Object hierarchy

From Gerris

Contents 1 Introduction 2 Common objects 2.1 Solvers 2.2 Functions and macros 2.3 Variables 2.4 Parameters 2.5 Solid boundaries 2.6 General orthogonal coordinates 2.7 Topology 2.8 Boundary conditions 2.9 Initial mesh refinement 2.10 Initialisation of fields 2.11 Adaptive mesh refinement 2.12 Various events 2.13 Source terms 2.14 Outputs 3 Modules 3.1 Map 3.2 Terrain 3.3 Wavewatch 3.4 Okada 3.5 Tide 3.6 DF3 3.7 Particulates 3.7.1 Bubbles 3.8 Ode 3.9 Hypre 3.10 Electrohydro 3.10.1 See also 3.11 Skewsymmetric 3.12 FFT 3.13 Culvert 3.14 GfsView 3.15 Topics 4 Command-line programs

Introduction

This page describes all the objects which can be used in Gerris parameter files. The syntax of each object is given using a simple convention which expresses "inheritance" from the parent object. This is more simply explained using an example e.g. GfsOutputScalarSum. The syntax of this object is described as

[ GfsOutputScalar ]

which means that this object is a descendant of GfsOutputScalar. Following the link gives the syntax of GfsOutputScalar as

[ GfsOutput ] {
  v = [ GfsFunction ]
  maxlevel = 6
  min = -12.1
  max = 1e3
  box = -0.1,-0.1,0.1,0.1
}

which in turns means that this object is a descendant of GfsOutput but also takes the additional arguments described. Similarly GfsOutput is a descendent of GfsEvent and finally GfsEvent is a "root object class" which has no parent. Putting it all together, an example of use of GfsOutputScalarSum is

GfsOutputScalarSum { istep = 1 } sum { v = U }

where the red text is "inherited" from the GfsEvent great-grandparent, the blue text from the GfsOutput grandparent and the green text from the GfsOutputScalar parent.

Common objects

Note that the way the following list is indented reflects the inheritance hierarchy of each object.

Solvers

• GfsSimulation — Incompressible Euler and Navier-Stokes solver
  • GfsAxi — Cylindrical (axisymmetric) coordinates
  • GfsSimulationMoving — Integration of moving solid boundaries
  • GfsOcean
  • GfsAdvection
  • GfsPoisson
  • GfsWave — Spectral wave model
  • GfsRiver — Solves the Saint-Venant equations

Functions and macros

• GfsGlobal — Global functions

• GfsFunction — Numerical constants and expressions

• GfsDefine — Text macros

Variables

• GfsEvent
  • GfsVariable — Scalar fields
    • GfsVariableTracer — Advected scalar fields
      • GfsVariableTracerVOF — Volume-Of-Fluid advection
        • GfsVariableTracerVOFHeight — Volume-Of-Fluid advection (new implementation)
      • GfsVariableVOFConcentration — Concentration associated with a VOF phase
    • GfsVariableResidual
    • GfsVariableFiltered — Spatial filtering
    • GfsVariableFunction — Optimising function evaluations
      • GfsVariableStreamFunction — Maintaining a velocity field defined by a stream function
      • GfsVariablePoisson — Maintaining a scalar field solution of a Poisson equation
      • GfsVariableAverage
      • GfsVariableLaplacian — Laplacian of a function
    • GfsVariableCurvature — Curvature of an interface
      • GfsVariablePosition — Coordinates of a VOF interface
    • GfsVariableDistance — Signed distance to a VOF interface
    • GfsVariableBoolean — Boolean value consistent with adaptive refinement
    • GfsVariableAge — How old is this cell?
    • GfsHydrostaticPressure — Hydrostatic pressure integration
  • GfsConstant — Spatially-constant but time-dependent variables
    • GfsDischargeElevation — Elevation for a given discharge
    • GfsSpatialSum — Compute spatial sum of GfsFunction

Parameters

• GfsPhysicalParams — Tuning box size, gravity and density
• GfsProjectionParams — Tuning the Poisson solver
• GfsAdvectionParams — Tuning the advection schemes

