GB Kinetics
  • Download
  • Installation
    • Pre-installed programs
    • Install GB Kinetics
      • Windows
      • Mac/Linux
      • Conda
    • Workflow
    • Usage
  • Theory
    • Construction of STGB microstate
    • Enumeration of disconnection modes
    • Construction of atomistic GB migration images
    • Mapping the atomic shuffles
    • Evaluation of the energy barrier and trajectories
      • References
  • Data
  • Grid Search Example
    • Output
  • GB Kinetics Example
    • User input
    • Command line Output
    • Output
      • References
    • Summary of important functions/classes used in the workflow
  • Source
    • GBKineticsRunController module
      • runGBkinetics()
      • runGridSearch()
    • IO module
      • find_gb_location()
      • read_LAMMPS_datafile()
      • read_LAMMPS_dumpfile()
      • read_gridsearch_results()
      • read_neb_output_data()
      • write_LAMMPSoutput_tstep()
      • write_gridsearch_results()
      • write_lammps_datafile()
    • bicrystal module
      • bicrystal
        • bicrystal.__init__()
        • bicrystal.create_disconnection_containing_bicrystal()
        • bicrystal.create_fix_eco_orientationfile()
        • bicrystal.create_flat_gb_bicrystal()
        • bicrystal.ordered_write()
        • bicrystal.write()
    • bicrystallography module
      • bicrystallography
        • bicrystallography.sigma
        • bicrystallography.misorientation
        • bicrystallography.inclination
        • bicrystallography.axis
        • bicrystallography.lattice_parameter
        • bicrystallography.__init__()
        • bicrystallography.gb_props()
    • min_shuffle module
      • min_shuffle
        • min_shuffle.__init__()
        • min_shuffle.format_input()
        • min_shuffle.gb_info()
        • min_shuffle.load_data()
        • min_shuffle.pbcdist()
        • min_shuffle.pbcwrap()
        • min_shuffle.plot_min_shuffle_2d()
        • min_shuffle.plot_min_shuffle_3d()
        • min_shuffle.replicate()
        • min_shuffle.run()
        • min_shuffle.write_images()
    • plastic_slip module
      • dislocation_dipole
        • dislocation_dipole.dislocation_points
        • dislocation_dipole.period
        • dislocation_dipole.burgers_vector
        • dislocation_dipole.dislocation_vector
        • dislocation_dipole.dislocation_distance
        • dislocation_dipole.__init__()
        • dislocation_dipole.plastic_displacement()
    • runLAMMPS module
      • run_LAMMPS
        • run_LAMMPS.folder
        • run_LAMMPS.element
        • run_LAMMPS.lattice_parameter
        • run_LAMMPS.sigma
        • run_LAMMPS.misorientation
        • run_LAMMPS.inclination
        • run_LAMMPS.size_along_gb_period
        • run_LAMMPS.potential
        • run_LAMMPS.mpi_location
        • run_LAMMPS.lammps_location
        • run_LAMMPS.output_filename_gridsearch
        • run_LAMMPS.gridsearch_output_setting
        • run_LAMMPS.gridsearch_output_folder
        • run_LAMMPS.lammps_input_filename
        • run_LAMMPS.neb_images
        • run_LAMMPS.number_of_images_provided
        • run_LAMMPS.burgers_vec
        • run_LAMMPS.step_height
        • run_LAMMPS.neb_output_folder
        • run_LAMMPS.__init__()
        • run_LAMMPS.post_process_gridsearch_data()
        • run_LAMMPS.post_process_neb_output()
        • run_LAMMPS.run_grid_search()
        • run_LAMMPS.run_minimization()
        • run_LAMMPS.run_neb_calc()
        • run_LAMMPS.write_lammps_gridsearch_input()
        • run_LAMMPS.write_lammps_neb_input_script()
        • run_LAMMPS.write_minimization_input()
GB Kinetics
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