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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -66.049529 0.0000000) to (38.133713 66.049529 5.9798434) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6262856 5.0529694 5.9798434 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -66.049529 0.0000000) to (38.133713 66.049529 5.9798434) create_atoms CPU = 0.009 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6262856 5.0529694 5.9798434 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -66.049529 0.0000000) to (38.133713 66.049529 5.9798434) create_atoms CPU = 0.009 seconds 1465 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 34 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2925 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 7.012 | 7.012 | 7.012 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12624.068 0 -12624.068 39126.726 96 0 -13131.266 0 -13131.266 16365.925 Loop time of 11.2998 on 1 procs for 96 steps with 2925 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 = -12624.0684066436 -13131.2536935342 -13131.2659421522 Force two-norm initial, final = 609.37018 0.42096071 Force max component initial, final = 150.81315 0.088023957 Final line search alpha, max atom move = 1.0000000 0.088023957 Iterations, force evaluations = 96 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.026 | 11.026 | 11.026 | 0.0 | 97.57 Neigh | 0.15239 | 0.15239 | 0.15239 | 0.0 | 1.35 Comm | 0.067054 | 0.067054 | 0.067054 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05467 | | | 0.48 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13903.0 ave 13903 max 13903 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: 582850.0 ave 582850 max 582850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582850 Ave neighs/atom = 199.26496 Neighbor list builds = 2 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.77 | 10.77 | 10.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -13131.266 0 -13131.266 16365.925 30123.028 102 0 -13132.37 0 -13132.37 -7.3170657 30242.979 Loop time of 0.540651 on 1 procs for 6 steps with 2925 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13131.2659421523 -13132.3601232524 -13132.3701873218 Force two-norm initial, final = 579.74429 1.0351095 Force max component initial, final = 493.22928 0.68369735 Final line search alpha, max atom move = 2.6729150e-05 1.8274649e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52796 | 0.52796 | 0.52796 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028872 | 0.0028872 | 0.0028872 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0098 | | | 1.81 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13805.0 ave 13805 max 13805 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: 582960.0 ave 582960 max 582960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582960 Ave neighs/atom = 199.30256 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 10.29 | 10.29 | 10.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13132.37 0 -13132.37 -7.3170657 Loop time of 6.285e-06 on 1 procs for 0 steps with 2925 atoms 175.0% 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 | | 6.285e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13829.0 ave 13829 max 13829 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: 582556.0 ave 582556 max 582556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582556 Ave neighs/atom = 199.16444 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 10.29 | 10.29 | 10.29 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 -13132.37 -13132.37 38.107186 132.74751 5.978487 -7.3170657 -7.3170657 19.761482 -5.5007912 -36.211888 2.1503876 990.54898 Loop time of 6.735e-06 on 1 procs for 0 steps with 2925 atoms 282.1% 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 | | 6.735e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13829.0 ave 13829 max 13829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291278.0 ave 291278 max 291278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 582556.0 ave 582556 max 582556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582556 Ave neighs/atom = 199.16444 Neighbor list builds = 0 Dangerous builds = 0 2925 -13132.370187329 eV 2.15038758771002 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13