Solid boundaries

• GfsSolid — Solid boundaries
  • GfsSolidMoving — Moving solid boundaries

• GfsSurfaceBc — Boundary conditions for diffusion and Poisson equations

General orthogonal coordinates

• GfsMetric — Analytical metrics
• GfsMetricLonLat
• GfsMetricCubed
• GfsMetricStretch — Anisotropic mesh stretching
• GfsMetricLaplace — Numerically-defined transformation
• GfsMap — Coordinates transformations
  • GfsMapTransform — Isometric coordinates transformations
  • GfsMapFunction

Topology

• GfsBox
• GfsGedge

Boundary conditions

• GfsBoundary — Default boundary conditions (symmetry)
  • GfsBoundaryInflowConstant — Constant inflow
  • GfsBoundaryOutflow — Free outflow/inflow
  • GfsBoundaryPeriodic
    • GfsBoundaryMpi

• GfsBc — Base class for boundary conditions on individual variables
  • GfsBcDirichlet — Dirichlet boundary condition (i.e. value)
  • GfsBcNeumann — Neumann boundary condition (i.e. value of the normal derivative)
  • GfsBcNavier — Navier slip/Robin boundary condition
  • GfsBcAngle — Contact angle boundary condition for interfaces
  • GfsBcFlather — "Flather" boundary conditions for barotropic flows
  • GfsBcSubcritical

Initial mesh refinement

• GfsRefine — Simple definition of the refinement levels
  • GfsRefineSolid — Refine embedded solid surfaces
  • GfsRefineSurface — Refine cells cut by a surface
    • GfsRefineDistance — Refine cells as a function of the distance from a surface
• GfsInitMask — "Masking out" part of the mesh

Initialisation of fields

• GfsEvent — Any action to be performed at a given time
  • GfsInit — Initialising variables
  • GfsInitFraction — Initialising volume fractions from interface shapes
  • GfsInitVorticity — Initialising a vorticity field
  • GfsInitWave — Initial wave spectrum for wave model

Adaptive mesh refinement

• GfsEvent
  • GfsAdapt — Base class for adaptive refinement criteria
    • GfsAdaptVorticity — Adapting cells depending on the local vorticity
    • GfsAdaptGradient — Adapting cells depending on the local gradient of a variable
      • GfsAdaptError — Adapting using an a posteriori error estimate
    • GfsAdaptFunction — Adapting cells depending on the value of a function
    • GfsAdaptThickness — Adapting cells according to the thickness of interfacial films

Various events

• GfsEvent
  • GfsEventSum — Time-integral of a variable or function
  • GfsEventHarmonic — Harmonic decomposition of a variable
  • GfsEventStop — Stopping when steady-state is reached
  • GfsEventScript — Executing a shell-script at given times
  • GfsEventBalance — Dynamic load-balancing
  • GfsRemoveDroplets — Controlling the topology of interfaces
  • GfsRemovePonds — Controlling the domain topology
  • GfsEventFilter — Exponential filtering of variables
  • GfsEventList — A List of events

Source terms

• GfsEvent
  • GfsSourceGeneric — Abstract class for source terms
    • GfsSourceScalar — Source terms for scalar variables
      • GfsSource — Source defined by a function
      • GfsSourceControl — Controlling the spatially-averaged value of a scalar
        • GfsSourceControlField — Controlling the value of a scalar averaged at a given spatial scale
        • GfsSourceFlux — Adding a flux on a given area or volume
      • GfsSourceDiffusion — Scalar diffusion
        • GfsSourceDiffusionExplicit — Time-explicit scalar diffusion
    • GfsSourceVelocity — Source terms for velocity
      • GfsSourceViscosity — Viscous terms
        • GfsSourceViscosityExplicit
      • GfsSourceFriction
      • GfsSourceCoriolis — Coriolis acceleration and linear friction
        • GfsSourceTension — Surface tension
        • GfsSourceTensionCSS
      • GfsSourceHydrostatic
    • GfsSourcePipe — Pipes and culverts models for GfsRiver

