Periodic Energy Decomposition Analysis - PEDA
*********************************************

BAND Bonding Analysis Energy Decomposition Analysis

This tutorial will teach you how to perform a Periodic Energy
Decomposition Analysis (PEDA) for periodic systems with BAND.


Set up the system - CO@MgO(100) (√2×√2)-R45°
============================================

Start AMSinput in a clean directory and switch to Band:

   **1.** Switch to the **BAND panel**: [image: ADFPanel][image] **→** [image: BANDPanel][image]
   **2.** Copy-paste the following coordinates directly into AMSinput

   Mg       0.59538358       0.59538226       0.20750000
   Mg       2.08384335      -0.89307752      -1.89750000
   Mg      -2.38153597       0.59538226       0.20750000
   Mg      -0.89307620      -0.89307752      -1.89750000
   O        2.08384335      -0.89307752       0.20750000
   O       -0.89307620      -0.89307752       0.20750000
   O        0.59538358       0.59538226      -1.89750000
   O       -2.38153597       0.59538226      -1.89750000
   O        0.59538553       0.59539200       3.95250000
   C        0.59538493       0.59538903       2.80750000
   VEC1     2.97691955      -2.97691955       0.00000000
   VEC2     2.97691955       2.97691955       0.00000000

   **3.** Set **View →  View Direction →  Along Y-axis** (CTRL+2)
   **4.** Deselect **View →  Periodic →  Show Lattice Vectors** (if it was selected)
 [image]


Set up the PEDA calculation
===========================

To run the PEDA for the adsorption of CO on MgO, you have to define
the fragments. Therefore switch to Regions menu.

   **1.** Panel bar **Model → Regions**
   **2.** Select the CO fragment and add a new region by clicking on the '+' button (or Ctrl+G)
   **3.** De-select the currently selected atoms by clicking in an empty space of the molecule drawing area
   **4.** Select the MgO fragment and add a new region by clicking on the '+' button (or Ctrl+G)
   **5.** You may want to rename "Region_1" to CO and "Region_2" to MgO. (optional)
 [image]

We now enable the PEDA calculation:

   **1.** Panel bar **MultiLevel → Fragments**
   **2.** check the "Use fragments" box. This will trigger the PEDA.

   [image]

Go back to the main panel set some calculation options for BAND:

   **1.** Panel bar **Main**
   **2.** **XC Functional → GGA → PBE**
   **3.** **Basis set → DZP**
   **4.** **Frozen core → Small**
   **5.** **Numerical quality → Basic** (this is just to make the calculation run faster! For production results, don't use "basic" numerical quality)
 [image]


Run the calculation check the results
=====================================

Now you can save and run the calculation:

   **File → Save**, give it a name and press Save.
   **File → Run**

After the calculations of the fragments and the PEDA finished you can
look for the PEDA results. Open the "Output" using the SCM dropdown
menu:

   **SCM → Output**

You can jump to the 'PEDA Energy Terms' via the corresponding button
in the 'Properties' drop-down menu.

   **Properties → PEDA Energy Terms**

Reference results:

[image]

In addition to these energy terms the summed preparation energies of
the fragments and the (negative) bond dissociation energy are usually
given. Therefore you have to calculate the energy difference between
the electronically and structurally relaxed fragments (which can be
accessed by a geometry optimization of the separated fragments) and
the promoted fragments (which are already calculated and used for the
PEDA). Adding this energy difference, which is equal to the
preparation energy, to the interaction energy will give you the
negative bond dissociation energy.


Plot the deformation density with respect to the fragments
==========================================================

Fire up amsview

   **SCM → View**

and select add -> Isosurface: With Phase. At the bottom you can now
open the selector, and this shows an extra item "Fragment related
densities". Select "Deformation density w.r.t. sum-of-fragments". You
should see

[image]

Make sure that you select View→ View Direction→ Along Y-axis, change
the isovalue from 0.03 to 0.001, and deselect View→ Periodic→ Show
Lattice Vectors. As you can see, more is happening on the CO than on
the MgO surface. One could improve the picture by using Fields→ Grid→
Medium, for example.

You can also visualize the same, but obtained with via the fitted
density. This is faster, but is an approximation. In this case they
look pretty much the same.
