Path optimization by a variational reaction coordinate method. I. Development of formalism and algorithms.
@article{Birkholz2015PathOB,
title={Path optimization by a variational reaction coordinate method. I. Development of formalism and algorithms.},
author={Adam B. Birkholz and H. Bernhard Schlegel},
journal={The Journal of chemical physics},
year={2015},
volume={143 24},
pages={
244101
}
}The development of algorithms to optimize reaction pathways between reactants and products is an active area of study. Existing algorithms typically describe the path as a discrete series of images (chain of states) which are moved downhill toward the path, using various reparameterization schemes, constraints, or fictitious forces to maintain a uniform description of the reaction path. The Variational Reaction Coordinate (VRC) method is a novel approach that finds the reaction path by…
8 Citations
Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation.
- Computer ScienceThe Journal of chemical physics
- 2016
Methods for incorporating redundant internal coordinates and potential energy surface interpolation into the VRC method are described, and the per-iteration cost of theVRC method is reduced while the high algorithmic efficiency is maintained.
Geodesic interpolation for reaction pathways.
- Computer ScienceThe Journal of chemical physics
- 2019
This work reformulate the problem of interpolation between endpoint geometries as a search for the geodesic curve on a Riemannian manifold and is able to generate paths from reactants to products which are remarkably close to the true minimum energy path.
Calculus of variations as a basic tool for modelling of reaction paths and localisation of stationary points on potential energy surfaces
- MathematicsMolecular Physics
- 2019
ABSTRACT The theory of calculus of variations is a mathematical tool which is widely used in different scientific areas in particular in physics and chemistry. This theory is strongly related with…
Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method
- ChemistryJ. Comput. Chem.
- 2017
The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching…
Expansive Quantum Mechanical Exploration of Chemical Reaction Paths.
- ChemistryAccounts of chemical research
- 2021
Explorative approaches are likely to replace the current state of the art in computational chemistry, because they reduce the human effort to be invested in reaction path elucidations, they are less prone to errors and bias-free, and they cover more extensive regions of the relevant configuration space.
Dynamics Sampling in Transition Pathway Space.
- PhysicsJournal of chemical theory and computation
- 2018
An enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, is developed to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways.
Simultaneously improving reaction coverage and computational cost in automated reaction prediction tasks
- ChemistryNature Computational Science
- 2021
It is shown that cost can be reduced and reaction coverage can be increased simultaneously by relatively straightforward modifications of the reaction enumeration, geometry initialization and transition state convergence algorithms that are common to many prediction methodologies.
Construction of elementary reaction paths of pure and mixed Argon-Xenon clusters : a parallel tempering based study
- Computer ScienceStructural Chemistry
- 2020
To understand the working principles of the parallel tempering method, distribution of structures found in different replicas has been analyzed, and insights have been given as to how parallel Tempering can be use effectively to handle this problem effectively.
References
SHOWING 1-10 OF 30 REFERENCES
The reaction path intrinsic reaction coordinate method and the Hamilton-Jacobi theory.
- Computer ScienceThe Journal of chemical physics
- 2005
The characterization of the local minima character of the intrinsic reaction coordinate is proved and leads to a numerical algorithm to find intrinsic reaction coordinates paths based on the successive minimizations of the Weierstrass E-function evaluated on a guess curve connecting the initial and final points of the desired path.
A combined method for determining reaction paths, minima, and transition state geometries
- Chemistry
- 1997
Mapping out a reaction mechanism involves optimizing the reactants and products, finding the transition state and following the reaction path connecting them. Transition states can be difficult to…
Applications of analytic and geometry concepts of the theory of Calculus of Variations to the Intrinsic Reaction Coordinate model
- Mathematics
- 2007
A mathematical analysis of several algorithms, for the integration of the differential equation associated to the Intrinsic Reaction Coordinate path, is performed. This analysis first shows that the…
Quadratic string method for determining the minimum-energy path based on multiobjective optimization.
- Computer ScienceThe Journal of chemical physics
- 2006
A new quadratic string method for finding the minimum-energy path that eliminates the need for predetermining such parameters as step size and spring constants, and is applicable to reactions with multiple barriers.
Chemical reaction paths and calculus of variations
- Computer Science
- 2008
The theoretical definitions of different forms of reaction pathways are analyzed in the light of the abstract theory of calculus of variations such as steepest descent from saddle point, the intrinsic reaction coordinate, Newton trajectory, variationally optimized reaction paths and others.
Reaction Path Optimization without NEB Springs or Interpolation Algorithms.
- PhysicsJournal of chemical theory and computation
- 2013
This letter describes a chain-of-states method that optimizes reaction paths under the sole constraint of equally spaced structures that requires no spring forces, interpolation algorithms, or other heuristics to control structure distribution.
Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications.
- Computer ScienceJournal of chemical theory and computation
- 2011
A new method for interpolating and reparameterizing nodes within the growing string method using the linear synchronous transit method of Halgren and Lipscomb is presented.
Optimization of equilibrium geometries and transition structures
- Chemistry
- 1982
A modified conjugate gradient algorithm for geometry optimization is outlined for use with ab initio MO methods. Since the computation time for analytical energy gradients is approximately the same…
Location of saddle points and minimum energy paths by a constrained simplex optimization procedure
- Chemistry
- 1979
Two methods are proposed, one for the location of saddle points and one for the calculation of steepest-descent paths on multidimensional surfaces. Both methods are based on a constrained simplex…
Single‐ended transition state finding with the growing string method
- Computer ScienceJ. Comput. Chem.
- 2015
A single‐ended growing string method (GSM) is introduced which allows for reaction path searches starting from a single structure and can be even more computationally efficient than the already rapid double‐ended method.






