I refined my XRD data and exported the PCR file to visualize it, with minimum refinement I am getting structure as ordinary crystal files ( almost matches with original cod data. But when I refine it to accurate refinements which mean fully converged my crystal structure having white partition? What is meant for white partition for the same atom? I did not change colors, Original file structure I am getting I attached below, What is it represents? kindly help me
Dear Atchaya Sundararajan ,
without further information is hard to answer your question. Nevertheless, it could represent thermal parameters without octant, a CIF file sharing a specific site with two different atoms controlled by occupancy, pre defined atoms color, two different atoms sharing the same symmetry operator, and so on.
The CIF file may provide the answer.
Best regards
WNM
Answer by Wagner Da Nova Mussel is fully ok. However, one more general advice/comment. A PCR file contains the information extracted by Rietveld refinement using the Fullprof software. A CIF file is a standardised way to contain crystal structure information, which can be automatically read in in the structure drawing program VESTA. The present case for me is a typical example that people start to think in terms of their files instead of thinking in terms of the physical information contained in these files. If this information is not properly understood, you cannot use it adequately.
Atchaya Sundararajan : This is a simple crystal structure which you show, and I am convinced it is not a new one. Have you ever thought to enter this crystal structure "by hand" into VESTA starting from the information listed in a proper paper. This helps you to get a feeling about what the different quantities you enter (and which can automatically entered by importing the cif file) mean. As indicated above, a crucial factor is the occupancy, which is apparently 1/2 for the red atoms, and likely incorrectly. One frequent issue is the different ways to enter occupancies in software. There are different ways to do this and there pitfalls upon handling them correctly and there may also be errors upon exporting/importing.
Wagner Da Nova Mussel Thank you sir, I was in a confusion that whether this colour variation or has some conceptual meanigs. That's why I didn't include the CIF file. Now I found that the technical error.
Andreas Leineweber Thank you sir.
Yes, Sir, I refined my XRD data using FUll PROF. I checked the PCR data and concluded that the formations are correct, But even though I got the variations. Now I found that there is atom style configuration setting We can Highlight ionic, Radii, Vanderwall's bonding visualizations using the Ball style and Ellipsoids option. When I changed these balls and ellipsoids configuration I can get bicolor In my case White color indicates Radii and Ions. That's why I got two colors and I am analyzing whether it indicates the edge-sharing or some other parameters.
Thank you sir
Atchaya Sundararajan, please note that the two modes of representation do not visualize the same information:
If you show the atoms as thermal ellipsoids, the shape and size of those ellipsoids will reflect the thermal displacement parameters. If you used isotropic displacement parameters, the atoms will appear to be spherical. In this representation, VESTA does not indicate the occupancy of the atomic sites.
If you show the atoms as balls, a spherical representation is used no matter what the anisotropic displacement parameters are. In this case, VESTA will include the occupancy of the sites but not the thermal displacement parameters.
Atoms having two colors means in this representation means that two things (elements, vacancies) occupy this site with the fraction represented by the portion of each color. The default settings are that red represents oxygen, the white color represents a vacancy. Therefore, it seems like your oxygen site is only occupied to roughly 50%. The numerical values for the occupancies (Occ.) can be found in the "structure parameters" menu.
In some ionic compounds, the occupancies can/need to be lower than 100% to ensure charge balance.
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