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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -45.232469 0.0000000) to (22.157312 45.232469 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9086166 5.4274109 6.6060342 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -45.232469 0.0000000) to (22.157312 45.232469 9.9090513) create_atoms CPU = 0.001 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9086166 5.4274109 6.6060342 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -45.232469 0.0000000) to (22.157312 45.232469 9.9090513) create_atoms CPU = 0.001 seconds 612 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 29 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 1176 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3918.8554 0 -3918.8554 -2223.0904 55 0 -3935.2637 0 -3935.2637 -9175.1206 Loop time of 3.26874 on 1 procs for 55 steps with 1176 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 = -3918.85540719037 -3935.26016963337 -3935.26369130103 Force two-norm initial, final = 8.6079573 0.12599362 Force max component initial, final = 1.1735634 0.0087794843 Final line search alpha, max atom move = 1.0000000 0.0087794843 Iterations, force evaluations = 55 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2601 | 3.2601 | 3.2601 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032192 | 0.0032192 | 0.0032192 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005385 | | | 0.16 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3421.00 ave 3421 max 3421 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: 62760.0 ave 62760 max 62760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62760 Ave neighs/atom = 53.367347 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3935.2637 0 -3935.2637 -9175.1206 19862.296 62 0 -3935.8144 0 -3935.8144 -1825.382 19654.637 Loop time of 0.284838 on 1 procs for 7 steps with 1176 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 = -3935.26369130104 -3935.81285741253 -3935.81441134779 Force two-norm initial, final = 144.86699 0.37101498 Force max component initial, final = 110.00356 0.19416965 Final line search alpha, max atom move = 0.00029317820 5.6926307e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28302 | 0.28302 | 0.28302 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025952 | 0.00025952 | 0.00025952 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001558 | | | 0.55 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3577.00 ave 3577 max 3577 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: 63408.0 ave 63408 max 63408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63408 Ave neighs/atom = 53.918367 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.681 | 4.681 | 4.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3935.8144 0 -3935.8144 -1825.382 Loop time of 1.694e-06 on 1 procs for 0 steps with 1176 atoms 177.1% 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 | | 1.694e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3616.00 ave 3616 max 3616 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: 63504.0 ave 63504 max 63504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63504 Ave neighs/atom = 54.000000 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.681 | 4.681 | 4.681 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 -3935.8144 -3935.8144 22.013661 90.464939 9.8694387 -1825.382 -1825.382 15.430722 -5507.3415 15.764749 2.5884803 952.30958 Loop time of 1.95e-06 on 1 procs for 0 steps with 1176 atoms 205.1% 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 | | 1.95e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3616.00 ave 3616 max 3616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31752.0 ave 31752 max 31752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63504.0 ave 63504 max 63504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63504 Ave neighs/atom = 54.000000 Neighbor list builds = 0 Dangerous builds = 0 1176 -3935.81441134779 eV 2.58848030183247 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03