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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -37.802674 0.0000000) to (46.298631 37.802674 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8925530 5.4985707 5.8858683 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -37.802674 0.0000000) to (46.298631 37.802674 8.8288024) create_atoms CPU = 0.002 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8925530 5.4985707 5.8858683 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.802674 0.0000000) to (46.298631 37.802674 8.8288024) create_atoms CPU = 0.002 seconds 1323 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 27 atoms, new total = 2613 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9538.2013 0 -9538.2013 127555.66 351 0 -11090.824 0 -11090.824 -14276.899 Loop time of 60.1138 on 1 procs for 351 steps with 2613 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 = -9538.20130697259 -11090.8145265406 -11090.8235516239 Force two-norm initial, final = 2441.9730 0.30970850 Force max component initial, final = 490.94855 0.085687851 Final line search alpha, max atom move = 1.0000000 0.085687851 Iterations, force evaluations = 351 616 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 59.716 | 59.716 | 59.716 | 0.0 | 99.34 Neigh | 0.25261 | 0.25261 | 0.25261 | 0.0 | 0.42 Comm | 0.056742 | 0.056742 | 0.056742 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08858 | | | 0.15 Nlocal: 2613.00 ave 2613 max 2613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6467.00 ave 6467 max 6467 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: 198596.0 ave 198596 max 198596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198596 Ave neighs/atom = 76.003062 Neighbor list builds = 14 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 351 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.554 | 5.554 | 5.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 351 0 -11090.824 0 -11090.824 -14276.899 30904.552 361 0 -11093.187 0 -11093.187 48.79753 30625.531 Loop time of 1.04256 on 1 procs for 10 steps with 2613 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 = -11090.8235516239 -11093.1861798307 -11093.1867683626 Force two-norm initial, final = 529.22983 2.2024593 Force max component initial, final = 386.07249 1.1653366 Final line search alpha, max atom move = 0.00024173697 0.00028170493 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0372 | 1.0372 | 1.0372 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066479 | 0.00066479 | 0.00066479 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004713 | | | 0.45 Nlocal: 2613.00 ave 2613 max 2613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6484.00 ave 6484 max 6484 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: 198760.0 ave 198760 max 198760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198760 Ave neighs/atom = 76.065825 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.692 | 5.692 | 5.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11093.187 0 -11093.187 48.79753 Loop time of 2.147e-06 on 1 procs for 0 steps with 2613 atoms 139.7% 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 | | 2.147e-06 | | |100.00 Nlocal: 2613.00 ave 2613 max 2613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6471.00 ave 6471 max 6471 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: 202614.0 ave 202614 max 202614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202614 Ave neighs/atom = 77.540758 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.692 | 5.692 | 5.692 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 -11093.187 -11093.187 46.051665 74.972835 8.8702193 48.79753 48.79753 40.215455 60.454624 45.72251 2.2916558 13278.591 Loop time of 2.62e-06 on 1 procs for 0 steps with 2613 atoms 229.0% 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 | | 2.62e-06 | | |100.00 Nlocal: 2613.00 ave 2613 max 2613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6471.00 ave 6471 max 6471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101307.0 ave 101307 max 101307 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202614.0 ave 202614 max 202614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202614 Ave neighs/atom = 77.540758 Neighbor list builds = 0 Dangerous builds = 0 2613 -11093.1867683626 eV 2.29165576138723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:01