xdatbus.utils
=============

.. py:module:: xdatbus.utils


Functions
---------

.. autoapisummary::

   xdatbus.utils.read_lat_vec
   xdatbus.utils.unwrap_pbc_dis
   xdatbus.utils.update_folder
   xdatbus.utils.remove_file
   xdatbus.utils.skip_comments
   xdatbus.utils.filter_files
   xdatbus.utils.gauss_pot_1d
   xdatbus.utils.gauss_pot_2d
   xdatbus.utils.gauss_pot_3d


Module Contents
---------------

.. py:function:: read_lat_vec(xdatcar_dir)

   Read the lattice vectors from the first image of the XDATCAR file.


.. py:function:: unwrap_pbc_dis(coord_1, coord_2, box_length)

   Unwrap the distance between two coordinates.

       Parameters
       ----------
       coord_1 : ndarray
           The first coordinate
       coord_2 : ndarray
           The second coordinate
       box_length :
           The length of the box

       Returns
       -------
       float
           The unwrapped distance between the two coordinates


.. py:function:: update_folder(folder)

   Delete the folder and create a new one.

       Parameters
       ----------
       folder : str
           The path of the folder


.. py:function:: remove_file(file_path)

   Delete the file.

       Parameters
       ----------
       file_path : str
           The path of the file


.. py:function:: skip_comments(file)

.. py:function:: filter_files(files, pattern)

.. py:function:: gauss_pot_1d(x: numpy.ndarray, x0: float, height: float, width: float) -> numpy.ndarray

   Calculate the Gaussian potential energy.

   Parameters:
   - x (np.ndarray): Array of positions at which to evaluate the potential.
   - x0 (float): The position of the potential minimum.
   - height (float): The height of the Gaussian potential.
   - width (float): The standard deviation (controls the width of the Gaussian).

   Returns:
   - np.ndarray: The potential energy at each position x.


.. py:function:: gauss_pot_2d(x: numpy.ndarray, y: numpy.ndarray, x0: float, y0: float, height: float, width: float) -> numpy.ndarray

   Calculate the Gaussian potential energy.

   Parameters:
   - x (np.ndarray): Array of x positions at which to evaluate the potential.
   - y (np.ndarray): Array of y positions at which to evaluate the potential.
   - x0 (float): The x position of the potential minimum.
   - y0 (float): The y position of the potential minimum.
   - height (float): The height of the Gaussian potential.
   - width (float): The standard deviation (controls the width of the Gaussian).

   Returns:
   - np.ndarray: The potential energy at each position (x, y).


.. py:function:: gauss_pot_3d(x: numpy.ndarray, y: numpy.ndarray, z: numpy.ndarray, x0: float, y0: float, z0: float, height: float, width: float) -> numpy.ndarray

   Calculate the Gaussian potential energy.

   Parameters:
   - x (np.ndarray): Array of x positions at which to evaluate the potential.
   - y (np.ndarray): Array of y positions at which to evaluate the potential.
   - z (np.ndarray): Array of z positions at which to evaluate the potential.
   - x0 (float): The x position of the potential minimum.
   - y0 (float): The y position of the potential minimum.
   - z0 (float): The z position of the potential minimum.
   - height (float): The height of the Gaussian potential.
   - width (float): The standard deviation (controls the width of the Gaussian).

   Returns:
   - np.ndarray: The potential energy at each position (x, y, z).