From 8c5d1d9e24758aa70d9f92826144cf7eb4e38d2a Mon Sep 17 00:00:00 2001 From: Kane Shenton Date: Tue, 9 Dec 2025 17:43:15 +0000 Subject: [PATCH] Add links and instructions for the marimo apps --- docs/workshop/03_geometry.md | 9 +++++++++ docs/workshop/04_nmr_shiedling_efg.md | 8 ++++++++ 2 files changed, 17 insertions(+) diff --git a/docs/workshop/03_geometry.md b/docs/workshop/03_geometry.md index c8c92fb..94f101a 100644 --- a/docs/workshop/03_geometry.md +++ b/docs/workshop/03_geometry.md @@ -187,3 +187,12 @@ and let all angles relax independently. This is similar to the `%block lattice_a For the mathematically minded, this is taking the limit that the interlayer spacing, controlled by the out-of-plane lattice vector, goes to infinity! Practically, we cannot actually set the lattice parameter to infinity - try varying it and seeing how it converges with distance. + + +## Further Resources + +There is a web app here: + +[Geometry optimisation visualiser web app](https://jkshenton.github.io/marimo_notebooks/apps/castep_geomopt_summary.html) + +which allows you to explore the progress of your geometry optimisation by plotting energies, forces, stresses and displacements with each iteration. \ No newline at end of file diff --git a/docs/workshop/04_nmr_shiedling_efg.md b/docs/workshop/04_nmr_shiedling_efg.md index 562a33a..64cca50 100644 --- a/docs/workshop/04_nmr_shiedling_efg.md +++ b/docs/workshop/04_nmr_shiedling_efg.md @@ -332,3 +332,11 @@ INSTRUCTIONS: The Collaborative Computational Project for NMR Crystallography (CCP-NC) has a number of [tools](https://www.ccpnc.ac.uk/software) and [resources](https://www.ccpnc.ac.uk/docs) to help with CASTEP. In addtion is the graphical user interface, MagresView mentioned above, the Soprano python library can be a useful way to analyse CASTEP output. There are NMR-specific tutorials here: and a command line interface for commond NMR tasks with .magres files here: . Soprano is installed on the VM (Applications -> Software -> Soprano). +There is also an interactive notebook on the VM under `/shared_materials/magres_analyser.py`. To use this you need to open a terminal on the VM and then run the following two commands: + +``` +python3.11 -m pip install uv +uvx marimo run /shared_materials/magres_analyser.py --sandbox +``` + +a browser window should open with the notebook. This notebook will allow you to explore different NMR tensor conventions.