.. _geometry_optimization :

Geometry Optimization
=====================

Overview
--------

Geometry Optimization calculations adjust the atomic positions of a molecule to find a
stable structure with minimal electronic energy. 
This is essential for determining equilibrium geometries, transition states, and reaction pathways.

Check the :ref:`visualiser-input` section for the allowed input types and how to upload the files.

Modules Available
-----------------

Three modules are currently available:

1. **DFT** - Density Functional Theory (highest accuracy)
2. **GFN2-XTB** - Tight-binding semi-empirical method (fast and reasonably accurate)
3. **Hybrid ML model** - Fastest and DFT-accurate using machine learning

..
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Hybrid ML Module Input Fields
-----------------------------

Upon selecting the **Hybrid ML** module, following inputs have to be provided:


.. grid:: 1 2 2 2
   :gutter: 2


   .. grid-item-card:: **Charge**
      :text-align: left

      Total charge of the molecule (e.g., 0)


   .. grid-item-card:: **Multiplicity**
      :text-align: left

      Spin mulitplicity = 2S+1 (e.g., 1 for singlet)

GFN2-XTB Module Input Fields
----------------------------


If the **GFN2-XTB** module is selected, the following inputs must be provided:


.. grid:: 1 2 2 2
   :gutter: 2


   .. grid-item-card:: **Charge**
      :text-align: left


      Total charge of the molecule (e.g., 0)


   .. grid-item-card:: **Multiplicity**
      :text-align: left


      Spin multiplicity = 2S+1 (e.g., 1 for singlet)


   .. grid-item-card:: **Include Solvent**
      :text-align: left


      Toggle to include solvent effects


   .. grid-item-card:: **Solvent**
      :text-align: left
     
      Select a solvent (e.g., water, ethanol)

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DFT Module Input Fields
-----------------------

Upon selecting the **DFT** module, the following inputs must be provided:

.. grid:: 1 2 2 2
   :gutter: 2

   .. grid-item-card:: **Charge**
      :text-align: left

      Total charge of the molecule (e.g., 0)

   .. grid-item-card:: **Multiplicity**
      :text-align: left

      Spin multiplicity = 2S+1 (e.g., 1 for singlet)

   .. grid-item-card:: **Constrained Optimization**
      :text-align: left

      Toggle to enable constrained optimization (e.g., fix certain bond lengths)

      **More About Constrained Optimization**

      See the :ref:`constrained_optimization_details` section for details on how to freeze or set specific geometric parameters.

   .. grid-item-card:: **Basis Set Category**
      :text-align: left

      Select the basis set family (e.g., Pople, Dunning)

   .. grid-item-card:: **Basis Set**
      :text-align: left

      Select the basis set (e.g., 6-31G, 6-31+Gss)

   .. grid-item-card:: **DFT Functional**
      :text-align: left

      Choose an exchange-correlation functional (e.g., M06)

   .. grid-item-card:: **Include Solvent**
      :text-align: left

      Toggle to include solvent effects

   .. grid-item-card:: **Solvent**
      :text-align: left

      Select a solvent (e.g., water, ethanol)

   .. grid-item-card:: **Solvent Model**
      :text-align: left

      Choose the solvation model (e.g., PCM, SMD)

   .. grid-item-card:: **Include Dispersion Correction**
      :text-align: left

      Toggle to enable dispersion correction (e.g., D3BJ)

   .. grid-item-card:: **Dispersion Correction**
      :text-align: left

      Choose a dispersion correction model

.. _constrained_optimization_details :

Constrained Optimization Details
--------------------------------

If you want to freeze any bond, angle, or dihedral during optimization, use the following syntax (atom indices are used):

Note : Atom index can not be zero (0)

- **Freeze a parameter**:

If you wish to fix a bond of your given input then,
  ::

    freeze
    distance 1 2

If you wish to fix a angle of your given input then,
  ::

    freeze
    angle 1 2 3

If you wish to fix a dihedral angle of your given input then,
  ::

    freeze
    dihedral 1 2 3 4

If you want to set a specific value during optimization (distance in angstroms, angles in degrees):
  ::

- **Set a parameter**:

If you wish to fix a bond at specific value in angstroms,
  ::

    set
    distance 1 2 1.0

If you wish to fix a angle at specific value (value in degree),
  ::

    set
    angle 1 2 3 60.0

If you wish to fix a dihedral at specific value (value in degree),
  ::

    set
    dihedral 1 2 3 4 120.0

.. note::
    We have LDA, PBE, PBE0, M06, B3LYP, CAM-B3LYP, and WB97X functionals
    available right now for the GPU calculations.

Finally, click the **Run Optimization** button to start the simulation.

Output Details
--------------

The following options are available to explore and save the results of your geometry optimization:

.. grid:: 1 1 1 1
   :gutter: 2

   .. grid-item-card:: **View Trajectory**
      :text-align: left

      To see the optimization trajectory, click the "Trajectory View" button at the top left of the visualiser and press "Start".

      .. image:: ../_static/images/tasks/geom-output-traj.jpg
         :width: 100%
         :align: center
         :alt: Trajectory View Interface

      *Figure: The Trajectory View interface showing the animation controls.*

   .. grid-item-card:: **Energy Graph**
      :text-align: left

      Click the "Energy Graph" checkbox to display the variation of energy with optimization steps.

   .. grid-item-card:: **Save Results**
      :text-align: left

      In the bottom right corner, you can save the "Trajectory" and "Optimized Structure". These are in XYZ file format.