Problem Setup

A complete problem setup in NekRS requires a set of case files which are used for defining the geometry and physics of a problem. Details of how to setup a case in NekRS are outlined in the following sections:

• Case files
  • Parameter File (.par)
    • User Sections
    • General Parameters
    • OCCA Parameters
    • Problem Type Parameters
    • Mesh Parameters
    • Field Settings
      • Common Field Settings
    • CVODE Parameters
    • NekNek Parameters
  • User-Defined Host File (.udf)
    • OKL block
    • UDF_Setup0
    • UDF_LoadKernels
    • UDF_Setup
    • UDF_ExecuteStep
  • Legacy Nek5000 User File (.usr)
    • Legacy Data Interface
  • Mesh File (.re2)
  • NekNek Session File (.sess)
  • Trigger File (nekrs.upd)
  • NekRS Files & Extensions
• Boundary conditions
  • Basic boundary conditions
    • Zero-value BC
    • User-value BC
    • Internal / periodic BC
  • Special cases
    • NekNek coupling
    • Turbulent inflow
    • Velocity recycling
    • Stabilized outflow [Dong]
• Initial conditions
  • Specification in .udf File
  • Restarting from Field File(s)
  • Legacy useric in .usr File
• Physical properties
  • Constant Properties
  • Variable Properties
  • Conjugate Heat Transfer
• Models and Source Terms
  • Turbulence models
    • Large Eddy Simulation (LES)
      • High pass filter relaxation
    • RANS models
  • Low-Mach Compressible Model
  • Custom Source Terms
    • Momentum Equation
      • Implicit Linearized Momentum Source
    • Scalar Equations
• Mesh & Meshing
  • Runtime Setup
    • Coordinates Modification
    • Sidesets & Boundary Tags
    • Connectivity
  • Nek5000 Meshing Tools
    • genbox
    • n2to3
    • reatore2
  • Convert External Meshes
    • Gmsh (gmsh2nek)
    • Exodus II (exo2nek)
    • Tet-to-Hex
  • Moving Mesh
  • Conjugate Heat Transfer
  • h-Refinement
  • Miscellaneous Tips
• Postprocessing
  • Checkpointing & Visualization
    • Adding Custom Fields
    • Adding Custom Output File
    • Element Filter
  • Compute Derived Quantity
    • Array Operators
    • Spatial Derivatives
    • Spatial Integrals
    • Strain & Rotation Rate
    • Aero-Forces
    • Q criterion
  • Averaging
    • Time Averaging
    • Time Averaging (Legacy Mode)
    • Planar Averaging
  • ADIOS2 Format (.bp/)
  • Data Extraction
  • Insitu Visualization
  • Legacy Support (userchk)
• Running
  • Native Running
    • MPI launch scripts
  • Running on HPC Systems
  • Runtime Control with Signals
• Debugging Tips
  • Just-in-time Compilation
  • Verbose and Debug Mode
  • Check Device Arrays
  • Kernel in Serial Mode
  • Synchronization
  • Using gdb
    • Attaching to a Process
    • Attach Mode
    • Launch NekRS under gdb