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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -52.428711 0.0000000) to (30.267395 52.428711 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4858704 6.2410317 7.0055407 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.428711 0.0000000) to (30.267395 52.428711 7.0055407) create_atoms CPU = 0.004 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4858704 6.2410317 7.0055407 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.428711 0.0000000) to (30.267395 52.428711 7.0055407) create_atoms CPU = 0.004 seconds 676 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 30 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1328 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_058537087384_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4427.6486 0 -4427.6486 1060.5959 65 0 -4445.8662 0 -4445.8662 -4321.5818 Loop time of 17.2006 on 1 procs for 65 steps with 1328 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 = -4427.64860622893 -4445.86198894947 -4445.86618430635 Force two-norm initial, final = 21.319138 0.15252891 Force max component initial, final = 4.3769938 0.0094398618 Final line search alpha, max atom move = 1.0000000 0.0094398618 Iterations, force evaluations = 65 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.13 | 17.13 | 17.13 | 0.0 | 99.59 Neigh | 0.036696 | 0.036696 | 0.036696 | 0.0 | 0.21 Comm | 0.014967 | 0.014967 | 0.014967 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01864 | | | 0.11 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5260.00 ave 5260 max 5260 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: 104672.0 ave 104672 max 104672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104672 Ave neighs/atom = 78.819277 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -4445.8662 0 -4445.8662 -4321.5818 22233.912 68 0 -4445.9739 0 -4445.9739 -1053.5603 22140.271 Loop time of 0.703633 on 1 procs for 3 steps with 1328 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 = -4445.86618430634 -4445.97269317771 -4445.97394031722 Force two-norm initial, final = 72.123816 1.4612727 Force max component initial, final = 53.321943 1.2691579 Final line search alpha, max atom move = 0.00014958014 0.00018984082 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70083 | 0.70083 | 0.70083 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053312 | 0.00053312 | 0.00053312 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002274 | | | 0.32 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5197.00 ave 5197 max 5197 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: 103856.0 ave 103856 max 103856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103856 Ave neighs/atom = 78.204819 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.200 | 5.200 | 5.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4445.9739 0 -4445.9739 -1053.5603 Loop time of 6.275e-06 on 1 procs for 0 steps with 1328 atoms 191.2% 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 | | 6.275e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5230.00 ave 5230 max 5230 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: 108744.0 ave 108744 max 108744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108744 Ave neighs/atom = 81.885542 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.200 | 5.200 | 5.200 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 -4445.9739 -4445.9739 30.198149 104.85742 6.9920325 -1053.5603 -1053.5603 -50.895505 -3201.4508 91.665274 2.6230065 1155.6633 Loop time of 6.415e-06 on 1 procs for 0 steps with 1328 atoms 296.2% 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 | | 6.415e-06 | | |100.00 Nlocal: 1328.00 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5230.00 ave 5230 max 5230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54372.0 ave 54372 max 54372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108744.0 ave 108744 max 108744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108744 Ave neighs/atom = 81.885542 Neighbor list builds = 0 Dangerous builds = 0 1328 -4445.97394031722 eV 2.62300648062406 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18