Commit c7d3303e authored by rym's avatar rym
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Added py3Dmol and jupyter dependencies; updated .extend_vdW_layers to... 

Added py3Dmol and jupyter dependencies; updated .extend_vdW_layers to correctly map layers back to cell; updated example.ipynb to use view_structure fxn, which uses py3Dmol
parent d26ad8ff

README.md

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# vdW_structures



## Overview

`vdW_structures` is a Python package built on `ase` and `pymatgen` that facilitates the construction of van der Waals (vdW) layered materials.

`vdW_structures` is a Python package built on `ase` and `pymatgen` that facilitates the construction of van der Waals (vdW) layered materials. It requires 'jupyter' and 'py3Dmol' for testing and visualization. 



## Features

- Allows the user to extract and recombine individual layers of vdW materials.

- Improves `pymatgen`'s CoherentInterfaceBuilder() handling of vdW heterostructure construction.

- Supports common vdW structural transformations (e.g., x, y and z-direction shifts of individual layers).



- NOTE: Solving for and setting vdW layers is currently only supported along c-lattice vectors with no x or y components, e.g., [0, 0, z]. 



## Installation

You can install `vdW_structures` using pip:
@@ -15,7 +17,7 @@ You can install `vdW_structures` using pip: 
pip install git+https://github.com/yourusername/vdW_structures.git

```



Alternatively, if you're developing the package, clone the repository and install it in editable mode. 

Alternatively, if you'd like to make local changes to the package, clone the repository and install it in editable mode. 



```bash

git clone https://github.com/yourusername/vdW_structures.git

pyproject.toml

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@@ -14,7 +14,9 @@ authors = [ 
dependencies = [

    "numpy",  # Add your dependencies here

    "ase",

    "pymatgen"

    "jupyter",

    "pymatgen",

    "py3Dmol"

]



[tool.setuptools]

tests/.ipynb_checkpoints/example-checkpoint.ipynb

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tests/example.ipynb

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vdW_structures/vdW_structure.py

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@@ -10,7 +10,7 @@ from copy import deepcopy 




class VdWStructure:

    def __init__(self, structure: Structure, minimum_vdW_gap: Union[int, float]):

    def __init__(self, structure: Structure, minimum_vdW_gap: Union[int, float], shift_gap=True):

        """Identify van der Waals layers based on if the spacing between atomic layers exceeds the minimum_vdW_gap."""

        if not isinstance(structure, Structure):

            raise TypeError(f"Expected a pymatgen Structure object, got {type(structure).__name__}")
@@ -29,7 +29,11 @@ class VdWStructure: 
            except:

                raise ValueError(f"No van der Waals layers found with a gap of {minimum_vdW_gap} Å.")

        

        if shift_gap:

            self.structure = self.shift_to_vdW_gap(structure, self.vdW_layers, self.layer_images).get_sorted_structure()

        else:

            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)
@@ -296,4 +300,11 @@ class VdWStructure: 
                

        no_spacing_extended_structure = self._add_vdW_sites(new_layer_numbers)

        correct_spacing_structure = self._rescale_vdW_lattice(new_layer_numbers, no_spacing_extended_structure)



        # Might need to adjust this depending on the gap location        

        correct_spacing_vdW = VdWStructure(correct_spacing_structure.get_sorted_structure(), self.minimum_vdW_gap)

        correct_spacing_atoms = correct_spacing_structure.to_ase_atoms()

        correct_spacing_atoms.center(axis=2, vacuum=correct_spacing_vdW.vdW_spacings[0]/2) # Set to bottom gap

        correct_spacing_structure = self.ase_atoms_adaptor.get_structure(correct_spacing_atoms)

        

        return VdWStructure(correct_spacing_structure.get_sorted_structure(), self.minimum_vdW_gap)