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 -51.792002 0.0000000) to (18.311238 51.792002 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7473580 5.7546669 4.9836877 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -51.792002 0.0000000) to (18.311238 51.792002 4.9836877) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7473580 5.7546669 4.9836877 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.792002 0.0000000) to (18.311238 51.792002 4.9836877) create_atoms CPU = 0.001 seconds 434 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 = 5 24 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 = 862 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 = 5 24 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) = 7.726 | 7.726 | 7.726 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2986.547 0 -2986.547 163982.65 86 0 -3813.429 0 -3813.429 5258.2192 Loop time of 2.89923 on 1 procs for 86 steps with 862 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2986.54700051461 -3813.42585150762 -3813.42895725823 Force two-norm initial, final = 1357.2575 0.19279863 Force max component initial, final = 341.78093 0.050037044 Final line search alpha, max atom move = 1.0000000 0.050037044 Iterations, force evaluations = 86 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8631 | 2.8631 | 2.8631 | 0.0 | 98.75 Neigh | 0.01153 | 0.01153 | 0.01153 | 0.0 | 0.40 Comm | 0.014838 | 0.014838 | 0.014838 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009757 | | | 0.34 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8131.00 ave 8131 max 8131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108324.0 ave 108324 max 108324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108324 Ave neighs/atom = 125.66589 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 : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.736 | 7.736 | 7.736 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -3813.429 0 -3813.429 5258.2192 9452.8165 89 0 -3813.4899 0 -3813.4899 1.6602752 9479.633 Loop time of 0.116898 on 1 procs for 3 steps with 862 atoms 88.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3813.42895725823 -3813.48815370986 -3813.48989454291 Force two-norm initial, final = 58.326695 0.73541673 Force max component initial, final = 48.384687 0.54975529 Final line search alpha, max atom move = 0.00015015104 8.2546331e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11457 | 0.11457 | 0.11457 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043428 | 0.00043428 | 0.00043428 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001898 | | | 1.62 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555.00 ave 8555 max 8555 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107984.0 ave 107984 max 107984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107984 Ave neighs/atom = 125.27146 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 = 5 24 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) = 7.367 | 7.367 | 7.367 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3813.4899 0 -3813.4899 1.6602752 Loop time of 2.191e-06 on 1 procs for 0 steps with 862 atoms 136.9% 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 | | 2.191e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555.00 ave 8555 max 8555 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107844.0 ave 107844 max 107844 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 = 107844 Ave neighs/atom = 125.10905 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) = 7.367 | 7.367 | 7.367 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 -3813.4899 -3813.4899 18.32402 103.80311 4.9837976 1.6602752 1.6602752 -92.980376 30.26452 67.696682 2.2885516 456.3627 Loop time of 2.391e-06 on 1 procs for 0 steps with 862 atoms 209.1% 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 | | 2.391e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555.00 ave 8555 max 8555 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107844.0 ave 107844 max 107844 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215688.0 ave 215688 max 215688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215688 Ave neighs/atom = 250.21810 Neighbor list builds = 0 Dangerous builds = 0 862 -3813.48989454291 eV 2.28855164328445 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03