qharv.cross package

Submodules

qharv.cross.pqscf module

qharv.cross.pqscf.ase_tile(cell, tmat)

Create supercell from primitive cell and tiling matrix

Parameters

• cell (pyscf.Cell) – cell object

• tmat (np.array) – 3x3 tiling matrix e.g. 2*np.eye(3)

Returns

supercell

Return type

pyscf.Cell

qharv.cross.pqscf.atom_text(elem, pos)

convert elem,pos to text representation

for example, elem = [‘C’,’C’], pos = [[0,0,0],[0.5,0.5,0.5]] will be converted to ‘C 0 0 0;C 0.5 0.5 0.5’

Parameters

• elem (list) – a list of atomic symbols such as ‘H’,’C’,’O’

• pos (list) – a list of atomic positions, assume in 3D

Returns

atomic string accepted by pyscf

Return type

str

qharv.cross.pqscf.check_grid_shape(grid_shape, gvecs)

qharv.cross.pqscf.mf_from_chkfile(chkfile, scf_class=None, pbc=True)

qharv.cross.pqscf.pw_to_r(gvecs, psig, grid_shape=None)

convert a 3D function from plane-wave to real-space basis

plane wave basis is assumed to be in reciprocal-lattice units real-space basis will be in grid units axes/grid_shape

Parameters

• gvecs (np.array) – dtype=int & shape = (npw,ndim), npw is the number of plane waves, and ndim is the number of spatial dimensions. ndim is expected to be 3. Each entry in gvecs should be a 3D vector of integers. Each gvec specify a plane wave basis element exp(i*gvec*rvec).

• psig (np.array) – dtype=complex & shape = (npw,). Expansion coefficients in PW basis.

• grid_shape (np.array) – dtype=int & shape = (ndim,). Shape of real-space grid.

Returns

(grid_shape,moR), grid_shape is input if given. Otherwise constructed in function to hold all information from the plane-wave representation. moR has dtype=complex & shape = grid_shape. moR is the 3D function in real-space basis. Typically a molecular orbital.

Return type

(np.array,np.array)

qharv.cross.pqscf.r_to_pw(moR0, grid_shape, gvecs=None)

convert a 3D function from real-space to plane-wave basis

This function is essentially the inverse of pw_to_r, but assumes that the real space grid is built around (0,0,0)

Parameters

• moR0 (np.array) – dtype=complex & shape = (ngrid,), ngrid is the number of grid points. 3D function in real-space grid basis.

• grid_shape (np.array) – dtype=int & shape = (ndim,). Shape of real-space grid.

Returns

(gvecs,psig), gvecs is input if given. Otherwise internally constructed. psig has dtype=complex & shape = (npw,). psig is the 3D function in plane-wave basis. Typically a molecular orbital.

Return type

(np.array,np.array)

qharv.cross.pwscf module

qharv.cross.pwscf.copy_charge_density(scf_dir, nscf_dir, execute=True)

Copy charge density files from scf folder to nscf folder.

Parameters

• scf_dir (str) – scf folder

• nscf_dir (str) – nscf folder

• execute (bool, optional) – perform file system operations, default True if execute is False, then description of operations will be printed.

qharv.cross.pwscf.input_keywords(scf_in)

Extract all keywords from a quantum espresso input file

Parameters

scf_in (str) – path to input file

Returns

a dictionary of inputs

Return type

dict

qharv.cross.pwscf.ktext_frac(kpts)

Write K_POINTS card assuming fractional kpoints with uniform weight.

Parameters

kpts (np.array) – kpoints in reciprocal lattice units

Returns

ktext to be fed into pw.x input

Return type

str

Module contents