jarvis.core package

Submodules

jarvis.core.atoms module

This module provides classes to specify atomic structure.

class jarvis.core.atoms.Atoms(lattice_mat=None, coords=None, elements=None, props=None, cartesian=False, show_props=False)

Bases: object

Generate Atoms python object.

apply_strain(strain)

Apply a strain(e.g. 0.01, [0,0,.01]) to the lattice.

ase_converter(pbc=True)

Get ASE representation of the atoms object.

atomic_numbers

Get list of atomic numbers of atoms in the atoms object.

center(axis=2, vacuum=18.0, about=None)

Center structure with vacuum padding.

Args:

vacuum:vacuum size

axis: direction

center_around_origin(new_origin=[0.0, 0.0, 0.5])

Center around given origin.

check_polar

Check if the surface structure is polar.

Comparing atom types at top and bottom. Applicable for sufcae with vaccums only.

Args:

file:atoms object (surface with vacuum)

Returns:

polar:True/False

composition

Get composition of the atoms object.

density

Get density in g/cm3 of the atoms object.

static from_cif(filename='atoms.cif')

Read .cif format file.

classmethod from_dict(d={})

Form atoms object from the dictionary.

classmethod from_poscar(filename='POSCAR')

Read POSCAR/CONTCAR file from to make Atoms object.

classmethod from_xyz(filename='dsgdb9nsd_057387.xyz', box_size=40)

Read XYZ file from to make Atoms object.

get_center_of_mass()

Get center of mass of the atoms object.

get_lll_reduced_structure()

Get LLL algorithm based reduced structure.

get_origin()

Get center of mass of the atoms object.

get_primitive_atoms

Get primitive Atoms using spacegroup information.

get_string(cart=True, sort_order='X')

Convert Atoms to string.

Optional arguments below.

Args:

cart:True/False for cartesian/fractional coords.

sort_order: sort by chemical properties of

elements. Default electronegativity.

get_xyz_string

Get xyz string for atoms.

lattice_points_in_supercell(supercell_matrix)

Adapted from Pymatgen.

Returns the list of points on the original lattice contained in the supercell in fractional coordinates (with the supercell basis). e.g. [[2,0,0],[0,1,0],[0,0,1]] returns [[0,0,0],[0.5,0,0]]

Args:

supercell_matrix: 3x3 matrix describing the supercell

Returns:

numpy array of the fractional coordinates

make_supercell(dim=[2, 2, 2])

Make supercell of dimension dim.

make_supercell_matrix(scaling_matrix)

Adapted from Pymatgen.

Makes a supercell. Allowing to have sites outside the unit cell.

Args:

scaling_matrix: A scaling matrix for transforming the lattice vectors. Has to be all integers. Several options are possible: a. A full 3x3 scaling matrix defining the linear combination

the old lattice vectors. E.g., [[2,1,0],[0,3,0],[0,0, 1]] generates a new structure with lattice vectors a’ = 2a + b, b’ = 3b, c’ = c where a, b, and c are the lattice vectors of the original structure.

2. An sequence of three scaling factors. E.g., [2, 1, 1]

specifies that the supercell should have dimensions 2a x b x c.

3. A number, which simply scales all lattice vectors by the

same factor.

Returns:

Supercell structure. Note that a Structure is always returned, even if the input structure is a subclass of Structure. This is to avoid different arguments signatures from causing problems. If you prefer a subclass to return its own type, you need to override this method in the subclass.

num_atoms

Get number of atoms.

packing_fraction

Get packing fraction of the atoms object.

phonopy_converter(pbc=True)

Get phonopy representation of the atoms object.

pymatgen_converter()

Get pymatgen representation of the atoms object.

raw_angle_matrix

Provide distance matrix.

raw_distance_matrix

Provide distance matrix.

remove_site_by_index(site=0)

Remove an atom by its index number.

spacegroup(symprec=0.001)

Get spacegroup of the atoms object.

to_dict()

Provide dictionary representation of the atoms object.

uniq_species

Get unique elements.

volume

Get volume of the atoms object.

write_cif(filename='atoms.cif', comment=None, with_spg_info=True)

Write CIF format file from Atoms object.

Caution: can’t handle fractional occupancies right now

write_poscar(filename='POSCAR')

Write POSCAR format file from Atoms object.

write_xyz(filename='atoms.xyz')

Write XYZ format file.

class jarvis.core.atoms.VacuumPadding(atoms, vacuum=20.0)

Bases: object

Adds vaccum padding to make 2D structure or making molecules.

get_effective_2d_slab()

Add 2D vacuum to a system.

get_effective_molecule()

Add vacuum around a system.

jarvis.core.atoms.add_atoms(top, bottom, distance=[0, 0, 1], apply_strain=False)

Add top and bottom Atoms with a distance array.

