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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -37.233734 0.0000000) to (45.597971 37.233734 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2111967 4.7867898 5.1383093 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -37.233734 0.0000000) to (45.597971 37.233734 7.7074639) create_atoms CPU = 0.005 seconds 841 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2111967 4.7867898 5.1383093 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -37.233734 0.0000000) to (45.597971 37.233734 7.7074639) create_atoms CPU = 0.004 seconds 841 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1682 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.649 | 4.649 | 4.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11242.19 0 -11242.19 31367.35 39 0 -11376.54 0 -11376.54 16760.905 Loop time of 5.17208 on 1 procs for 39 steps with 1682 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 = -11242.1901613689 -11376.5319141317 -11376.5399229812 Force two-norm initial, final = 67.293126 1.2020478 Force max component initial, final = 10.990836 0.38853613 Final line search alpha, max atom move = 0.31102298 0.12084366 Iterations, force evaluations = 39 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1354 | 5.1354 | 5.1354 | 0.0 | 99.29 Neigh | 0.018327 | 0.018327 | 0.018327 | 0.0 | 0.35 Comm | 0.0067056 | 0.0067056 | 0.0067056 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01163 | | | 0.22 Nlocal: 1682.00 ave 1682 max 1682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4691.00 ave 4691 max 4691 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: 96570.0 ave 96570 max 96570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96570 Ave neighs/atom = 57.413793 Neighbor list builds = 1 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -11376.54 0 -11376.54 16760.905 26171.198 44 0 -11377.162 0 -11377.162 6072.2443 26275.895 Loop time of 0.621772 on 1 procs for 5 steps with 1682 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 = -11376.5399229812 -11377.1536047843 -11377.1623951657 Force two-norm initial, final = 316.43566 16.044159 Force max component initial, final = 290.19559 15.437433 Final line search alpha, max atom move = 3.4550099e-05 0.00053336484 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61767 | 0.61767 | 0.61767 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067146 | 0.00067146 | 0.00067146 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003434 | | | 0.55 Nlocal: 1682.00 ave 1682 max 1682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4537.00 ave 4537 max 4537 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: 96400.0 ave 96400 max 96400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96400 Ave neighs/atom = 57.312723 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.785 | 4.785 | 4.785 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11377.162 0 -11377.162 6072.2443 Loop time of 6.375e-06 on 1 procs for 0 steps with 1682 atoms 203.9% 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 | | 6.375e-06 | | |100.00 Nlocal: 1682.00 ave 1682 max 1682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 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: 96380.0 ave 96380 max 96380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96380 Ave neighs/atom = 57.300832 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.785 | 4.785 | 4.785 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 -11377.162 -11377.162 45.787335 74.467468 7.7062939 6072.2443 6072.2443 945.20882 17015.678 255.84577 2.2803827 2098.0147 Loop time of 7.256e-06 on 1 procs for 0 steps with 1682 atoms 248.1% 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 | | 7.256e-06 | | |100.00 Nlocal: 1682.00 ave 1682 max 1682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48190.0 ave 48190 max 48190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96380.0 ave 96380 max 96380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96380 Ave neighs/atom = 57.300832 Neighbor list builds = 0 Dangerous builds = 0 1682 -11377.1623951657 eV 2.28038273317788 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06