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2. Revision of Python and best practices. Coding Molecular Dynamics


Teaching: min
Exercises: min

Table of Content

  1. Brief Python overview
  2. Best practices
  3. Working on collaborative projects with Git and GitHub
  4. Constructing MD integrators

1. Python introduction

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My best referece is this site

Copy the example from


or from:

2. Best practices

This section can also be found here

I also recommend this reference

And a more complete documentation

Below I will summarize the list of most important Git commands. Note that the names in the UPPER CASE have to be substituted with the actual names specific to your work.

2.1. Working locally (development and info)

2.1.1. Initializing an empty repo

To create a brand-new Git repo with nothig else

git init

2.1.2. The status of your repo

To shows the current state of your project. This will show which files/directories are in unstaged/staged/commited/uncommited as well as the branch on which you are currently on

git status

2.1.3. The history of commits

To show the history of all commits and the development tree, highlights the sections

git log

A better version of this

git log --graph --pretty=format:'%C(magenta)%h%C(blue)%d%Creset %s %C(blue bold)- %an, %ar%Creset'


git log --decorate

2.1.4. Diff

To show the changes of the present state made w.r.t. the latest commit

git diff

2.1.5. Adding files and directories in the repo

To add the FILES-OR-DIRECTORIES to a so-called “staging” area (think of concert) - something you are working with at the moment. The FILES-OR-DIRECTORIES are the names of the files or directories to add. You can use an asterisk to match multiple files


2.1.6. Commiting

This will commit the files in the current “staging” area to the development history of the code - this way you save the most valuable and recent state of the project. You can also think of this as making a snapshot of the history of your code. The message should be informative and must describe clearly what changes have you made in the present version w.r.t. the older state of the code.

git commit -m "Some-message"

2.2. Working with branches

2.2.1. Find out the current branch

To show the list of available branches and highlight the active branch

git branch

or slightly more verbose

git branch -rv

2.2.2. Creating a new branch

To create a new branch called BRANCH-NAME. The present repository in its present state will be copied into the new branch.

git branch BRANCH-NAME

2.2.3. Deleting a branch

To delete a branch called BRANCH-NAME.

git branch -d BRANCH-NAME

2.2.4. Switching into a new branch

To switch into the existing BRANCH-NAME branch. This will bring up all the files at the stage of the last commit on that branch. Be careful - this may override your existing files, so you’d need to commit all the changes you have made to those files, otherwise all those changes will be lost. Also - this is a way to “recover” accidentally deleted files or “roll back” to the latest commited stage.

git checkout BRANCH-NAME

2.2.5. Merging

To merge the branch called BRANCH-NAME into your currently active branch

git merge BRANCH-NAME

2.2. Working with remotes

2.2.1. cloning

To clone another repository located at the REPOSITORY_URL (remote = e.g. GitHub repo) to your current repository (local computer)

git clone REPOSITORY_URL.git

2.2.2. Info on the remotes

To show the list of available remotes

git remote -v

2.2.3. Adding a remote

Add a “remote” you can pull from and push to. The REMOTE-NAME will be a short name of the remote, whereas REMOTE-URL is the actual link to the remote repository (ending with .git).

There are couple standard names of the remotes:

2.2.4. Renaming a remote

To rename the name of the already existing remote


2.2.5. Removing a remote

To remove the remote (a link to the remote repository, known to your git package) named REMOTE-NAME. This will remote the name of the remote from your list of available remotes. This doesn’t change the remote repository, of course

git remote rm REMOTE-NAME

2.2.6. Pulling

To get the latest version of the REMOTE-BRANCH branch on the remote repository REMOTE-NAME and merge it into you presently chosen branch.


2.2.7. Pushing

To update the branch REMOTE-BRANCH of a remote reporisotry you have (write) access to called REMOTE-NAME with the latests updates (commits) on the branch of a local repository you are currently in


2.3. Using GIT - practical exercies

git clone<your-account>/Cyber_Training_Workshop_2021.git
git remote add origin<your-account>/Cyber_Training_Workshop_2021.git
cd course_work
mkdir my_name
git add my_name
git commit -m "Added my stuff"
git push origin main

A typical session is:

git init
git status
git add
git status
git commit -m "Added my new code"
git status
git push origin master

A session with branching and external repo

git clone
git branch my_new_feature
git branch    
git add
git commit -m "fixed a bug"
git remote add origin
git push origin my_new_feature

A session with merging and upstream update

git remote add origin
git remote add upstream
git pull upstream master   
git branch my_new_feature
git branch    
git add
git commit -m "fixed a bug"
git status
git checkout master 
git merge my_new_feature
git push origin master

3. Working on collaborative projects with Git and GitHub

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4. Molecular Dynamics

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Key Points