Bottom Atoms lattice-matrix is chosen as final lattice.

jarvis.core.atoms.ase_to_atoms(ase_atoms='')

Convert ase structure to Atoms.

jarvis.core.atoms.fix_pbc(atoms)

Use for making Atoms with vacuum.

jarvis.core.atoms.get_supercell_dims(atoms, enforce_c_size=10, extend=1)

Get supercell dimensions.

jarvis.core.atoms.pmg_to_atoms(pmg='')

Convert pymatgen structure to Atoms.

jarvis.core.composition module

Modules handling chemical composition.

class jarvis.core.composition.Composition(content={}, sort=False)

Bases: object

Generate composition python object.

formula

Get total chemical formula.

classmethod from_dict(d={})

Load the class from a dictionary.

static from_string(value, sort=True)

Generate composition from string.

prototype

Get chemical prototypes such as A, AB etc.

reduce()

Reduce chemical formula.

reduced_formula

Get reduced formula.

to_dict()

Return dictionary format.

weight

Get atomic weight.

jarvis.core.graphs module

Module to generate networkx graphs.

class jarvis.core.graphs.Graph(nodes=[], node_attributes=[], edges=[], edge_attributes=[], color_map=None, labels=None)

Bases: object

Generate a graph object.

adjacency_matrix

Provide adjacency_matrix of graph.

static from_atoms(atoms=None, lengthscale=0.5, variance=1.0, get_prim=False, zero_diag=False, node_atomwise_angle_dist=False, node_atomwise_rdf=False, features='basic', enforce_c_size=10.0, max_n=100, max_cut=5.0, verbose=False, make_colormap=True)

Get Networkx graph. Requires Networkx installation.

Args:

atoms: jarvis.core.Atoms object.

rcut: cut-off after which distance will be set to zero

in the adjacency matrix.

features: Node features.

‘atomic_number’: graph with atomic numbers only. ‘cfid’: 438 chemical descriptors from CFID. ‘basic’:10 features array: array with CFID chemical descriptor names. See: jarvis/core/specie.py

enforce_c_size: minimum size of the simulation cell in Angst.

classmethod from_dict(d={})

Constuct class from a dictionary.

num_edges

Return number of edges in the graph.

num_nodes

Return number of nodes in the graph.

to_dict()

Provide dictionary representation of the Graph object.

to_networkx()

Get networkx representation.

jarvis.core.image module

Module for processing image files.

class jarvis.core.image.Image(values=[], pbc_params=[])

Bases: object

Module for processing image files.

black_and_white(threshold=127)

Make black and white image.

crop_square(size=None)

Crop an image.

fourier_transform2D(zoom_factor=30, interpol_factor=1, use_crop=True, pad_bright_spot=True)

Make 2D FT.

static from_file(path)

Load image frim file.

gaussian_filter(sigma=10)

Apply Gaussian filter to an image.

rgb_to_gray()

Make RGB to Grey scale image.

rotate(angle=45)

Rotate an image.

save(filename)

Save an image.

zoom_interp_2d(FFT_image, zoom_factor=40, interpol_factor=1)

Zoom and interpolate an image.

jarvis.core.kpoints module

Module for k-points used n various calculations.

class jarvis.core.kpoints.HighSymmetryKpoint3DFactory(kpoints=[], path=[], name=None)

Bases: object

High-symmetry k-points for different crystal-systems.

bcc()

Bcc HighSymmKPath, return: Dict.

bctet1(c, a)

BCT1 HighSymmKPath, return: Dict.

bctet2(c, a)

BCT2 HighSymmKPath, return: Dict.

cubic()

Cubic HighSymmKPath, return: Dict.

fcc()

Fcc HighSymmKPath, return: Dict.

hex()

Hexagonal HighSymmKPath, return: Dict.

mcl(b, c, beta)

Monoclinic 1 HighSymmKPath, return: Dict.

mclc1(a, b, c, alpha)

Monoclinic C1 HighSymmKPath, return: Dict.

mclc2(a, b, c, alpha)

Monoclinic C2 HighSymmKPath, return: Dict.

mclc3(a, b, c, alpha)

Monoclinic C3 HighSymmKPath, return: Dict.

mclc4(a, b, c, alpha)

Monoclinic C4 HighSymmKPath, return: Dict.

