forte2.system.geom_utils
========================

.. py:module:: forte2.system.geom_utils






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

.. py:function:: parse_geometry(geom, unit)

   
   Parse a geometry string (XYZ or Z-matrix) into a list of atoms.


   :Parameters:

       **geom** : str
           Geometry string in XYZ or Z-matrix format.

       **unit** : str
           Coordinate unit, "bohr" or "angstrom".



   :Returns:

       **atoms** : list[tuple(int, NDArray)]
           List of (Z, coords) tuples in Bohr.











   ..
       !! processed by numpydoc !!

.. py:function:: parse_xyz(lines, unit)

   
   Parse an XYZ string into a list of atoms.


   :Parameters:

       **lines** : list[str]
           The lines containing the XYZ atom symbols and coordinates.

       **unit** : str
           The unit of the coordinates, either "bohr" or "angstrom".



   :Returns:

       **atoms** : list[tuple(int, NDArray)]
           A list of tuples, each containing the atomic number and a numpy array of coordinates.




   :Raises:

       ValueError
           If a line in the XYZ string does not match the expected format or has an incorrect number of coordinates.






   .. rubric:: Examples

   >>> xyz = "Li 0.0 0.0 0.0\nN -10 0 0\n"
   >>> parse_xyz(xyz, "bohr")
   [(3, array([0., 0., 0.])), (7, array([-10., 0., 0.]))]

   >>> xyz = "Li 0.0 0.0\nN -10 0\n"
   >>> parse_xyz(xyz, "angstrom")
   Traceback (most recent call last):
       ... ValueError: Invalid line in XYZ file: Li 0.0 0.0. Expected 3 coordinates, found 2.

   ..
       !! processed by numpydoc !!

.. py:function:: parse_zmatrix(lines, unit)

   
   Parse a Z-matrix string into a list of atoms.


   :Parameters:

       **lines** : list[str]
           The lines containing the Z-matrix atom symbols and coordinates.

       **unit** : str
           The unit of the coordinates, either "bohr" or "angstrom".



   :Returns:

       **atoms** : list[tuple(int, NDArray)]
           A list of tuples, each containing the atomic number and a numpy array of coordinates.




   :Raises:

       ValueError
           If a line in the Z-matrix string does not match the expected format.






   .. rubric:: Examples

   Unit bohr:
   H
   O 1 0.9
   O 2 1.4 1 105.0
   H 3 0.9 2 105.0 1 120.0

   Should return:
   [[ 0.          0.          0.        ]
   [ 1.70075351  0.          0.        ]
   [ 2.38548947  0.         -2.55546938]
   [ 3.29283067  1.42270804 -2.76806356]]

   ..
       !! processed by numpydoc !!

.. py:class:: GeometryHelper

   
   Helper class to process geometry data.
















   ..
       !! processed by numpydoc !!

   .. py:attribute:: atoms
      :type:  list[tuple[int, numpy.ndarray]]


   .. py:attribute:: tol
      :type:  float
      :value: 0.0001



   .. py:attribute:: symmetry
      :type:  bool
      :value: False