Module 2

2.1.1 Berkeley Overview of Computational Nanoscience (on nanoHUB) (From Schiller)

The Berkeley Overview of Computational Nanoscience on introduces a broad range of computational tools in a self-contained nanoHUB tool. It includes introductions to classical, quantum, and statistical methods and provides easy-to-understand interfaces to codes including molecular dynamics, Monte Carlo methods, density functional theory, and quantum chemistry. The tool can be used in conjunction with the Berkeley Computational Nanoscience course lectures, also available on the nanoHUB.

2.1.2 From Atoms to Materials: Predictive Theory and Simulations (on nanoHUB) (From Schiller)

This web-based course was developed by Purdue University Professor of Materials Engineering Alejandro Strachan. It develops a unified framework for understanding essential physics that govern materials at atomic scales and relate these processes to the macroscopic world. The course is suitable for beginning graduate students. The course can be taken online at https://nanohub.org/courses/FATM.

2.1.3 CECAM-MARVEL Classics in molecular and materials modeling (From Kuksenok)

Lectures dedicated to pioneering contributions in molecular and materials simulations.

Level: intermediate/ advanced (graduate students)

format: video recording of lectures, time: 2-3 hr per lecture/ Q&A

Video Link

2.1.4 Molecular Chemical Engineering (From Getman)

Courses that I’ve developed on modeling are here: https://lor.instructure.com/search?q=rachel%20getman. Choose the ones about Molecular Chemical Engineering (three of them).

2.1.5 Software Carpentry (From Schiller)

The Software Carpentry, now part of The Carpentries, teaches basic lab skills for scientific research computing. The workshop lessons are developed collaboratively on Github. The Software Carpentry workshops cover the following core topics: the Unix shell, version control with Git, and a programming language (Python or R). Curricula for these lessons are available in English and Spanish (select lessons only) online at https://software-carpentry.org/lessons/. The materials are suitable for undergraduate and graduate students.

2.1.6 Getting Started in Computational Chemistry (From Shields) – this is the basics

Level: beginners (UG/graduate students)

Format: online tutorials at own pace on the very basics (terminal) https://education.molssi.org/getting-started-computational-chemistry/

2.1.7 Quantum Mechanics Tools (From Shields) – the basics of QM

Level: beginners/intermediates (UG/graduate students)

Format: Online tutorials at own pace cover Geometry Optimization, Potential Energy Surfaces, Basis Set Convergence, Redox Potentials, and Version control and making changes in existing codes. https://education.molssi.org/qm-tools/

2.1.8 Molecular Mechanics Tools (From Shields) – the basics of MM

Level: beginners/intermediates (UG/graduate students)

Format: Online tutorials at own pace cover MD simulation of Alkanes, MD simulation of a Protein, sharing and revising code with Git and GitHub. https://education.molssi.org/mm-tools/

2.1.9 LAMMPS manual and tutorials (From Kuksenok)

Level: beginners to advanced (UG/graduate students)

Format: tutorials are taken at own pace

LAMMPS manual https://docs.lammps.org/

LAMMPS tutorial for beginners/intermediate (S. Plimpton): Link

Modifying LAMMPS: Link (advanced level only)

2.1.10 Molecular Modeling and Simulation with LAMMPS (From Schiller)

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular dynamics program from Sandia National Laboratories that is widely used for atomistic and coarse-grained particle-based simulations. The code is open-source, and the program is available on many computing systems. The LAMMPS website has links to tutorial materials the LAMMPS developers have used. Undergraduate and graduate students intending to use LAMMPS will benefit from completing the set of tutorials created by the Center for Advanced Vehicular Systems (CAVS) group at Mississippi State University.