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Computing

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Acknowledgement: This webpage was modifed based on the content from Prof. Piero Canepa's website.

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.

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.

tip

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

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​

Xcode tools (for Mac users)​

You will first need to download and install some basic compilers and libraries:

  • Xcode – This provides the gcc compiler. Install it from the App Store.
  • Xcode command line tools - After installing XCode, type the following in your terminal:
xcode-select --install

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.

iTerm2​

iTerm2 is a good looking terminal app for MacOS.

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.

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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 WSL). Please find more information here: homebrew. Packages such as wget and gfortran can be installed using homebrew.

Miniconda​

Conda is a package manager that makes it a lot easier to work with different python versions and packages. Download Miniconda from the webpage: https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/. After downloading the miniconda installer, install it using bash. There is a separate page for Miniconda.

Now, you should start a new terminal before proceeding.

Graphics and Design​

Adobe Creative Cloud​

Staff members have free access to Adobe Creative Cloud. We use Illustrator to create and modify vector images, e.g. plots.

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

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.

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. 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.

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