# Persson Group Handbook

## Persson Group Handbook

- [Persson Group Handbook](https://materialsproject.gitbook.io/persson-group-handbook/master.md)
- [(Materials Project Handbook)](https://materialsproject.gitbook.io/persson-group-handbook/mp-handbook.md)
- [Before you Arrive](https://materialsproject.gitbook.io/persson-group-handbook/getting-started/before-you-arrive.md): A brief guide on things to do before your first day in the group.
- [After you Arrive](https://materialsproject.gitbook.io/persson-group-handbook/getting-started/after-you-arrive.md): Checklists for your first day and week in the group.
- [Coming Onsite](https://materialsproject.gitbook.io/persson-group-handbook/getting-started/coming-onsite.md): Instructions and tips for the first time you come onsite to LBL.
- [Getting a Computer](https://materialsproject.gitbook.io/persson-group-handbook/getting-started/getting-a-computer.md): Advice on purchasing laptop for your research.
- [Workspace Setup](https://materialsproject.gitbook.io/persson-group-handbook/getting-started/workspace-setup.md): A brief guide on how to set up your workspace for ergonomic comfort and optimal productivity.
- [Getting Settled](https://materialsproject.gitbook.io/persson-group-handbook/getting-started/getting-settled.md): Things to be aware of in the first months in your new position.
- [Meetings](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/meetings.md): Info about 1) mentoring, 2) big group meeting, 3) subgroups, and 4) group time.
- [Leave Time](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/leave-time.md)
- [Purchasing](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/purchasing.md)
- [Bear Buy](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/purchasing/bear-buy.md)
- [Travel](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/conference-travel.md): Going to a conference, DOE meeting, or other visit? Find more info below.
- [Writing/Submitting Your Paper](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/writing-submitting-your-paper.md): An overview of our group's recommendations regarding paper submission to scientific journals.
- [Group Agreements](https://materialsproject.gitbook.io/persson-group-handbook/group-policies/group-values.md)
- [Setting up your computer](https://materialsproject.gitbook.io/persson-group-handbook/computing/computer-setup.md): This page describes how to set up your new computer with the software our group members commonly use.
- [Software](https://materialsproject.gitbook.io/persson-group-handbook/computing/software.md): This page provides an overview of software used by our group. Detailed descriptions of simulation codes and other python codes (i.e., fireworks, atomate) are on following pages in this section.
- [High Performance Computing (HPC)](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing.md): This section and its subpages describe how to set up and run calculations on various computing resources that our group has access to, as well as how to backup your data.
- [NERSC (Perlmutter)](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing/nersc-perlmutter.md): This page describes setup for running calculations at NERSC's Perlmutter HPC.
- [Conda Environments](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing/nersc-perlmutter/conda-environments.md): Using Conda environments on NERSC systems
- [Frequently encountered blockers](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing/nersc-perlmutter/frequently-encountered-blockers.md): Find solutions to frequently encountered issues here
- [BRC (Savio)](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing/brc-savio.md): This page describes how to get setup at the Berkeley Research Computing center (BRC) on Savio.
- [LRC (Lawrencium)](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing/lrc-lawrencium.md): This page describes how to get set up to run calculations at LRC on the Lawrencium cluster.
- [NREL (Kestrel)](https://materialsproject.gitbook.io/persson-group-handbook/computing/high-performance-computing/nrel-kestrel.md): This page describes how to get setup at the National Renewable Energy Laboratory (NREL) on Kestrel.
- [Simulation Codes](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes.md)
- [VASP](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes/ab-initio.md)
- [Q-Chem](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes/ab-initio-1.md)
- [Gaussian](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes/ab-initio-2.md)
- [OpenMM](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes/molecular-dynamics.md)
- [LAMMPS](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes/molecular-dynamics-1.md)
- [GROMACS](https://materialsproject.gitbook.io/persson-group-handbook/computing/simulation-codes/molecular-dynamics-2.md)
- [Fireworks & Atomate](https://materialsproject.gitbook.io/persson-group-handbook/computing/atomate-setup.md): This page describes the setup procedure for using fireworks and atomate on high performance computing systems. These instructions are intended for first time users.
- [Setup](https://materialsproject.gitbook.io/persson-group-handbook/computing/atomate-setup/setup.md): This page describes how to set up fireworks and atomate.
- [Fireworks: Advanced Usage](https://materialsproject.gitbook.io/persson-group-handbook/computing/atomate-setup/atomate-setup.md): This page builds upon the Fireworks + Atomate Setup page to provide practical tips and advice for more advanced use cases which may be helpful once your start running a larger number of calculations.
- [Machine Learning (ML)](https://materialsproject.gitbook.io/persson-group-handbook/computing/machine-learning-ml.md): Set up a conda environment for machine learning.
- [Group Meeting Schedule](https://materialsproject.gitbook.io/persson-group-handbook/group-resources/group-meeting-schedule.md)
- [Group Jobs (Summer 2026)](https://materialsproject.gitbook.io/persson-group-handbook/group-resources/group-jobs.md): Last updated:07/21/2026
- [Physical Resources (printers, etc.)](https://materialsproject.gitbook.io/persson-group-handbook/group-resources/group-resources.md): Resources for the group at our LBL office in B33.
- [Undergraduate Research Mentoring](https://materialsproject.gitbook.io/persson-group-handbook/group-resources/undergraduate-research-mentoring.md)
- [Contributing to Handbook](https://materialsproject.gitbook.io/persson-group-handbook/group-resources/contributing.md)
- [Group Roster](https://materialsproject.gitbook.io/persson-group-handbook/group-resources/group-roster.md)
- [Tutorials and Helpful Links](https://materialsproject.gitbook.io/persson-group-handbook/health-and-well-being/tutorials-and-helpful-links.md)
- [Group Member Expertise](https://materialsproject.gitbook.io/persson-group-handbook/health-and-well-being/group-member-expertise.md): This page contains information regarding group members' research interests and expertise. This can include what one works on, which packages/techniques one is familiar with, etc.
- [Professional development](https://materialsproject.gitbook.io/persson-group-handbook/health-and-well-being/professional-development.md): \[WIP] Collection of professional development opportunities for group members in the field of sustainable materials science and beyond. This is meant to be a living document, please add to it!
- [Health and wellbeing](https://materialsproject.gitbook.io/persson-group-handbook/health-and-well-being/resources.md)
- [UAW 4811 Contracts](https://materialsproject.gitbook.io/persson-group-handbook/finishing-your-phd/uaw-4811-contracts.md): The information here is an overview of major points in our GSI and GSR contracts; it is not fully comprehensive but covers many aspects of the most common issues you might face in your workplace.
- [Research Credits (298/299)](https://materialsproject.gitbook.io/persson-group-handbook/finishing-your-phd/research-credits-298-299.md): Resources and requirements specific to graduate students taking research credit courses.
- [Course Recommendations](https://materialsproject.gitbook.io/persson-group-handbook/finishing-your-phd/course-recommendations.md)
- [How to Qual (MSE)](https://materialsproject.gitbook.io/persson-group-handbook/finishing-your-phd/how-to-qual.md): This page describes the process for taking the Berkeley MSE department's Qualifying Exam (QE) for the PhD program, which is a ~3hr oral presentation and Q\&A on your dissertation topic.
- [How to Graduate](https://materialsproject.gitbook.io/persson-group-handbook/finishing-your-phd/how-to-graduate.md): A guide to getting to the PhinisheD line in the Persson group! Remember that everyone's academic and research path is unique and there are no set timelines for finishing a PhD.