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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -53.666577 0.0000000) to (32.863933 53.666577 9.9088485) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9752605 6.0984747 6.6058990 Created 1049 atoms using lattice units in orthogonal box = (0.0000000 -53.666577 0.0000000) to (32.863933 53.666577 9.9088485) create_atoms CPU = 0.002 seconds 1049 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9752605 6.0984747 6.6058990 Created 1073 atoms using lattice units in orthogonal box = (0.0000000 -53.666577 0.0000000) to (32.863933 53.666577 9.9088485) create_atoms CPU = 0.002 seconds 1073 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 3 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2112 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_658278549784_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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.463 | 6.463 | 6.463 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7184.5922 0 -7184.5922 2283.3378 36 0 -7195.3912 0 -7195.3912 2089.5006 Loop time of 1.60425 on 1 procs for 36 steps with 2112 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7184.59220004592 -7195.3873891843 -7195.39117091605 Force two-norm initial, final = 10.030290 0.10799617 Force max component initial, final = 1.8888698 0.0075058088 Final line search alpha, max atom move = 1.0000000 0.0075058088 Iterations, force evaluations = 36 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.589 | 1.589 | 1.589 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0067875 | 0.0067875 | 0.0067875 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008488 | | | 0.53 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9303.00 ave 9303 max 9303 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: 472082.0 ave 472082 max 472082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 472082 Ave neighs/atom = 223.52367 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.463 | 6.463 | 6.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -7195.3912 0 -7195.3912 2089.5006 34952.369 42 0 -7195.6393 0 -7195.6393 109.19216 35039.013 Loop time of 0.186235 on 1 procs for 6 steps with 2112 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7195.39117091622 -7195.63835787363 -7195.6393243462 Force two-norm initial, final = 105.65529 4.4398014 Force max component initial, final = 102.61282 3.7047230 Final line search alpha, max atom move = 0.00025394116 0.00094078165 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18152 | 0.18152 | 0.18152 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064801 | 0.00064801 | 0.00064801 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004063 | | | 2.18 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9312.00 ave 9312 max 9312 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: 468534.0 ave 468534 max 468534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468534 Ave neighs/atom = 221.84375 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.601 | 6.601 | 6.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7195.6393 0 -7195.6393 109.19216 Loop time of 2.364e-06 on 1 procs for 0 steps with 2112 atoms 169.2% 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 | | 2.364e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9312.00 ave 9312 max 9312 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: 466936.0 ave 466936 max 466936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466936 Ave neighs/atom = 221.08712 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.601 | 6.601 | 6.601 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 -7195.6393 -7195.6393 32.805488 107.88907 9.8998334 109.19216 109.19216 72.59151 170.27771 84.707249 2.7314856 825.15238 Loop time of 2.63e-06 on 1 procs for 0 steps with 2112 atoms 342.2% 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 | | 2.63e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9312.00 ave 9312 max 9312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233468.0 ave 233468 max 233468 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 466936.0 ave 466936 max 466936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466936 Ave neighs/atom = 221.08712 Neighbor list builds = 0 Dangerous builds = 0 2112 -7195.6393243462 eV 2.7314856427067 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02