PEDA-NOCV for Spin Unrestricted Calculations

This tutorial will teach you how to:

  • perform a periodic energy decomposition analysis (PEDA) combined with the natural orbitals for chemical valency (NOCV) method (pEDA-NOCV) for extended systems with the BAND-GUI, where the bond is described by open-shell, spin unrestricted fragments
  • where to look for the results

Step 1: Start ADFinput

Start ADFinput in a clean directory. (according to Step 1 of the With a Grain of Salt Tutorial)

/scm-uploads/doc.2016/Tutorials/_images/adfinput_BAND_Main.png

Step 2: Set up the system - Ethane

An easy and non-timeconsuming testsystem is the C-C bond analysis in an ethane molecule. Here, two methyl radicals with opposite spin-polarization do 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
VEC1      10.00000000       0.00000000       0.00000000
/scm-uploads/doc.2016/Tutorials/_images/adfinput_BAND_MainA_Tut4b.png

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).
  • Then 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)
/scm-uploads/doc.2016/Tutorials/_images/adfinput_BAND_Model_RegionsB_Tut4b.png

Step 3b: Details for the calculation

Go to the Main menu,

Panel bar Main

and change the calculation setup (XC functional, basis set, frozen core, numerical quality and unrestricted calculation) according to the following picture.

/scm-uploads/doc.2016/Tutorials/_images/adfinput_BAND_MainB_Tut4b.png

Since the PEDA-NOCV does only work for the \(\Gamma\)-point in reciprocal space, you have to specify this in the Details menu.

Panel bar Details
Set Kspace to Gamma Only
/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_Details.png

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).
/scm-uploads/doc.2016/Tutorials/_images/adfinput_BAND_MultiLevel_FragmentsC_Tut4b.png

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
/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_Properties.png

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-NOCV Energy Terms’ via the corresponding button in the ‘Properties’ dropdown menu.

Properties → PEDA-NOCV Energy Terms

Reference results:

/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_Results.png

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

Depending on your preferences (w.r.t. showing atoms of neighboring cells) you will end up with the following representation of ADFview.

(new Image compare to other PEDANOCV tutorial)

You can now add an isosurface (Double(+/-)) via the dropdown menu ‘Add’, or via ‘Ctrl+D’.

Add → Isosurface (Double(+/-)
/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_adfview1.png

Step 5a: Plotting NOCV deformation densities

To get an overview of the NOCV deformation densities click on ‘Select Field ...’ and then on ‘NOCV deformation densities’. The following window should appear.

/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_adfview2.png

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. (Be aware of the small isovalue of 0.001 in the following picture!)

/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_adfview4.png

You see the transfer of charge density from red to blue lobes from one methylradical (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 methylradical with spin B excess to the methylradical with spin A excess.

/scm-uploads/doc.2016/Tutorials/_images/PEDANOCV_Unrest_adfview3.png