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Spatial bining display

Dear developers,

I hava problems with spatial bining modifier in the ovito pro. This modifier is really helperful but I can not make the image achieve high quality. Here is my steps:

  1. compute a specific property, e.g. stress
  2. use spatial bining
  3. use color coding modifier on Voxel grid property
  4. In visual elements window, hide particles, show bining grid (don't highlight grid lines)

Then I get a stress distribution figure. But problems is that the region without atoms is colored, because the bin value is zero and zero color is not white or transparent. This make the background (vacuum region) is unacceptable. Is there a method to fix it or have a different way to realize the same aim.

Thanks for your time.

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Is it possible to map the bin value to the respective atoms in specific spatial bin? Then I can use the great renderer in ovito pro.

Hi,

Currently, there is no option in OVITO to make certain voxel grid cells transparent or invisible. However, giving some cells a special color if they contain a special value can be accomplished using the Compute Property modifier. Attached is an example showing a structure for which the centrosymmetry parameter has been calculated for each atom. This parameter typically has a positive value. Voxel grid cells containing no atoms at all will have a centrosymmetry value of exact zero. The Computer Property modifier is used to give these cells a white color, overriding the original colors assigned by the Color Coding modifier.

-Alex

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Quote from wang xin on July 12, 2020, 11:29 am

Is it possible to map the bin value to the respective atoms in specific spatial bin? Then I can use the great renderer in ovito pro.

This is a good idea, but there is no built-in function for mapping information from the voxel grid cells back to the atoms. We can try to develop a Python script for that, which uses each atom's coordinates to look up the corresponding grid cell and then assigning the local value as a property to the atom. But that will require some work.

Another option you have is to avoid using the Spatial Binning modifier altogether and instead perform a spatial averaging of the stress property of the atoms. For this purpose OVITO's Compute Property modifier provides the neighbour calculation mode. It allows you to sum up the atomic stress values within a spherical cutoff around each atom. Using this technique you can also achieve a smoothing effect to reduce fluctuations in the local atomic values.

Quote from Alexander Stukowski on July 14, 2020, 9:14 am
Quote from wang xin on July 12, 2020, 11:29 am

Is it possible to map the bin value to the respective atoms in specific spatial bin? Then I can use the great renderer in ovito pro.

This is a good idea, but there is no built-in function for mapping information from the voxel grid cells back to the atoms. We can try to develop a Python script for that, which uses each atom's coordinates to look up the corresponding grid cell and then assigning the local value as a property to the atom. But that will require some work.

Another option you have is to avoid using the Spatial Binning modifier altogether and instead perform a spatial averaging of the stress property of the atoms. For this purpose OVITO's Compute Property modifier provides the neighbour calculation mode. It allows you to sum up the atomic stress values within a spherical cutoff around each atom. Using this technique you can also achieve a smoothing effect to reduce fluctuations in the local atomic values.

Thanks a lot! You and your friends make ovito really strong and convenient. Without the beneficial communication with you, I may miss such a great feature! I thick I should read more about SUPPORT FORUM and docs to explore ovito.