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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -63.753432 0.0000000) to (22.538997 63.753432 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0470481 5.4420656 4.9780318 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.753432 0.0000000) to (22.538997 63.753432 4.9780318) create_atoms CPU = 0.005 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0470481 5.4420656 4.9780318 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.753432 0.0000000) to (22.538997 63.753432 4.9780318) create_atoms CPU = 0.005 seconds 658 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5762.7756 0 -5762.7756 5214.084 33 0 -5791.6157 0 -5791.6157 -6638.0834 Loop time of 1.76219 on 1 procs for 33 steps with 1304 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 = -5762.77559379376 -5791.61001002835 -5791.61574410404 Force two-norm initial, final = 44.044642 0.25257232 Force max component initial, final = 13.061608 0.023924061 Final line search alpha, max atom move = 1.0000000 0.023924061 Iterations, force evaluations = 33 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7008 | 1.7008 | 1.7008 | 0.0 | 96.52 Neigh | 0.03837 | 0.03837 | 0.03837 | 0.0 | 2.18 Comm | 0.013184 | 0.013184 | 0.013184 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009836 | | | 0.56 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10342.0 ave 10342 max 10342 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: 292724.0 ave 292724 max 292724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292724 Ave neighs/atom = 224.48160 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -5791.6157 0 -5791.6157 -6638.0834 14306.25 35 0 -5791.6589 0 -5791.6589 -2963.471 14276.55 Loop time of 0.126209 on 1 procs for 2 steps with 1304 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 = -5791.61574410404 -5791.65430672711 -5791.65894235069 Force two-norm initial, final = 54.012432 4.2692414 Force max component initial, final = 48.672575 4.2484258 Final line search alpha, max atom move = 6.0395225e-05 0.00025658463 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12296 | 0.12296 | 0.12296 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085905 | 0.00085905 | 0.00085905 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002392 | | | 1.90 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10333.0 ave 10333 max 10333 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: 292728.0 ave 292728 max 292728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292728 Ave neighs/atom = 224.48466 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5791.6589 0 -5791.6589 -2963.471 Loop time of 6.444e-06 on 1 procs for 0 steps with 1304 atoms 186.2% 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 | | 6.444e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10333.0 ave 10333 max 10333 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: 292804.0 ave 292804 max 292804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292804 Ave neighs/atom = 224.54294 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.687 | 5.687 | 5.687 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 -5791.6589 -5791.6589 22.527247 127.50686 4.9702884 -2963.471 -2963.471 476.52825 -9329.6532 -37.287948 2.3137874 414.92484 Loop time of 6.445e-06 on 1 procs for 0 steps with 1304 atoms 294.8% 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 | | 6.445e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10333.0 ave 10333 max 10333 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146402.0 ave 146402 max 146402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292804.0 ave 292804 max 292804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292804 Ave neighs/atom = 224.54294 Neighbor list builds = 0 Dangerous builds = 0 1304 -5756.14930576509 eV 2.31378741073518 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02