Nek5000 User Documentation

Paul Fischer, James Lottes, Stefan Kerkemeier, Oana Marin, Katherine Heisey, Aleks Obabko, Elia Merzari, Yulia Peet

August 25, 2016
Contents
 Executive Summary
 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
 2.2 The SVN Repository
 2.3 A Worked Example
 2.4 Viewing the First 2D Example
3 User files
 3.1 Case set-up .usr
 3.2 Problem size file SIZE
 3.3 Geometry and Parameters file .rea
 3.4 Data Layout
4 Geometry
 4.1 Setting up the geometry
 4.2 Extrusion/Mirroring
 4.3 Moving Geometry
 4.4 Boundary and 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
 7.2 Appendix B. Extensive list of parameters SIZE file
 7.3 Appendix C. The fld file format
Bibliography