0 -9070.4436 0 -9070.4436 28.116942 25079.019 Loop time of 6.94832 on 1 procs for 32 steps with 2128 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 = -9046.33906455451 -9070.44279575402 -9070.4436254857 Force two-norm initial, final = 1166.5495 6.9570560 Force max component initial, final = 795.02596 4.8199808 Final line search alpha, max atom move = 0.00096281705 0.0046407597 Iterations, force evaluations = 32 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.877 | 6.877 | 6.877 | 0.0 | 98.97 Neigh | 0.050202 | 0.050202 | 0.050202 | 0.0 | 0.72 Comm | 0.0036628 | 0.0036628 | 0.0036628 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01747 | | | 0.25 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9599.00 ave 9599 max 9599 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: 239848.0 ave 239848 max 239848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239848 Ave neighs/atom = 112.71053 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.772 | 5.772 | 5.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9070.4436 0 -9070.4436 28.116942 Loop time of 2.343e-06 on 1 procs for 0 steps with 2128 atoms 170.7% 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 | | 2.343e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9606.00 ave 9606 max 9606 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: 239916.0 ave 239916 max 239916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239916 Ave neighs/atom = 112.74248 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.772 | 5.772 | 5.772 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 -9070.4436 -9070.4436 41.301021 121.87482 4.9823679 28.116942 28.116942 304.2385 30.862891 -250.75056 2.348569 5128.289 Loop time of 2.583e-06 on 1 procs for 0 steps with 2128 atoms 232.3% 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 | | 2.583e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9606.00 ave 9606 max 9606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119958.0 ave 119958 max 119958 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 239916.0 ave 239916 max 239916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239916 Ave neighs/atom = 112.74248 Neighbor list builds = 0 Dangerous builds = 0 2128 -9070.4436254857 eV 2.34856900029829 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:23