PyPWDFT

https://ifilot.github.io/pypwdft/
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PyPWDFT is a pure-Python package for performing plane-wave DFT calculations, designed with the aim...
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### Install PyPWDFT with PyPI

Source: https://ifilot.github.io/pypwdft/installation.html

Use this command in a terminal to install PyPWDFT and its dependencies via pip.

```bash
pip install pypwdft mendeleev pyfftw

```

--------------------------------

### Verify PyPWDFT Installation

Source: https://ifilot.github.io/pypwdft/installation.html

Run this Python code snippet to check if PyPWDFT is installed correctly and print its version.

```python
import pypwdft
print(pypwdft.__version__)

```

--------------------------------

### Install PyPWDFT with Anaconda

Source: https://ifilot.github.io/pypwdft/installation.html

Use this command in an Anaconda command prompt to install PyPWDFT and its dependencies.

```bash
conda install -c ifilot pypwdft mendeleev pyfftw

```

--------------------------------

### PeriodicSystem.get_ct

Source: https://ifilot.github.io/pypwdft/api.html

Gets the FFT transformation constant, used for converting between canonical FFT and FFTs with normalized plane wave basis sets.

```APIDOC
## PeriodicSystem.get_ct

### Description
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
```

--------------------------------

### SystemBuilder.from_file

Source: https://ifilot.github.io/pypwdft/api.html

Constructs a system from a specified input file.

```APIDOC
## SystemBuilder.from_file

### Description
Build a system from a file.

### Parameters
* **filepath** (str) – Path to the input file.
```

--------------------------------

### SystemBuilder.from_name

Source: https://ifilot.github.io/pypwdft/api.html

Constructs a system from a predefined material name.

```APIDOC
## SystemBuilder.from_name

### Description
Build a system from a material name.

### Parameters
* **name** (str) – Name of the material.
```

--------------------------------

### Set up and Perform SCF Calculation

Source: https://ifilot.github.io/pypwdft/usage.html

This snippet demonstrates how to create a periodic system, initialize the PyPWDFT calculator, and run the self-consistent field (SCF) procedure. It shows setting up a CH4 molecule in a cubic lattice and performing the SCF calculation with verbose output and a specified tolerance.

```python
from pypwdft import PyPWDFT, PeriodicSystem, SystemBuilder

# create cubic periodic system with lattice size of 10 Bohr units
npts = 32   # number of grid points
sz = 10

# construct CH4 molecule system via SystemBuilder
s = SystemBuilder().from_name('CH4', sz=sz, npts=npts)

# construct calculator object
calculator = PyPWDFT(s)

# perform self-consistent field procedure and store results in res object
res = calculator.scf(tol=1e-5, verbose=True)

```

--------------------------------

### PyPWDFT.__init__

Source: https://ifilot.github.io/pypwdft/api.html

Initializes the main PyPWDFT calculator class.

```APIDOC
## PyPWDFT.__init__

### Description
Initializes the PyPWDFT calculator.
```

--------------------------------

### SystemBuilder.__init__

Source: https://ifilot.github.io/pypwdft/api.html

Initializes the SystemBuilder class, used for constructing system objects.

```APIDOC
## SystemBuilder.__init__

### Description
Initializes the SystemBuilder.
```

--------------------------------

### SystemBuilder.from_file

Source: https://ifilot.github.io/pypwdft/api.html

Constructs a PeriodicSystem instance from a .xyz file. This method allows specifying the file path, the edge size of the unit cell, and the number of sampling points.

```APIDOC
## SystemBuilder.from_file

### Description
Constructs a PeriodicSystem instance from a .xyz file.

### Method
`from_file(_path: str_, _sz: float = 10_, _npts: int = 32_)`

### Parameters
#### Path Parameters
- **path** (str) - Path to .xyz file
#### Optional Parameters
- **sz** (float) - Edge size of the cubic unit cell in a.u. Defaults to 10 a.u.
- **npts** (int) - Number of sampling points per Cartesian direction. Defaults to 32.

### Returns
PeriodicSystem instance encapsulating the specified molecule.

### Return Type
PeriodicSystem
```

