Understanding advanced molecular simulation

CH-420

Setup your Computational Environment

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Overview

In the course, you will need to modify and run some simple Python scripts and plot the output. The Python scripts are Jupiter notebook format i.e., .ipynb. Therefore, Anaconda / Miniconda(light version)/ Mamba (C++ version) is required to construct your Python virtual environment. In this environment, you need to install the molsim python package (i.e., molsim-source-solutions.zip). Because the molsim package is based on C++ language,  you need to use the "apt install" command to install some packages on your computers. You can follow the tutorial (i.e., Installation.pdf) to set up your computer. After you finish the setup, you can run "test.ipynb" to check everything is fine. All files mentioned here can be found below.


For window user

If you use a Windows computer, you need to install WSL on your computer, which can create a Linux environment. In this environment, you can follow the Linux part in the tutorial to install everything.

Step 1. Enable WSL on Windows: 
    • Go to "Control Panel"
    • Navigate to "Program and Features"
    • Click on "Turn Windows features on or off"
    • Select "Windows Subsytem for Linux"
    • Restart your computer
    • (For older versions) If needed, turn on "Developer Mode": Start menu -> Settings -> search for "developer settings" -> Turn on "Developer Mode".
Step 2. Install Ubuntu from the Microsoft Store
    • Go to "Microsoft Store"
    • Go to "Apps" 
    • Search for "Ubuntu 20.04.5 LTS"
    • Select "Get"
If your Microsoft store also does not work, you have to download Ubuntu 18 and install it by hand. 

Step 3. Create a Linux account

Step 4. Follow the tutorial for Linux.


Visual Studio Code

VSCode is a lightweight but powerful source code editor that is available for Windows, macOS, and Linux. We recommend you use it to run the notebooks. We attach an introduction to VS code.