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Onboarding and documentation for the BMD Lab.
- Want to run a calculation? Start with Using BMD Compute. Linux, SSH, SLURM and running VASP by hand are not prerequisites; VASP — fundamentals (under Computing foundations) is useful background.
- Calculation stuck or looks wrong? See BMD Agent, a command-line tool for understanding a calculation's progress or problems.
- What's happening under the hood? See Computing foundations below.
- Looking for specialist methods? See Research methods below.
The sections below are suggestions, not prerequisites. What you need depends on your project, and your supervisor may recommend a different route.
What BMD Compute runs and why.
| BMD Compute reference |
Language |
|---|---|
| What is BMD Compute? | Using BMD Compute |
| BMD Compute Workflows | English |
| BMD Compute INCARs | English |
| BMD Compute Advanced Options | English |
Often useful during an MSc, or whenever you want to understand and control what BMD Compute automates. Tutorials 1–11 build on one another and are best followed in order. VASP — fundamentals is also useful background for any BMD Compute user.
| Computing foundations |
Language |
|---|---|
| Linux | |
| Tutorial 01- Installing linux (for Windows machines) | English/Hebrew |
| Tutorial 02- Navigating with linux | English/Hebrew |
| Tutorial 03- Reading or editing files | English/Hebrew |
| Remote computing and POWER | |
| Tutorial 04- Connecting to other computers | English/Hebrew |
| Tutorial 05- Sending or receiving files | English/Hebrew |
| Tutorial 06- Working on the TAU supercomputer "POWER" | English |
| Tutorial 07- Options and outputs | English/Hebrew |
| Tutorial 08- Automating tasks | English/Hebrew |
| Python and pymatgen | |
| Tutorial 9- Installing Python on POWER and your PC | English |
| Tutorial 10- Using Python | English |
| Tutorial 11- Using the Python Materials Genomics (PyMatGen) toolkit | English |
| Running calculations yourself | |
| VASP — fundamentals (Vienna Ab initio Simulation Package) | English |
| Working with the Materials Project | English |
| Calculating Band Structures in VASP (manual HSE06 workflow) | English |
Often useful during a PhD or a specialised project. Pick the topics your research needs.
| Topic |
Page | Language |
|---|---|---|
| Disorder and alloys | The Special Quasirandom Structures (SQS) Method | English |
| Crystal structure prediction | Universal Structure Predictor: Evolutionary Xtallography (USPEX) | English/Hebrew |
| XtalOpt | English | |
| Scaling up | High-throughput computing on POWER | English |
| Research practice (any stage) | Publishing results | English |
| Funding opportunities | English |