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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -37.515894 0.0000000) to (26.525720 37.515894 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9350178 4.7981787 4.0451344 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -37.515894 0.0000000) to (26.525720 37.515894 4.0451344) create_atoms CPU = 0.001 seconds 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9350178 4.7981787 4.0451344 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -37.515894 0.0000000) to (26.525720 37.515894 4.0451344) create_atoms CPU = 0.001 seconds 346 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 = 7 20 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 12 atoms, new total = 680 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 = 7 20 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) = 4.928 | 4.928 | 4.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2867.133 0 -2867.133 -4078.5783 181 0 -2935.3676 0 -2935.3676 -2424.8072 Loop time of 1.97363 on 1 procs for 181 steps with 680 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 = -2867.13295342421 -2935.36479474572 -2935.3675940417 Force two-norm initial, final = 50.373182 0.24002026 Force max component initial, final = 10.246016 0.044111632 Final line search alpha, max atom move = 1.0000000 0.044111632 Iterations, force evaluations = 181 354 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9281 | 1.9281 | 1.9281 | 0.0 | 97.69 Neigh | 0.020324 | 0.020324 | 0.020324 | 0.0 | 1.03 Comm | 0.014719 | 0.014719 | 0.014719 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01047 | | | 0.53 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5731.00 ave 5731 max 5731 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: 112552.0 ave 112552 max 112552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112552 Ave neighs/atom = 165.51765 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 = 7 20 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 : 181 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press Volume 181 0 -2935.3676 0 -2935.3676 -2424.8072 8050.9187 249 0 -2953.3971 0 -2953.3971 -34763.82 8106.0278 Loop time of 0.45538 on 1 procs for 68 steps with 680 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 = -2935.36759404167 -2953.39448956639 -2953.39705007134 Force two-norm initial, final = 613.48890 6.0396550 Force max component initial, final = 561.32270 4.3785842 Final line search alpha, max atom move = 0.00012563909 0.00055012132 Iterations, force evaluations = 68 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43125 | 0.43125 | 0.43125 | 0.0 | 94.70 Neigh | 0.0065158 | 0.0065158 | 0.0065158 | 0.0 | 1.43 Comm | 0.0031682 | 0.0031682 | 0.0031682 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01445 | | | 3.17 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5523.00 ave 5523 max 5523 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: 111584.0 ave 111584 max 111584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111584 Ave neighs/atom = 164.09412 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2953.3971 0 -2953.3971 -34763.82 Loop time of 1.669e-06 on 1 procs for 0 steps with 680 atoms 179.7% 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 | | 1.669e-06 | | |100.00 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5510.00 ave 5510 max 5510 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: 111600.0 ave 111600 max 111600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111600 Ave neighs/atom = 164.11765 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 = 7 20 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) = 5.064 | 5.064 | 5.064 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 -2953.3971 -2953.3971 25.479566 75.031788 4.240048 -34763.82 -34763.82 -534.03932 -102850.28 -907.13889 2.4019006 2597.0794 Loop time of 1.764e-06 on 1 procs for 0 steps with 680 atoms 226.8% 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 | | 1.764e-06 | | |100.00 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5510.00 ave 5510 max 5510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55800.0 ave 55800 max 55800 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111600.0 ave 111600 max 111600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111600 Ave neighs/atom = 164.11765 Neighbor list builds = 0 Dangerous builds = 0 680 -2953.39705007134 eV 2.40190061805547 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02