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#17 Electron Charge Density, Allowing Visual Check of Electron Distribution

Viewed : 816 times,  2019-09-18 16:23:33

The electron charge density, displaying the density of electrons in space, is good to visually check the electron distribution in materials. [1]

In particular, as calculating the difference in charge densities shows the difference in the electron distribution of the two structures, if a defect occurs or a molecule is adsorbed, you can see what happens on the electron structure at a glance.
With a DFT calculation, you can calculate an electron charge density. With Materials Square, you can conveniently find and visualize the charge density data by carrying out a plane-wave basis DFT calculation of Quantum Espresso.
This weekly tip describes how to find a charge density with Materials Square.

 

1. How to Calculate Charge Density

You can find a charge density with Materials Square as follows:

  1. Model your system on the Structure builder module.
  2. Perform DFT calculation on the Quantum Espresso module.
  3. Check the charge density on the charge density module.

The post-processing calculation is required to get a charge density. To get the charge density data, add the post-processing tab like the following.

The charge density of a silicon bulk unit cell is calculated as follows:

👉 Check the result of Charge Density

The visualizer has a menu that can adjust the calculated charge density and isovalue. ρ(max) indicates the maximum charge density; and ρ(min), the minimum charge density.
The isovalue menu allows selecting an isovalue value and its unit. Setting the isovalue displays only those that have the same value corresponding to the isovalue, among the charge densities distributed at space. The electron density increases when closing to the nucleus of an atom. Thus, the higher the isovalue is, the smaller the volume of the charge density displayed becomes. Set a value to clearly see the characteristics.

 

2. How to Calculate Charge Density Difference

If you get two or more charge density data by carrying out an SCF calculation of two structures, you can find the difference in the charge densities.
When performing an SCF calculation to find the charge density difference, you need to note that. As the location of atoms should be exactly the same when finding the difference, it is good to carry out an SCF calculation that only calculates the electron structure in the given atom location. If the atom location is optimized through the (vc-)Relax, the atomic coordinates of the two structures may change, and the difference may not be accurately calculated.
If one silicon atom is substituted with phosphorous in a silicon unit cell to get the charge density data, you can have the charge density difference by taking the difference from the silicon bulk calculated above.
Connect the charge density module to two Quantum Espresso module to activate the 'Diff' tab.

 

👉 Check the result of Charge Density Difference

Basically, the ρ12 data is displayed. To adjust that, write the desired formula to the 'Formula' input.

Calculating the difference between the charge density of a silicon bulk unit cell and that of a structure where a silicon is substituted with P allows you to check if there is some electron near P. As Si has four valence electrons and P has five, it can be interpreted that a part doped with P has a large electron density.

 

3. How to Check PBC

The last weekly tip mentioned that enough amount of vacuum to 10–15 Å needs to be added to a calculation model when calculating a single atom or a molecule. If so, how can we know that the vacuum added does not interact with the neighboring atoms/molecules?
You can conduct a convergence test that can check if energy decreases when the volume of vacuum increases, but it can also be done by finding a charge density. Setting isovalue to a very small value close to 0 visually displays how charges are distributed in the vacuum section. If the set vacuum is smaller than the required volume, the ratio that charges are displayed in the entire cell with the same isovalue value will be large. Then, we can estimate that more interaction may occur.

 

👉 Check the Data of ρBA

 

Sample Data Calculation

Name TYPE Node ppn Duration Cost
Silicon Conventional cell QE 1 36 00:00:23 $ 0.064
Si-P doped structure QE 1 36 00:00:21 $ 0.058
Silicon Single Atom (Vacuum 20 Å) QE 1 36 00:00:47 $ 0.131
Total       00:01:31 $ 0.253

 

This weekly tip looks into how to calculate a charge density and a charge density difference in Materials Square. A charge density can be used to find out the characteristics of a structure by displaying the distribution of electrons. In particular, a charge density difference can selectively visualize the density of the desired part among complex charge densities, and you can use it in various ways.
Moreover, with Materials Square, you can easily get a charge density by simply clicking a couple of menus.
Why don’t you have the charge density and the charge density difference of a structure of interest?

 


[1] Gatti, C., & Macchi, P. (2011). A Guided Tour Through Modern Charge Density Analysis. In Modern Charge-Density Analysis (pp. 1-78). Springer, Dordrecht.

 


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