Plotting Charge Density in 3D: Can My Data Be Formatted as an XYZ File?

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SUMMARY

The discussion centers on formatting charge density data for 3D plotting, specifically whether it can be converted into an XYZ file format. The user is currently utilizing gopenmol, which requires plt format, but seeks to convert their grid point data into XYZ format. However, it is concluded that XYZ files are typically reserved for atomic coordinates and may not be suitable for charge density data. Alternative software options suggested for 3D plotting of charge density include Xcrysden and VESTA.

PREREQUISITES
  • Understanding of charge density data representation
  • Familiarity with XYZ file format specifications
  • Knowledge of gopenmol software for plotting
  • Experience with alternative visualization tools like Xcrysden and VESTA
NEXT STEPS
  • Research how to format charge density data for Xcrysden
  • Explore VESTA's capabilities for 3D charge density visualization
  • Learn about the plt format used by gopenmol
  • Investigate data conversion techniques between different file formats
USEFUL FOR

This discussion is beneficial for researchers and scientists working with charge density data, computational chemists, and anyone involved in visualizing 3D data using software like gopenmol, Xcrysden, or VESTA.

Morberticus
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I have a charge density I would like to plot in 3D

The data is currently in the format

x1 y1 z1 density
x2 y2 z2 density
etc
etc

where x,y,z are grid points. Can this kind of data be formatted as an xyz file? I know xyz is normally atom locations (I have no explicit atoms), but I have heard it can be done.

The program I am using to plot it is gopenmol, which expects plt format. I can convert xyz to plt but not sure how to convert my data to xyz

Thanks
 
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It doesn't sound like it. It sounds to me like an xyz file represents a different kind of data. I'd suggest looking at xcrysden or vesta for plotting charge density in 3D.
 

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