mclc5(a, b, c, alpha)

Monoclinic C5 HighSymmKPath, return: Dict.

orc()

Orthorhombic HighSymmKPath, return: Dict.

orcc(a, b, c)

Orthorhombic C HighSymmKPath, return: Dict.

orcf1(a, b, c)

Orthorhombic f1 HighSymmKPath, return: Dict.

orcf2(a, b, c)

Orthorhombic f2 HighSymmKPath, return: Dict.

orcf3(a, b, c)

Orthorhombic f3 HighSymmKPath, return: Dict.

orci(a, b, c)

Orthorhombic I HighSymmKPath, return: Dict.

rhl1(alpha)

Rhombohedral 1 HighSymmKPath, return: Dict.

rhl2(alpha)

Rhombohedral 2 HighSymmKPath, return: Dict.

tet()

Tetragonal HighSymmKPath, return: Dict.

to_dict()

Get dictionary representation.

tria()

Trigonal a HighSymmKPath, return: Dict.

trib()

Trigonal b HighSymmKPath, return: Dict.

class jarvis.core.kpoints.Kpoints3D(kpoints=[[1, 1, 1]], labels=[], kpoints_weights=[], kpoint_mode='automatic', header='Gamma')

Bases: object

Handle k-points python object.

automatic_length_mesh(lattice_mat=[], length=20, header='Gamma')

Length based automatic k-points.

classmethod from_dict(d={})

Build class from a dictionary representation.

high_kpath(atoms)

Get high symmetry path as a dictionary.

high_symm_path(atoms)

Get high symmetry k-points for given Atoms.

interpolated_points(atoms, line_density=20, coords_are_cartesian=False)

Provide bandstructure k-points, controlled by the line_density.

kpath(atoms, line_density=20, weights=[], unique_kp_only=False, coords_are_cartesian=False)

Get k-path for bandstructure calculations.

kpoints_per_atom(atoms=None, kppa=1000)

Return Kpoints object for kpoints per atom for a cell.

kpts

Return k-points arrays.

labels

Return k-points labels, used for high BZ points.

to_dict()

Provide dictionary representation.

write_file(filename='')

Write k-point object to a files.

jarvis.core.kpoints.generate_kgrid(grid=[5, 5, 5])

Generate k-mesh of size grid.

jarvis.core.kpoints.generate_kpath(kpath=[[0, 0, 0], [0, 0.5, 0.5]], num_k=5)

Generate k-path with distance num_k k-points between them.

jarvis.core.lattice module

Modules for handing crystallographic lattice-parameters.

class jarvis.core.lattice.Lattice(lattice_mat=None, round_off=5)

Bases: object

Construct Lattice parameter object.

a

Return a lattice vector length.

abc

Return lattice vector lengths.

alpha

Return alpha lattice vector angle.

angles

Return lattice vector angles.

b

Return b lattice vector length.

beta

Return beta lattice vector angle.

c

Return c lattice vector length.

cart_coords(frac_coords)

Return cartesian coords from fractional coords using Lattice.

static cubic(a)

Construct cubic Lattice from lattice parameter information.

find_all_matches(other_lattice, ltol=1e-05, atol=1)

Find all lattice mappings, adapted from pymatgen.

find_matches(other_lattice, ltol=1e-05, atol=1)

Find matches with length and angle tolerances.

frac_coords(cart_coords)

Return fractional coords from cartesian coords using Lattice.

classmethod from_dict(d)

Construct Lattice from lattice matrix dictionary.

static from_parameters(a, b, c, alpha, beta, gamma)

Construct Lattice from lattice parameter information.

gamma

Return gamma lattice vector angle.

get_lll_reduced_lattice(delta=0.75)

Get LLL reduced lattice.

Adpted from pymatgen. Args:

delta: Delta parameter.

Returns:

LLL reduced Lattice.

get_points_in_sphere(frac_points, center, r)

Find all points within a sphere from the point.

