FHDeX Documentation

FHDeX is a collection of solvers for fluctuating hydrodynamics (FHD) and related particle methods, built on the AMReX software framework. It simulates fluids at mesoscopic scales, where thermal fluctuations matter: incompressible and compressible flows, multispecies mixtures, chemical reactions, charged species, and fluids coupled to particles and immersed boundaries. All solvers run in parallel with MPI and on GPUs.

Source code	https://github.com/AMReX-FHD/FHDeX
AMReX documentation	https://amrex-codes.github.io/amrex/docs_html/

This guide explains how to build and run the FHDeX applications, how the source code is organised, and which runtime parameters they accept. FHDeX relies heavily on AMReX, so this guide does not repeat material that the AMReX documentation already covers. Instead it links to the relevant AMReX section wherever an AMReX concept (MultiFab, ParmParse, plotfiles, the GNU Make build system and so on) comes up.

New users should read Getting Started first and then the page for the application they want to run under Applications.

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
• 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