PEDA-NOCV for Spin Unrestricted Calculations
********************************************

BAND Bonding Analysis Energy Decomposition Analysis Unrestricted

This tutorial will teach you how to:

* perform an Periodic Energy Decomposition Analysis (PEDA) combined
  with the natural orbitals for chemical valency (NOCV) method (pEDA-
  NOCV) for extended and/or molecular systems with BAND, where the
  bond is described by open-shell, **spin unrestricted** fragments

* where to look for the results


Step 1: Start AMSinput
======================

Start AMSinput in a clean directory.

   Switch to the **BAND** panel: [image: ADFPanel][image] **→** [image: BANDPanel][image]
   Chose **Periodicity**: *None*.
 [image]


Step 2: Set up the system - Ethane
==================================

An easy and non-time-consuming test system is the C-C bond analysis in
an ethane molecule. Here, two methyl radicals with opposite spin-
polarization interact to form the shared electron C-C bond. Hence, the
fragments and the PEDA-NOCV calculation have to be carried out as
unrestricted DFT calculations.

You can copy-paste the following geometry information into the GUI
directly.

   C          1.54081631       0.00000000       0.00000000
   H          1.90061013       0.71448558       0.72714386
   H          1.90061011      -0.98692880       0.25534173
   H          1.90084793       0.27238885      -0.98228957
   C          0.00000000       0.00000000       0.00000000
   H         -0.35953041      -0.27213306       0.98136715
   H         -0.36080772       0.98640196      -0.25411759
   H         -0.36080775      -0.71466441      -0.72582318

[image]


Step 3: Running the PEDA-NOCV calculation
=========================================


Step 3a: Setting up the fragments
---------------------------------

To run the PEDA and PEDA-NOCV you have to define fragments. Therefore
switch to Regions menu.

   Panel bar **Model → Regions**
   Select one methyl fragment and add a new region by clicking on the '+' button (or Ctrl+G).
   Select the other methyl fragment and add a new region by clicking on the '+' button (or Ctrl+G).
   You may want to rename "Region_1" to "H3C_A" and "Region_2" to "H3C_B". (optional)
 [image]


Step 3b: Details for the calculation
------------------------------------

Go to the Main menu,

   Panel bar **Main**
   Check the **Unrestricted** checkbox
   Select **XC functional → GGA-D → BP86-D3(BJ)**
   Select **Basis set → TZ2P** and **Frozen core → Small**
 [image]


Step 3c: Enabling the PEDA-NOCV
-------------------------------

Go to the Fragments menu,

   Panel bar **MultiLevel → Fragments**
   Check the "Use fragments" box. This will trigger the PEDA.
   Define the **spin** polarization of the fragments. One shall be **+1** (excess of 1 electron with spin up) and the other **-1** (excess of 1 electron with spin down).
 [image]

Furthermore, enable the PEDA-NOCV calculation as follows:

   Panel bar **Properties → PEDA-NOCV**
   Check the **Perform PEDA-NOCV analysis** box
   Set **Use NOCVs with eV larger than:** to 0.001
 [image]


Step 3d: Save and run the calculation
-------------------------------------

Now you can save and run the calculation.

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


Step 4: Checking the results
============================

After the calculations of the fragments and the PEDA-NOCV finished you
can look for the PEDA results. Therefore, 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' dropdown 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 these energy differences, which are equal to the
preparation energy, to the interaction energy will give you the
negative bond dissociation energy.

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

   **Properties → PEDA-NOCV Energy Terms**

Reference results:

[image]


Step 5: Plotting NOCV orbitals and deformation densities
========================================================

You can visualize the charge NOCV deformation densities which describe
the charge flow between the fragments. Therefore, open the "View"
using the SCM dropdown menu.

   **SCM → View**
   **Fields → Grid → Medium**

You can now add an isosurface with phase via the dropdown menu 'Add',
or via 'Ctrl+B'.

   **Add → Isosurface: With Phase**
 [image]


Step 5a: Plotting NOCV deformation densities
--------------------------------------------

To get an overview of the NOCV deformation densities click on 'Select
Field ...' and then on 'NOCV Def densities'.

[image]

You can see that there are NOCV deformation densities for electron
spin A and B.

You can visualize the first NOCV deformation density of spin A:

   Click on the first NOCV Def density in the table
   Set the **isovalue** to 0.001
   Opionally, click on the tiny arrow next to "Isosurface with phase" to toggle details controls, and set **opacity** to 50
 [image]

You see the transfer of charge density from red to blue lobes from one
methyl radical (with spin A excess) to the other (with spin B excess).
The first NOCV deformation density for spin B is giving the same
picture but the other way around. So, transfer of charge density from
the methyl radical with spin B excess to the methyl radical with spin
A excess.

[image]
