jarvis.core.atoms

This module provides classes to specify atomic structure.

Attributes

amu_gm
ang_cm
mineral_json_file

Classes

Atoms	Generate Atoms python object.
VacuumPadding	Adds vaccum padding to make 2D structure or making molecules.
OptimadeAdaptor	Module to work with optimade.

Functions

fix_pbc(atoms)	Use for making Atoms with vacuum.
add_atoms(top, bottom[, distance, apply_strain, add_tags])	Add top and bottom Atoms with a distance array.
get_supercell_dims(atoms[, enforce_c_size, extend])	Get supercell dimensions.
pmg_to_atoms([pmg])	Convert pymatgen structure to Atoms.
ase_to_atoms([ase_atoms, cartesian])	Convert ase structure to Atoms.
crop_square([atoms, csize])	Crop a sqaur portion from a surface/2D system.
compare_atoms([atoms1, atoms2, primitive_cell, verbose])	Compare atomic strutures.
build_xanes_poscar([atoms, selected_element, prefix, ...])	Generate POSCAR file for XANES, note the element ordering.

Module Contents

jarvis.core.atoms.amu_gm = 1.66054e-24

jarvis.core.atoms.ang_cm = 1e-08

jarvis.core.atoms.mineral_json_file

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.

>>> box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
>>> coords = [[0, 0, 0], [0.25, 0.2, 0.25]]
>>> elements = ["Si", "Si"]
>>> Si = Atoms(lattice_mat=box, coords=coords, elements=elements)
>>> print(round(Si.volume,2))
40.03
>>> Si.composition
{'Si': 2}
>>> round(Si.density,2)
2.33
>>> round(Si.packing_fraction,2)
0.28
>>> Si.atomic_numbers
[14, 14]
>>> Si.num_atoms
2
>>> Si.frac_coords[0][0]
0
>>> Si.cart_coords[0][0]
0.0
>>> coords = [[0, 0, 0], [1.3575 , 1.22175, 1.22175]]
>>> round(Si.density,2)
2.33
>>> Si.spacegroup()
'C2/m (12)'
>>> Si.pymatgen_converter()!={}
True

lattice_mat

show_props = False

lattice

coords

elements = None

cartesian = False

props = None

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

static read_with_cif2cell(filename='1000000.cif', get_primitive_atoms=False)

Use cif2cell package to read cif files.

static from_pdb_old(filename='abc.pdb')

Read PDB file, kept of checking, use from_pdb instead.

static from_pdb(filename='abc.pdb', max_lat=200)

Read pdb/sdf/mol2 etc. file and make Atoms object, using pytraj.

static from_cif(filename='atoms.cif', from_string='', get_primitive_atoms=True, use_cif2cell=True)

Read .cif format file.

write_poscar(filename='POSCAR')

Write POSCAR format file from Atoms object.

property get_xyz_string

Get xyz string for atoms.

write_xyz(filename='atoms.xyz')

Write XYZ format file.

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

Read XYZ file from to make Atoms object.

classmethod from_poscar(filename='POSCAR')

Read POSCAR/CONTCAR file from to make Atoms object.

property 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

strain_atoms(strain)

Apply volumetric strain to atoms.

apply_strain(strain)

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

to_dict()

Provide dictionary representation of the atoms object.

classmethod from_dict(d={})

Form atoms object from the dictionary.

remove_site_by_index(site=0)

Remove an atom by its index number.

remove_sites_by_indices(indices=[0], in_place=False)

Remove multiple atoms by their corresponding indices number.

add_site(element='Si', coords=[0.1, 0.1, 0.1], props=[], index=0)

Ad an atom, coords in fractional coordinates.

property get_conventional_atoms

Get conventional Atoms using spacegroup information.

property get_spacegroup

Get spacegroup information.

property get_primitive_atoms

Get primitive Atoms using spacegroup information.

get_all_neighbors(r=5, bond_tol=0.15)

Get neighbors for each atom in the unit cell, out to a distance r.

Contains [index_i, index_j, distance, image] array. Adapted from pymatgen.

get_neighbors_cutoffs(max_cut=10, r=5, bond_tol=0.15)

Get neighbors within cutoff.

rotate_pos(phi=0.0, theta=90.0, psi=0.0, center=(0, 0, 0))

Rotate atom sites via Euler angles (in degrees).

