Hybrid Monte Carlo

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Table of contents

General Introduction
1 Simulation method review
1.1 The need for large-scale simulation
1.1.1 Examples
1.1.2 State of the art
1.2 Molecular dynamics
1.2.1 Integrator
1.2.2 Long-range algorithms
1.2.3 Event-driven molecular dynamics
1.3 Traditional Monte Carlo
1.3.1 Properties of transition matrix
1.3.2 Tricks by modifying target distribution
1.3.3 Several reversible algorithms
1.4 Irreversible Monte Carlo
1.4.1 Non-lifting irreversible Monte Carlo
1.4.2 Lifting irreversible Monte Carlo
1.5 Models and measurements
1.5.1 Molecular models
1.5.2 Measurements
2 Event-chain Monte Carlo
2.1 Introduction
2.2 Basics
2.2.1 Lifted configurations
2.2.2 Factor event rate
2.2.3 Factorization
2.3 Fast implementation
2.3.1 Event-driven approach
2.3.2 Bounding potential
2.3.3 Sampling
2.3.4 Direction switching and restarts
3 Event-chain Monte Carlo for long-range interaction
3.1 Long-range system
3.2 Calculation of pairwise Coulomb interaction
3.2.1 Ewald summation
3.2.2 Line-charge method
3.2.3 Higher-order methods
3.2.4 Interpolation
3.2.5 Separate-image method
3.3 ECMC cell-veto algorithm
3.3.1 Description
3.3.2 Cell-veto event rate
3.3.3 Walker’s method
3.4 Coulomb bounding potential
3.5 Dipole factors
3.5.1 Two-dipole case
3.5.2 Homogeneous systems
3.5.3 Dipole lifting schemes
3.6 Numerical tests
3.6.1 Dipole system
3.6.2 SPC/Fw water model
4 JeLLyFysh architecture
4.1 Issues of application development
4.2 Features of JELLYFYSH-V1.0
4.3 Basic concepts
4.3.1 Event flow
4.3.2 Units
4.3.3 Global state and internal state
4.4 Essential modules
4.4.1 Mediator
4.4.2 Event handler
4.4.3 Activator
4.4.4 State handler
4.4.5 Scheduler
4.4.6 Input-output handler
4.5 Important tools
4.5.1 Globally used modules
4.5.2 Cells and cell occupancy
4.5.3 Initializer
4.5.4 Potentials, estimator
4.5.5 Lifting schemes
5 JELLYFYSH simulation
5.1 Event handlers of JELLYFYSH-V1.0
5.1.1 Event handler for two-body invertible potentials
5.1.2 Event handlers for non-invertible potentials
5.1.3 Cell-veto event handler
5.1.4 Event handlers for composite object motion
5.1.5 Sampling event handler and end-of-chain event handler .
5.1.6 Other helping event handlers
5.2 Factory
5.2.1 Running
5.2.2 Customization
5.3 Verifications
5.3.1 Coulomb atoms
5.3.2 Dipoles
5.3.3 SPC/Fw water
6 Realistic water system
6.1 Speeding up JELLYFYSH
6.1.1 Fast track for unconfirmed events
6.1.2 Other improvements
6.2 Coulomb event profiling
6.2.1 Charge-water estimator
6.2.2 Optimizing cell-veto events
6.2.3 Dipole factor vs. atomic factor
6.3 Water system benchmark
6.3.1 Chain state
6.3.2 Molecular translation
6.3.3 Discussions
7 Sequential Monte Carlo
7.1 Single-dipole system
7.1.1 Configuration
7.1.2 Sequential Monte Carlo method
7.1.3 Validation
7.2 Rotational dynamics
7.2.1 Zigzag and excursion
7.2.2 Large-time limit
7.3 Mixing of orientation
General Conclusion
Bibliography