--------------------------------

### Create Periodic System Manually

Source: https://ifilot.github.io/pypwdft/usage.html

Manually create a cubic periodic system by defining lattice size and grid points.

```python
from pypwdft import PeriodicSystem

npts = 32   # number of grid points
sz = 10     # edge size of cubic unit cell
s = PeriodicSystem(sz, npts)

```

--------------------------------

### Build CH4 System Automatically

Source: https://ifilot.github.io/pypwdft/usage.html

Use SystemBuilder to create a cubic periodic system for a CH4 molecule. Specify lattice size and grid points.

```python
from pypwdft import SystemBuilder, PeriodicSystem

# create cubic periodic system with lattice size of 10 Bohr units
npts = 16   # number of grid points
sz = 10

# construct CH4 molecule system via SystemBuilder
s = SystemBuilder().from_name('CH4', sz=sz, npts=npts)

```

--------------------------------

### pypwdft.SystemBuilder methods

Source: https://ifilot.github.io/pypwdft/genindex.html

Methods available for the SystemBuilder class, used for constructing system objects.

```APIDOC
## __init__() SystemBuilder

### Description
Initializes a SystemBuilder object. This is a constructor method.

### Method
Constructor

### Parameters
None explicitly documented.

### Response
Initializes a SystemBuilder object.
```

```APIDOC
## from_file() SystemBuilder

### Description
Builds a system from a file.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns a system object built from the file.
```

```APIDOC
## from_name() SystemBuilder

### Description
Builds a system from a name.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns a system object built from the name.
```

--------------------------------

### Perform SCF Calculation and Generate Isosurfaces

Source: https://ifilot.github.io/pypwdft/usage.html

This snippet demonstrates a full workflow: setting up a periodic system, performing a Self-Consistent Field (SCF) calculation, interpolating the resulting scalar fields using quintic interpolation, and generating isosurfaces for molecular orbitals using PyTessel. It includes generating positive and negative real and imaginary isosurfaces for different orbitals.

```python
import numpy as np
from pytessel import PyTessel
from scipy.interpolate import RegularGridInterpolator
from pypwdft import PyPWDFT, SystemBuilder, PeriodicSystem

def main():
    # create cubic periodic system with lattice size of 10 Bohr units
    npts = 32       # number of grid points
    sz = 10

    # construct CO molecule system via SystemBuilder
    s = SystemBuilder().from_name('CO', sz=sz, npts=npts)

    # construct calculator object
    calculator = PyPWDFT(s)

    # perform self-consistent field procedure and store results in res object
    res = calculator.scf(tol=1e-5, nsol=9, verbose=True)

    # generate PyTessel object
    pytessel = PyTessel()

    for i in range(2,9):
        print('Building isosurfaces: %02i' % (i+1))
        scalarfield = interpolate_grid(res['orbc_rs'][i], sz, npts, 4)
        unitcell = np.identity(3) * sz

        # build positive real isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.real.flatten(), scalarfield.shape, unitcell.flatten(), 0.1)
        pytessel.write_ply('MO_PR_%02i.ply' % (i+1), vertices, normals, indices)

        # build negative real isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.real.flatten(), scalarfield.shape, unitcell.flatten(), -0.1)
        pytessel.write_ply('MO_NR_%02i.ply' % (i+1), vertices, normals, indices)

        # build positive imaginary isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.imag.flatten(), scalarfield.shape, unitcell.flatten(), 0.1)
        pytessel.write_ply('MO_PI_%02i.ply' % (i+1), vertices, normals, indices)

        # build negative imaginary isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.imag.flatten(), scalarfield.shape, unitcell.flatten(), -0.1)
        pytessel.write_ply('MO_NI_%02i.ply' % (i+1), vertices, normals, indices)

def interpolate_grid(scalarfield, sz, npts, amp=2):
    x = np.linspace(0, sz, npts)
    interp = RegularGridInterpolator((x,x,x), scalarfield, method='quintic')
    s = PeriodicSystem(sz, npts * amp)
    points = s.get_r()

    return interp(points)

if __name__ == '__main__':
    main()

```

--------------------------------

### PeriodicSystem.__init__

Source: https://ifilot.github.io/pypwdft/api.html

Initializes a PeriodicSystem object to represent a cubic unit cell with periodic boundary conditions. It sets up the sampling grid for nuclei and electrons.

```APIDOC
## PeriodicSystem.__init__

### Description
Build a periodic system.

### Parameters
* **sz** (float) – edge size of the cubic unit cell
* **npts** (int) – number of sampling points per Cartesian direction
```

