How to predict the volume of diffusion pathways in structure?

Guancred · November 12, 2022, 2:05pm

Hi, I am trying to calculate (or predict) the volume of diffusion pathways in structure, but it seems pymatgen can not meet my requirement. Any quick suggestions a will help me a lot here.

jshen · November 15, 2022, 6:41pm

This is kind of possible we have done something similar with when integrating charge in a tube between two sites, if you have the exact path you can also set up a grid and then move a sphere along the path slowly and get the integrated volume:
You can look at my code here for an example of how this can be done:

github.com

materialsvirtuallab/pymatgen-analysis-diffusion/blob/8f88dc888c54401cdf6446694ae6d5e57c255eba/pymatgen/analysis/diffusion/neb/full_path_mapper.py#L600-L654


      
          def _get_chg_between_sites_tube(self, migration_hop, mask_file_seedname=None):
              """
              Calculate the amount of charge that a migrating ion has to move through in order to complete a hop
              Args:
                  migration_hop: MigrationHop object that represents a given hop
                  mask_file_seedname(string): seedname for output of the migration path masks (for debugging and
                      visualization) (Default value = None)
              Returns:
                  float: The total charge density in a tube that connects two sites of a given edges of the graph
              """
              try:
                  self._tube_radius
              except NameError:
                  logger.warning("The radius of the tubes for charge analysis need to be defined first.")
              ipos = migration_hop.isite.frac_coords
              epos = migration_hop.esite.frac_coords
          
          
    cart_ipos = np.dot(ipos, self.potential_field.structure.lattice.matrix)
              cart_epos = np.dot(epos, self.potential_field.structure.lattice.matrix)
              pbc_mask = np.zeros(self._uc_grid_shape, dtype=bool).flatten()

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