Takes into account periodic boundary conditions. This includes sites in other periodic images. Adapted from pymatgen.

static hexagonal(a, c)

Construct hexagonal Lattice from lattice parameter information.

inv_lattice()

Return inverse lattice matrix.

inv_matrix

Return inverse lattice matrix.

lat_angles(tol=0.01, radians=False)

Return lattice vector angles in radians or degree.

lat_lengths()

Return lattice vectors’ lengths.

lattice()

Return lattice matrix.

matrix

Return lattice matrix.

static monoclinic(a, b, c, beta)

Construct monoclinic Lattice from lattice parameter information.

static orthorhombic(a, b, c)

Construct orthorhombic Lattice.

parameters

Return lattice vector angles in radians or degree.

reciprocal_lattice()

Return reciprocal Lattice.

reciprocal_lattice_crystallographic()

Return reciprocal Lattice without 2 * pi.

static rhombohedral(a, alpha)

Construct rhombohedral Lattice.

static tetragonal(a, c)

Construct tetragonal Lattice from lattice parameter information.

to_dict()

Return lattice parameter information as a dictionary.

volume

Return volume given a lattice object.

jarvis.core.lattice.abs_cap(val, max_abs_val=1)

Return the value with its absolute value capped at max_abs_val.

Particularly useful in passing values to trignometric functions where numerical errors may result in an argument > 1 being passed in.

Args:

val (float): Input value.

max_abs_val (float): The maximum absolute value for val. Defaults to 1.

Returns:

val if abs(val) < 1 else sign of val * max_abs_val.

jarvis.core.lattice.lattice_coords_transformer(old_lattice_mat=[], new_lattice_mat=[], cart_coords=[])

Transform coords to a new lattice.

jarvis.core.pdb_atoms module

Modules for handling PDB Protein Data Bank files.

jarvis.core.pdb_atoms.read_pdb(filename='')

Read PDB file and make Atoms object.

jarvis.core.specie module

Modules related to chemistry of periodic-table elements.

class jarvis.core.specie.Specie(symbol='')

Bases: object

Specie object for chemistry information.

Used in defining chemistry of a material.

>>> el = Specie('Al')
>>> el.Z
13
>>> round(el.atomic_mass,2)
26.98
>>> el.symbol
'Al'
>>> round(el.get_chgdescrp_arr[1],2)
12.17
>>> round(el.get_descrp_arr[1],2)
2792.11
>>> el = Specie('asdfg')
>>> el.element_property("asdfg")
nan

Z

Get atomic number.

atomic_mass

Get atomic mass.

atomic_rad

Get atomic radii.

element_property(key='')

Get element property from the list of keys.

These 84 keys are: keys = [

“is_halogen”, “row”, “GV”, “nfunfill”, “C-9”, “C-8”, “C-7”, “C-6”, “C-5”, “C-4”, “C-3”, “C-2”, “C-1”, “C-0”, “me1”, “me3”, “me2”, “max_oxid_s”, “npvalence”, “mp”, “first_ion_en”, “ndunfill”, “op_eg”, “jv_enp”, “nfvalence”, “polzbl”, “oq_bg”, “atom_rad”, “atom_mass”, “is_alkali”, “C-13”, “C-12”, “C-11”, “C-10”, “C-17”, “C-16”, “C-15”, “C-14”, “C-19”, “C-18”, “voro_coord”, “is_noble_gas”, “e1”, “e3”, “e2”, “is_lanthanoid”, “ndvalence”, “KV”, “min_oxid_s”, “nsunfill”, “C-26”, “X”, “is_actinoid”, “C-28”, “C-29”, “C-27”, “C-24”, “C-25”, “C-22”, “C-23”, “C-20”, “C-21”, “avg_ion_rad”, “nsvalence”, “is_metalloid”, “elec_aff”, “coulmn”, “mol_vol”, “bp”, “C-31”, “C-30”, “C-33”, “C-32”, “C-35”, “C-34”, “is_transition_metal”, “block”, “therm_cond”, “Z”, “is_alkaline”, “npunfill”, “oq_enp”, “mop_eg”, “hfus”,

]

get_chgdescrp_arr

Get charge descriptors for an element.

Gives 378 array data.

Args:

elm: element name

Returns:

arr: array value

get_descrp_arr

Get chemical descriptors for an element.

Gives 438 array data.

Args:

elm: element name

Returns:

arr: array value

jarvis.core.specie.get_descrp_arr_name(elm='Al')

Get chemical descriptors for an element.

Can be used in JARVIS-ML.

