LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -45.030006 0) to (31.841023 45.030006 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1781089 6.7208965 5.5012908 Created 536 atoms using lattice units in orthogonal box = (0 -45.030006 0) to (31.841023 45.030006 5.5012908) create_atoms CPU = 0.001 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1781089 6.7208965 5.5012908 Created 538 atoms using lattice units in orthogonal box = (0 -45.030006 0) to (31.841023 45.030006 5.5012908) create_atoms CPU = 0.000 seconds 538 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 21 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 4 atoms, new total = 1070 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:187) 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 21 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) = 7.728 | 7.728 | 7.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3310.6992 0 -3310.6992 133988.95 81 0 -4151.4022 0 -4151.4022 605.25349 Loop time of 0.864105 on 1 procs for 81 steps with 1070 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 = -3310.69917463661 -4151.39802941135 -4151.40218011731 Force two-norm initial, final = 1102.766 0.22812339 Force max component initial, final = 328.38474 0.055897367 Final line search alpha, max atom move = 1 0.055897367 Iterations, force evaluations = 81 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85304 | 0.85304 | 0.85304 | 0.0 | 98.72 Neigh | 0.0045502 | 0.0045502 | 0.0045502 | 0.0 | 0.53 Comm | 0.004107 | 0.004107 | 0.004107 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002411 | | | 0.28 Nlocal: 1070 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7366 ave 7366 max 7366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106546 ave 106546 max 106546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106546 Ave neighs/atom = 99.575701 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.728 | 7.728 | 7.728 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4151.4022 0 -4151.4022 605.25349 15775.518 85 0 -4151.5093 0 -4151.5093 70.034737 15778.779 Loop time of 0.0355384 on 1 procs for 4 steps with 1070 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 = -4151.40218011732 -4151.50824615976 -4151.5092713726 Force two-norm initial, final = 54.679046 2.3962264 Force max component initial, final = 47.316842 2.1108706 Final line search alpha, max atom move = 9.79449e-05 0.00020674901 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034732 | 0.034732 | 0.034732 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016538 | 0.00016538 | 0.00016538 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006409 | | | 1.80 Nlocal: 1070 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6943 ave 6943 max 6943 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106640 ave 106640 max 106640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106640 Ave neighs/atom = 99.663551 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) 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 21 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) = 7.356 | 7.356 | 7.356 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4151.5093 0 -4151.5093 70.034737 Loop time of 5.91e-07 on 1 procs for 0 steps with 1070 atoms 338.4% 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 | | 5.91e-07 | | |100.00 Nlocal: 1070 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7019 ave 7019 max 7019 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106580 ave 106580 max 106580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106580 Ave neighs/atom = 99.607477 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.356 | 7.356 | 7.356 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 -4151.5093 -4151.5093 31.761196 90.327977 5.4998933 70.034737 70.034737 -80.590269 76.411232 214.28325 2.5595934 624.06727 Loop time of 5.01e-07 on 1 procs for 0 steps with 1070 atoms 199.6% 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 | | 5.01e-07 | | |100.00 Nlocal: 1070 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7019 ave 7019 max 7019 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106580 ave 106580 max 106580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 213160 ave 213160 max 213160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213160 Ave neighs/atom = 199.21495 Neighbor list builds = 0 Dangerous builds = 0 1070 -4151.5092713726 eV 2.55959341765652 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00