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 -56.639256 0) to (28.319628 56.639256 3.8900001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8089934 4.8089934 3.8900001 Created 424 atoms using lattice units in orthogonal box = (0 -56.639256 0) to (28.319628 56.639256 3.8900001) create_atoms CPU = 0.000 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8089934 4.8089934 3.8900001 Created 426 atoms using lattice units in orthogonal box = (0 -56.639256 0) to (28.319628 56.639256 3.8900001) create_atoms CPU = 0.000 seconds 426 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 = 7 26 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 2 atoms, new total = 848 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 = 7 26 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) = 7.281 | 7.281 | 7.281 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2877.6101 0 -2877.6101 103322.99 82 0 -3283.631 0 -3283.631 10287.068 Loop time of 0.707044 on 1 procs for 82 steps with 848 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2877.61009628699 -3283.62786407072 -3283.63097028406 Force two-norm initial, final = 708.79379 0.19998163 Force max component initial, final = 231.91988 0.030413023 Final line search alpha, max atom move = 1 0.030413023 Iterations, force evaluations = 82 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69787 | 0.69787 | 0.69787 | 0.0 | 98.70 Neigh | 0.0018933 | 0.0018933 | 0.0018933 | 0.0 | 0.27 Comm | 0.0050123 | 0.0050123 | 0.0050123 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002267 | | | 0.32 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8680 ave 8680 max 8680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84330 ave 84330 max 84330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84330 Ave neighs/atom = 99.445755 Neighbor list builds = 1 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.281 | 7.281 | 7.281 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -3283.631 0 -3283.631 10287.068 12479.141 91 0 -3284.0036 0 -3284.0036 16.706172 12543.07 Loop time of 0.0588064 on 1 procs for 9 steps with 848 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3283.63097028405 -3284.00328091551 -3284.00364251815 Force two-norm initial, final = 146.42692 0.63725488 Force max component initial, final = 117.92368 0.28722689 Final line search alpha, max atom move = 0.00071737223 0.00020604859 Iterations, force evaluations = 9 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057091 | 0.057091 | 0.057091 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039447 | 0.00039447 | 0.00039447 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001321 | | | 2.25 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8698 ave 8698 max 8698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84388 ave 84388 max 84388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84388 Ave neighs/atom = 99.514151 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 = 7 26 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) = 6.912 | 6.912 | 6.912 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3284.0036 0 -3284.0036 16.706172 Loop time of 5.41e-07 on 1 procs for 0 steps with 848 atoms 369.7% 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 | | 5.41e-07 | | |100.00 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8710 ave 8710 max 8710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84288 ave 84288 max 84288 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 = 84288 Ave neighs/atom = 99.396226 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) = 6.912 | 6.912 | 6.912 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 -3284.0036 -3284.0036 28.284317 114.15741 3.8846691 16.706172 16.706172 6.2937996 7.1863571 36.63836 2.5356014 435.68028 Loop time of 7.21e-07 on 1 procs for 0 steps with 848 atoms 277.4% 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 | | 7.21e-07 | | |100.00 Nlocal: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8710 ave 8710 max 8710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84288 ave 84288 max 84288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168576 ave 168576 max 168576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168576 Ave neighs/atom = 198.79245 Neighbor list builds = 0 Dangerous builds = 0 848 -3284.00364251815 eV 2.5356014120606 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00