Tutorials

The direct problem solver, sim_trhepd_rheed, is based on the Reflection-High-Energy Electron Diffraction (RHEED, TRHEPD) analysis software developed by Prof. Takashi Hanada at Tohoku University.

In TRHEPD, when atomic coordinates are given, diffraction data is given as a simulation result. Therefore, we are dealing with the direct problem from atomic coordinates to diffraction data. On the other hand, in many cases, diffraction data is given experimentally, and the atomic coordinates are required to reproduce the experimental data. These are inverse problems to the above direct problems.

In ODAT-SE, the algorithms for solving the inverse problem can be selected as following algorithms:

• minsearch

  Nelder-Mead method.

• mapper_mpi

  Searching the entire search grid for a given parameter.

• bayes

  Bayesian optimization.

• exchange

  Sampling by the replica exchange Monte Carlo method.

• pamc

  Sampling by the population annealing Monte Carlo method.

In this tutorial, we will first introduce how to run the direct problem solver sim-trhepd-rheed. Then we will instruct how to run minsearch , mapper_mpi, bayes, exchange, and pamc. Hereinafter, we use odatse-STR program included in odatse-STR with input files in TOML format.

At the end of the tutorial, we will explain how to write your own main program for analyses.

• Direct Problem Solver
• Optimization by Nelder-Mead method
• Optimization by Grid search
• Optimization by Bayesian Optimization
• Optimization by replica exchange Monte Carlo method
• Optimization by population annealing Monte Carlo method
• Analyses by user programs