jarvis.analysis.structure.spacegroup
====================================

.. py:module:: jarvis.analysis.structure.spacegroup

.. autoapi-nested-parse::

   Modules for handling crystallographic Spacegroup related operations.



Attributes
----------

.. autoapisummary::

   jarvis.analysis.structure.spacegroup.wyckoff_file


Classes
-------

.. autoapisummary::

   jarvis.analysis.structure.spacegroup.Spacegroup3D


Functions
---------

.. autoapisummary::

   jarvis.analysis.structure.spacegroup.unique_rows_2
   jarvis.analysis.structure.spacegroup.symmetrically_distinct_miller_indices
   jarvis.analysis.structure.spacegroup.parse_wyckoff_csv
   jarvis.analysis.structure.spacegroup.read_wyckoff_csv
   jarvis.analysis.structure.spacegroup.get_wyckoff_position_operators
   jarvis.analysis.structure.spacegroup.parse_xyz_string
   jarvis.analysis.structure.spacegroup.operate_affine
   jarvis.analysis.structure.spacegroup.get_new_coord_for_xyz_sym
   jarvis.analysis.structure.spacegroup.check_duplicate_coords


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

.. py:function:: unique_rows_2(a)

   Remove duplicate rows.


.. py:function:: symmetrically_distinct_miller_indices(max_index=3, cvn_atoms=None)

   Get unique miller indices for max_index.


.. py:data:: wyckoff_file
   :value: ''


.. py:function:: parse_wyckoff_csv(wyckoff_file)

   Parse Wyckoff.csv from spglib.

   There are 530 data sets. For one example:
   9:C 1 2 1:::::::
   ::4:c:1:(x,y,z):(-x,y,-z)::
   ::2:b:2:(0,y,1/2):::
   ::2:a:2:(0,y,0):::


.. py:function:: read_wyckoff_csv(filename)

   Read wyckoff_csv file.


.. py:function:: get_wyckoff_position_operators(hall_number)

   Get all Wyckoff operations for Hall number.


.. py:class:: Spacegroup3D(atoms=[], dataset={}, symprec=0.01, angle_tolerance=5)

   Bases: :py:obj:`object`


   Provide spacegroup related data for Atoms object.

   Currently uses spglib to derive spacegroup
   related information for 3D materials mainly


   .. py:attribute:: _dataset


   .. py:attribute:: _atoms
      :value: []



   .. py:attribute:: _symprec
      :value: 0.01



   .. py:attribute:: _angle_tolerance
      :value: 5



   .. py:method:: spacegroup_data()

      Provide spacegroup data from spglib.



   .. py:property:: space_group_symbol

      Get spacegroup symbol.



   .. py:property:: space_group_number

      Get spacegroup number.



   .. py:property:: primitive_atoms

      Get primitive atoms.



   .. py:property:: refined_atoms

      Refine atoms based on spacegroup data.



   .. py:property:: crystal_system

      Get crystal system.



   .. py:property:: lattice_system

      Get lattice system.



   .. py:property:: point_group_symbol

      Get pointgroup.



   .. py:property:: conventional_standard_structure

      Give a conventional cell according to certain conventions.

      The conventionss are defined in Setyawan, W., & Curtarolo,
      S. (2010). High-throughput electronic band structure calculations:
      Challenges and tools. Computational Materials Science,
      49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010
      They basically enforce as much as possible
      norm(a1)<norm(a2)<norm(a3)
      Returns:
          The structure in a conventional standardized cell



.. py:function:: parse_xyz_string(xyz_string)

   Convert xyz info to translation and rotation vectors.

   Adapted from pymatgen.
   Args:
       xyz_string: string of the form 'x, y, z', '-x, -y, z',
           '-2y+1/2, 3x+1/2, z-y+1/2', etc.
   Returns:
       translation and rotation vectors.


.. py:function:: operate_affine(cart_coord=[], affine_matrix=[])

   Operate affine method.


.. py:function:: get_new_coord_for_xyz_sym(frac_coord=[], xyz_string='')

   Obtain new coord from xyz string.


.. py:function:: check_duplicate_coords(coords=[], coord=[])

   Check if a coordinate exists.