Args:

elm: element name

Returns:

arr: array value

jarvis.core.spectrum module

Module to process spectrum like data.

class jarvis.core.spectrum.Spectrum(x=[], y=[], linewidth=5.0, resolution=0.1)

Bases: object

Module for spectrum like data, e.g. IR, Raman, DOS, epsilon.

get_interpolated_values(new_dist=array([ 0., 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1., 1.05, 1.1, 1.15, 1.2, 1.25, 1.3, 1.35, 1.4, 1.45, 1.5, 1.55, 1.6, 1.65, 1.7, 1.75, 1.8, 1.85, 1.9, 1.95, 2., 2.05, 2.1, 2.15, 2.2, 2.25, 2.3, 2.35, 2.4, 2.45, 2.5, 2.55, 2.6, 2.65, 2.7, 2.75, 2.8, 2.85, 2.9, 2.95, 3., 3.05, 3.1, 3.15, 3.2, 3.25, 3.3, 3.35, 3.4, 3.45, 3.5, 3.55, 3.6, 3.65, 3.7, 3.75, 3.8, 3.85, 3.9, 3.95, 4., 4.05, 4.1, 4.15, 4.2, 4.25, 4.3, 4.35, 4.4, 4.45, 4.5, 4.55, 4.6, 4.65, 4.7, 4.75, 4.8, 4.85, 4.9, 4.95, 5., 5.05, 5.1, 5.15, 5.2, 5.25, 5.3, 5.35, 5.4, 5.45, 5.5, 5.55, 5.6, 5.65, 5.7, 5.75, 5.8, 5.85, 5.9, 5.95, 6., 6.05, 6.1, 6.15, 6.2, 6.25, 6.3, 6.35, 6.4, 6.45, 6.5, 6.55, 6.6, 6.65, 6.7, 6.75, 6.8, 6.85, 6.9, 6.95, 7., 7.05, 7.1, 7.15, 7.2, 7.25, 7.3, 7.35, 7.4, 7.45, 7.5, 7.55, 7.6, 7.65, 7.7, 7.75, 7.8, 7.85, 7.9, 7.95, 8., 8.05, 8.1, 8.15, 8.2, 8.25, 8.3, 8.35, 8.4, 8.45, 8.5, 8.55, 8.6, 8.65, 8.7, 8.75, 8.8, 8.85, 8.9, 8.95, 9., 9.05, 9.1, 9.15, 9.2, 9.25, 9.3, 9.35, 9.4, 9.45, 9.5, 9.55, 9.6, 9.65, 9.7, 9.75, 9.8, 9.85, 9.9, 9.95, 10., 10.05, 10.1, 10.15, 10.2, 10.25, 10.3, 10.35, 10.4, 10.45, 10.5, 10.55, 10.6, 10.65, 10.7, 10.75, 10.8, 10.85, 10.9, 10.95, 11., 11.05, 11.1, 11.15, 11.2, 11.25, 11.3, 11.35, 11.4, 11.45, 11.5, 11.55, 11.6, 11.65, 11.7, 11.75, 11.8, 11.85, 11.9, 11.95, 12., 12.05, 12.1, 12.15, 12.2, 12.25, 12.3, 12.35, 12.4, 12.45, 12.5, 12.55, 12.6, 12.65, 12.7, 12.75, 12.8, 12.85, 12.9, 12.95, 13., 13.05, 13.1, 13.15, 13.2, 13.25, 13.3, 13.35, 13.4, 13.45, 13.5, 13.55, 13.6, 13.65, 13.7, 13.75, 13.8, 13.85, 13.9, 13.95, 14., 14.05, 14.1, 14.15, 14.2, 14.25, 14.3, 14.35, 14.4, 14.45, 14.5, 14.55, 14.6, 14.65, 14.7, 14.75, 14.8, 14.85, 14.9, 14.95]))

Get interpolated grid on a fixed grid.

get_peak_indices(window=array([1, 2, 3, 4, 5, 6, 7, 8, 9]))

Get peak indices for non-zero peaks.

max_x

Get maximum mode frequency.

min_x

Get minimum mode frequency.

num_modes

Get number of modes.

rescale(mode='max', scaling_factor=1.0)

Rescale the spectrum.

smoothen_spiky_spectrum()

Smoothen peak for delta function like peaks.

jarvis.core.utils module

Set of useful utility functions.

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

Convert 1D arry to string.

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

Check if a coordinate exists.

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.chunks(lst, n)

Split successive n-sized chunks from list.

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

GCD module from ase.

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

Get angle between three vectors.

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.get_new_coord_for_xyz_sym(frac_coord=[], xyz_string='')

Obtain new coord from xyz string.

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

Get Lorentzian of a function.

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

Operate affine method.

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.rand_select(x=[])

Select randomly with index info.

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

Generate random colors for atom coloring.

jarvis.core.utils.rec_dict()

Make a recursion dictionary.

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.stringdict_to_xml(d={}, enforce_string=False)

Convert string dictionary to XML.

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

Return update dictionary.

jarvis.core.utils.xml_to_dict(fname)

Parse XML file.

Module contents

Some of the core modules for JARVIS-Tools.