Topic: force fields and empirical potentials, classical molecular dynamics, statistical physics, melting and solidification
Download these recitation files and Lab 2 examples for octane and NaCl. Be prepared: LAMMPS is needed
Lecture slides (slides from 2021, slides from 2022)
Practice slides
Practice
Useful materials
- Lammps docs: unpad, ...
- Lammps tutorial: Gravelle, ...
- To create data file with crystal structure (.inp or .lmpdat) from xyz or other format use Openbabel (http://openbabel.org/docs/Installation/install.html).
- To visualize dump files use Ovito. To read dump output use Pizza python tools.
- Interatomic potentials: NIST, ...
- Universal interatomic ML potentials for Lammps https://github.com/MDIL-SNU/SevenNet
- Python scripts for LAMMPS: Pizza
- Conformer search: Avogadro (ver1, ver2, ver2_bin), mcsorkun
- Packmol to pack molecules in a box, e.g. water https://m3g.github.io/packmol/
- Moltemplate to construct complex systems https://www.moltemplate.org/
- Automated Topology Builder (ATB) and Repository https://atb.uq.edu.au/
- Force field generator for organic molecules https://traken.chem.yale.edu/ligpargen/
- Tutorials https://www.scm.com/doc/Tutorials/MolecularDynamicsAndMonteCarlo/index.html
Reading
- Jensen chapter 2 till 2.8; 13.1, 13.4, 14.1, 14.2, 14.3
- Cramer chapter 2, chapter 3 till 3.5
- Wikipedia for Interatomic potential and "See also" concepts
- LAMMPS Benchmark of Interatomic Potentials
- A F Voter, F Montalenti, T C Germann, Extending the Time Scale in Atomistic Simulation of Materials, Annu Rev Mater Res 32, 321 (2002)