Hamiltonian Computational Chemistry: Geometrical Structures in Chemical Dynamics and Kinetics
Abstract
:1. Introduction
2. Geometrical Structures in Chemical Dynamics
2.1. Canonical Classical Mechanics
2.1.1. Manifolds and Maps
2.1.2. Equations of Motion
- is bilinear,
- antisymmetric,
- , and
- (Jacobi identity).
2.1.3. Integrable Hamiltonian Systems
2.1.4. Complexification of Classical Hamilton’s Equations
2.1.5. Jacobi Fields and Variational Equations
2.2. Geometrical Quantum Mechanics
2.2.1. Manifolds and Maps
2.2.2. Projective Hilbert Space
2.2.3. Realification of Hilbert Space and Kähler Manifolds
2.2.4. Equations of Motion
2.2.5. Quantum Systems as Totally Integrable Hamiltonian Systems
3. Hamiltonian Chemical Thermodynamics
3.1. Manifolds and Maps
3.2. Equations of Motion
3.2.1. Contact Equations of Motion
3.2.2. Riemannian Metric on Lagrangian Submanifold
3.3. Embedding Systems in Homogeneous Media
3.4. Chemical Kinetics
3.4.1. Thermodynamics of Chemical Reactions
3.4.2. Thermodynamic Hamiltonian in Massieu-Gibbs Representation
4. Numerical Implementations
4.1. High-Order Finite-Difference and Pseudospectral Methods
4.2. The Hénon–Heiles Model
4.2.1. A Classical Time-Dependent Hénon–Heiles System
4.2.2. The Quantum Hénon–Heiles System
4.2.3. Energy Dissipation of Hénon–Heiles System in Homogeneous Media
5. Conclusions
Funding
Data Availability Statement
Conflicts of Interest
Abbreviations
FD | Finite Difference |
PS | Pseudospectral |
DOF | degrees of freedom |
TEPS | Thermodynamic Extended Phase Space |
TEPSS | Thermodynamic Extended Physical State Submanifold |
TCS | Thermodynamic Contact Space |
PTS | Physical Thermodynamic Submanifold |
ODEs | Ordinary Differential Equations |
HNN | Hamiltonian neural networks |
PNN | Physics neural networks |
nD | dimensional |
Appendix A
Appendix A.1. Proof of Equation (89)
Appendix A.2. Proof of Equation (90)
Appendix A.3. Proof of Equation (152)
Appendix A.4. Tables
Appendix A.4.1. Projection Maps between Thermodynamic Extended Phase Space and Thermodynamic Contact Space
Appendix A.4.2. Thermodynamic Manifolds in Entropy Representation
Manifold | |||
Coordinates | |||
Momenta | |||
form | |||
form | |||
PTS | (TEPSS) | ||
Metric |
Appendix A.4.3. Thermodynamic Manifolds in Energy Representation
Manifold | |||
Coordinates | |||
Momenta | |||
form | |||
form | |||
PTS | (TEPSS) | ||
Metric | |||
Appendix A.5. Hamiltonian Chemical Kinetics: A Simple Chemical Kinetic Example: Consecutive First-Order Elementary Reactions
Appendix A.5.1. Discussion
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Farantos, S.C. Hamiltonian Computational Chemistry: Geometrical Structures in Chemical Dynamics and Kinetics. Entropy 2024, 26, 399. https://doi.org/10.3390/e26050399
Farantos SC. Hamiltonian Computational Chemistry: Geometrical Structures in Chemical Dynamics and Kinetics. Entropy. 2024; 26(5):399. https://doi.org/10.3390/e26050399
Chicago/Turabian StyleFarantos, Stavros C. 2024. "Hamiltonian Computational Chemistry: Geometrical Structures in Chemical Dynamics and Kinetics" Entropy 26, no. 5: 399. https://doi.org/10.3390/e26050399