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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -46.785002 0.0000000) to (33.081992 46.785002 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1547893 5.9841282 5.0449565 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -46.785002 0.0000000) to (33.081992 46.785002 5.0449565) create_atoms CPU = 0.002 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1547893 5.9841282 5.0449565 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -46.785002 0.0000000) to (33.081992 46.785002 5.0449565) create_atoms CPU = 0.002 seconds 690 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1372 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.659 | 4.659 | 4.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5400.0732 0 -5400.0732 53196.665 320 0 -5793.9596 0 -5793.9596 54648.508 Loop time of 25.8904 on 1 procs for 320 steps with 1372 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 = -5400.07324936514 -5793.95481379092 -5793.95956001044 Force two-norm initial, final = 549.76707 0.29963244 Force max component initial, final = 119.86782 0.051294029 Final line search alpha, max atom move = 1.0000000 0.051294029 Iterations, force evaluations = 320 626 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.785 | 25.785 | 25.785 | 0.0 | 99.59 Neigh | 0.014797 | 0.014797 | 0.014797 | 0.0 | 0.06 Comm | 0.04126 | 0.04126 | 0.04126 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0491 | | | 0.19 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5388.00 ave 5388 max 5388 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: 83688.0 ave 83688 max 83688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83688 Ave neighs/atom = 60.997085 Neighbor list builds = 2 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 320 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.659 | 4.659 | 4.659 Mbytes Step Temp E_pair E_mol TotEng Press Volume 320 0 -5793.9596 0 -5793.9596 54648.508 15616.573 336 0 -5799.6242 0 -5799.6242 -414.19641 15942.151 Loop time of 0.732573 on 1 procs for 16 steps with 1372 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 = -5793.95956001044 -5799.62348559754 -5799.62419507763 Force two-norm initial, final = 927.62329 8.4371280 Force max component initial, final = 611.07859 5.9573220 Final line search alpha, max atom move = 0.00030973360 0.0018451828 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71879 | 0.71879 | 0.71879 | 0.0 | 98.12 Neigh | 0.0071025 | 0.0071025 | 0.0071025 | 0.0 | 0.97 Comm | 0.0010261 | 0.0010261 | 0.0010261 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005655 | | | 0.77 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5274.00 ave 5274 max 5274 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: 79508.0 ave 79508 max 79508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79508 Ave neighs/atom = 57.950437 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5799.6242 0 -5799.6242 -414.19641 Loop time of 2.618e-06 on 1 procs for 0 steps with 1372 atoms 191.0% 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 | | 2.618e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5280.00 ave 5280 max 5280 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: 79224.0 ave 79224 max 79224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79224 Ave neighs/atom = 57.743440 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.797 | 4.797 | 4.797 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 -5799.6242 -5799.6242 33.251213 94.989473 5.0473561 -414.19641 -414.19641 -412.15518 -231.44203 -598.99202 2.3922548 2407.3708 Loop time of 2.919e-06 on 1 procs for 0 steps with 1372 atoms 274.1% 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 | | 2.919e-06 | | |100.00 Nlocal: 1372.00 ave 1372 max 1372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5280.00 ave 5280 max 5280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39612.0 ave 39612 max 39612 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79224.0 ave 79224 max 79224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79224 Ave neighs/atom = 57.743440 Neighbor list builds = 0 Dangerous builds = 0 1372 -5799.62419507763 eV 2.39225475671392 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27