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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -42.532616 0.0000000) to (52.091603 42.532616 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950853 5.2437472 5.7481757 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -42.532616 0.0000000) to (52.091603 42.532616 8.6222635) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950853 5.2437472 5.7481757 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -42.532616 0.0000000) to (52.091603 42.532616 8.6222635) 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 3490 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13677.406 0 -13677.406 129763.92 60 0 -15471.958 0 -15471.958 314.84199 Loop time of 3.96655 on 1 procs for 60 steps with 3490 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13677.4058283463 -15471.9445063185 -15471.9583286028 Force two-norm initial, final = 2379.5166 0.39001238 Force max component initial, final = 363.08628 0.028776728 Final line search alpha, max atom move = 1.0000000 0.028776728 Iterations, force evaluations = 60 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8338 | 3.8338 | 3.8338 | 0.0 | 96.65 Neigh | 0.091321 | 0.091321 | 0.091321 | 0.0 | 2.30 Comm | 0.017951 | 0.017951 | 0.017951 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0235 | | | 0.59 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13009.0 ave 13009 max 13009 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: 779280.0 ave 779280 max 779280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 779280 Ave neighs/atom = 223.28940 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -15471.958 0 -15471.958 314.84199 38206.839 61 0 -15471.97 0 -15471.97 -462.65527 38223.398 Loop time of 0.116615 on 1 procs for 1 steps with 3490 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 = -15471.9583286028 -15471.9583286028 -15471.9695562618 Force two-norm initial, final = 34.193118 20.870543 Force max component initial, final = 21.476400 17.512343 Final line search alpha, max atom move = 4.6562738e-05 0.00081542265 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11464 | 0.11464 | 0.11464 | 0.0 | 98.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033548 | 0.00033548 | 0.00033548 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001638 | | | 1.40 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12916.0 ave 12916 max 12916 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: 779396.0 ave 779396 max 779396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 779396 Ave neighs/atom = 223.32264 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.30 | 11.30 | 11.30 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15471.97 0 -15471.97 -462.65527 Loop time of 2.337e-06 on 1 procs for 0 steps with 3490 atoms 171.2% 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 | | 2.337e-06 | | |100.00 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12878.0 ave 12878 max 12878 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: 779398.0 ave 779398 max 779398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 779398 Ave neighs/atom = 223.32321 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 11.30 | 11.30 | 11.30 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 -15471.97 -15471.97 52.110982 85.035302 8.6258276 -462.65527 -462.65527 -248.32732 -733.7912 -405.84727 2.2835966 1451.7407 Loop time of 2.925e-06 on 1 procs for 0 steps with 3490 atoms 239.3% 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 | | 2.925e-06 | | |100.00 Nlocal: 3490.00 ave 3490 max 3490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12878.0 ave 12878 max 12878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 389699.0 ave 389699 max 389699 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 779398.0 ave 779398 max 779398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 779398 Ave neighs/atom = 223.32321 Neighbor list builds = 0 Dangerous builds = 0 3490 -15376.8272639798 eV 2.28359660992925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05