Commit 7fe52c8f authored by rym's avatar rym
Browse files

Updated VdWStructure class to map input structures to unit cell during initialization

parent 0f070528

vdW_structures/vdW_structure.py

+5 −2
Original line number Diff line number Diff line
@@ -17,10 +17,14 @@ class VdWStructure: 
        if not isinstance(minimum_vdW_gap, (float, int)):

            raise TypeError(f"Expected a float/int for minimum_vdW_gap, got {type(minimum_vdW_gap).__name__}")



        # Map all atoms back to unit cell

        self.minimum_vdW_gap = minimum_vdW_gap

        structure = Structure(lattice=structure.lattice, 

                              species=[site.species for site in structure], 

                              coords=[site.frac_coords for site in structure], 

                              site_properties=structure.site_properties, to_unit_cell=True)

        

        self.vdW_layers, self.layer_images, self.vdW_spacings = self.get_vdW_layers(structure)

        #print(self.vdW_layers, self.layer_images, self.vdW_spacings)

        

        if len(self.vdW_layers) == 1:

            try:
@@ -35,7 +39,6 @@ class VdWStructure: 
            self.structure = structure 

 

        self.vdW_layers, self.layer_images, self.vdW_spacings = self.get_vdW_layers(self.structure)

        #print(self.vdW_layers, self.layer_images, self.vdW_spacings)

        

        self.ase_atoms_adaptor = AseAtomsAdaptor()

        self.layer_shifter = LayerShifter()