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 -51.230198 0.0000000) to (24.148300 51.230198 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0838527 6.2909467 5.5400000 Created 460 atoms using lattice units in orthogonal box = (0.0000000 -51.230198 0.0000000) to (24.148300 51.230198 5.5400000) create_atoms CPU = 0.004 seconds 460 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0838527 6.2909467 5.5400000 Created 460 atoms using lattice units in orthogonal box = (0.0000000 -51.230198 0.0000000) to (24.148300 51.230198 5.5400000) create_atoms CPU = 0.003 seconds 460 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 = 8 32 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 24 atoms, new total = 896 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 = 8 32 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5129.2502 0 -5129.2502 -3112.8652 47 0 -5144.4827 0 -5144.4827 -16648.773 Loop time of 3.02282 on 1 procs for 47 steps with 896 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 = -5129.25021619754 -5144.47771136885 -5144.48265797871 Force two-norm initial, final = 12.450436 0.23964832 Force max component initial, final = 2.8935348 0.023728799 Final line search alpha, max atom move = 1.0000000 0.023728799 Iterations, force evaluations = 47 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0027 | 3.0027 | 3.0027 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010091 | 0.010091 | 0.010091 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009986 | | | 0.33 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4543.00 ave 4543 max 4543 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: 68680.0 ave 68680 max 68680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68680 Ave neighs/atom = 76.651786 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 = 8 32 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -5144.4827 0 -5144.4827 -16648.773 13707.314 53 0 -5144.844 0 -5144.844 -7034.6669 13629.429 Loop time of 0.272016 on 1 procs for 6 steps with 896 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5144.4826579787 -5144.83957612197 -5144.84400986868 Force two-norm initial, final = 143.80857 5.2659773 Force max component initial, final = 124.47501 4.3296778 Final line search alpha, max atom move = 0.00010621353 0.00045987035 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26798 | 0.26798 | 0.26798 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091613 | 0.00091613 | 0.00091613 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003121 | | | 1.15 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4536.00 ave 4536 max 4536 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: 69120.0 ave 69120 max 69120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69120 Ave neighs/atom = 77.142857 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 = 8 32 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5144.844 0 -5144.844 -7034.6669 Loop time of 6.364e-06 on 1 procs for 0 steps with 896 atoms 172.8% 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 | | 6.364e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4543.00 ave 4543 max 4543 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: 69120.0 ave 69120 max 69120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69120 Ave neighs/atom = 77.142857 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 = 8 32 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) = 4.722 | 4.722 | 4.722 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 -5144.844 -5144.844 24.016978 102.4604 5.5386417 -7034.6669 -7034.6669 -506.19759 -20248.302 -349.50078 2.573926 647.18952 Loop time of 6.726e-06 on 1 procs for 0 steps with 896 atoms 297.4% 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: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4543.00 ave 4543 max 4543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34560.0 ave 34560 max 34560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69120.0 ave 69120 max 69120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69120 Ave neighs/atom = 77.142857 Neighbor list builds = 0 Dangerous builds = 0 896 -5144.84400986868 eV 2.57392600548266 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03