See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation. Adapted from https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate center :

The point to rotate about. A sequence of length 3 with the coordinates.

phi :

The 1st rotation angle around the z axis.

theta :

Rotation around the x axis.

psi :

2nd rotation around the z axis.

rotate_cell(phi=0.0, theta=90.0, psi=0.0, center=(0, 0, 0))

Rotate atom cell via Euler angles (in degrees).

See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation. Adapted from https://wiki.fysik.dtu.dk/ase/_modules/ase/atoms.html#Atoms.rotate center :

The point to rotate about. A sequence of length 3 with the coordinates.

phi :

The 1st rotation angle around the z axis.

theta :

Rotation around the x axis.

psi :

2nd rotation around the z axis.

atomwise_angle_and_radial_distribution(r=5, bond_tol=0.15, c_size=10, verbose=False)

Get atomwise distributions.

property raw_distance_matrix

Provide distance matrix.

property raw_angle_matrix

Provide distance matrix.

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

Center structure with vacuum padding.

Args:

vacuum:vacuum size

axis: direction

property volume

Get volume of the atoms object.

property composition

Get composition of the atoms object.

property density

Get density in g/cm3 of the atoms object.

plot_atoms(colors=[], sizes=[], cutoff=1.9, opacity=0.5, bond_width=2, filename=None)

Plot atoms using plotly.

property atomic_numbers

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

property num_atoms

Get number of atoms.

property uniq_species

Get unique elements.

get_center_of_mass()

Get center of mass of the atoms object.

get_origin()

Get center of mass of the atoms object.

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

Center around given origin.

pymatgen_converter()

Get pymatgen representation of the atoms object.

phonopy_converter(pbc=True)

Get phonopy representation of the atoms object.

ase_converter(pbc=True)

Get ASE representation of the atoms object.

spacegroup(symprec=0.001)

Get spacegroup of the atoms object.

property packing_fraction

Get packing fraction of the atoms object.

get_alignn_feats(model_name='jv_formation_energy_peratom_alignn', max_neighbors=12, neighbor_strategy='k-nearest', use_canonize=True, atom_features='cgcnn', line_graph=True, cutoff=8, model='')

Get ALIGNN features.

get_mineral_prototype_name(prim=True, include_c_over_a=False, digits=3)

Get mineral_prototype_name.

get_minaral_name(model='')

Get mineral prototype.

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

describe(xrd_peaks=5, xrd_round=1, cutoff=4, take_n_bonds=2, include_spg=True, include_mineral_name=False)

Describe for NLP applications.

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.

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

Make supercell of dimension dim.

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

Make supercell of dimension dim using for loop.

get_lll_reduced_structure()

Get LLL algorithm based reduced structure.

__repr__()

Get representation during print statement.

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.

clone()

Clones the class instance.

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

Bases: object

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

atoms

vacuum = 20.0

get_effective_2d_slab()

Add 2D vacuum to a system.

get_effective_molecule()

Add vacuum around a system.

jarvis.core.atoms.fix_pbc(atoms)

Use for making Atoms with vacuum.

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

Add top and bottom Atoms with a distance array.

Bottom Atoms lattice-matrix is chosen as final lattice.

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.atoms.ase_to_atoms(ase_atoms='', cartesian=True)

Convert ase structure to Atoms.

jarvis.core.atoms.crop_square(atoms=None, csize=10)

Crop a sqaur portion from a surface/2D system.

class jarvis.core.atoms.OptimadeAdaptor(atoms=None)

Bases: object

Module to work with optimade.

atoms = None

reduce(content={})

Reduce chemical formula.

optimade_reduced_formula(content={}, sort_alphabetical=True)

Get chemical formula.

get_optimade_prototype(content={})

Get chemical prototypes such as A, AB etc.

get_optimade_species()

Get optimade species.

from_optimade(info={})

Get Atoms from optimade.

to_optimade(idx='x', itype='structures', source='JARVIS-DFT-3D', reference_url='https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/', now=datetime.datetime.now(datetime.timezone.utc).isoformat())

Get optimade format data.

jarvis.core.atoms.compare_atoms(atoms1=[], atoms2=[], primitive_cell=True, verbose=True)

Compare atomic strutures.

jarvis.core.atoms.build_xanes_poscar(atoms=None, selected_element='Si', prefix='-', extend=1, enforce_c_size=12, dir='.', filename_with_prefix=False)

Generate POSCAR file for XANES, note the element ordering.