Welcome to the SabIA Group How-To Examples

In this webpage, you will find a collection of “How-To” explanations compiled by the SabIA group from 2024 onwards. We hope this is useful!

The Simulations from Ab Initio Approaches (SabIA) group is hosted at the MPI for the Structure and Dynamics of Matter in Hamburg, Germany. Check out our webpage too, under this link.

Contributions come from all members of the group.

If you find this useful

Cite the webpage as (authors are members of the group, in alphabetical order):

Hannah Bertschi, Krystof Brezina, Jorge Castro, Paolo Lazzaroni, Zekun Lou, Jan-Niklas Mohr, Mariana Rossi, Shubham Sharma, Elia Stocco, George Trenins, “SabIA Group How-Tos”, URL: https://how-tos.readthedocs.io (2025)

Note

This project is under active development.

How To …

• Nudged Elastic Band (NEB) Calculations
  • ASE driver
• Creating AFM and STM images
  • STM simulations
  • AFM simulations
• Ehrenfest dynamics in FHI-aims
  • Set up the control.in file
  • Set up the geometry.in file
  • Created output
• Linear absorption spectra
  • Theory
  • Example of benzene
• Transition tube sampling
  • How to use TTS
  • Code documentation
  • References
• Remote Development on MPCDF Clusters
  • MPCDF SSH Configurations
  • VS Code + Remote Development Extension
  • Best Practices
• Normal and Phonon Modes
  • Normal Modes
• Phonopy in Python
  • Generate displaced structures
  • Calculate forces and then compute force constants
  • Plot and save phonon band structure
  • Phonopy using command line for FHI-aims
  • Phonon mode visualization
  • Rendering phonon modes with OVITO
• Time Correlation Functions
  • Cross Correlation
  • Infrared Spectrum
  • A common trick
• Dissipative Baths
  • Basics
  • Bath discretization
• GLE for a harmonic oscillator
  • wnle_cqq()
  • gle_cxx()
  • get_Aqp()
  • get_Dqp()
  • get_Cqp()
  • get_Cqp_canonical()
• Unit systems
  • SI
  • atomic
  • hartAng
  • kcalAfs
  • kcalAamu
  • eVAamu
  • Physical constants
  • Dimensions
  • Unit conversion
• Stochastic Thermostats
  • Test System
  • Langevin Themostat
  • Generalized Langevin Equation thermostat (GLE)
  • Stochastic velocity rescaling (SVR)
• Temperature spacing for replica exchange molecular dynamics simulations
  • Replica Exchange Molecular Dynamics (REMD)
  • Questions ?
• RPMD, TRPMD and CMD Simulations
  • Equilibrating the system
  • Starting the RPMD/TRPMD/CMD simulations
• Momentum distributions from open path PIMD
  • Background
  • i-pi inputs
  • Processing the simulation output
• Farthest Point Sampling (FPS)
  • How to perfrom FPS on a pool of data points?
  • Diving into the code
• 2D-VDOS correlation plots
  • Reading and projecting trajectories
  • Dynamic spectrum from VDOS blocks
  • 2D Correlations
• Visualizing Molecular Orbitals
  • Electronic structure calculation
  • Data visualization
• Simulating tip-enhanced Raman spectroscopy (TERS) images
  • Theory fundamentals
  • Implementation
  • Code documentation
  • References