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_NiRh__SM_306597220004_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239998 3.5239998 3.5239998 Created orthogonal box = (0.0000000 -43.589470 0.0000000) to (20.548273 43.589470 4.9836883) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0436097 5.9828684 4.9836883 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -43.589470 0.0000000) to (20.548273 43.589470 4.9836883) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0436097 5.9828684 4.9836883 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -43.589470 0.0000000) to (20.548273 43.589470 4.9836883) create_atoms CPU = 0.001 seconds 412 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 5 20 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 = 816 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_306597220004_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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 5 20 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) = 7.687 | 7.687 | 7.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2134.7588 0 -2134.7588 241557.03 56 0 -3610.9039 0 -3610.9039 7529.2926 Loop time of 1.60693 on 1 procs for 56 steps with 816 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 = -2134.75881296252 -3610.90073782267 -3610.90387505658 Force two-norm initial, final = 1932.3418 0.18288336 Force max component initial, final = 455.63436 0.019966933 Final line search alpha, max atom move = 1.0000000 0.019966933 Iterations, force evaluations = 56 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5857 | 1.5857 | 1.5857 | 0.0 | 98.68 Neigh | 0.0061433 | 0.0061433 | 0.0061433 | 0.0 | 0.38 Comm | 0.0091005 | 0.0091005 | 0.0091005 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005993 | | | 0.37 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102388.0 ave 102388 max 102388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102388 Ave neighs/atom = 125.47549 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.687 | 7.687 | 7.687 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3610.9039 0 -3610.9039 7529.2926 8927.6628 60 0 -3611.0159 0 -3611.0159 3.4505268 8964.0382 Loop time of 0.11158 on 1 procs for 4 steps with 816 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 = -3610.90387505658 -3611.01496117055 -3611.01587334107 Force two-norm initial, final = 77.557007 0.63300636 Force max component initial, final = 63.977919 0.44753985 Final line search alpha, max atom move = 0.00018936834 8.4749877e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10916 | 0.10916 | 0.10916 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042922 | 0.00042922 | 0.00042922 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001993 | | | 1.79 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7857.00 ave 7857 max 7857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101932.0 ave 101932 max 101932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101932 Ave neighs/atom = 124.91667 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 = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 5 20 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) = 7.319 | 7.319 | 7.319 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3611.0159 0 -3611.0159 3.4505268 Loop time of 1.976e-06 on 1 procs for 0 steps with 816 atoms 151.8% 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 | | 1.976e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7857.00 ave 7857 max 7857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101768.0 ave 101768 max 101768 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 = 101768 Ave neighs/atom = 124.71569 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) = 7.319 | 7.319 | 7.319 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 -3611.0159 -3611.0159 20.558357 87.439351 4.9866441 3.4505268 3.4505268 80.029747 0.56884367 -70.24701 2.3773377 500.87848 Loop time of 2.36e-06 on 1 procs for 0 steps with 816 atoms 254.2% 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 | | 2.36e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7857.00 ave 7857 max 7857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101768.0 ave 101768 max 101768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203536.0 ave 203536 max 203536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203536 Ave neighs/atom = 249.43137 Neighbor list builds = 0 Dangerous builds = 0 816 -3611.01587334107 eV 2.37733768886909 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02