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 # Using KIM Simulator Model : Sim_LAMMPS_ADP_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -64.982862 0.0000000) to (32.489669 64.982862 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9690082 4.9690082 3.5239994 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -64.982862 0.0000000) to (32.489669 64.982862 3.5239994) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9690082 4.9690082 3.5239994 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -64.982862 0.0000000) to (32.489669 64.982862 3.5239994) create_atoms CPU = 0.002 seconds 682 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 8 30 1 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 8 atoms, new total = 1356 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/SM_559286646876_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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 7.921 | 7.921 | 7.921 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5950.8701 0 -5950.8701 22771.692 79 0 -6010.286 0 -6010.286 -1634.0198 Loop time of 7.48106 on 1 procs for 79 steps with 1356 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 = -5950.87012284161 -6010.28176030332 -6010.28604461699 Force two-norm initial, final = 68.977928 0.23061827 Force max component initial, final = 17.371690 0.042587346 Final line search alpha, max atom move = 1.0000000 0.042587346 Iterations, force evaluations = 79 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3925 | 7.3925 | 7.3925 | 0.0 | 98.82 Neigh | 0.019884 | 0.019884 | 0.019884 | 0.0 | 0.27 Comm | 0.043597 | 0.043597 | 0.043597 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02512 | | | 0.34 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14170.0 ave 14170 max 14170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171392.0 ave 171392 max 171392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171392 Ave neighs/atom = 126.39528 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.925 | 7.925 | 7.925 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -6010.286 0 -6010.286 -1634.0198 14880.24 80 0 -6010.291 0 -6010.291 -449.21971 14870.714 Loop time of 0.162738 on 1 procs for 1 steps with 1356 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6010.28604461699 -6010.28604461699 -6010.29099747476 Force two-norm initial, final = 19.453212 4.7463975 Force max component initial, final = 18.487976 4.4922872 Final line search alpha, max atom move = 5.4089208e-05 0.00024298426 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15983 | 0.15983 | 0.15983 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088825 | 0.00088825 | 0.00088825 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002023 | | | 1.24 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14115.0 ave 14115 max 14115 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170660.0 ave 170660 max 170660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170660 Ave neighs/atom = 125.85546 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.556 | 7.556 | 7.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6010.291 0 -6010.291 -449.21971 Loop time of 6.525e-06 on 1 procs for 0 steps with 1356 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14115.0 ave 14115 max 14115 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170740.0 ave 170740 max 170740 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170740 Ave neighs/atom = 125.91445 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.556 | 7.556 | 7.556 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 -6010.291 -6010.291 32.473994 129.96572 3.5234433 -449.21971 -449.21971 -163.09452 -1668.489 483.92438 2.2552831 142.05872 Loop time of 7.256e-06 on 1 procs for 0 steps with 1356 atoms 317.0% 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 | | 7.256e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14115.0 ave 14115 max 14115 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170740.0 ave 170740 max 170740 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 341480.0 ave 341480 max 341480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341480 Ave neighs/atom = 251.82891 Neighbor list builds = 0 Dangerous builds = 0 1356 -6010.29099747476 eV 2.25528311398691 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08