jarvis.analysis.interface.zur
=============================

.. py:module:: jarvis.analysis.interface.zur

.. autoapi-nested-parse::

   Design interface using Zur algorithm and Anderson rule.



Classes
-------

.. autoapisummary::

   jarvis.analysis.interface.zur.ZSLGenerator


Functions
---------

.. autoapisummary::

   jarvis.analysis.interface.zur.gen_sl_transform_matricies
   jarvis.analysis.interface.zur.rel_strain
   jarvis.analysis.interface.zur.rel_angle
   jarvis.analysis.interface.zur.fast_norm
   jarvis.analysis.interface.zur.vec_angle
   jarvis.analysis.interface.zur.vec_area
   jarvis.analysis.interface.zur.reduce_vectors
   jarvis.analysis.interface.zur.get_factors
   jarvis.analysis.interface.zur.make_interface
   jarvis.analysis.interface.zur.get_hetero_type
   jarvis.analysis.interface.zur.mismatch_strts
   jarvis.analysis.interface.zur.get_hetero


Module Contents
---------------

.. py:class:: ZSLGenerator(max_area_ratio_tol=0.09, max_area=400, max_length_tol=0.03, max_angle_tol=0.01)

   Bases: :py:obj:`object`


   Uses Zur algorithm to find best matched interfaces.

   This class is modified from pymatgen.


   .. py:attribute:: max_area_ratio_tol
      :value: 0.09



   .. py:attribute:: max_area
      :value: 400



   .. py:attribute:: max_length_tol
      :value: 0.03



   .. py:attribute:: max_angle_tol
      :value: 0.01



   .. py:method:: is_same_vectors(vec_set1, vec_set2)

      Check two sets of vectors are the same.

      Args:
          vec_set1(array[array]): an array of two vectors

          vec_set2(array[array]): second array of two vectors



   .. py:method:: generate_sl_transformation_sets(film_area, substrate_area)

      Generate transformation sets for film/substrate.

      The transformation sets map the film and substrate unit cells to super
      lattices with a maximum area.

      Args:

          film_area(int): the unit cell area for the film.

          substrate_area(int): the unit cell area for the substrate.

      Returns:
          transformation_sets: a set of transformation_sets defined as:
              1.) the transformation matricies for the film to create a
              super lattice of area i*film area
              2.) the tranformation matricies for the substrate to create
              a super lattice of area j*film area



   .. py:method:: get_equiv_transformations(transformation_sets, film_vectors, substrate_vectors)

      Apply the transformation_sets to the film and substrate vectors.

      Generate super-lattices and checks if they matches.
      Returns all matching vectors sets.

      Args:
          transformation_sets(array): an array of transformation sets:
              each transformation set is an array with the (i,j)
              indicating the area multipes of the film and subtrate it
              corresponds to, an array with all possible transformations
              for the film area multiple i and another array for the
              substrate area multiple j.

          film_vectors(array): film vectors to generate super lattices.

          substrate_vectors(array): substrate vectors to generate super
              lattices



   .. py:method:: __call__(film_vectors, substrate_vectors, lowest=False)

      Run the ZSL algorithm to generate all possible matching.



   .. py:method:: match_as_dict(film_sl_vectors, substrate_sl_vectors, film_vectors, substrate_vectors, match_area, film_transformation, substrate_transformation)

      Return dict which contains ZSL match.

      Args:
          film_miller(array)

          substrate_miller(array)



.. py:function:: gen_sl_transform_matricies(area_multiple)

   Generate the transformation matricies.

   Convert a set of 2D vectors into a super
   lattice of integer area multiple as proven
   in Cassels:
   Cassels, John William Scott. An introduction to the geometry of
   numbers. Springer Science & Business Media, 2012.

   Args:
       area_multiple(int): integer multiple of unit cell area for super
       lattice area.

   Returns:
       matrix_list: transformation matricies to covert unit vectors to
       super lattice vectors.


.. py:function:: rel_strain(vec1, vec2)

   Calculate relative strain between two vectors.


.. py:function:: rel_angle(vec_set1, vec_set2)

   Calculate the relative angle between two vector sets.

   Args:
       vec_set1(array[array]): an array of two vectors.

       vec_set2(array[array]): second array of two vectors.


.. py:function:: fast_norm(a)

   Much faster variant of numpy linalg norm.


.. py:function:: vec_angle(a, b)

   Calculate angle between two vectors.


.. py:function:: vec_area(a, b)

   Area of lattice plane defined by two vectors.


.. py:function:: reduce_vectors(a, b)

   Generate independent and unique basis vectors based on Zur et al.


.. py:function:: get_factors(n)

   Generate all factors of n.


.. py:function:: make_interface(film='', subs='', atol=1, ltol=0.05, max_area=500, max_area_ratio_tol=1.0, seperation=3.0, vacuum=8.0, apply_strain=False)

   Use as main function for making interfaces/heterostructures.

   Return mismatch and other information as info dict.

   Args:
      film: top/film material.

      subs: substrate/bottom/fixed material.

      seperation: minimum seperation between two.

      vacuum: vacuum will be added on both sides.
      So 2*vacuum will be added.


.. py:function:: get_hetero_type(A={}, B={})

   Provide heterojunction classification using Anderson rule.


.. py:function:: mismatch_strts()

   Return mismatch and other information as info dict.

   Deprecated, preserved here so legacy imports work.


.. py:function:: get_hetero()

   Generate heterostructure. Deprecated also.