luchem/KEMM30

KEMM30

Course files for KEMM30.

Running

Here are three ways you can run this:

1. Log into Google Colab and navigate to Github and search for luchem. Open the first notebook.
2. Run using the free My Binder server by clicking launch binder above.
3. On local Jupyter server. Download and unzip the code. Then launch a local server by typing jupyter lab or jupyter notebook on a command line (the adress field in any windows browser window is a command line).
   • if this fails with "can not find command" it means that anaconda is not in the search path. You can then either start a specified server/command line by starting anaconda command prompt or by starting a server and navigating to the folder with your notebooks
   • add the python script folder to your environment variables. This folder can be in different location but is usually easy to find. You search for the Anaconda3 folder either at: C:\Anaconda3, at C:\Programs\Anaconda3, C:\Users\my_name\Anaconda3,... or using the search function. At the university computers in Lund/chemistry the folder you need to add is c:\Anaconda3\Scripts. For windows there is a small bat file in the main directory called add_anaconda_scripts_to_path.bat that will do that for you (so simply double click on it).

Usage without environment

The first (lecture) notebooks only use the standard scientific packages and you can start working directly. only for the last notebook you will need an additional package that you can install from within any notebook with !pip install lmfit (and then restart the kernel to use it)

For the project notebooks you will need a number of extra packages. If you run from within any notebook this command you will install the in one go your installation folder (or the user folder in case of lacking rights)

!pip install lmfit ipympl lxml nglview ipywidgets brewer2mpl rdkit ffmpeg nmrglue.

Usage with environment

At Lund installing an environement is very slow. So we recommend to install only the minimum using conda and then install the rest via pip. To do this run the following commands:

conda env create -f environment_mini.yml
conda activate KEMM30
pip install lmfit ipympl lxml nglview ipywidgets brewer2mpl rdkit ffmpeg nmrglue
jupyter nbextension enable rubberband/main
jupyter nbextension enable exercise2/main
jupyter nbextension enable --py widgetsnbextension
jupyter-notebook

At home you can install all packages automatically. Install python via Miniconda or the full anaconda from Anaconda and then make sure all required packages are loaded by issuing the following terminal commands:

conda env create -f environment.yml
conda activate KEMM30
jupyter nbextension enable rubberband/main
jupyter nbextension enable exercise2/main
jupyter nbextension enable --py widgetsnbextension
jupyter-notebook

The before each usage you must "activate" the environment by typing activate KEMM30.