Some molecules bind on graphene in our project and we got output files from bader charge analysis by Henkelman group theory. we want to visualize the whole charge density profile from this output. So, how could i visualize this.
Hi Delowar,
I don't know about the software that you are using, but if the output is a text file, then you can use textscan function of MATLAB to read the data from the .dat/.txt file and plot out your required data.
Thanks.
Raihan
Hello Delowar Hossain, according to the page of Henkelman
http://theory.cm.utexas.edu/henkelman/code/bader/
You can visualize the results using several packages. Among them, I think VESTA is the best choice to get very nice figures.
Thank you very much@Sinhué López. I have tried by using this link but i couldn't . Do you know which package is suitable for obtaining whole structure charge density?
Besides the Bader analysis mentioned in your question, you could perform DDEC6 analysis to compute the net atomic charges and bond orders. The program mentioned below outputs the results to xyz files that are readable by Jmol visualization program. You can use Jmol to display the chemical structure and either label each atom by the numeric property (net atomic charge, atomic spin moment (for magnetic materials), sum of bond orders, etc.) or if desired you can ask Jmol to color each atom by the value of the computed property. The method for doing this is explained in the Chargemol program manual (http://ddec.sourceforge.net). It's really easy to create graphics in Jmol where the atoms are labeled or colored by the computed scalar property for each atom.
The DDEC6 method has a lot of useful properties. See the following papers for details:
(1) T. A. Manz and N. Gabaldon Limas, “Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology,” RSC Advances, 6 (2016) 47771-47801 (http://dx.doi.org/10.1039/C6RA04656H).
(2) N. Gabaldon Limas and T. A. Manz, “Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials,” RSC Advances, 6 (2016) 45727-45747 (http://dx.doi.org/10.1039/C6RA05507A).
(3) T. A. Manz, "Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute bond orders," RSC Advances, 7 (2017) 45552-45581 (http://dx.doi.org/10.1039/C7RA07400J ). (open access)
The DDEC6 method is available in the free Chargemol program (http://ddec.sourceforge.net) which can analyze the outputs of VASP, Gaussian, and other quantum chemistry programs.
- Badges
- Science topic
- Similar topics
- Statistics
- Survey