API

PeriodicSystem —

class pypwdft.PeriodicSystem(sz: float, npts: int)

Class that encapsulates a cubic unitcell with periodic boundary conditions and which can host the nuclei and electrons

__init__(sz: float, npts: int)

Build a periodic system

Parameters:

  • sz (float) – edge size of the cubic unit cell

  • npts (int) – number of sampling points per Cartesian direction

add_atom(x: float, y: float, z: float, charge: float, unit: str = 'bohr')

Add an atom to the unit cell

Parameters:

  • x (float) – x-coordinate

  • y (float) – y-coordinate

  • z (float) – z-coordinate

  • charge (float) – charge of the atom

  • unit (str, optional) – Which length unit, ‘bohr’ or ‘angstrom’. Defaults to ‘bohr’.

Raises:

Exception – Invalid unit received.

calculate_ewald_sum(gcut: float = 2, gamma: float = 1e-08) → float

Calculate Ewald sum

Parameters:

  • gcut (float, optional) – Plane wave cut off energy in Ht. Defaults to 2.

  • gamma (float, optional) – Separation parameter. Defaults to 1e-8.

Returns:

Ewald sum in Ht

Return type:

float

calculate_vpot() → ndarray

Construct the nuclear attraction potential

Returns:

nuclear attraction potential in real-space

Return type:

np.ndarray

get_atom_charges() → ndarray

Get the atomic charges

Returns:

atomic charges

Return type:

np.ndarray

get_atom_positions() → ndarray

Get atomic positions in real-space

Returns:

atomic positions

Return type:

np.ndarray

get_ct() → float
Get the FFT transformation constant from canonical FFT to an FFT using

a normalized plane wave basis set.

Returns:

FFT transformation constant

Return type:

float

get_nelec() → int

Get the number of electrons

Returns:

number of electrons

Return type:

int

get_npts() → int

Get the number of sampling points per Cartesian direction

Returns:

number of sampling points per Cartesian direction

Return type:

int

get_omega() → float

Get unitcell volume

Returns:

volume of the unit cell

Return type:

float

get_pw_k() → ndarray

Get the plane wave vectors

Returns:

plane wave vectors

Return type:

np.ndarray

get_pw_k2() → ndarray

Get the squared length of the plane wave vectors

Returns:

squared length of plane wave vectors

Return type:

np.ndarray

get_r() → ndarray

Get the sampling vectors in real-space

Returns:

real-space sampling vectors

Return type:

np.ndarray

get_r_norms() → ndarray

Get real-space sampling vector lengths

Returns:

real-space sampling vector lengths

Return type:

np.ndarray

translate(dist: ndarray)

Translate all atoms in unit cell

Parameters:

dist (np.ndarray) – displacement vector

PyPWDFT

class pypwdft.PyPWDFT(sys: PeriodicSystem, fft: str = 'pyfftw')

Class that encapsulates the planewave DFT method

__init__(sys: PeriodicSystem, fft: str = 'pyfftw')

Build PyPWDFT class

Parameters:

  • sys (PeriodicSystem) – periodic system

  • fft (str, optional) – which FFT algorithm to use. Defaults to ‘pyfftw’.

scf(tol: float = 1e-05, nsol: int = None, verbose: bool = False) → dict

Perform self-consistent field procedure

Parameters:

  • tol (float, optional) – electronic convergence criterion. Defaults to 1e-5.

  • nsol (int, optional) – number of solutions to find. Defaults to None.

  • verbose (bool, optional) – whether verbose output should be given. Defaults to False.

Returns:

Dictionary containing system results

Return type:

dict

SystemBuilder

class pypwdft.SystemBuilder

Class that builds molecules from templates or from point group descriptions

__init__()

Create the object

from_file(path: str, sz: float = 10, npts: int = 32) → PeriodicSystem

Construct a PeriodicSystem instance from a .xyz file

Parameters:

  • path (str) – path to .xyz file

  • sz (float, optional) – edge size of the cubic unit cell in a.u. Defaults to 10 a.u.

  • npts (int, optional) – number of sampling points per Cartesian direction. Defaults to 32.

Returns:

PeriodicSystem instance encapsulating the specified molecule

Return type:

PeriodicSystem

from_name(molname: str, sz: float = 10, npts: int = 32) → PeriodicSystem

Create a PeriodicSystem instance by specifying the name of the molecule

Parameters:

  • molname (str) – name of the molecule

  • sz (float, optional) – edge size of the cubic unit cell in a.u. Defaults to 10 a.u.

  • npts (int, optional) – number of sampling points per Cartesian direction. Defaults to 32.

Returns:

PeriodicSystem instance encapsulating the specified molecule

Return type:

PeriodicSystem