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- .github/workflows/environments/environment.yaml+1-1
- .github/workflows/environments/py313-conda-lock.yml+789-768
- .github/workflows/environments/update-lockfiles.sh+1-1
- .github/workflows/test.yaml+4-4
- .pre-commit-config.yaml+1-1
- 03-Parallel-Simulations-With-MPI/04-Running-Multiple-Simulations-With-Partitions.ipynb+5-2
- 05-Organizing-and-Executing-Simulations/.gitignore+3-2
- 05-Organizing-and-Executing-Simulations/00-index.ipynb+6-6
- 05-Organizing-and-Executing-Simulations/01-Organizing-Data.ipynb+22-20
- 05-Organizing-and-Executing-Simulations/02-Executing-Simulations.ipynb+283-182
- 05-Organizing-and-Executing-Simulations/03-Continuing-Simulations.ipynb+264-236
- 05-Organizing-and-Executing-Simulations/04-Submitting-Cluster-Jobs.ipynb+192-515
- 05-Organizing-and-Executing-Simulations/Tutorial concept map.pptx
- 05-Organizing-and-Executing-Simulations/compress.py+55
- 05-Organizing-and-Executing-Simulations/create_simulation.py+23
- 05-Organizing-and-Executing-Simulations/equilibrate.py+92
- 05-Organizing-and-Executing-Simulations/project.py+22-154
- 05-Organizing-and-Executing-Simulations/project_partitioned.py-170
- 05-Organizing-and-Executing-Simulations/randomize.py+20
- 10-Modelling-Flexible-Active-Interfaces/00-index.ipynb+61
- 10-Modelling-Flexible-Active-Interfaces/01-Describing-Membranes-As-Meshes.ipynb+303
- 10-Modelling-Flexible-Active-Interfaces/02-Vesicle-MD.ipynb+597
- 10-Modelling-Flexible-Active-Interfaces/2D_triangulation.svg+2.9k
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- 10-Modelling-Flexible-Active-Interfaces/sphere_triangulation.png
- AUTHORS.md+2
- README.md+4-2
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