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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -42.256701 0.0000000) to (14.940000 42.256701 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9800000 5.8689862 4.9800000 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -42.256701 0.0000000) to (14.940000 42.256701 4.9800000) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9800000 5.8689862 4.9800000 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -42.256701 0.0000000) to (14.940000 42.256701 4.9800000) create_atoms CPU = 0.001 seconds 292 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 576 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_000553624872_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2423.5071 0 -2423.5071 68392.763 43 0 -2550.484 0 -2550.484 14803.458 Loop time of 1.68982 on 1 procs for 43 steps with 576 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 = -2423.5070704825 -2550.48207705697 -2550.48401462552 Force two-norm initial, final = 245.30768 0.16576870 Force max component initial, final = 54.357750 0.027202744 Final line search alpha, max atom move = 1.0000000 0.027202744 Iterations, force evaluations = 43 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.68 | 1.68 | 1.68 | 0.0 | 99.42 Neigh | 0.0036354 | 0.0036354 | 0.0036354 | 0.0 | 0.22 Comm | 0.0030564 | 0.0030564 | 0.0030564 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003111 | | | 0.18 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3277.00 ave 3277 max 3277 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: 44904.0 ave 44904 max 44904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44904 Ave neighs/atom = 77.958333 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -2550.484 0 -2550.484 14803.458 6287.8984 52 0 -2550.9044 0 -2550.9044 -96.145082 6337.6794 Loop time of 0.258014 on 1 procs for 9 steps with 576 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 = -2550.48401462552 -2550.90427996061 -2550.90439268607 Force two-norm initial, final = 118.88474 1.0052624 Force max component initial, final = 107.75910 0.77874320 Final line search alpha, max atom move = 0.00080760838 0.00062891954 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25565 | 0.25565 | 0.25565 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040207 | 0.00040207 | 0.00040207 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001964 | | | 0.76 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3304.00 ave 3304 max 3304 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: 44832.0 ave 44832 max 44832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44832 Ave neighs/atom = 77.833333 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2550.9044 0 -2550.9044 -96.145082 Loop time of 2.353e-06 on 1 procs for 0 steps with 576 atoms 170.0% 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 | | 2.353e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3255.00 ave 3255 max 3255 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: 44784.0 ave 44784 max 44784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44784 Ave neighs/atom = 77.750000 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 ghost atom cutoff = 6 binsize = 3, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.643 | 4.643 | 4.643 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 -2550.9044 -2550.9044 14.95543 85.158552 4.9762602 -96.145082 -96.145082 -197.07098 -114.39301 23.028748 2.3206347 401.88465 Loop time of 2.384e-06 on 1 procs for 0 steps with 576 atoms 167.8% 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 | | 2.384e-06 | | |100.00 Nlocal: 576.000 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3255.00 ave 3255 max 3255 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22392.0 ave 22392 max 22392 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44784.0 ave 44784 max 44784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44784 Ave neighs/atom = 77.750000 Neighbor list builds = 0 Dangerous builds = 0 576 -2550.90439268607 eV 2.32063468372658 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02