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 = 2.8553125 2.8553125 2.8553125 Created orthogonal box = (0.0000000 -56.532304 0.0000000) to (34.618825 56.532304 6.9940587) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0035375 4.0380217 4.6627058 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -56.532304 0.0000000) to (34.618825 56.532304 6.9940587) create_atoms CPU = 0.005 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0035375 4.0380217 4.6627058 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.532304 0.0000000) to (34.618825 56.532304 6.9940587) create_atoms CPU = 0.005 seconds 1182 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 = 10 31 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 6 atoms, new total = 2352 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_143977152728_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 = 10 31 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) = 6.100 | 6.100 | 6.100 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6357.4372 0 -6357.4372 252590.76 76 0 -9397.8605 0 -9397.8605 7438.2601 Loop time of 4.76226 on 1 procs for 76 steps with 2352 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 = -6357.43721368786 -9397.85325593113 -9397.86051392413 Force two-norm initial, final = 5046.3567 0.29837421 Force max component initial, final = 702.83532 0.032306865 Final line search alpha, max atom move = 1.0000000 0.032306865 Iterations, force evaluations = 76 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6472 | 4.6472 | 4.6472 | 0.0 | 97.58 Neigh | 0.048559 | 0.048559 | 0.048559 | 0.0 | 1.02 Comm | 0.033064 | 0.033064 | 0.033064 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03347 | | | 0.70 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9549.00 ave 9549 max 9549 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: 321336.0 ave 321336 max 321336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321336 Ave neighs/atom = 136.62245 Neighbor list builds = 1 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 = 10 31 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.095 | 6.095 | 6.095 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -9397.8605 0 -9397.8605 7438.2601 27375.892 82 0 -9398.4378 0 -9398.4378 -287.40463 27497.98 Loop time of 0.276451 on 1 procs for 6 steps with 2352 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 = -9397.86051392413 -9398.4353610505 -9398.43781170827 Force two-norm initial, final = 254.12979 9.9243653 Force max component initial, final = 229.88500 8.3895952 Final line search alpha, max atom move = 7.7650340e-05 0.00065145492 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26844 | 0.26844 | 0.26844 | 0.0 | 97.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001528 | 0.001528 | 0.001528 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006482 | | | 2.34 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8940.00 ave 8940 max 8940 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: 319992.0 ave 319992 max 319992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319992 Ave neighs/atom = 136.05102 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 = 10 32 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) = 6.234 | 6.234 | 6.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9398.4378 0 -9398.4378 -287.40463 Loop time of 6.755e-06 on 1 procs for 0 steps with 2352 atoms 177.6% 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 | | 6.755e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949.00 ave 8949 max 8949 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: 319692.0 ave 319692 max 319692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319692 Ave neighs/atom = 135.92347 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 = 10 32 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) = 6.234 | 6.234 | 6.234 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 -9398.4378 -9398.4378 34.603856 113.66609 6.9910978 -287.40463 -287.40463 -488.61046 -76.603457 -296.99998 2.228071 1023.9139 Loop time of 8.259e-06 on 1 procs for 0 steps with 2352 atoms 217.9% 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 | | 8.259e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949.00 ave 8949 max 8949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159846.0 ave 159846 max 159846 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 319692.0 ave 319692 max 319692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319692 Ave neighs/atom = 135.92347 Neighbor list builds = 0 Dangerous builds = 0 2352 -9398.43781170828 eV 2.2280710150312 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06