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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -55.403427 0.0000000) to (33.927532 55.403427 8.6176017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4721825 5.3616220 5.7450678 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -55.403427 0.0000000) to (33.927532 55.403427 8.6176017) create_atoms CPU = 0.002 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4721825 5.3616220 5.7450678 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -55.403427 0.0000000) to (33.927532 55.403427 8.6176017) create_atoms CPU = 0.002 seconds 1491 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 ghost atom cutoff = 8 binsize = 4, bins = 9 28 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2976 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_832600236922_005#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 ghost atom cutoff = 8 binsize = 4, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.365 | 7.365 | 7.365 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11040.208 0 -11040.208 155755.57 68 0 -13012.121 0 -13012.121 6568.2958 Loop time of 3.68821 on 1 procs for 68 steps with 2976 atoms 96.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11040.2080923705 -13012.1088740735 -13012.1209499456 Force two-norm initial, final = 2252.9672 0.34594635 Force max component initial, final = 326.25936 0.081916730 Final line search alpha, max atom move = 1.0000000 0.081916730 Iterations, force evaluations = 68 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5396 | 3.5396 | 3.5396 | 0.0 | 95.97 Neigh | 0.10617 | 0.10617 | 0.10617 | 0.0 | 2.88 Comm | 0.020496 | 0.020496 | 0.020496 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02196 | | | 0.60 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11285.0 ave 11285 max 11285 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: 591256.0 ave 591256 max 591256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 591256 Ave neighs/atom = 198.67473 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 ghost atom cutoff = 8 binsize = 4, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.367 | 7.367 | 7.367 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -13012.121 0 -13012.121 6568.2958 32397.038 73 0 -13012.593 0 -13012.593 -44.996799 32520.895 Loop time of 0.196597 on 1 procs for 5 steps with 2976 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 = -13012.1209499457 -13012.5918332708 -13012.5926771199 Force two-norm initial, final = 261.46766 3.7495192 Force max component initial, final = 234.13385 2.8248413 Final line search alpha, max atom move = 9.4023858e-05 0.00026560248 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19197 | 0.19197 | 0.19197 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064325 | 0.00064325 | 0.00064325 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00398 | | | 2.02 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11601.0 ave 11601 max 11601 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: 591732.0 ave 591732 max 591732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 591732 Ave neighs/atom = 198.83468 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 ghost atom cutoff = 8 binsize = 4, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.505 | 7.505 | 7.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13012.593 0 -13012.593 -44.996799 Loop time of 2.047e-06 on 1 procs for 0 steps with 2976 atoms 195.4% 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 | | 2.047e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11601.0 ave 11601 max 11601 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: 591342.0 ave 591342 max 591342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 591342 Ave neighs/atom = 198.70363 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 ghost atom cutoff = 8 binsize = 4, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.505 | 7.505 | 7.505 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 -13012.593 -13012.593 33.924745 111.26284 8.6158026 -44.996799 -44.996799 -139.15739 86.801234 -82.634246 2.18341 871.85912 Loop time of 2.595e-06 on 1 procs for 0 steps with 2976 atoms 269.7% 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 | | 2.595e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11601.0 ave 11601 max 11601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 295671.0 ave 295671 max 295671 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 591342.0 ave 591342 max 591342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 591342 Ave neighs/atom = 198.70363 Neighbor list builds = 0 Dangerous builds = 0 2976 -13012.5926771199 eV 2.1834100331192 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04