FHDeX

User Guide

  • 1. Introduction
    • 1.1. What is fluctuating hydrodynamics?
    • 1.2. Solver families
    • 1.3. Relationship to AMReX
    • 1.4. Repository layout
  • 2. Getting Started
    • 2.1. Prerequisites
    • 2.2. Downloading the code
    • 2.3. Building exec/hydro
    • 2.4. Running a test problem
    • 2.5. Output
  • 3. Theory and Numerical Methods
    • 3.1. Fluctuating hydrodynamics
    • 3.2. Incompressible flow
    • 3.3. The Stokes solver
    • 3.4. Multispecies mixtures
    • 3.5. Compressible flow
    • 3.6. Chemistry and reaction–diffusion
    • 3.7. Particle methods
    • 3.8. Random numbers
    • 3.9. References
  • 4. Code Structure
    • 4.1. How an application is assembled
    • 4.2. Source libraries
      • 4.2.1. Infrastructure
      • 4.2.2. Physics solvers
      • 4.2.3. Particles and immersed boundaries
      • 4.2.4. Multiscale coupling
      • 4.2.5. Other directories
  • 5. Applications
    • 5.1. exec/hydro – incompressible fluctuating hydrodynamics
    • 5.2. exec/multispec – low-Mach multispecies mixtures
    • 5.3. exec/compressible_stag – compressible staggered-grid FHD
    • 5.4. exec/reactDiff – stochastic reaction–diffusion
    • 5.5. exec/DSMC – direct simulation Monte Carlo
    • 5.6. exec/immersedIons – Brownian ions in a fluctuating fluid
    • 5.7. Other applications
  • 6. Analysis and Output
    • 6.1. Plotfiles
    • 6.2. Structure factors
    • 6.3. Means, variances and correlations
    • 6.4. Checkpoint and restart
    • 6.5. Python tools
  • 7. Runtime Parameters
    • 7.1. common
    • 7.2. gmres
    • 7.3. multispec
    • 7.4. compressible
    • 7.5. chemistry
    • 7.6. reactDiff
    • 7.7. MFsurfchem
    • 7.8. dsmc
    • 7.9. surfchem_mui
  • 8. Developer Guide
    • 8.1. Adding a new application
    • 8.2. Adding a runtime parameter
    • 8.3. GPU support
    • 8.4. Single precision
    • 8.5. Style
    • 8.6. Documentation

Project

  • Contributing to This Documentation
    • Editing a page
    • Runtime parameters
    • Building locally
    • Publishing
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