GAP Documentation

Contents:

  • Introduction
    • Overview
    • First exmaple
  • Installation
    • Precompiled Containers
    • Compilation Instructions
      • Quick start
      • Step by step
      • Installing the Jupyter notebook
    • Custom settings
    • Common Problems
      • Permission errors when installing
      • Installing on Mac OS X with macports
      • RuntimeError when importing
      • ImportError when importing
      • Possible problems installing atomeye module
      • Error compiling IPModel_GAP
      • Warning about quippy.castep when importing quippy
      • Internal compiler error with ifort
      • Linking error on Mac OS X
      • Segmentation Faults with OpenBLAS
  • Learning GAP
    • Gaussian Approximation Potentials
    • Additional helper
  • Descriptors
    • List of descriptors
  • Using Potentials
    • QUIP
      • Potentials implemented in QUIP
      • Performing calculations
      • Creating a Potential
    • GAP
      • XML functions
  • Tutorials
    • Using Quippy to compute descriptors of atomic environments
      • A simple descriptor: pairwise distances
      • A many-body descriptor: SOAP
      • General_monomer example: benzene
    • How to train a GAP model from scratch
      • steps
      • here we will fit twice, to see the difference between a 2b-only and a 2b+3b fit
      • generating data only with ASE, using the EMT calculator
      • get e0 for H and O - energies of the isolated atoms
      • separate the dataset into a training and a validation set
      • train our GAP model from the command line
      • notice, that the script is running in parallel, using all 8 cores of the current machine
      • use the potential with QUIP on trani.xyz and validate.xyz
      • make simple plots of the energies and forces on the EMT and GAP datas
      • train our GAP_3b model from the command line
      • both training and quip takes significantly more time than the last one!!!
      • use the potential with QUIP on trani.xyz and validate.xyz
      • look at the outputs - clear improvement
GAP Documentation
  • Docs »
  • Tutorials
  • View page source

TutorialsΒΆ

The following tutorials are currently available:

  • Using Quippy to compute descriptors of atomic environments
    • A simple descriptor: pairwise distances
    • A many-body descriptor: SOAP
    • General_monomer example: benzene
  • How to train a GAP model from scratch
    • steps
    • here we will fit twice, to see the difference between a 2b-only and a 2b+3b fit
    • generating data only with ASE, using the EMT calculator
    • get e0 for H and O - energies of the isolated atoms
    • separate the dataset into a training and a validation set
    • train our GAP model from the command line
    • notice, that the script is running in parallel, using all 8 cores of the current machine
    • use the potential with QUIP on trani.xyz and validate.xyz
    • make simple plots of the energies and forces on the EMT and GAP datas
    • train our GAP_3b model from the command line
    • both training and quip takes significantly more time than the last one!!!
    • use the potential with QUIP on trani.xyz and validate.xyz
    • look at the outputs - clear improvement
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