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 -37.958159 0.0000000) to (18.977318 37.958159 3.5239994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5807318 4.5807318 3.5239994 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -37.958159 0.0000000) to (18.977318 37.958159 3.5239994) create_atoms CPU = 0.002 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5807318 4.5807318 3.5239994 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -37.958159 0.0000000) to (18.977318 37.958159 3.5239994) create_atoms CPU = 0.001 seconds 233 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 18 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 6 atoms, new total = 460 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 18 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) = 7.135 | 7.135 | 7.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2016.8504 0 -2016.8504 13576.087 27 0 -2031.0613 0 -2031.0613 -1600.0788 Loop time of 0.767192 on 1 procs for 27 steps with 460 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 = -2016.85039729829 -2031.05969553248 -2031.06133130767 Force two-norm initial, final = 27.997817 0.12702326 Force max component initial, final = 10.308660 0.034074291 Final line search alpha, max atom move = 0.86192964 0.029369641 Iterations, force evaluations = 27 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75004 | 0.75004 | 0.75004 | 0.0 | 97.76 Neigh | 0.0069476 | 0.0069476 | 0.0069476 | 0.0 | 0.91 Comm | 0.006244 | 0.006244 | 0.006244 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003965 | | | 0.52 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6685.00 ave 6685 max 6685 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57407.0 ave 57407 max 57407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57407 Ave neighs/atom = 124.79783 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.135 | 7.135 | 7.135 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -2031.0613 0 -2031.0613 -1600.0788 5076.9839 29 0 -2031.0702 0 -2031.0702 626.54974 5070.7855 Loop time of 0.0956935 on 1 procs for 2 steps with 460 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2031.06133130767 -2031.06887111405 -2031.07021507466 Force two-norm initial, final = 13.605596 0.41107984 Force max component initial, final = 12.610438 0.31329864 Final line search alpha, max atom move = 0.00036348513 0.00011387940 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.093012 | 0.093012 | 0.093012 | 0.0 | 97.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064912 | 0.00064912 | 0.00064912 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002032 | | | 2.12 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6697.00 ave 6697 max 6697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57445.0 ave 57445 max 57445 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57445 Ave neighs/atom = 124.88043 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 18 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) = 6.767 | 6.767 | 6.767 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2031.0702 0 -2031.0702 626.54974 Loop time of 8.791e-06 on 1 procs for 0 steps with 460 atoms 147.9% 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 | | 8.791e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729.00 ave 6729 max 6729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57484.0 ave 57484 max 57484 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 = 57484 Ave neighs/atom = 124.96522 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) = 6.767 | 6.767 | 6.767 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 -2031.0702 -2031.0702 18.949276 75.916318 3.5249055 626.54974 626.54974 -98.844254 2051.2879 -72.794432 2.2561798 272.73235 Loop time of 9.582e-06 on 1 procs for 0 steps with 460 atoms 250.5% 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 | | 9.582e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729.00 ave 6729 max 6729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57484.0 ave 57484 max 57484 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114968.0 ave 114968 max 114968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114968 Ave neighs/atom = 249.93043 Neighbor list builds = 0 Dangerous builds = 0 460 -2031.07021507466 eV 2.25617975897883 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01