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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -39.840000 0.0000000) to (17.251226 39.840000 6.0992295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7504087 4.9800000 6.0992295 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -39.840000 0.0000000) to (17.251226 39.840000 6.0992295) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7504087 4.9800000 6.0992295 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.840000 0.0000000) to (17.251226 39.840000 6.0992295) create_atoms CPU = 0.001 seconds 396 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 = 6 25 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 = 772 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_500937681860_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 = 6 25 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) = 4.572 | 4.572 | 4.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3050.7081 0 -3050.7081 121688.41 59 0 -3412.4949 0 -3412.4949 26869.92 Loop time of 4.51777 on 1 procs for 59 steps with 772 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 = -3050.70810898584 -3412.49234723403 -3412.49492582253 Force two-norm initial, final = 464.87406 0.23670936 Force max component initial, final = 99.008051 0.055245325 Final line search alpha, max atom move = 1.0000000 0.055245325 Iterations, force evaluations = 59 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5001 | 4.5001 | 4.5001 | 0.0 | 99.61 Neigh | 0.00585 | 0.00585 | 0.00585 | 0.0 | 0.13 Comm | 0.0054438 | 0.0054438 | 0.0054438 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006359 | | | 0.14 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3974.00 ave 3974 max 3974 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: 69720.0 ave 69720 max 69720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69720 Ave neighs/atom = 90.310881 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 25 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -3412.4949 0 -3412.4949 26869.92 8383.8648 74 0 -3414.2758 0 -3414.2758 -93.506065 8501.7823 Loop time of 0.688393 on 1 procs for 15 steps with 772 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 = -3412.49492582253 -3414.27535075524 -3414.27575524976 Force two-norm initial, final = 283.05979 1.2858873 Force max component initial, final = 258.39014 0.59733484 Final line search alpha, max atom move = 0.00046151703 0.00027568020 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6785 | 0.6785 | 0.6785 | 0.0 | 98.56 Neigh | 0.0056264 | 0.0056264 | 0.0056264 | 0.0 | 0.82 Comm | 0.00071214 | 0.00071214 | 0.00071214 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003558 | | | 0.52 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3974.00 ave 3974 max 3974 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: 67504.0 ave 67504 max 67504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67504 Ave neighs/atom = 87.440415 Neighbor list builds = 1 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 = 6 25 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) = 4.710 | 4.710 | 4.710 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3414.2758 0 -3414.2758 -93.506065 Loop time of 2.466e-06 on 1 procs for 0 steps with 772 atoms 202.8% 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 | | 2.466e-06 | | |100.00 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3974.00 ave 3974 max 3974 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: 67520.0 ave 67520 max 67520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67520 Ave neighs/atom = 87.461140 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 = 6 25 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) = 4.710 | 4.710 | 4.710 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 -3414.2758 -3414.2758 17.236293 80.812531 6.1036187 -93.506065 -93.506065 -64.289396 -114.16884 -102.05996 2.2224495 471.53726 Loop time of 2.346e-06 on 1 procs for 0 steps with 772 atoms 426.3% 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 | | 2.346e-06 | | |100.00 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3974.00 ave 3974 max 3974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33760.0 ave 33760 max 33760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67520.0 ave 67520 max 67520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67520 Ave neighs/atom = 87.461140 Neighbor list builds = 0 Dangerous builds = 0 772 -3414.27575524976 eV 2.2224495303492 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05