--------------------------------

### Frequency Domain Upsampling for Molecular Orbitals

Source: https://ifilot.github.io/pypwdft/usage.html

This script demonstrates frequency domain upsampling to visualize molecular orbitals. It sets up a periodic system, performs SCF calculations, and generates isosurfaces for both real and imaginary parts of the orbitals using marching cubes. The `upsample_grid` function handles the frequency domain upsampling.

```python
import numpy as np
from pytessel import PyTessel
from pypwdft import PyPWDFT, SystemBuilder

def main():
    # create cubic periodic system with lattice size of 10 Bohr units
    npts = 32       # number of grid points
    sz = 10

    # construct CO molecule system via SystemBuilder
    s = SystemBuilder().from_name('CH4', sz=sz, npts=npts)

    # construct calculator object
    calculator = PyPWDFT(s)

    # perform self-consistent field procedure and store results in res object
    res = calculator.scf(tol=1e-5, verbose=True)

    # print molecular orbital energies
    print(res['orbe'])

    # generate PyTessel object
    pytessel = PyTessel()

    for i in range(5):
        print('Building isosurfaces: %02i' % (i+1))
        scalarfield = upsample_grid(res['orbc_fft'][i], sz**3, 4)
        unitcell = np.identity(3) * sz

        # build positive real isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.real.flatten(), scalarfield.shape, unitcell.flatten(), 0.03)
        pytessel.write_ply('MO_PR_%02i.ply' % (i+1), vertices, normals, indices)

        # build negative real isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.real.flatten(), scalarfield.shape, unitcell.flatten(), -0.03)
        pytessel.write_ply('MO_NR_%02i.ply' % (i+1), vertices, normals, indices)

        # build positive imaginary isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.imag.flatten(), scalarfield.shape, unitcell.flatten(), 0.03)
        pytessel.write_ply('MO_PI_%02i.ply' % (i+1), vertices, normals, indices)

        # build negative imaginary isosurface
        vertices, normals, indices = pytessel.marching_cubes(scalarfield.imag.flatten(), scalarfield.shape, unitcell.flatten(), -0.03)
        pytessel.write_ply('MO_NI_%02i.ply' % (i+1), vertices, normals, indices)

def upsample_grid(scalarfield_fft, Omega, upsample=4):
    Nx, Ny, Nz = scalarfield_fft.shape
    Nx_up = Nx * upsample
    Ny_up = Nx * upsample
    Nz_up = Nx * upsample

    # shift the frequencies
    fft = np.fft.fftshift(scalarfield_fft)

    # perform padding
    fft_upsampled = np.pad(fft, [((Nz_up-Nz)//2,), 
                                ((Ny_up-Ny)//2,),
                                ((Nx_up-Nx)//2,)], 'constant')

    # shift back
    fft_hires = np.fft.ifftshift(fft_upsampled)

    return np.fft.ifftn(fft_hires) * np.prod([Nx_up, Ny_up, Nz_up]) / np.sqrt(Omega)

if __name__ == '__main__':
    main()

```

--------------------------------

### SystemBuilder.from_name

Source: https://ifilot.github.io/pypwdft/api.html

Creates a PeriodicSystem instance by specifying the name of the molecule. This method is useful for building systems from a predefined list of molecules and allows setting the unit cell size and sampling points.

```APIDOC
## SystemBuilder.from_name

### Description
Creates a PeriodicSystem instance by specifying the name of the molecule.

### Method
`from_name(_molname: str_, _sz: float = 10_, _npts: int = 32_)`

### Parameters
#### Path Parameters
- **molname** (str) - Name of the molecule
#### Optional Parameters
- **sz** (float) - Edge size of the cubic unit cell in a.u. Defaults to 10 a.u.
- **npts** (int) - Number of sampling points per Cartesian direction. Defaults to 32.

### Returns
PeriodicSystem instance encapsulating the specified molecule.

### Return Type
PeriodicSystem
```

--------------------------------

### Print System Details

Source: https://ifilot.github.io/pypwdft/usage.html

Print the unit cell matrix and atomic coordinates of a defined system.

```python
print(s)

