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 = 3.5898365 3.5898365 3.5898365 Created orthogonal box = (0.0000000 -38.328965 0.0000000) to (27.102671 38.328965 5.0767954) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2303400 6.0519418 5.0767954 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.328965 0.0000000) to (27.102671 38.328965 5.0767954) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2303400 6.0519418 5.0767954 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.328965 0.0000000) to (27.102671 38.328965 5.0767954) create_atoms CPU = 0.001 seconds 458 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 21 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2611.5701 0 -2611.5701 98931.638 150 0 -3178.394 0 -3178.394 4180.753 Loop time of 4.11716 on 1 procs for 150 steps with 908 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2611.57010545563 -3178.3910648878 -3178.39404368003 Force two-norm initial, final = 940.14881 0.18628335 Force max component initial, final = 223.72426 0.050476333 Final line search alpha, max atom move = 1.0000000 0.050476333 Iterations, force evaluations = 150 287 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0551 | 4.0551 | 4.0551 | 0.0 | 98.49 Neigh | 0.027951 | 0.027951 | 0.027951 | 0.0 | 0.68 Comm | 0.018339 | 0.018339 | 0.018339 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01577 | | | 0.38 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5860.00 ave 5860 max 5860 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: 146364.0 ave 146364 max 146364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146364 Ave neighs/atom = 161.19383 Neighbor list builds = 3 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 150 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 150 0 -3178.394 0 -3178.394 4180.753 10547.726 154 0 -3178.4723 0 -3178.4723 179.86485 10579.371 Loop time of 0.0771144 on 1 procs for 4 steps with 908 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 = -3178.39404368003 -3178.471618367 -3178.47231338118 Force two-norm initial, final = 55.070002 2.7537589 Force max component initial, final = 50.014136 2.0528272 Final line search alpha, max atom move = 0.00022649448 0.00046495404 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075608 | 0.075608 | 0.075608 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027625 | 0.00027625 | 0.00027625 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00123 | | | 1.60 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5884.00 ave 5884 max 5884 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: 146848.0 ave 146848 max 146848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146848 Ave neighs/atom = 161.72687 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.123 | 5.123 | 5.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3178.4723 0 -3178.4723 179.86485 Loop time of 2.217e-06 on 1 procs for 0 steps with 908 atoms 135.3% 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 | | 2.217e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5884.00 ave 5884 max 5884 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: 144548.0 ave 144548 max 144548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144548 Ave neighs/atom = 159.19383 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.123 | 5.123 | 5.123 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 -3178.4723 -3178.4723 27.098431 76.890221 5.0774375 179.86485 179.86485 -44.232658 311.82931 271.99789 2.3351332 721.83993 Loop time of 1.929e-06 on 1 procs for 0 steps with 908 atoms 207.4% 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 | | 1.929e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5884.00 ave 5884 max 5884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72274.0 ave 72274 max 72274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 144548.0 ave 144548 max 144548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144548 Ave neighs/atom = 159.19383 Neighbor list builds = 0 Dangerous builds = 0 908 -3178.47231338118 eV 2.33513323963785 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04