Totally Accurate Pathway Simulator

Totally Accurate Pathway Simulator (TAPS) is a pathway simulation tool contains coordinate representation tools, projection tools, model for potential energy surface, modularized pathway optimization tools, database for machine learning, data driven potential energy surface etc.

Contents

• About
• Install
• Tutorial
  • Muller Brown potential
  • Müller Brown I
    • Construction of a pathway
    • Potential calculation
    • Visualization
    • Direct Action Optimization
  • Müller Brown II
    • Previously on Müller Brown I
    • Müller Brown II
    • Pathway optimization on the sine components.
    • Results in the previous example, Müller Brown I
    • Database construction
    • Gaussian Potential
    • Pathway optimization perfomed
  • GPAO I
    • Pathway optimization on the projected space.
    • Iteration reduced from 1100 to
    • Database construction
    • Gaussian Potential
    • Pathway optimization perfomed
  • Gaussian process action optimization
    • Muller Brown GPAO
    • Iteration reduced from 1100 to
    • Database construction
    • Gaussian Potential
    • Pathway optimization perfomed
  • Alanine dipeptide
    • Inverse Projector
    • Trajectory writing
    • VASP calculator
    • Atomic model
    • Paths construction
    • Effective mass
    • VASP Alanine dipeptide with velocity applied
• TAPS
  • Paths
    • Overall Structure
    • Load & Save
    • List of all Methods
  • Cartesian
    • Array Order
    • Calculate Kinetic energy
    • Cartesian representation
    • Array like
    • List of all Methods
  • Model
    • Example
    • Model as a super class
      • Cache
    • Model as a subclass of Model
      • MullerBrown
        • List of Methods
      • AtomicModel
    • List of all Methods
  • Path finder
    • Nudged Elastic Band
    • Direct Action Optimizer
    • Gaussian process assisted action optimizer

Indices and tables

• Index

• Module Index

• Search Page