Outputs

• GfsEvent
  • GfsOutput — Writing simulation data
    • GfsOutputTime — Model time, timestep and computing times
    • GfsOutputProgress
    • GfsOutputProjectionStats
    • GfsOutputDiffusionStats
    • GfsOutputSolidStats
    • GfsOutputAdaptStats — Information about the mesh adaptation
    • GfsOutputTiming
    • GfsOutputBalance — Writing simulation size statistics
    • GfsOutputSolidForce — Forces and moments on the embedded solid boundaries
    • GfsOutputLocation — Writing the values of variables at specified locations
    • GfsOutputSimulation — Writing the whole simulation
    • GfsOutputBoundaries
    • GfsOutputParticle — Tracking Lagrangian particles
    • GfsOutputScalar — Generic output of scalar fields
      • GfsOutputScalarNorm — Computing the norms of a scalar field
      • GfsOutputScalarStats — Computing simple statistics for a scalar field
      • GfsOutputScalarSum — Computing the sum of a scalar field
      • GfsOutputScalarMaxima
      • GfsOutputScalarHistogram — Computing histograms
      • GfsOutputDropletSums — Computing sums for each droplet
      • GfsOutputErrorNorm — Computing differences to a reference solution
        • GfsOutputCorrelation
      • GfsOutputSquares
      • GfsOutputStreamline
      • GfsOutputPPM — Writing 2D images
      • GfsOutputGRD — Writing 2D ESRI raster files
    • GfsOutputObject — Calling the write method of a given object
    • GfsOutputSectionFlux — Writing the the fluxes of tracers through specified planar slices either due to advection and diffusion

Modules

Map

The Map module defines the objects used to perform cartographic projections within Gerris. As all modules, it is optional and depends on the availability of the PROJ.4 cartographic projections library on your system. The module is initialised in parameter files using

GModule map

and defines the GfsMapProjection object with the following inheritance hierarchy

• GfsMap
  • GfsMapProjection — Geographic transformations of model coordinates

Terrain

The Terrain module contains a set of objects which can be used to define solid boundaries using large Digital Terrain Model (DTM) databases. The databases are only limited in size by the amount of disk space available and include an Kd-tree spatial index for efficient retrieval of subsets of the original data. The module is initialised in parameter files using

GModule terrain

and defines the GfsRefineTerrain, GfsTerrain and GfsVariableTerrain objects with the following inheritance hierarchy

• GfsRefine
  • GfsRefineTerrain — Refines the mesh and creates the corresponding terrain model

• GfsSolid
  • GfsTerrain — Creates a solid boundary following a given terrain model

• GfsVariable
  • GfsVariableTerrain — Defines a variable containing the terrain height

Real terrains are often defined in a geographic coordinate system (e.g. longitude, latitude and height) and in practice this module is often combined with the Map module.

The terrain databases used by GfsRefineTerrain and GfsVariableTerrain need to be created in a pre-processing step using the xyz2kdt command-line utility.

Wavewatch

The Wavewatch module can be used only in GfsWave simulations. When this module is included, the GfsWave simulation will call the source terms routines (wind, wave breaking etc...) of the WaveWatch III spectral wave model. The module is initialised in parameter files using

GModule wavewatch

The wind field is defined by the U10 and V10 variables: the coordinates of the local wind vector (in m/sec and at a reference height of 10 m).

If the AS field is defined an "atmospheric stability correction" is applied to the wind field (see Section 2.3.5 of WaveWatch manual version 3.12). The AS field must be initialised with the air/sea temperature difference in degree Celsius.

Note that due to the license of recent versions of WaveWatch III, the wavewatch module is not provided in pre-compiled binaries of Gerris. It needs to be installed from source first.

Okada

The Okada module defines objects computing displacement solutions for the Okada fault model. The module is initialised in parameter files using

GModule okada

and defines the GfsInitOkada object with the following inheritance hierarchy

• GfsInit
  • GfsInitOkada — Initialises a field with the vertical displacement of an Okada fault model

Tide

DF3

The DF3 module allows to create a POV-Ray DF3 file mapping values of a variable from a simulation to a cube. Such output can be used to visualize a variable in 3D using POV-Ray. The module is initialised in parameter files using

GModule df3

and defines the GfsOutputPovrayDF3 object with the following inheritance hierarchy.

