pyvibdmc.simulation_utilities.initial_conditioner
=================================================

.. py:module:: pyvibdmc.simulation_utilities.initial_conditioner


Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/pyvibdmc/simulation_utilities/initial_conditioner/finite_difference/index
   /autoapi/pyvibdmc/simulation_utilities/initial_conditioner/harmonic_analysis/index
   /autoapi/pyvibdmc/simulation_utilities/initial_conditioner/initial_conditioner/index


Classes
-------

.. autoapisummary::

   pyvibdmc.simulation_utilities.initial_conditioner.MolFiniteDifference
   pyvibdmc.simulation_utilities.initial_conditioner.HarmonicAnalysis
   pyvibdmc.simulation_utilities.initial_conditioner.InitialConditioner


Package Contents
----------------

.. py:class:: MolFiniteDifference

   Helper to calculate derivatives of some value as a function of Cartesian displacements in a molecule.


   .. py:attribute:: weights_der1


   .. py:attribute:: weights_der2


   .. py:method:: displace_molecule(eq_geom, atm_cd, dx, num_disps)
      :staticmethod:


      Displace atm along cd
      :param eq_geom: Geometry from which you will be displaced
      :param atm_cd: a tuple that has a paricular atom of interest to displace in a particular dimension (x,y,or,z)
      :param dx: The amount each geometry will be replaced
      :param num_disps: int of how many displacements to do, will take the form of 3 or 5 for harmonic analysis.
      :return: Displaced coordinates in a 3D array (n,m,3). If displaced in two directions, then still (n,m,3)



   .. py:method:: differentiate(values, dx, num_points, der)
      :classmethod:



.. py:class:: HarmonicAnalysis(eq_geom, atoms, potential, masses=None, dx=0.001, points_diag=5, points_off_diag=3, dipole=None)

   .. py:attribute:: eq_geom


   .. py:attribute:: atoms


   .. py:attribute:: potential


   .. py:attribute:: masses
      :value: None



   .. py:attribute:: dx
      :value: 0.001



   .. py:attribute:: points_diag
      :value: 5



   .. py:attribute:: points_off_diag
      :value: 3



   .. py:attribute:: num_elems


   .. py:attribute:: dipole
      :value: None



   .. py:method:: generate_hessian()


   .. py:method:: dipole_derivs()


   .. py:method:: diagonalize(hessian)


   .. py:method:: run()


.. py:class:: InitialConditioner(coord, atoms, num_walkers, technique, technique_kwargs, masses=None)

   If given a minimum energy geometry of the system you are trying to run, it will generate a preliminary ensemble.
   In one instance, you can calculate the harmonic frequencies and normal modes, and then sample the harmonic 3N-6
   ground state wave function along those  normal modes. Will, in the future, handle other initial conditions.


   .. py:attribute:: coord


   .. py:attribute:: atoms


   .. py:attribute:: masses
      :value: None



   .. py:attribute:: num_walkers


   .. py:attribute:: technique


   .. py:attribute:: technique_kwargs


   .. py:method:: gen_disps(sigmas)


   .. py:method:: displace_along_nms(freqz, nmz, massez, ensemble)


   .. py:method:: run_harm()


   .. py:method:: run_permute()

      Must pass in a list of lists.



   .. py:method:: run()