CUBE doesn't open

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1

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I believe this to be a bug with Avogadro:
I try to open MultiWFN generated cube from ORCA output but orbitals are not plotted.

Environment Information

Avogadro version: 1.100.0
Operating system and version: MacOS Sequioa

Expected Behavior

Orbitals shall appear

Actual Behavior

Orbitals do not appear although SURFACES is ticked

Steps to Reproduce

Load the file via Avogadro

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)
CUBE.tar.gz (7.9 MB)

2

Okay, I understand your UI confusion - I’ll think about the best way to address that…

In the meantime, you’ll want to create a mesh:

  • Go to Analyze ⇒ Create Surfaces…
  • Pick “From File” (which probably should also be the default option in this case)

Create Surfaces Dialog
Create Surfaces Dialog1110×1018 81.1 KB

It’ll create a mesh of the orbital for you and render it.

I think your point from a user perspective is “I loaded this Cube file, I’d like to see the orbital automagically” which totally makes sense. I have to think a little bit about the best way to make that happen.

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3

Okay, this patch should do it (i.e., if you read in a file with cubes, it will display a mesh by default)

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4

Apparently, my version of Avogadro doesn’t have an option to load a surface from a file. Is it a nightly build?

By the way, which files should I delete to reset all settings to factory defaults? I changed some options and would like to revert everything.
It would be helpful to have a “Reset to Defaults” button somewhere in the toolbar?

Zrzut ekranu 2025-06-23 o 08.14.36
Zrzut ekranu 2025-06-23 o 08.14.36894×504 58.4 KB

5

Yes, it’s a nightly build. If you have a GitHub account, you can try this build. At the moment, Apple Silicon builds are offline. (I’m working to move them from a desktop in my lab to GitHub.)

On a Mac, you can find all your preferences in ~/Library/Preferences. Avogadro2 is org.openchemistry.Avogadro but it’s often interesting to sort by date.

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6

Oh well… I’m not very comfortable compiling software, so it looks like I’ll need to wait until a ready-to-run MacOS build is available.
Would you be able to upload a .dmg file directly?

7

Yes, it should be available through the (Intel) macOS nightly build.

The link I indicated was a DMG - but you need a GitHub account to download it.

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8

I have a GitHub account, but earlier, downloading the file didn’t give me a DMG — it was some CMake config file instead. Interestingly, now it downloaded the DMG properly. Though, ARM Mac here

9

Yes - the Apple Silicon builds have been off a desktop in my lab, but there’s an Xcode issue at the moment and I’d like to move them to GitHub.

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10

I see. However, the file from your link is macOS.dmg.zip that upon extracting yields „AvogadroCPackOptions.cmake” file; this is not an executable

11

BUMP

The nightly builds from:

include both Intel and ARM64 versions. However:

  • Downloading the Intel version yields a file named AvogadroCPackOptions.cmake, not a .dmg.
  • The ARM64 version correctly downloads a .dmg, but it does not include surface options.
12

You don’t need to bump the thread. I’m a Mac user. I’m well aware of the problem:

  • The Intel builds are intermittent because creating a disk image on a build server randomly fails with macOS 13. Apple fixed it in macOS 14, but GitHub only has ARM servers for that.
  • The ARM build is likely quite old because I only got that build server back online yesterday afternoon.

I would guess that the next nightly build for ARM should be up-to-date.

The longer term solution is to get the Mac Qt6 builds working, but I don’t have time this week to deal with CMake.

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13

Oh, okay. Sorry for the bump, then.

14

No worries - I understand the frustration.

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