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 -43.589465 0.0000000) to (14.529822 43.589465 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2734770 4.2734770 3.5239994 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -43.589465 0.0000000) to (14.529822 43.589465 3.5239994) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2734770 4.2734770 3.5239994 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.589465 0.0000000) to (14.529822 43.589465 3.5239994) create_atoms CPU = 0.000 seconds 206 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 = 4 20 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 2 atoms, new total = 408 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 = 4 20 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) = 7.125 | 7.125 | 7.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1631.8142 0 -1631.8142 124272.28 54 0 -1803.3055 0 -1803.3055 11728.507 Loop time of 0.847988 on 1 procs for 54 steps with 408 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1631.81423982658 -1803.30417158286 -1803.30547989823 Force two-norm initial, final = 498.96861 0.12442989 Force max component initial, final = 168.85203 0.020552038 Final line search alpha, max atom move = 1.0000000 0.020552038 Iterations, force evaluations = 54 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83441 | 0.83441 | 0.83441 | 0.0 | 98.40 Neigh | 0.0026515 | 0.0026515 | 0.0026515 | 0.0 | 0.31 Comm | 0.0070514 | 0.0070514 | 0.0070514 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003879 | | | 0.46 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6126.00 ave 6126 max 6126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52476.0 ave 52476 max 52476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52476 Ave neighs/atom = 128.61765 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.125 | 7.125 | 7.125 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1803.3055 0 -1803.3055 11728.507 4463.83 62 0 -1803.4795 0 -1803.4795 269.25379 4491.3987 Loop time of 0.090129 on 1 procs for 8 steps with 408 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 = -1803.30547989823 -1803.47925584404 -1803.4795240906 Force two-norm initial, final = 60.984774 1.5899089 Force max component initial, final = 51.172489 1.3490578 Final line search alpha, max atom move = 0.00057850229 0.00078043304 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087286 | 0.087286 | 0.087286 | 0.0 | 96.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052653 | 0.00052653 | 0.00052653 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002317 | | | 2.57 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6156.00 ave 6156 max 6156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51050.0 ave 51050 max 51050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51050 Ave neighs/atom = 125.12255 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 = 4 20 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) = 6.756 | 6.756 | 6.756 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1803.4795 0 -1803.4795 269.25379 Loop time of 1.914e-06 on 1 procs for 0 steps with 408 atoms 156.7% 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 | | 1.914e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6156.00 ave 6156 max 6156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50854.0 ave 50854 max 50854 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 = 50854 Ave neighs/atom = 124.64216 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) = 6.756 | 6.756 | 6.756 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 -1803.4795 -1803.4795 14.525112 87.795529 3.5220029 269.25379 269.25379 279.91601 484.64103 43.204349 2.299087 184.27371 Loop time of 2.34e-06 on 1 procs for 0 steps with 408 atoms 213.7% 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 | | 2.34e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6156.00 ave 6156 max 6156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50854.0 ave 50854 max 50854 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101708.0 ave 101708 max 101708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101708 Ave neighs/atom = 249.28431 Neighbor list builds = 0 Dangerous builds = 0 408 -1803.4795240906 eV 2.29908704562808 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01