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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -42.527316 0.0000000) to (52.080802 42.527316 8.6204757) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9940495 5.2426599 5.7469838 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -42.527316 0.0000000) to (52.080802 42.527316 8.6204757) create_atoms CPU = 0.002 seconds 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9940495 5.2426599 5.7469838 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -42.527316 0.0000000) to (52.080802 42.527316 8.6204757) create_atoms CPU = 0.002 seconds 1758 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 60 atoms, new total = 3456 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.382 | 7.382 | 7.382 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15259.416 0 -15259.416 1706.8645 54 0 -15322.595 0 -15322.595 -18612.002 Loop time of 2.63681 on 1 procs for 54 steps with 3456 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15259.4164500236 -15322.5826774979 -15322.5950569926 Force two-norm initial, final = 58.708824 0.38877900 Force max component initial, final = 9.5139996 0.021280828 Final line search alpha, max atom move = 0.90064569 0.019166486 Iterations, force evaluations = 54 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6123 | 2.6123 | 2.6123 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010073 | 0.010073 | 0.010073 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01439 | | | 0.55 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10965.0 ave 10965 max 10965 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: 598416.0 ave 598416 max 598416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 598416 Ave neighs/atom = 173.15278 Neighbor list builds = 0 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.382 | 7.382 | 7.382 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -15322.595 0 -15322.595 -18612.002 38186.237 60 0 -15324.293 0 -15324.293 -4065.9303 37871.549 Loop time of 0.205326 on 1 procs for 6 steps with 3456 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 = -15322.5950569924 -15324.2892927262 -15324.2931845735 Force two-norm initial, final = 568.82883 0.63370684 Force max component initial, final = 443.45210 0.24984405 Final line search alpha, max atom move = 5.9727048e-05 1.4922447e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20076 | 0.20076 | 0.20076 | 0.0 | 97.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006342 | 0.0006342 | 0.0006342 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003932 | | | 1.92 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10992.0 ave 10992 max 10992 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: 597864.0 ave 597864 max 597864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 597864 Ave neighs/atom = 172.99306 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.520 | 7.520 | 7.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15324.293 0 -15324.293 -4065.9303 Loop time of 2.001e-06 on 1 procs for 0 steps with 3456 atoms 149.9% 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 | | 2.001e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10992.0 ave 10992 max 10992 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: 598884.0 ave 598884 max 598884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 598884 Ave neighs/atom = 173.28819 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.520 | 7.520 | 7.520 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 -15324.293 -15324.293 51.808577 85.054632 8.5943579 -4065.9303 -4065.9303 -10.51454 -12179.934 -7.3418294 2.1775624 1465.397 Loop time of 2.177e-06 on 1 procs for 0 steps with 3456 atoms 229.7% 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 | | 2.177e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10992.0 ave 10992 max 10992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 299442.0 ave 299442 max 299442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 598884.0 ave 598884 max 598884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 598884 Ave neighs/atom = 173.28819 Neighbor list builds = 0 Dangerous builds = 0 3456 -15324.2931845735 eV 2.17756240758258 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03