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 -55.499522 0.0000000) to (33.984219 55.499522 8.6320004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4813257 5.3705804 5.7546669 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -55.499522 0.0000000) to (33.984219 55.499522 8.6320004) create_atoms CPU = 0.002 seconds 1491 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4813257 5.3705804 5.7546669 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -55.499522 0.0000000) to (33.984219 55.499522 8.6320004) create_atoms CPU = 0.002 seconds 1491 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 25 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 30 atoms, new total = 2952 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 25 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) = 9.332 | 9.332 | 9.332 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13007.648 0 -13007.648 6479.6224 62 0 -13068.815 0 -13068.815 -8061.536 Loop time of 5.67339 on 1 procs for 62 steps with 2952 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 = -13007.6477123623 -13068.8034255286 -13068.8151693649 Force two-norm initial, final = 87.614117 0.37509519 Force max component initial, final = 15.398529 0.061331337 Final line search alpha, max atom move = 1.0000000 0.061331337 Iterations, force evaluations = 62 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6254 | 5.6254 | 5.6254 | 0.0 | 99.15 Neigh | 0.017537 | 0.017537 | 0.017537 | 0.0 | 0.31 Comm | 0.015509 | 0.015509 | 0.015509 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0149 | | | 0.26 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13069.0 ave 13069 max 13069 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 368945.0 ave 368945 max 368945 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368945 Ave neighs/atom = 124.98137 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 9.333 | 9.333 | 9.333 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -13068.815 0 -13068.815 -8061.536 32561.769 65 0 -13069.035 0 -13069.035 -2400.373 32461.096 Loop time of 0.301829 on 1 procs for 3 steps with 2952 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 = -13068.8151693649 -13069.0338298692 -13069.0348154414 Force two-norm initial, final = 193.81156 0.39241447 Force max component initial, final = 156.61404 0.073167315 Final line search alpha, max atom move = 0.00012984082 9.5001039e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29855 | 0.29855 | 0.29855 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055388 | 0.00055388 | 0.00055388 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002726 | | | 0.90 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13177.0 ave 13177 max 13177 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 369358.0 ave 369358 max 369358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369358 Ave neighs/atom = 125.12127 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 25 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) = 8.964 | 8.964 | 8.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13069.035 0 -13069.035 -2400.373 Loop time of 1.732e-06 on 1 procs for 0 steps with 2952 atoms 173.2% 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 | | 1.732e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13189.0 ave 13189 max 13189 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 369956.0 ave 369956 max 369956 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 = 369956 Ave neighs/atom = 125.32385 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) = 8.964 | 8.964 | 8.964 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 -13069.035 -13069.035 33.947017 110.99904 8.6147431 -2400.373 -2400.373 -2.014875 -7198.5516 -0.55247872 2.2492192 891.01348 Loop time of 1.96e-06 on 1 procs for 0 steps with 2952 atoms 255.1% 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 | | 1.96e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13189.0 ave 13189 max 13189 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 369956.0 ave 369956 max 369956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 739912.0 ave 739912 max 739912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739912 Ave neighs/atom = 250.64770 Neighbor list builds = 0 Dangerous builds = 0 2952 -13069.0348154414 eV 2.2492192425451 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06