activity prep

README.md

@@ -1,31 +1,85 @@
 # IMD Workshop 2024
 
-## Getting a codespace 
+Welcome to the interactive portion of the workshop! 
+To get started, we recommend using VSCode
+in the browser with the Github codespace we've provided 
+which includes all the tools you'll need to get started with live
+simulation streaming.
 
-To get access to the workshop environment, you have two options:
+# 1. Codespace environment setup
 
-### 1. In the browser
+## i. Github codespaces in the browser (recommend)
 
-The easiest way is to simply click the "+" in the codespaces menu in this repo (shown below) to create a new codespace. A workshop environment will be created and VSCode will automatically run in your browser
-with the extensions and packages you'll need already installed, including GROMACS, LAMMPS, NAMD, MDAnalysis, and IMDClient.
+The easiest way is to simply use this repository to create a codespace.
+A workshop environment will be created and VSCode will automatically run in your browser.
 
-![alt text](.media/browser.png)
+### Step 1.
 
-### 2. In your IDE
+Select the "new with options" codespace button.
 
-You can also use your own IDE to spin up and connect to a codespace. If you have VSCode installed, you can install the 
+![alt text](.media/browser_1.png)
+
+### Step 2.
+
+Select the region closest to you.
+
+![alt text](.media/browser_2.png)
+
+### Step 3.
+
+Finally, select "Create codespace" to launch the codespace.
+
+## ii. Github codespaces tunnel from your IDE (VSCode and Pycharm)
+
+You can use your own IDE to spin up and connect to a codespace (which GitHub will host). 
+
+If you are using VSCode, follow these steps:
+
+### Step 1.
+
+If you have VSCode installed, you can install the 
 [codespace extension](https://marketplace.visualstudio.com/items?itemName=GitHub.codespaces). 
-After installing, you'll see the "remote explorer" icon on the left. 
-Click "Create Codespace" and type in "Becksteinlab/imd-workshop-2024" and select the "main" branch and a 2-core CPU.
 
-![alt text](.media/ide.png)
+### Step 2.
+
+After installing, you'll see the "remote explorer" icon on the left. Click this and select "Github codespaces"
+in the dropdown.
+
+![alt text](.media/ide_1.png)
+![alt text](.media/ide_1.png)
+
+### Step 3.
+
+Select the "+"
+
+![alt text](.media/ide_3.png)
+
+For the repository, enter "ljwoods2/imd-workshop-2024"
+For the branch, select "main"
+For the machine type, select "2 cores, 8GB RAM, 32 GB storage"
 
 After that, VSCode will automatically launch a new window which is executing in the codespace workshop environment.
 To troubleshoot, see the documentation [here](https://docs.github.com/en/codespaces/developing-in-a-codespace/using-github-codespaces-in-visual-studio-code).
 
-An extension is also available [for Pycharm](https://plugins.jetbrains.com/plugin/20060-github-codespaces).
+### Pycharm
+
+A codespace extension is also available for [Pycharm](https://plugins.jetbrains.com/plugin/20060-github-codespaces).
 
-## Setting up the activity notebook
+## iii. Local codespace in IDE (VSCode only) (slow, not recommend)
+
+You can also run the workshop activity locally if you have the [devcontainers VScode extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers)
+and [docker](https://docs.docker.com/engine/install/) installed. 
+
+After docker is installed & enabled and your user has been added to the docker group, run:
+```bash
+git clone https://github.com/ljwoods2/imd-workshop-2024.git
+code imd-workshop-2024
+```
+In VSCode, enter CTRL+SHIFT+P and type: "Dev Containers: Open Folder in Container..." and select
+the root of the cloned repo as the folder path. A new window will open which is executing 
+in the workshop activity codespace.
+
+# 2. Getting started with the activity
 
 First, open the "activity/activity.ipynb" jupyter notebook from this repo in your codespace environment.
 
@@ -34,5 +88,5 @@ in the upper right corner of the jupyter notebook. You may have to restart the k
 
 After that, follow the instruction in the notebook to run the simulation engines and your analysis code!
 
-
-
+![alt text](.media/codespace_1.png)
+![alt text](.media/codespace_2.png)

activity/run.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+mkdir -p sample_simulation
+cd sample_simulation
+# if [ ! -f sample_simulation/topol.tpr ]; then
+# echo "Running grompp"
+# gmx grompp -f imd.mdp -c start.gro -p topol.top -o >& grompp.out
+# fi
+echo "Starting mdrun"
+# modify gromacs execution string according to available resources
+# here we use 2 parallel threads
+gmx mdrun -v -nt 2 -imdwait -imdport 8889
+cd ..

gromacs-demos/distances/imd.mdp → activity/sample_simulation/imd.mdp

@@ -52,6 +52,6 @@ IMD-time                = yes
 IMD-box                 = yes
 IMD-coords              = yes
 IMD-unwrap              = yes
-IMD-forces              = no
-IMD-vels                = no
+IMD-forces              = yes
+IMD-vels                = yes
 IMD-energies            = no

activity/utils.py

@@ -0,0 +1,15 @@
+import matplotlib.pyplot as plt
+from IPython.display import display, clear_output
+
+
+def start_interactive_display():
+    plt.ion()  # Turn on interactive mode
+
+
+def stop_interactive_display():
+    plt.ioff()
+
+
+def update_display(obj):
+    clear_output(wait=True)
+    display(obj)