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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -81.202452 0.0000000) to (46.882258 81.202452 7.0148235) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2976167 6.4638768 7.0148235 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.202452 0.0000000) to (46.882258 81.202452 7.0148235) create_atoms CPU = 0.011 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2976167 6.4638768 7.0148235 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.202452 0.0000000) to (46.882258 81.202452 7.0148235) create_atoms CPU = 0.010 seconds 1610 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3214 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.626 | 6.626 | 6.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10515.563 0 -10515.563 20050.974 124 0 -10872.634 0 -10872.634 2079.7462 Loop time of 8.66645 on 1 procs for 124 steps with 3214 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 = -10515.5634832626 -10872.6235714559 -10872.6342688121 Force two-norm initial, final = 450.99337 0.27212671 Force max component initial, final = 169.27264 0.055042828 Final line search alpha, max atom move = 1.0000000 0.055042828 Iterations, force evaluations = 124 221 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2767 | 8.2767 | 8.2767 | 0.0 | 95.50 Neigh | 0.25738 | 0.25738 | 0.25738 | 0.0 | 2.97 Comm | 0.059391 | 0.059391 | 0.059391 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07295 | | | 0.84 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10730.0 ave 10730 max 10730 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: 394864.0 ave 394864 max 394864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394864 Ave neighs/atom = 122.85750 Neighbor list builds = 5 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 124 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.626 | 6.626 | 6.626 Mbytes Step Temp E_pair E_mol TotEng Press Volume 124 0 -10872.634 0 -10872.634 2079.7462 53410.225 128 0 -10872.833 0 -10872.833 -26.347645 53556.09 Loop time of 0.263626 on 1 procs for 4 steps with 3214 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 = -10872.6342688122 -10872.8323344379 -10872.8331046069 Force two-norm initial, final = 141.18520 3.3040821 Force max component initial, final = 124.53856 3.1858411 Final line search alpha, max atom move = 0.00011300628 0.00036002007 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25529 | 0.25529 | 0.25529 | 0.0 | 96.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015876 | 0.0015876 | 0.0015876 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006744 | | | 2.56 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10733.0 ave 10733 max 10733 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: 402672.0 ave 402672 max 402672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402672 Ave neighs/atom = 125.28687 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.382 | 6.382 | 6.382 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10872.833 0 -10872.833 -26.347645 Loop time of 6.565e-06 on 1 procs for 0 steps with 3214 atoms 213.3% 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 | | 6.565e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10721.0 ave 10721 max 10721 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: 388104.0 ave 388104 max 388104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388104 Ave neighs/atom = 120.75420 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.382 | 6.382 | 6.382 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 -10872.833 -10872.833 46.905022 162.91313 7.008635 -26.347645 -26.347645 -95.353454 -7.24811 23.558629 2.5693303 1402.0223 Loop time of 6.795e-06 on 1 procs for 0 steps with 3214 atoms 294.3% 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 | | 6.795e-06 | | |100.00 Nlocal: 3214.00 ave 3214 max 3214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10721.0 ave 10721 max 10721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 194052.0 ave 194052 max 194052 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 388104.0 ave 388104 max 388104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388104 Ave neighs/atom = 120.75420 Neighbor list builds = 0 Dangerous builds = 0 3214 -10872.8331046069 eV 2.56933025296477 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09