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 -70.655968 0.0000000) to (40.793242 70.655968 6.1037460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4796893 5.6243557 6.1037460 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.655968 0.0000000) to (40.793242 70.655968 6.1037460) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4796893 5.6243557 6.1037460 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.655968 0.0000000) to (40.793242 70.655968 6.1037460) create_atoms CPU = 0.003 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 10 32 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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 = 10 32 2 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) = 16.13 | 16.13 | 16.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12540.521 0 -12540.521 113546.99 94 0 -14239.169 0 -14239.169 6806.2737 Loop time of 13.9412 on 1 procs for 94 steps with 3216 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12540.5207074224 -14239.1561430107 -14239.1691166042 Force two-norm initial, final = 1773.7174 0.43176045 Force max component initial, final = 357.58807 0.094850192 Final line search alpha, max atom move = 1.0000000 0.094850192 Iterations, force evaluations = 94 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.794 | 13.794 | 13.794 | 0.0 | 98.94 Neigh | 0.04409 | 0.04409 | 0.04409 | 0.0 | 0.32 Comm | 0.059029 | 0.059029 | 0.059029 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04429 | | | 0.32 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17548.0 ave 17548 max 17548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 402974.0 ave 402974 max 402974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402974 Ave neighs/atom = 125.30286 Neighbor list builds = 2 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.13 | 16.13 | 16.13 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -14239.169 0 -14239.169 6806.2737 35185.484 99 0 -14239.749 0 -14239.749 -74.673269 35315.408 Loop time of 0.535018 on 1 procs for 5 steps with 3216 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 = -14239.1691166042 -14239.748522085 -14239.7489483612 Force two-norm initial, final = 315.08299 3.2011542 Force max component initial, final = 288.58947 2.6585745 Final line search alpha, max atom move = 0.00018075019 0.00048053784 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52711 | 0.52711 | 0.52711 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013304 | 0.0013304 | 0.0013304 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006578 | | | 1.23 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17564.0 ave 17564 max 17564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401480.0 ave 401480 max 401480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401480 Ave neighs/atom = 124.83831 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 = 10 32 2 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) = 15.02 | 15.02 | 15.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14239.749 0 -14239.749 -74.673269 Loop time of 2.35e-06 on 1 procs for 0 steps with 3216 atoms 170.2% 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 | | 2.35e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17540.0 ave 17540 max 17540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 400966.0 ave 400966 max 400966 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 = 400966 Ave neighs/atom = 124.67848 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) = 15.02 | 15.02 | 15.02 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 -14239.749 -14239.749 40.808508 141.87777 6.0995693 -74.673269 -74.673269 -120.65837 -69.747722 -33.613714 2.2421802 1039.0795 Loop time of 2.79e-06 on 1 procs for 0 steps with 3216 atoms 286.7% 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 | | 2.79e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17540.0 ave 17540 max 17540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 400966.0 ave 400966 max 400966 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 801932.0 ave 801932 max 801932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 801932 Ave neighs/atom = 249.35697 Neighbor list builds = 0 Dangerous builds = 0 3216 -14239.7489483612 eV 2.24218019226001 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15