```

--------------------------------

### Visualize Molecular Orbitals in 2D Projections

Source: https://ifilot.github.io/pypwdft/usage.html

This script visualizes the real part, imaginary part, and electron density of molecular orbitals from a CH4 molecule calculation. It uses matplotlib to display 2D slices of the orbitals at a specific z-layer.

```python
# import the required libraries for the test
from pypwdft import PyPWDFT, PeriodicSystem, SystemBuilder
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable

def main():
    # create cubic periodic system with lattice size of 10 Bohr units
    npts = 32   # number of grid points
    sz = 10

    # construct CH4 molecule system via SystemBuilder
    s = SystemBuilder().from_name('CH4', sz=sz, npts=npts)

    # construct calculator object
    calculator = PyPWDFT(s)

    # perform self-consistent field procedure and store results in res object
    res = calculator.scf(tol=1e-1, verbose=True)

    # visualize the occupied molecular orbitals
    fig, im = plt.subplots(3,5, dpi=300, figsize=(16,8))
    extent=[-sz/2,sz/2,-sz/2,sz/2]
    orbe = res['orbe']
    fig.suptitle('Occupied molecular orbitals of CH$_{4}$')
    m = np.empty((3,5), dtype=object) # create placeholder for maps

    for i in range(0,5):
        # visualize the real part of the wave function
        field = np.real(res['orbc_rs'][i][npts//2, :, :])
        maxval = max(np.max(np.abs(field)), 0.1)
        m[0][i] = im[0,i].imshow(field, origin='lower',
                interpolation='bicubic', extent=extent, cmap='PiYG',
                vmin=-maxval, vmax=maxval)
        im[0,i].set_title(r'$\\mathbb{R}\\;[\\psi_{%i}]$' % (i+1))

        # visualize the imaginary part of the wave function
        field = np.imag(res['orbc_rs'][i][npts//2, :, :])
        maxval = max(np.max(np.abs(field)), 0.001)
        m[1][i] = im[1,i].imshow(field, origin='lower',
                interpolation='bicubic', extent=extent, cmap='PiYG',
                vmin=-maxval, vmax=maxval)
        im[1,i].set_title(r'$\\mathbb{I}\\;[\\psi_{%i}]$' % (i+1))

        # visualize the electron density
        m[2][i] = im[2,i].imshow(np.real(res['orbc_rs'][i][npts//2, :, :].conj() *
                            res['orbc_rs'][i][npts//2, :, :])),
                    origin='lower', interpolation='bicubic', extent=extent)
        im[2,i].set_title(r'$\\rho_{%i}$' % (i+1))

    for j in range(0,3):
        for i in range(0,5):
            im[j,i].set_xlabel('$x$-position [a.u.]')
            im[j,i].set_ylabel('$y$-position [a.u.]')

            divider = make_axes_locatable(im[j,i])
            cax = divider.append_axes('right', size='5%', pad=0.05)
            fig.colorbar(m[j][i], cax=cax, orientation='vertical')

    plt.tight_layout()

if __name__ == '__main__':
    main()

```

--------------------------------

### pypwdft.PeriodicSystem methods

Source: https://ifilot.github.io/pypwdft/genindex.html

Methods available for the PeriodicSystem class, used for managing and querying properties of a periodic system.

```APIDOC
## __init__() PeriodicSystem

### Description
Initializes a PeriodicSystem object. This is a constructor method.

### Method
Constructor

### Parameters
None explicitly documented.

### Response
Initializes a PeriodicSystem object.
```

```APIDOC
## add_atom() PeriodicSystem

### Description
Adds an atom to the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Adds an atom to the system.
```

```APIDOC
## calculate_ewald_sum() PeriodicSystem

### Description
Calculates the Ewald sum for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the calculated Ewald sum.
```

```APIDOC
## calculate_vpot() PeriodicSystem

### Description
Calculates the potential of the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the calculated potential.
```

```APIDOC
## get_atom_charges() PeriodicSystem

### Description
Retrieves the charges of the atoms in the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the atom charges.
```

```APIDOC
## get_atom_positions() PeriodicSystem

### Description
Retrieves the positions of the atoms in the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the atom positions.
```

```APIDOC
## get_ct() PeriodicSystem

### Description
Retrieves the CT value for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the CT value.
```

```APIDOC
## get_nelec() PeriodicSystem

### Description
Retrieves the number of electrons in the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the number of electrons.
```

```APIDOC
## get_npts() PeriodicSystem

### Description
Retrieves the number of points in the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the number of points.
```

```APIDOC
## get_omega() PeriodicSystem

### Description
Retrieves the omega value for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the omega value.
```

```APIDOC
## get_pw_k() PeriodicSystem

### Description
Retrieves the pw_k value for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the pw_k value.
```

```APIDOC
## get_pw_k2() PeriodicSystem

### Description
Retrieves the pw_k2 value for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the pw_k2 value.
```

```APIDOC
## get_r() PeriodicSystem

### Description
Retrieves the R value for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the R value.
```

```APIDOC
## get_r_norms() PeriodicSystem

### Description
Retrieves the R norms for the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the R norms.
```

```APIDOC
## translate() PeriodicSystem

### Description
Translates the periodic system.

### Method
Method

### Parameters
None explicitly documented.

### Response
Translates the system.
```

