PovRay Mesh Colors / Transparency Not Exported Correctly

[maciekofficial]

In Avogadro 1.2 one can export PovRay file to generate high resolution image. In Avogadro 1.97 the feature is there in File->Export->Molecule, but it exports only molecule without mesh/surface. It would be great to export molecule along with the surface.

[ghutchis]

That was a bit weird - it actually computed the mesh, but didn't write it to the file. Check out #1180 - but if you have an example file or two, it would help a lot. Not sure this is exactly correct.

[maciekofficial]

First, sorry for delayed answer...

I did some small testing on Kubuntu 20.04.5 LTS with Avogadro 1.93.0 (from the Ubuntu repository), 1.97.0 and 1.97.0_Nightly, both in AppImage format. I used a small cube file with spin density generated in ORCA 5.0.3 (oSQ_spindens.cube.zip).

The cube file opens well in all tested versions and mesh can be generated.

The command used in testing for rendering with PovRay was:
povray +Iname.pov +Oname.png +W1024 +H768 +V +D +FN +Q9 +P +UD +UL +UV +A +AM2 +UA

In Avogadro 1.93.0 in menu File->Export there is an option "PovRay Render". It exports *.pov files, however they do not include the mesh that has been calculated and displayed. The pov and rendered png files are given as avogadro_1.93.0.zip

In Avogadro 1.97.0 and 1.97.0_Nightly the option "PovRay Render" is not available in File->Export. I exported the pov file using File->Export->Molecule. This option generates pov files using Open Babel and thus file babel_povray3.inc is required for PovRay rendering. The data for mesh rendering are not included in the pov file and final molecule result is significantly different from what is displayed in Avogadro (different style). Results are enclosed as avogadro_1.97.0_Nightly.zip and avogadro_1.97.0.zip. The file babel_povray3.inc used in rendering is also attached.
In Avogadro 1.93.0 File->Export->Molecule can also be used but to the same end.

Hope this will be somewhat helpful.

If there is any more testing that I can do, please let me know.

With best of regards,
Maciek

oSQ_spindens.cube.zip
avogadro_1.93.0.zip
avogadro_1.97.0.zip
avogadro_1.97.0_Nightly.zip
babel_povray3.inc.zip

[ghutchis]

Can you send me a screenshot of your File => Export submenu? I don't know how it wouldn't show up...

The build at #1180 would have mesh support .. at the very least I can see that it writes out the mesh data and it seems comparable to Avogadro 1.x.

Obviously 1.93 and 1.97 wouldn't have mesh support because it's only in the #1180 branch for now.

And no, export to Open Babel would not include the mesh because Open Babel doesn't have a concept of a mesh - it's a cheminformatics library.

Did you try the AppImage from #1180?

[maciekofficial]

Using the AppImage from #1180, I think I've found the source of the problem. When user interface language is set to American English, the sub menu File => Export shows up as it should:

I had interface set to British English (exported from system language) and then some options from this sub menu were missing:

The problem exists for Canadian and Australian English, polski/Polish, espanol de Espana/Spanish, but not for Deutsch/German, and it also affects the Win64 version.

The build at #1180 exports mesh to a pov file, however it seems that in the process:

• mesh transparency is set to 100%, so the mesh doesn't show up in rendering and this happens regardless of "Opacity" slider setting in View Configuration
  
• colors for the positive and negative parts of the mesh are the same

Both can be fixed in the pov file. Just in case, I am sending the original and corrected pov file (pov_files.zip). I changed line 21105 and line 82134

line 21105:	pigment { rgbt <1.0, 0.0, 0.0, 0.0> }  // WAS: pigment { rgbt <1.0, 0.0, 0.0, 1.0> }
line 82134:	pigment { rgbt <1.0, 0.0, 0.0, 0.0> }  // WAS: pigment { rgbt <1.0, 0.0, 0.0, 1.0> }

Render results:
povray +Iname.pov +Oname.png +W1024 +H768 +V +D +FN +Q9 +P +UD +UL +UV +A +AM2 +UA

1. Pov file as exported from Avogadro2
   

2. Fixed transparency in line 21105
   

3. Fixed transparency and color in line 82134:
   

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-Latest.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
macOS.dmg
Ubuntu-Latest.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
Avogadro2.AppImage
Ubuntu-Latest.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.