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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -52.428710 0.0000000) to (30.267395 52.428710 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4858703 6.2410316 7.0055406 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.428710 0.0000000) to (30.267395 52.428710 7.0055406) create_atoms CPU = 0.005 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4858703 6.2410316 7.0055406 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.428710 0.0000000) to (30.267395 52.428710 7.0055406) create_atoms CPU = 0.004 seconds 676 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 33 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1328 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_099716416216_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4427.6593 0 -4427.6593 1125.0725 69 0 -4445.8792 0 -4445.8792 -4264.1135 Loop time of 12.4502 on 1 procs for 69 steps with 1328 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 = -4427.65934121038 -4445.87554441812 -4445.87921537365 Force two-norm initial, final = 21.375923 0.12848677 Force max component initial, final = 4.4487013 0.0079936526 Final line search alpha, max atom move = 1.0000000 0.0079936526 Iterations, force evaluations = 69 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.388 | 12.388 | 12.388 | 0.0 | 99.50 Neigh | 0.028713 | 0.028713 | 0.028713 | 0.0 | 0.23 Comm | 0.014512 | 0.014512 | 0.014512 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01878 | | | 0.15 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5065.00 ave 5065 max 5065 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: 101320.0 ave 101320 max 101320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101320 Ave neighs/atom = 76.295181 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4445.8792 0 -4445.8792 -4264.1135 22233.911 72 0 -4445.9836 0 -4445.9836 -1051.1094 22141.718 Loop time of 0.49023 on 1 procs for 3 steps with 1328 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 = -4445.87921537366 -4445.9830110759 -4445.98362504399 Force two-norm initial, final = 71.022774 1.0021250 Force max component initial, final = 51.782819 0.86185237 Final line search alpha, max atom move = 0.00021404364 0.00018447402 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48754 | 0.48754 | 0.48754 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054203 | 0.00054203 | 0.00054203 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002144 | | | 0.44 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5122.00 ave 5122 max 5122 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: 101688.0 ave 101688 max 101688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101688 Ave neighs/atom = 76.572289 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.184 | 5.184 | 5.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4445.9836 0 -4445.9836 -1051.1094 Loop time of 6.295e-06 on 1 procs for 0 steps with 1328 atoms 174.7% 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 | | 6.295e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5137.00 ave 5137 max 5137 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: 101800.0 ave 101800 max 101800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101800 Ave neighs/atom = 76.656627 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.184 | 5.184 | 5.184 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 -4445.9836 -4445.9836 30.200786 104.85742 6.991879 -1051.1094 -1051.1094 -35.349138 -3180.2212 62.24209 2.6204242 1155.6665 Loop time of 6.194e-06 on 1 procs for 0 steps with 1328 atoms 306.7% 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 | | 6.194e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5137.00 ave 5137 max 5137 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50900.0 ave 50900 max 50900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101800.0 ave 101800 max 101800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101800 Ave neighs/atom = 76.656627 Neighbor list builds = 0 Dangerous builds = 0 1328 -4445.98362504399 eV 2.62042422189051 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13