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Tutorial fixes for 5.0.
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@joaander
joaander committed Dec 2, 2024
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2 changes: 1 addition & 1 deletion sphinx-doc/tutorial
Submodule tutorial updated 64 files
+1 −5 .github/ISSUE_TEMPLATE/new_tutorial.md
+1 −2 .github/workflows/environments/environment.yaml
+828 −523 .github/workflows/environments/py312-conda-lock.yml
+6 −5 .github/workflows/test.yaml
+1 −1 .github/workflows/update-conda-lockfiles.yaml
+2 −2 .pre-commit-config.yaml
+4 −3 .ruff.toml
+2 −11 00-Introducing-HOOMD-blue/00-index.ipynb
+1 −10 00-Introducing-HOOMD-blue/01-The-Simulation-Object.ipynb
+4 −13 00-Introducing-HOOMD-blue/02-Performing-Hard-Particle-Monte-Carlo-Simulations.ipynb
+19 −22 00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb
+30 −33 00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb
+24 −27 00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb
+22 −25 00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb
+462 −363 00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.ipynb
+4 −10 01-Introducing-Molecular-Dynamics/00-index.ipynb
+147 −153 01-Introducing-Molecular-Dynamics/01-Molecular-Dynamics-Simulations.ipynb
+22 −19 01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb
+97 −93 01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb
+4 −10 02-Logging/00-index.ipynb
+251 −342 02-Logging/01-Logging-to-a-file.ipynb
+396 −402 02-Logging/02-Saving-Array-Quantities.ipynb
+13 −17 02-Logging/03-Storing-Particle-Shape.ipynb
+42 −48 02-Logging/04-Writing-Formatted-Output.ipynb
+3 −3 03-Parallel-Simulations-With-MPI/00-index.ipynb
+1 −1 03-Parallel-Simulations-With-MPI/03-Accessing-System-Configurations-With-MPI.ipynb
+2 −2 03-Parallel-Simulations-With-MPI/04-Running-Multiple-Simulations-With-Partitions.ipynb
+4 −4 03-Parallel-Simulations-With-MPI/domain_decomposition.py
+1 −1 03-Parallel-Simulations-With-MPI/global_snapshot.py
+1 −1 03-Parallel-Simulations-With-MPI/hello_hoomd.py
+1 −1 03-Parallel-Simulations-With-MPI/hello_partition.py
+1 −1 03-Parallel-Simulations-With-MPI/hello_world.py
+3 −3 03-Parallel-Simulations-With-MPI/lj_domain_error.py
+3 −3 03-Parallel-Simulations-With-MPI/lj_kinetic_energy.py
+5 −5 03-Parallel-Simulations-With-MPI/lj_partition.py
+4 −4 03-Parallel-Simulations-With-MPI/lj_performance.py
+4 −4 03-Parallel-Simulations-With-MPI/lj_trajectory.py
+1 −1 03-Parallel-Simulations-With-MPI/local_snapshot.py
+1 −1 04-Custom-Actions-In-Python/02-An-Initial-Custom-Action.ipynb
+3 −3 04-Custom-Actions-In-Python/03-Custom-Action-Features.ipynb
+9 −9 04-Custom-Actions-In-Python/04-Custom-Updater.ipynb
+32 −32 04-Custom-Actions-In-Python/05-Custom-Writer.ipynb
+5 −5 04-Custom-Actions-In-Python/06-Improving-Performance.ipynb
+5 −5 05-Organizing-and-Executing-Simulations/01-Organizing-Data.ipynb
+16 −16 05-Organizing-and-Executing-Simulations/02-Executing-Simulations.ipynb
+30 −30 05-Organizing-and-Executing-Simulations/03-Continuing-Simulations.ipynb
+1 −2 05-Organizing-and-Executing-Simulations/04-Submitting-Cluster-Jobs.ipynb
+29 −29 05-Organizing-and-Executing-Simulations/project.py
+30 −30 05-Organizing-and-Executing-Simulations/project_partitioned.py
+79 −79 06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb
+29 −25 06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb
+12 −8 06-Modelling-Rigid-Bodies/03-Preparing-a-General-Body.ipynb
+0 −3 07-Modelling-Patchy-Particles/00-index.ipynb
+0 −3 07-Modelling-Patchy-Particles/01-Kern-Frenkel-Model.ipynb
+556 −479 07-Modelling-Patchy-Particles/02-Simulating-a-System-of-Patchy-Particles-with-HPMC.ipynb
+16 −16 07-Modelling-Patchy-Particles/create-figures.ipynb
+23 −20 08-Placing-Barriers-in-the-Simulation-Box/02-Fixed-particles.ipynb
+19 −13 08-Placing-Barriers-in-the-Simulation-Box/04-Wall-potential-MD.ipynb
+17 −11 08-Placing-Barriers-in-the-Simulation-Box/05-Wall-potential-HPMC.ipynb
+31 −31 08-Placing-Barriers-in-the-Simulation-Box/create-figures.ipynb
+1 −2 09-Multiparticle-Collision-Dynamics/00-index.ipynb
+8 −8 09-Multiparticle-Collision-Dynamics/01-Pressure-Driven-Flow.ipynb
+13 −13 09-Multiparticle-Collision-Dynamics/02-Diffusion-in-Solution.ipynb
+1 −1 README.md

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