--------------------------------

### Perform DFT Calculation with PyPWDFT

Source: https://ifilot.github.io/pypwdft/index.html

This snippet demonstrates how to perform a self-consistent field calculation for a methane molecule using PyPWDFT. It requires importing necessary libraries, setting up the periodic system and molecule, initializing the calculator, and running the scf procedure.

```python
# import the required libraries for the test
from pypwdft import PyPWDFT, PeriodicSystem, MoleculeBuilder
import numpy as np

def main():
   # create cubic periodic system with lattice size of 10 Bohr
   npts = 16   # number of grid points
   sz = 10
   # construct CH4 molecule system via SystemBuilder
   s = SystemBuilder().from_name('CH4', sz=sz, npts=npts)

   # construct calculator object
   calculator = PyPWDFT(s)

   # perform self-consistent field procedure and store results in res object
   res = calculator.scf(tol=1e-1, verbose=True)

if __name__ == '__main__':
   main()

```

--------------------------------

### PeriodicSystem.get_r

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the sampling vectors in real-space.

```APIDOC
## PeriodicSystem.get_r

### Description
Get the sampling vectors in real-space.

### Returns
real-space sampling vectors

### Return type
np.ndarray
```

--------------------------------

### pypwdft.PyPWDFT methods

Source: https://ifilot.github.io/pypwdft/genindex.html

Methods available for the PyPWDFT class, used for performing DFT calculations.

```APIDOC
## __init__() PyPWDFT

### Description
Initializes a PyPWDFT object. This is a constructor method.

### Method
Constructor

### Parameters
None explicitly documented.

### Response
Initializes a PyPWDFT object.
```

```APIDOC
## scf() PyPWDFT

### Description
Performs a Self-Consistent Field (SCF) calculation.

### Method
Method

### Parameters
None explicitly documented.

### Response
Returns the result of the SCF calculation.
```

--------------------------------

### PeriodicSystem.calculate_vpot

Source: https://ifilot.github.io/pypwdft/api.html

Constructs the nuclear attraction potential in real-space, which is a key component in electronic structure calculations.

```APIDOC
## PeriodicSystem.calculate_vpot

### Description
Construct the nuclear attraction potential.

### Returns
nuclear attraction potential in real-space

### Return type
np.ndarray
```

--------------------------------

### Add Atoms to Periodic System

Source: https://ifilot.github.io/pypwdft/usage.html

Add atoms to a manually created PeriodicSystem by specifying their Cartesian coordinates and atomic charges.

```python
# atomic positions
atompos = np.array([[5.00000000, 5.00000000, 5.00000000],
                    [6.19575624, 6.19575624, 6.19575624],
                    [3.80424376, 3.80424376, 6.19575624],
                    [3.80424376, 6.19575624, 3.80424376],
                    [6.19575624, 3.80424376, 3.80424376]])

# atomic charges
charges = [6, 1, 1, 1, 1] # C + 4 x H

# add atoms to the system
for p,c in zip(atompos, charges):
    s.add_atom(p[0], p[1], p[2], c)

