Computing

General Office Works

Microsoft 365

You should install Microsoft 365 by login to the portal using your NUS email and password. It includes Word, Excel, Powerpoint, Outlook, and Teams.

LaTex

LaTex is used for writing papers and reports. For MacOS, we use MacTex. Sometimes, we also use Overleaf for collaboration. If you write in LaTex locally, then you can use free softwares such as TexShop (come with MacTex), VSCode (need to be configured), TexStudio, and Lyx. Texifier is also good but you have to pay for it.

Install Latex on macOS

On macOS you can install MacTex using homebrew (see below for installation guide)

brew install --cask mactex

If you don’t want GUI, e.g. you want to use VSCode to write LaTex:

brew install --cask mactex-no-gui

There are other type setting system such as tectonic and you can find the installation guide here.

For reference, usually we export the references from Zotero library as a .bib file, then we edit it using JabRef and include it in LaTex document.

Free Overleaf Premium for NUS

NUS has the subscription to Overleaf Premium. If you use VSCode, you can use Copilot for LaTex writing.

Large language model

Please see generative-ai for more details.

Zotero

For reference management, we use Zotero extensively and exclusively to enable collaboration and sharing of references. It has a plugin for Word.

Obsidian

Obsidian is a powerful and free note taking app which uses Markdown language. Like VSCode, it also has lots of 3rd party extensions. For example, you can use copilot extension to utilize local large language model such as Ollama to help your writing.

Tip

Markdown cheat-sheet https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet

Programming

VSCode

VSCode is a code editor developed by Microsoft with lots of plugins/extensions. Extensions such as vscode-remote and python are essential for our code development. You can also use it to write markdown document and even LaTex.

Terminal Emulator

• Terminal from Apple
• Windows Terminal from Microsoft
• iTerm2 is a good looking terminal app for macOS. It offers more customizable settings.

Git and Github and authentication

Create a Github account if you do not have one. Then add your ssh key (in $HOME/.ssh/id_rsa.pub. If it does not exist, create one using the ssh-keygen command) to your Github account under settings. Follow the instructions on this page https://help.github.com/articles/set-up-git. We have a guidance for git. Please also look at the security for more details about the data security concerns in our group.

Tip

Student and staff can register the Github Education Pack by verifying your educational email addresses and get free access to features such as unlimited private repositories and Copilot. Copilot is very powerful.

Homebrew

Homebrew is a package manager for MacOS and Linux (or WSL2). Please find more information here: homebrew. Packages such as wget and gfortran can be installed using homebrew.

Python

You can use venv to create an virtual environment. You can find more information about venv here.

Another way is to useconda, a package manager that makes it a lot easier to work with different python versions and packages. Download conda from the webpage: https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/. After downloading the miniconda installer, install it using bash. Now, you should start a new terminal before proceeding.

Graphics and Design

Adobe Create Cloud

Staff members have free access to Adobe Create Cloud. We use Illustrator to create and modify vector images, e.g. plots. However, this is not available to students.

Alternative solution for students

However, this is not available to students. Alternative solution to Adobe Illustrator:

• Inkscape (free and open-sourced)
• Affinity Designer (paid but not very expensive).
• draw.io (free and online) for creating beautiful flowchart.

Blender

Blender is an open-sourced and free software to render realistic/artistic figures. However, its learning curve is steep. It also needs a very good hardware to run.

• Useful tutorial: https://www.youtube.com/@ryomizutagraphics

VESTA

VESTA is a free and powerful visualization tool visualize crystal structure models. It supports MacOS, Windows and Linux.

Simulation Software

VASP

You need the VASP psuedopotential files in order to generate VASP input files. These are provided in the toolsforgreatcare repo under resources. Download the psuedopotentials from our resources forlder.

Setup Pymatgen

Add a VASPPSPDIR to your .pmgrc.yaml, by running the following:

pmg config --add PMG_VASP_PSP_DIR ~/bin/cd
>dft_codes/VASP_PAW_POTENTIALS/VASP_PSP

Test that you have set it up correctly by typing:

python -c 'from pymatgen.io.vasp import Potcar; print(Potcar(["Li_sv", "O"]))'

There should be no errors. Otherwise, you have not done setup correctly.

Awesome Mac

Please have a look at the Awesome Mac project where they have a collection of good software for macOS

Acknowledgement

This webpage used content from Prof. Piero Canepa’s website.