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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -42.376770 0.0000000) to (14.124284 42.376770 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4324169 5.4324169 3.9173716 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -42.376770 0.0000000) to (14.124284 42.376770 3.9173716) create_atoms CPU = 0.002 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4324169 5.4324169 3.9173716 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -42.376770 0.0000000) to (14.124284 42.376770 3.9173716) create_atoms CPU = 0.001 seconds 158 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 = 5 27 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 308 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_020840179467_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 = 5 27 2 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) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1757.9881 0 -1757.9881 2304.8593 39 0 -1767.9764 0 -1767.9764 -10061.741 Loop time of 0.968652 on 1 procs for 39 steps with 308 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 = -1757.98811767885 -1767.9746569166 -1767.97636746513 Force two-norm initial, final = 23.745408 0.16210895 Force max component initial, final = 8.9284441 0.035477286 Final line search alpha, max atom move = 1.0000000 0.035477286 Iterations, force evaluations = 39 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96063 | 0.96063 | 0.96063 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043152 | 0.0043152 | 0.0043152 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003705 | | | 0.38 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2396.00 ave 2396 max 2396 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: 23668.0 ave 23668 max 23668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23668 Ave neighs/atom = 76.844156 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 27 2 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -1767.9764 0 -1767.9764 -10061.741 4689.4192 43 0 -1768.033 0 -1768.033 -2597.2681 4669.0227 Loop time of 0.0934871 on 1 procs for 4 steps with 308 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 = -1767.97636746514 -1768.03207546433 -1768.03299165501 Force two-norm initial, final = 35.730804 0.21639621 Force max component initial, final = 26.838542 0.062028010 Final line search alpha, max atom move = 0.00036634364 2.2723567e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09178 | 0.09178 | 0.09178 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037302 | 0.00037302 | 0.00037302 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001334 | | | 1.43 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2428.00 ave 2428 max 2428 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: 23688.0 ave 23688 max 23688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23688 Ave neighs/atom = 76.909091 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 = 5 27 2 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) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1768.033 0 -1768.033 -2597.2681 Loop time of 6.957e-06 on 1 procs for 0 steps with 308 atoms 201.2% 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 | | 6.957e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2428.00 ave 2428 max 2428 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: 23688.0 ave 23688 max 23688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23688 Ave neighs/atom = 76.909091 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 = 5 27 2 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) = 4.562 | 4.562 | 4.562 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 -1768.033 -1768.033 14.106934 84.753539 3.9051301 -2597.2681 -2597.2681 -8.9638035 -7785.2254 2.3847824 2.5092762 189.53952 Loop time of 6.675e-06 on 1 procs for 0 steps with 308 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 | | 6.675e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2428.00 ave 2428 max 2428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11844.0 ave 11844 max 11844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23688.0 ave 23688 max 23688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23688 Ave neighs/atom = 76.909091 Neighbor list builds = 0 Dangerous builds = 0 308 -1768.03299165501 eV 2.5092761546125 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01