```

--------------------------------

### PyPWDFT.scf

Source: https://ifilot.github.io/pypwdft/api.html

Performs a self-consistent field (SCF) procedure to achieve electronic convergence for a given periodic system. It allows customization of the convergence criterion, the number of solutions, and verbosity.

```APIDOC
## PyPWDFT.scf

### Description
Performs a self-consistent field procedure to achieve electronic convergence.

### Method
`scf(_tol: float = 1e-05_, _nsol: int = None_, _verbose: bool = False_)`

### Parameters
#### Optional Parameters
- **tol** (float) - Electronic convergence criterion. Defaults to 1e-5.
- **nsol** (int) - Number of solutions to find. Defaults to None.
- **verbose** (bool) - Whether verbose output should be given. Defaults to False.

### Returns
A dictionary containing system results.

### Return Type
dict
```

--------------------------------

### PyPWDFT.scf

Source: https://ifilot.github.io/pypwdft/api.html

Performs the Self-Consistent Field (SCF) calculation for the system.

```APIDOC
## PyPWDFT.scf

### Description
Performs the Self-Consistent Field (SCF) calculation.
```

--------------------------------

### PeriodicSystem.get_nelec

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the total number of electrons in the system.

```APIDOC
## PeriodicSystem.get_nelec

### Description
Get the number of electrons.

### Returns
number of electrons

### Return type
int
```

--------------------------------

### PeriodicSystem.get_pw_k

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the plane wave vectors used in the calculation.

```APIDOC
## PeriodicSystem.get_pw_k

### Description
Get the plane wave vectors.

### Returns
plane wave vectors

### Return type
np.ndarray
```

--------------------------------

### PeriodicSystem.get_pw_k2

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the squared lengths of the plane wave vectors.

```APIDOC
## PeriodicSystem.get_pw_k2

### Description
Get the squared length of the plane wave vectors.

### Returns
squared length of plane wave vectors

### Return type
np.ndarray
```

--------------------------------

### PeriodicSystem.get_omega

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the volume of the unit cell.

```APIDOC
## PeriodicSystem.get_omega

### Description
Get unitcell volume.

### Returns
volume of the unit cell

### Return type
float
```

--------------------------------

### PeriodicSystem.get_npts

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the number of sampling points per Cartesian direction in the unit cell grid.

```APIDOC
## PeriodicSystem.get_npts

### Description
Get the number of sampling points per Cartesian direction.

### Returns
number of sampling points per Cartesian direction

### Return type
int
```

--------------------------------

### PeriodicSystem.get_atom_charges

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the charges of all atoms currently added to the unit cell.

```APIDOC
## PeriodicSystem.get_atom_charges

### Description
Get the atomic charges.

### Returns
atomic charges

### Return type
np.ndarray
```

--------------------------------

### PeriodicSystem.get_atom_positions

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the positions of all atoms in the unit cell in real-space coordinates.

```APIDOC
## PeriodicSystem.get_atom_positions

### Description
Get atomic positions in real-space.

### Returns
atomic positions

### Return type
np.ndarray
```

--------------------------------

### PeriodicSystem.translate

Source: https://ifilot.github.io/pypwdft/api.html

Translates all atoms within the unit cell by a given displacement vector.

```APIDOC
## PeriodicSystem.translate

### Description
Translate all atoms in unit cell.

### Parameters
* **dist** (np.ndarray) – displacement vector
```

--------------------------------

### PeriodicSystem.calculate_ewald_sum

Source: https://ifilot.github.io/pypwdft/api.html

Calculates the Ewald sum for the system, which is important for electrostatic interactions in periodic systems. It takes plane wave cutoff and separation parameters.

```APIDOC
## PeriodicSystem.calculate_ewald_sum

### Description
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
```

--------------------------------

### PeriodicSystem.get_r_norms

Source: https://ifilot.github.io/pypwdft/api.html

Retrieves the lengths of the real-space sampling vectors.

```APIDOC
## PeriodicSystem.get_r_norms

### Description
Get real-space sampling vector lengths.

### Returns
real-space sampling vector lengths

### Return type
np.ndarray
```

--------------------------------

### PeriodicSystem.add_atom

Source: https://ifilot.github.io/pypwdft/api.html

Adds an atom to the unit cell with specified coordinates, charge, and unit system. It supports both 'bohr' and 'angstrom' units.

```APIDOC
## PeriodicSystem.add_atom

### Description
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.
```
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