Added Natural Transition Orbital calculation and processing.#271
Added Natural Transition Orbital calculation and processing.#271hughf2468 wants to merge 10 commits into
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…he prototype model.
Fixed a bug where deselecting the "Calculate Natural Transition Orbitals" box would cause a crash loop.
…e prototype model.
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danielhollas
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danielhollas
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Amazing work, congrats! 🎉
I just have a couple of quick comments. Obviously we don't have time to do full review but that's fine. Good luck with your submission!
| Copy-paste the following profile configuration (substitute path to ORCA and the Docker image name if needed) | ||
| ``` | ||
| port = 8888 | ||
| default_apps = [ "aiidalab-ispg@git+https://github.com/ispg-group/aiidalab-ispg.git@main",] |
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I know this has caused problems for you at the beginning but it works now so please revert this change.
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Please run pre-commit to get rid of changes in this file:
The easiest way is perhaps to install uv package manager and then use
pip install uv
uvx pre-commit run --all-files
| structures_to_trajectory, | ||
| ) | ||
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| from aiida_shell import launch_shell_job |
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Can you please add aiida-shell as a dependency in pyproject.toml?
(also need to add cubehandler later, but now we cannot due to the python version dependency). If you open a PR on cubehandler, you can add the dependency on your specific branch like this
cubehandler@git+https://github.com/<username>/cubhandler@<your_branch>
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Superseded by #272 |
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Added steps to calculate NTOs when requested, convert to relevant ".cube" files, and compress these files.
Currently these files are stored in separate FolderData nodes (one for each conformer) and the PKs of these nodes are reported by each "NEA spectrum workflow". However, the code is compatible with a visualiser we have developed (https://github.com/AaronH-sys/atmospec-orbital-visualisation.git) with minor changes to enable it to accept multiple conformers if desired.
Requires "orca_plot" to be configured as an AiiDA code, as well as AiiDA shell and Cubehandler as additional dependencies. Cubehandler requires editing of its "pyproject.toml" to work under Python 3.9.