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 -61.083494 0.0000000) to (43.192553 61.083494 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8198768 6.9656616 5.7209934 Created 911 atoms using lattice units in orthogonal box = (0.0000000 -61.083494 0.0000000) to (43.192553 61.083494 5.7209934) create_atoms CPU = 0.002 seconds 911 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8198768 6.9656616 5.7209934 Created 915 atoms using lattice units in orthogonal box = (0.0000000 -61.083494 0.0000000) to (43.192553 61.083494 5.7209934) create_atoms CPU = 0.002 seconds 915 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 = 14 40 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1819 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 = 14 40 2 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5985.9658 0 -5985.9658 8464.4249 143 0 -6099.8684 0 -6099.8684 94.103999 Loop time of 16.4182 on 1 procs for 143 steps with 1819 atoms 93.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5985.96581021252 -6099.86273599374 -6099.86839631276 Force two-norm initial, final = 153.52838 0.17423128 Force max component initial, final = 37.154867 0.025352319 Final line search alpha, max atom move = 1.0000000 0.025352319 Iterations, force evaluations = 143 269 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.355 | 16.355 | 16.355 | 0.0 | 99.62 Neigh | 0.009158 | 0.009158 | 0.009158 | 0.0 | 0.06 Comm | 0.024393 | 0.024393 | 0.024393 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02964 | | | 0.18 Nlocal: 1819.00 ave 1819 max 1819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6575.00 ave 6575 max 6575 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: 99300.0 ave 99300 max 99300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99300 Ave neighs/atom = 54.590434 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 40 2 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 : 143 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -6099.8684 0 -6099.8684 94.103999 30187.99 145 0 -6099.8776 0 -6099.8776 12.514445 30191.368 Loop time of 0.233899 on 1 procs for 2 steps with 1819 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 = -6099.86839631277 -6099.87682024517 -6099.87757114108 Force two-norm initial, final = 14.411330 0.72867527 Force max component initial, final = 12.819269 0.60769037 Final line search alpha, max atom move = 0.00014928811 9.0720945e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23237 | 0.23237 | 0.23237 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024606 | 0.00024606 | 0.00024606 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001283 | | | 0.55 Nlocal: 1819.00 ave 1819 max 1819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 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: 98838.0 ave 98838 max 98838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98838 Ave neighs/atom = 54.336449 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 = 14 40 2 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) = 5.280 | 5.280 | 5.280 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6099.8776 0 -6099.8776 12.514445 Loop time of 2.264e-06 on 1 procs for 0 steps with 1819 atoms 176.7% 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 | | 2.264e-06 | | |100.00 Nlocal: 1819.00 ave 1819 max 1819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 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: 98842.0 ave 98842 max 98842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98842 Ave neighs/atom = 54.338648 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 = 14 40 2 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) = 5.280 | 5.280 | 5.280 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 -6099.8776 -6099.8776 43.183924 122.29012 5.717015 12.514445 12.514445 15.973049 32.281032 -10.710744 2.5686163 839.82896 Loop time of 2.52e-06 on 1 procs for 0 steps with 1819 atoms 277.8% 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 | | 2.52e-06 | | |100.00 Nlocal: 1819.00 ave 1819 max 1819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6592.00 ave 6592 max 6592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49421.0 ave 49421 max 49421 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98842.0 ave 98842 max 98842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98842 Ave neighs/atom = 54.338648 Neighbor list builds = 0 Dangerous builds = 0 1819 -6099.87757114108 eV 2.56861631333504 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17