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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -48.719303 0.0000000) to (59.668717 48.719303 9.8764362) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7216578 6.0064894 6.5842908 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -48.719303 0.0000000) to (59.668717 48.719303 9.8764362) create_atoms CPU = 0.003 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7216578 6.0064894 6.5842908 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -48.719303 0.0000000) to (59.668717 48.719303 9.8764362) create_atoms CPU = 0.002 seconds 1755 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.381 | 7.381 | 7.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11442.308 0 -11442.308 13231.791 60 0 -11746.045 0 -11746.045 4273.9627 Loop time of 3.29052 on 1 procs for 60 steps with 3504 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 = -11442.3076664463 -11746.0338966539 -11746.0452555242 Force two-norm initial, final = 92.630354 0.30237748 Force max component initial, final = 7.6665267 0.062912214 Final line search alpha, max atom move = 1.0000000 0.062912214 Iterations, force evaluations = 60 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2166 | 3.2166 | 3.2166 | 0.0 | 97.75 Neigh | 0.039193 | 0.039193 | 0.039193 | 0.0 | 1.19 Comm | 0.014476 | 0.014476 | 0.014476 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02027 | | | 0.62 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11139.0 ave 11139 max 11139 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: 605436.0 ave 605436 max 605436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605436 Ave neighs/atom = 172.78425 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.381 | 7.381 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -11746.045 0 -11746.045 4273.9627 57421.962 66 0 -11746.651 0 -11746.651 -2.1661509 57707.779 Loop time of 0.256038 on 1 procs for 6 steps with 3504 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 = -11746.0452555241 -11746.6502697391 -11746.6514813991 Force two-norm initial, final = 285.25746 0.74028468 Force max component initial, final = 232.71271 0.57955812 Final line search alpha, max atom move = 7.0440995e-05 4.0824650e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25009 | 0.25009 | 0.25009 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080239 | 0.00080239 | 0.00080239 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00515 | | | 2.01 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11140.0 ave 11140 max 11140 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: 606528.0 ave 606528 max 606528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 606528 Ave neighs/atom = 173.09589 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.519 | 7.519 | 7.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11746.651 0 -11746.651 -2.1661509 Loop time of 2.022e-06 on 1 procs for 0 steps with 3504 atoms 197.8% 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 | | 2.022e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11098.0 ave 11098 max 11098 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: 605214.0 ave 605214 max 605214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605214 Ave neighs/atom = 172.72089 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.519 | 7.519 | 7.519 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 -11746.651 -11746.651 59.729751 97.932546 9.8654434 -2.1661509 -2.1661509 -16.107087 3.0767456 6.5318884 2.5646096 2131.665 Loop time of 3.142e-06 on 1 procs for 0 steps with 3504 atoms 191.0% 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 | | 3.142e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11098.0 ave 11098 max 11098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302607.0 ave 302607 max 302607 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 605214.0 ave 605214 max 605214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605214 Ave neighs/atom = 172.72089 Neighbor list builds = 0 Dangerous builds = 0 3504 -11746.6514813991 eV 2.56460964671763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04