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
  • Requirements
  • Simple installation
• Tutorial
  • 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
    • \(\mu\) and \(\Sigma\) Maps
  • Machine Learning potential
  • GPAO I
    • Previously on Muller Brown II
    • One Image Method
  • GPAO II
  • Alanine dipeptide
    • Inverse Projector
    • Trajectory writing
    • VASP calculator
    • Atomic model
    • Paths construction
• TAPS
  • Paths
    • Overall Structure
    • Load & Save
    • List of all Methods
      • Paths
        • Paths.add_image_data()
        • Paths.copy()
        • Paths.get_accelerations()
        • Paths.get_covariance()
        • Paths.get_distances()
        • Paths.get_forces()
        • Paths.get_gradient()
        • Paths.get_gradients()
        • Paths.get_hessian()
        • Paths.get_higest_energy_idx()
        • Paths.get_image_data()
        • Paths.get_kinetic_energies()
        • Paths.get_kinetic_energy_gradients()
        • Paths.get_lowest_confident_idx()
        • Paths.get_momentums()
        • Paths.get_potential()
        • Paths.get_potential_energies()
        • Paths.get_potential_energy()
        • Paths.get_potentials()
        • Paths.get_properties()
        • Paths.get_total_energy()
        • Paths.get_velocities()
        • Paths.save()
        • Paths.search()
        • Paths.to_pickle()
  • Cartesian
    • Array Order
    • Calculate Kinetic energy
    • Cartesian representation
    • Array like
    • List of all Methods
      • Cartesian
        • Cartesian.accelerations()
        • Cartesian.displacements()
        • Cartesian.velocities()
  • Model
    • Example
    • Model as a super class
      • Cache
    • Model as a subclass of Model
      • MullerBrown
        • List of Methods
          • MullerBrown
            • MullerBrown.calculate()
    • 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