Contents

 Executive Summary
1 Introduction
 1.1 Incompressible Navier–Stokes equations
 1.2 Non-dimensional Navier-Stokes
 1.3 Energy equation
 1.4 Non-dimensional energy/passive scalar equation
 1.5 Passive scalars
 1.6 Unsteady Stokes
 1.7 Steady Stokes
 1.8 Linearized Equations
 1.9 Steady conduction
 1.10 Low-Mach Navier-Stokes
 1.11 Incompressible MHD equations
 1.12 Adaptive Lagrangian-Eulerian (ALE)
2 Quick start
 2.1 The Git Repositories
  2.1.1 Downloading the source code
  2.1.2 Downloading the example problems
  2.1.3 Tools and scripts
 2.2 The SVN Repository
  2.2.1 Downloading the source code and examples
  2.2.2 Tools and scripts
 2.3 A Worked Example
 2.4 Viewing the First 2D Example
  2.4.1 Modifying the First Example
3 User files
 3.1 Case set-up .usr
  3.1.1 Contents of .usr file
 3.2 Problem size file SIZE
  3.2.1 Memory Requirements
 3.3 Geometry and Parameters file .rea
  3.3.1 Parameters
 3.4 Data Layout
4 Geometry
 4.1 Setting up the geometry
  4.1.1 Uniformly Distributed Mesh
  4.1.2 Graded Mesh
  4.1.3 User-Specified Distribution
  4.1.4 Mesh Modification in Nek5000
  4.1.5 Cylindrical/Cartesian-transition Annuli
 4.2 Extrusion/Mirroring
  4.2.1 Building Extruded Meshes with n2to3
 4.3 Moving Geometry
 4.4 Boundary and initial conditions
  4.4.1 Boundary Conditions
  4.4.2 Fluid Velocity
  4.4.3 Internal Boundary Conditions
  4.4.4 Initial Conditions
 4.5 Mesh Partioning for Parallel Computing
5 Performing large scale simulations in Nek5000
 5.1 Large scale simulations
 5.2 Parallelism in Nek5000
6 Routines of interest
 6.1 Naming conventions
 6.2 Subroutines
 6.3 Functions
 6.4 An example of specifying surface normals in the .usr file
 6.5 Spectral Interpolation Tool
 6.6 Grid to Grid Interpolation
 6.7 Lagrangian Particle Tracking
7 Appendix
 7.1 Appendix A. Extensive list of parameters .rea file
  7.1.1 Parameters
  7.1.2 Available Parameters
  7.1.3 Available Logical Switches
  7.1.4 Logical switches
 7.2 Appendix B. Extensive list of parameters SIZE file
 7.3 Appendix C. The fld file format
  7.3.1 Header
  7.3.2 Data

Executive Summary

Abstract here.