Resolve "Support 3D simulations"

What does this MR do?

Fixes 3D instantiations and adds them to the default executables

Is there something that needs to be double checked?

No

Can this MR be accepted?

• Implemente
• Added/Updated tests
• Added/Updated documentation
• Pipelines passing
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  • 
  • 
• Delete branch option set
• Added entry to CHANGELOG.md

Related issues

Closes #31 (closed)