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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -67.341580 0.0000000) to (38.879679 67.341580 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363461 5.1518148 6.0968202 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.341580 0.0000000) to (38.879679 67.341580 6.0968202) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363461 5.1518148 6.0968202 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.341580 0.0000000) to (38.879679 67.341580 6.0968202) create_atoms CPU = 0.009 seconds 1466 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 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, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12499.008 0 -12499.008 36721.6 111 0 -12974.266 0 -12974.266 5746.0718 Loop time of 12.1266 on 1 procs for 111 steps with 2926 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 = -12499.0077062281 -12974.2542949594 -12974.2658243693 Force two-norm initial, final = 836.27941 0.53677187 Force max component initial, final = 247.18840 0.14566334 Final line search alpha, max atom move = 1.0000000 0.14566334 Iterations, force evaluations = 111 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.774 | 11.774 | 11.774 | 0.0 | 97.09 Neigh | 0.21788 | 0.21788 | 0.21788 | 0.0 | 1.80 Comm | 0.068671 | 0.068671 | 0.068671 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06607 | | | 0.54 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12348.0 ave 12348 max 12348 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: 519428.0 ave 519428 max 519428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519428 Ave neighs/atom = 177.52153 Neighbor list builds = 3 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.003 | 7.003 | 7.003 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -12974.266 0 -12974.266 5746.0718 31925.621 115 0 -12974.627 0 -12974.627 362.95078 32016.137 Loop time of 0.33848 on 1 procs for 4 steps with 2926 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 = -12974.2658243694 -12974.6205877076 -12974.6274743211 Force two-norm initial, final = 238.01495 13.942491 Force max component initial, final = 221.80231 11.753529 Final line search alpha, max atom move = 4.8242502e-05 0.00056701964 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33034 | 0.33034 | 0.33034 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019617 | 0.0019617 | 0.0019617 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006176 | | | 1.82 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12338.0 ave 12338 max 12338 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: 517192.0 ave 517192 max 517192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517192 Ave neighs/atom = 176.75735 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.141 | 7.141 | 7.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12974.627 0 -12974.627 362.95078 Loop time of 6.726e-06 on 1 procs for 0 steps with 2926 atoms 193.3% 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 | | 6.726e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12326.0 ave 12326 max 12326 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: 516144.0 ave 516144 max 516144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 516144 Ave neighs/atom = 176.39918 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.141 | 7.141 | 7.141 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 -12974.627 -12974.627 38.869587 135.11878 6.0959766 362.95078 362.95078 161.49729 590.08167 337.27339 2.2655822 915.6868 Loop time of 6.896e-06 on 1 procs for 0 steps with 2926 atoms 290.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12326.0 ave 12326 max 12326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 258072.0 ave 258072 max 258072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 516144.0 ave 516144 max 516144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 516144 Ave neighs/atom = 176.39918 Neighbor list builds = 0 Dangerous builds = 0 2926 -12974.6274743211 eV 2.26558222313732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13