Overview

Teaching: min
Exercises: min

Questions

Objectives

Table of Content

1. Constructing MD integrators
2. Introduction to Libra

1. Constructing MD integrators

Back to TOC

1.1. Presentation

1.2. Coding Exercises

• Euler MD
• Leap-frog (coordinate Verlet)
• Velocity verlet

1.3. Libra exmaples

• Runge-Kutta for classical MD

• Lattice MD

  cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra/demos_from_libra_code/notebooks/Example4_md/Example1_lattice

• Atomistic MD

  cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra/demos_from_libra_code/tests/test_md

2. Introduction to Libra

Back to TOC

2.1. Presentation

2.2. Get your copy of tutorials

git clone https://github.com/compchem-cybertraining/Tutorials_Libra.git

or

cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra

2.3. Examples

• Discuss data types

• Runge-Kutta for quantum dynamics

• Molecular integrals

   cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra/demos_from_libra_code/tests/test_libint2
  

• Built-in Electronic structure calculations:

   cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra/Tutorials_Libra/5_electronic_structure/1_eht/1_compact1
  

• Kinetic MC example to model diffusion

   cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra/demos_from_libra_code/notebooks/Example5_diffusion
  

• random number sampling - section 7.4

• crystal builder - section 12.1 (may be useful for the nano-qmflows/CAT tutorials)

• Molecular rotation

   cd /projects/academic/cyberwksp21/Instructors_material/alexeyak/libra/demos_from_libra_code/tests/example_8_rotation
  

  Exercise: can you combine examples showing py3Dmol, imageio, and the current rotation script to produce the animateg gifs of the rotation?

• define model Hamiltonians and plot properties, HDF5, exercises `
• Atomistic interfaces: Psi4 and DFTB+: LiH at CCSD/sto-3G

Key Points