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 -42.509621 0.0000000) to (52.063440 42.509621 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9923847 5.2409121 5.7450679 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -42.509621 0.0000000) to (52.063440 42.509621 8.6176019) create_atoms CPU = 0.007 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9923847 5.2409121 5.7450679 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.509621 0.0000000) to (52.063440 42.509621 8.6176019) create_atoms CPU = 0.006 seconds 1754 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3494 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11374.09 0 -11374.09 238433.44 71 0 -15264.715 0 -15264.715 3828.751 Loop time of 13.0979 on 1 procs for 71 steps with 3494 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 = -11374.0901997327 -15264.7015675477 -15264.7148447225 Force two-norm initial, final = 4076.6992 0.39743715 Force max component initial, final = 575.99260 0.054141118 Final line search alpha, max atom move = 1.0000000 0.054141118 Iterations, force evaluations = 71 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.76 | 12.76 | 12.76 | 0.0 | 97.42 Neigh | 0.24844 | 0.24844 | 0.24844 | 0.0 | 1.90 Comm | 0.04434 | 0.04434 | 0.04434 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04475 | | | 0.34 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13526.0 ave 13526 max 13526 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: 860664.0 ave 860664 max 860664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 860664 Ave neighs/atom = 246.32627 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -15264.715 0 -15264.715 3828.751 38144.903 76 0 -15265.192 0 -15265.192 -246.97872 38237.827 Loop time of 0.733736 on 1 procs for 5 steps with 3494 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15264.7148447225 -15265.1881909023 -15265.1915040516 Force two-norm initial, final = 229.33194 11.096698 Force max component initial, final = 225.65378 8.5172221 Final line search alpha, max atom move = 5.9800718e-05 0.00050933600 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72345 | 0.72345 | 0.72345 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001966 | 0.001966 | 0.001966 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008324 | | | 1.13 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13324.0 ave 13324 max 13324 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: 860688.0 ave 860688 max 860688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 860688 Ave neighs/atom = 246.33314 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.70 | 11.70 | 11.70 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15265.192 0 -15265.192 -246.97872 Loop time of 6.585e-06 on 1 procs for 0 steps with 3494 atoms 197.4% 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 | | 6.585e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13312.0 ave 13312 max 13312 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: 859496.0 ave 859496 max 859496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 859496 Ave neighs/atom = 245.99199 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.70 | 11.70 | 11.70 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 -15265.192 -15265.192 51.983438 85.388681 8.6144568 -246.97872 -246.97872 -356.3258 -107.65255 -276.95782 2.1531708 1320.6498 Loop time of 6.676e-06 on 1 procs for 0 steps with 3494 atoms 299.6% 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 | | 6.676e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13312.0 ave 13312 max 13312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 429748.0 ave 429748 max 429748 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 859496.0 ave 859496 max 859496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 859496 Ave neighs/atom = 245.99199 Neighbor list builds = 0 Dangerous builds = 0 3494 -15265.1915040516 eV 2.15317083800889 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15