• GfsOutputScalar
  • GfsOutputPovrayDF3 — Writes a POV-Ray df3 file

Particulates

The particulate module defines (active) Lagrangian particles coupled with the flow. GfsParticulates respond to forces (typically exerted by the fluid) and can exert forces on the fluid in response.

The module is initialised in parameter files using

GModule particulates

The module defines the following objects (in bold):

• GfsEvent
  • GfsEventList
    • GfsParticleList — List of GfsParticulates acted on by forces
      • GfsFeedParticle — Injection of particles
      • GfsDropletToParticle — Conversion of tracers to particles
  • GfsParticle
    • GfsParticulate — A GfsParticle which responds to forces

• GfsParticleForce — A force acting on a GfsParticulate
  • GfsForceBuoy — The buoyancy force
  • GfsForceCoeff — Generic class for forces with coefficients
    • GfsForceLift — The lift force
    • GfsForceDrag — The drag force

• GfsVariable
  • GfsParticulateField — Average density of particles

Bubbles

The module is initialised in parameter files using

GModule particulates
GModule bubbles

The module defines the following objects (in bold):

• GfsParticulate
  • GfsBubble — Compressible gas bubbles
• GfsParticulateField
  • GfsBubbleFraction — Kernel-averaged volume fraction of bubbles
    • GfsBubbleFractionDt — Time-derivative of volume fraction of bubbles

Ode

The Open Dynamics Engine module.

Hypre

This module uses the Hypre library (the algebraic multigrid (AMG) solver in particular) instead of Gerris' native multigrid solver to solve Poisson equations. The module is initialised in parameter files using

GModule hypre

This will use default settings which can be changed using an optional parameter block.

Electrohydro

This module can be used to solve 2D/3D electrohydrodynamics problems. The module is initialised in parameter files using

GModule electrohydro

The module defines the following objects:

• GfsSimulation
  • GfsElectroHydro — Electrohydrodynamics solver
    • GfsElectroHydroAxi — Axisymmetric electrohydrodynamics solver
• GfsSourceVelocity
  • GfsSourceElectric — Electric volumetric forces
• GfsOutput
  • GfsOutputPotentialStats — Convergence statistics for the electric potential

See also

J. M. Lopez-Herrera, S. Popinet, M. A. Herrada - A charge-conservative approach for simulating electrohydrodynamic two-phase flows using Volume-Of-Fluid

Journal of Computational Physics 230:1939-1955, 2010

Bibtex

Skewsymmetric

This module can be used to solve 2D/3D problems using the skew-symmetric formulation proposed by Verstappen (JCP, 2007). The module is initialised in parameter files using

GModule skewsymmetric

The module defines the following object:

• GfsSimulation
  • GfsSkewSymmetric — Skew-symmetric solver

FFT

This module computes FFTs of given variables

GModule fft

The module defines the following object:

• GfsOutput
  • GfsOutputSpectra — FFT output

Culvert

Modelling the effect of culverts within the GfsRiver solver. The module is initialised in parameter files using

GModule culvert

The module defines the following object:

• GfsSourcePipe
  • GfsSourceCulvert — Culvert model based on Boyd, 1987

GfsView

This module can be used to create GfsView visualisations from within Gerris. This eliminates the need to couple Gerris with GfsView through pipes and more importantly this means that the simulation does not need to be copied from Gerris into GfsView, thus saving CPU and memory. This can also be used to efficiently create visualisations of large-scale parallel computations: the visualisation itself is created in parallel for individual subdomains. The module is initialised in parameter files using

GModule gfsview

The module defines the following objects:

• GfsOutput
  • GfsOutputView — Batch visualisation with GfsView

Topics

This module implements initial conditions for the simulation of landslide generated tsunamis. It is a directly inspired from the software TOPICS developped by Dr. P. Watts. The sources are that used in the version 1.2 of TOPICS, last modified in August 2009 by Dr. P. Watts and published under the GPL license.

GModule topics

The module defines the following objects:

• GfsInit
  • GfsInitSubmarineLandslide — Initial conditions for the simulation of submarine landslide generated tsunamis in GfsRiver.
  • GfsInitSubmarineSlump — Initial conditions for the simulation of submarine slumps.
  • GfsInitSubaerialLandslide — