.. _reaction_path_search :

Reaction Path Search 
====================

Overview
--------

Estimate the minimum energy path from the reactants to the products and obtain an initial guess of the transition state structure. 

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

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

Four modules are currently available:

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

All the above three modules use the nudged elastic band (NEB) method for the reaction path search task. With GFN2-XTB, there is an additional option perform the same with meta-dynamics reaction path finder. 

In the meta-dynamics reaction path finder, a repulsive and an attractive potential is applied on the reatant and product structures, respectively. If the chosen potential is correct, xTB will yield the reaction path between reactant and product with a straight-forward geometry optimization.

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)
   
   .. grid-item-card:: **Number of Images**
      :text-align: left 

      Number of images for linear interpolation between initial and final systems. 

Following convergence parameters can also be set.

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

   .. grid-item-card:: **RMS Gradient**
      :text-align: left 

      Root mean square gradient 

   .. grid-item-card:: **Maximum Gradient**
     :text-align: left 

     Maximum gradient 

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

     Change in energy 

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

If **Nudged Elastic Band** is selected, the following inputs must be provided: 

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

   .. grid-item-card:: **Number of Points** 
      :text-align: left 

      Number of images for interpolation between initial and final systems. 

   .. grid-item-card:: **Max Force**
      :text-align: left 

      Maximum force 

If **meta-dynamics** is selected for reaction path search, 
then the following input parameters for repulsive and attractive 
potentials have to be provided.

.. grid:: 1 2 4 4 
   :gutter: 2 

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

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

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

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

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

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

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

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

   .. grid-item-card:: **Number of Points**
      :text-align: left

      Number of points along the path

   .. grid-item-card:: **Number of Runs**
      :text-align: left 

      Number of path search runs

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

      Alpha parameter for path optimization

   .. grid-item-card:: **K Push**
      :text-align: left 

      Push strength for meta-dynamics

   .. grid-item-card:: **K Pull**
      :text-align: left 

      Pull strength for meta-dynamics

   .. grid-item-card:: **P Pull**
      :text-align: left 

      Additional pull parameter

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

      Number of optimization cycles

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:: **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:: **Number of Images**
      :text-align: left

      Number of images for interpolation between initial and final systems.

      .. note::
         
         The number of images should be greater than 2. This number includes the reactant and product structures, 
         so the minimum value is 3.

   .. grid-item-card:: **Max Force**
      :text-align: left

      Maximum force 
  
Finally, click the **Run Reaction Path calculation** button to start the calculation.  

.. note:: 
   We have LDA, PBE, PBE0, M06, B3LYP, 
   CAM-B3LYP and wB97X functionals available 
   currently for the GPU-enabled runs.  

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:: **Paths**
      :text-align: left

      To see the reaction paths, click the "Path" dropdown at the top left of the visualiser.

      .. image:: ../_static/images/tasks/reaction_path.png
         :width: 100%
         :align: center
         :alt: Reaction path view

      *Figure: This viewer decpicting the the reaction path connecting reactants and products.*

   .. grid-item-card:: **Show Transition State**
      :text-align: left

      Tick the "Show Transition State" checkbox to view the initial guess transition state structure.

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

      In the bottom right corner, you can save the "Guess TS", "Reaction Paths", "Optimized reactants" and 
      "Optimized products" in xyz format.