:py:mod:`aiida_vasp.workchains.v2.common.transform`
===================================================

.. py:module:: aiida_vasp.workchains.v2.common.transform

.. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform
   :allowtitles:

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

Functions
~~~~~~~~~

.. list-table::
   :class: autosummary longtable
   :align: left

   * - :py:obj:`magnetic_structure_decorate <aiida_vasp.workchains.v2.common.transform.magnetic_structure_decorate>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.magnetic_structure_decorate
          :summary:
   * - :py:obj:`magnetic_structure_dedecorate <aiida_vasp.workchains.v2.common.transform.magnetic_structure_dedecorate>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.magnetic_structure_dedecorate
          :summary:
   * - :py:obj:`rattle <aiida_vasp.workchains.v2.common.transform.rattle>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.rattle
          :summary:
   * - :py:obj:`get_primitive <aiida_vasp.workchains.v2.common.transform.get_primitive>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_primitive
          :summary:
   * - :py:obj:`get_standard_primitive <aiida_vasp.workchains.v2.common.transform.get_standard_primitive>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_standard_primitive
          :summary:
   * - :py:obj:`spglib_refine_cell <aiida_vasp.workchains.v2.common.transform.spglib_refine_cell>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.spglib_refine_cell
          :summary:
   * - :py:obj:`get_standard_conventional <aiida_vasp.workchains.v2.common.transform.get_standard_conventional>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_standard_conventional
          :summary:
   * - :py:obj:`get_refined_structure <aiida_vasp.workchains.v2.common.transform.get_refined_structure>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_refined_structure
          :summary:
   * - :py:obj:`get_conventional_standard_structure <aiida_vasp.workchains.v2.common.transform.get_conventional_standard_structure>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_conventional_standard_structure
          :summary:
   * - :py:obj:`make_supercell <aiida_vasp.workchains.v2.common.transform.make_supercell>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.make_supercell
          :summary:
   * - :py:obj:`niggli_reduce <aiida_vasp.workchains.v2.common.transform.niggli_reduce>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.niggli_reduce
          :summary:
   * - :py:obj:`niggli_reduce_spglib <aiida_vasp.workchains.v2.common.transform.niggli_reduce_spglib>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.niggli_reduce_spglib
          :summary:
   * - :py:obj:`neb_interpolate <aiida_vasp.workchains.v2.common.transform.neb_interpolate>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.neb_interpolate
          :summary:
   * - :py:obj:`fix_atom_order <aiida_vasp.workchains.v2.common.transform.fix_atom_order>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.fix_atom_order
          :summary:
   * - :py:obj:`match_atomic_order_ <aiida_vasp.workchains.v2.common.transform.match_atomic_order_>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.match_atomic_order_
          :summary:
   * - :py:obj:`create_additional_species <aiida_vasp.workchains.v2.common.transform.create_additional_species>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.create_additional_species
          :summary:
   * - :py:obj:`convert_to_plain_list <aiida_vasp.workchains.v2.common.transform.convert_to_plain_list>`
     - .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.convert_to_plain_list
          :summary:

API
~~~

.. py:function:: magnetic_structure_decorate(structure, magmom)
   :canonical: aiida_vasp.workchains.v2.common.transform.magnetic_structure_decorate

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.magnetic_structure_decorate

.. py:function:: magnetic_structure_dedecorate(structure, mapping)
   :canonical: aiida_vasp.workchains.v2.common.transform.magnetic_structure_dedecorate

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.magnetic_structure_dedecorate

.. py:function:: rattle(structure, amp)
   :canonical: aiida_vasp.workchains.v2.common.transform.rattle

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.rattle

.. py:function:: get_primitive(structure)
   :canonical: aiida_vasp.workchains.v2.common.transform.get_primitive

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_primitive

.. py:function:: get_standard_primitive(structure, **kwargs)
   :canonical: aiida_vasp.workchains.v2.common.transform.get_standard_primitive

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_standard_primitive

.. py:function:: spglib_refine_cell(structure, symprec)
   :canonical: aiida_vasp.workchains.v2.common.transform.spglib_refine_cell

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.spglib_refine_cell

.. py:function:: get_standard_conventional(structure)
   :canonical: aiida_vasp.workchains.v2.common.transform.get_standard_conventional

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_standard_conventional

.. py:function:: get_refined_structure(structure, symprec, angle_tolerance)
   :canonical: aiida_vasp.workchains.v2.common.transform.get_refined_structure

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_refined_structure

.. py:function:: get_conventional_standard_structure(structure, symprec, angle_tolerance)
   :canonical: aiida_vasp.workchains.v2.common.transform.get_conventional_standard_structure

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.get_conventional_standard_structure

.. py:function:: make_supercell(structure, supercell, **kwargs)
   :canonical: aiida_vasp.workchains.v2.common.transform.make_supercell

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.make_supercell

.. py:function:: niggli_reduce(structure)
   :canonical: aiida_vasp.workchains.v2.common.transform.niggli_reduce

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.niggli_reduce

.. py:function:: niggli_reduce_spglib(structure)
   :canonical: aiida_vasp.workchains.v2.common.transform.niggli_reduce_spglib

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.niggli_reduce_spglib

.. py:function:: neb_interpolate(init_structure, final_strucrture, nimages)
   :canonical: aiida_vasp.workchains.v2.common.transform.neb_interpolate

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.neb_interpolate

.. py:function:: fix_atom_order(reference, to_fix)
   :canonical: aiida_vasp.workchains.v2.common.transform.fix_atom_order

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.fix_atom_order

.. py:function:: match_atomic_order_(atoms: ase.Atoms, atoms_ref: ase.Atoms) -> typing.Tuple[ase.Atoms, typing.List[int]]
   :canonical: aiida_vasp.workchains.v2.common.transform.match_atomic_order_

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.match_atomic_order_

.. py:function:: create_additional_species(species: list, magmoms: list)
   :canonical: aiida_vasp.workchains.v2.common.transform.create_additional_species

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.create_additional_species

.. py:function:: convert_to_plain_list(species: list, magmom_mapping: dict)
   :canonical: aiida_vasp.workchains.v2.common.transform.convert_to_plain_list

   .. autodoc2-docstring:: aiida_vasp.workchains.v2.common.transform.convert_to_plain_list