jarvis.core.utils
=================

.. py:module:: jarvis.core.utils

.. autoapi-nested-parse::

   Set of useful utility functions.



Functions
---------

.. autoapisummary::

   jarvis.core.utils.xml_to_dict
   jarvis.core.utils.get_factors
   jarvis.core.utils.get_counts
   jarvis.core.utils.gcd
   jarvis.core.utils.ext_gcd
   jarvis.core.utils.rand_select
   jarvis.core.utils.rec_dict
   jarvis.core.utils.random_colors
   jarvis.core.utils.get_angle
   jarvis.core.utils.recast_array_on_uniq_array_elements
   jarvis.core.utils.lorentzian
   jarvis.core.utils.stringdict_to_xml
   jarvis.core.utils.array_to_string
   jarvis.core.utils.chunks
   jarvis.core.utils.check_match
   jarvis.core.utils.update_dict
   jarvis.core.utils.get_new_coord_for_xyz_sym
   jarvis.core.utils.check_duplicate_coords
   jarvis.core.utils.parse_xyz_string
   jarvis.core.utils.operate_affine
   jarvis.core.utils.gaussian
   jarvis.core.utils.lorentzian2
   jarvis.core.utils.digitize_array
   jarvis.core.utils.bond_angle
   jarvis.core.utils.check_url_exists
   jarvis.core.utils.volumetric_grid_reshape
   jarvis.core.utils.cos_formula
   jarvis.core.utils.baseline_als
   jarvis.core.utils.recast_array


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

.. py:function:: xml_to_dict(fname)

   Parse XML file.


.. py:function:: get_factors(x, start=2)

   Get factors of a number.


.. py:function:: get_counts(array=['W', 'W', 'Mo', 'Mo', 'S', 'S'])

   Get number of unique elements and their counts.

   Uses OrderedDict.

   Args:
        array of elements

   Returns:
        ordereddict, e.g.OrderedDict([('W', 2), ('Mo', 2), ('S', 2)])


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

   Calculate the Greatest Common Divisor of a and b.

   Unless b==0, the result will have the same sign as b (so that when
   b is divided by it, the result comes out positive).


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

   GCD module from ase.


.. py:function:: rand_select(x=[])

   Select randomly with index info.


.. py:function:: rec_dict()

   Make a recursion dictionary.


.. py:function:: random_colors(number_of_colors=110)

   Generate random colors for atom coloring.


.. py:function:: get_angle(a=np.array([1, 2, 3]), b=np.array([4, 5, 6]), c=np.array([7, 8, 9]))

   Get angle between three vectors.


.. py:function:: recast_array_on_uniq_array_elements(uniq=['Si', 'Al', 'O'], arr=['Si', 'Si', 'Al', 'Al', 'Si', 'O', 'O', 'O', 'O'])

   Recast array on uniq array elements.


.. py:function:: lorentzian(x, y, x0, gamma)

   Get Lorentzian of a function.


.. py:function:: stringdict_to_xml(d={}, enforce_string=False)

   Convert string dictionary to XML.


.. py:function:: array_to_string(arr=[])

   Convert 1D arry to string.


.. py:function:: chunks(lst, n)

   Split successive n-sized chunks from list.


.. py:function:: check_match(a, b, tol=1e-08)

   Check if a and b are the same, taking into account PBCs.


.. py:function:: update_dict(main={}, extra={})

   Return update dictionary.


.. 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.


.. 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:: gaussian(x, sigma)

   Get Gaussian profile.


.. py:function:: lorentzian2(x, gamma)

   Get Lorentziann profile.


.. py:function:: digitize_array(values=[], max_len=10)

   Digitze an array.


.. py:function:: bond_angle(dist1, dist2, bondx1, bondx2, bondy1, bondy2, bondz1, bondz2)

   Get an angle.


.. py:function:: check_url_exists(url='https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-77580.xml')

   Check if a url exists.


.. py:function:: volumetric_grid_reshape(data=[], final_grid=[50, 50, 50])

   Reshape volumetric data.


.. py:function:: cos_formula(a, b, c)

   Get angle between three edges for oblique triangles.


.. py:function:: baseline_als(y, lam, p, niter=10)

   Adaptive Least Squares fitting for baseline correction

   Parameters:
   y: array_like
       Input signal
   lam: float
       Lambda (smoothness)
   p: float
       Asymmetry
   niter: int, optional
       Number of iterations

   Returns:
   array_like
       The estimated baseline


.. py:function:: recast_array(x_original=[], y_original=[], x_new=np.arange(0, 90, 1), tol=0.1)