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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -46.245318 0.0000000) to (32.700378 46.245318 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5829913 6.2036402 5.1069410 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.245318 0.0000000) to (32.700378 46.245318 5.1069410) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5829913 6.2036402 5.1069410 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.245318 0.0000000) to (32.700378 46.245318 5.1069410) create_atoms CPU = 0.002 seconds 660 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 35 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 1316 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5416.2678 0 -5416.2678 34727.79 68 0 -5573.7437 0 -5573.7437 9407.396 Loop time of 8.50331 on 1 procs for 68 steps with 1316 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 = -5416.2677912681 -5573.73906308051 -5573.74370556517 Force two-norm initial, final = 156.64422 0.25709264 Force max component initial, final = 32.783400 0.022139811 Final line search alpha, max atom move = 1.0000000 0.022139811 Iterations, force evaluations = 68 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4901 | 8.4901 | 8.4901 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0051714 | 0.0051714 | 0.0051714 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007997 | | | 0.09 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4504.00 ave 4504 max 4504 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: 71328.0 ave 71328 max 71328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71328 Ave neighs/atom = 54.200608 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.405 | 5.405 | 5.405 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -5573.7437 0 -5573.7437 9407.396 15445.834 76 0 -5574.335 0 -5574.335 -50.753948 15533.134 Loop time of 0.688876 on 1 procs for 8 steps with 1316 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 = -5573.74370556516 -5574.33487885668 -5574.33500318454 Force two-norm initial, final = 194.37171 1.4237836 Force max component initial, final = 183.64792 1.1654726 Final line search alpha, max atom move = 0.00043246642 0.00050402776 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68613 | 0.68613 | 0.68613 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041351 | 0.00041351 | 0.00041351 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002332 | | | 0.34 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4976.00 ave 4976 max 4976 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: 70984.0 ave 70984 max 70984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70984 Ave neighs/atom = 53.939210 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.543 | 5.543 | 5.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5574.335 0 -5574.335 -50.753948 Loop time of 1.723e-06 on 1 procs for 0 steps with 1316 atoms 174.1% 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 | | 1.723e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4964.00 ave 4964 max 4964 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: 70984.0 ave 70984 max 70984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70984 Ave neighs/atom = 53.939210 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.543 | 5.543 | 5.543 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 -5574.335 -5574.335 32.688576 93.114906 5.1032149 -50.753948 -50.753948 -120.17014 -62.230939 30.139239 2.3015618 540.07003 Loop time of 1.658e-06 on 1 procs for 0 steps with 1316 atoms 180.9% 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 | | 1.658e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4964.00 ave 4964 max 4964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35492.0 ave 35492 max 35492 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70984.0 ave 70984 max 70984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70984 Ave neighs/atom = 53.939210 Neighbor list builds = 0 Dangerous builds = 0 1316 -5574.33500318454 eV 2.30156180022952 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09