jarvis.core.utils

Set of useful utility functions.

Module Contents

Functions

xml_to_dict(fname)	Parse XML file.
get_factors(x[, start])	Get factors of a number.
get_counts([array])	Get number of unique elements and their counts.
gcd(a, b)	Calculate the Greatest Common Divisor of a and b.
ext_gcd(a, b)	GCD module from ase.
rand_select([x])	Select randomly with index info.
rec_dict()	Make a recursion dictionary.
random_colors([number_of_colors])	Generate random colors for atom coloring.
get_angle([a, b, c])	Get angle between three vectors.
recast_array_on_uniq_array_elements([uniq, arr])	Recast array on uniq array elements.
lorentzian(x, y, x0, gamma)	Get Lorentzian of a function.
stringdict_to_xml([d, enforce_string])	Convert string dictionary to XML.
array_to_string([arr])	Convert 1D arry to string.
chunks(lst, n)	Split successive n-sized chunks from list.
check_match(a, b[, tol])	Check if a and b are the same, taking into account PBCs.
update_dict([main, extra])	Return update dictionary.
get_new_coord_for_xyz_sym([frac_coord, xyz_string])	Obtain new coord from xyz string.
check_duplicate_coords([coords, coord])	Check if a coordinate exists.
parse_xyz_string(xyz_string)	Convert xyz info to translation and rotation vectors.
operate_affine([cart_coord, affine_matrix])	Operate affine method.
gaussian(x, sigma)	Get Gaussian profile.
lorentzian2(x, gamma)	Get Lorentziann profile.
digitize_array([values, max_len])	Digitze an array.
bond_angle(dist1, dist2, bondx1, bondx2, bondy1, ...)	Get an angle.
check_url_exists([url])	Check if a url exists.
volumetric_grid_reshape([data, final_grid])	Reshape volumetric data.
cos_formula(a, b, c)	Get angle between three edges for oblique triangles.

jarvis.core.utils.xml_to_dict(fname)

Parse XML file.

jarvis.core.utils.get_factors(x, start=2)

Get factors of a number.

jarvis.core.utils.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)])

jarvis.core.utils.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).

jarvis.core.utils.ext_gcd(a, b)

GCD module from ase.

jarvis.core.utils.rand_select(x=[])

Select randomly with index info.

jarvis.core.utils.rec_dict()

Make a recursion dictionary.

jarvis.core.utils.random_colors(number_of_colors=110)

Generate random colors for atom coloring.

jarvis.core.utils.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.

jarvis.core.utils.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.

jarvis.core.utils.lorentzian(x, y, x0, gamma)

Get Lorentzian of a function.

jarvis.core.utils.stringdict_to_xml(d={}, enforce_string=False)

Convert string dictionary to XML.

jarvis.core.utils.array_to_string(arr=[])

Convert 1D arry to string.

jarvis.core.utils.chunks(lst, n)

Split successive n-sized chunks from list.

jarvis.core.utils.check_match(a, b, tol=1e-08)

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

jarvis.core.utils.update_dict(main={}, extra={})

Return update dictionary.

jarvis.core.utils.get_new_coord_for_xyz_sym(frac_coord=[], xyz_string='')

Obtain new coord from xyz string.

jarvis.core.utils.check_duplicate_coords(coords=[], coord=[])

Check if a coordinate exists.

jarvis.core.utils.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.

jarvis.core.utils.operate_affine(cart_coord=[], affine_matrix=[])

Operate affine method.

jarvis.core.utils.gaussian(x, sigma)

Get Gaussian profile.

jarvis.core.utils.lorentzian2(x, gamma)

Get Lorentziann profile.

jarvis.core.utils.digitize_array(values=[], max_len=10)

Digitze an array.

jarvis.core.utils.bond_angle(dist1, dist2, bondx1, bondx2, bondy1, bondy2, bondz1, bondz2)

Get an angle.

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

Check if a url exists.

jarvis.core.utils.volumetric_grid_reshape(data=[], final_grid=[50, 50, 50])

Reshape volumetric data.

jarvis.core.utils.cos_formula(a, b, c)

Get angle between three edges for oblique triangles.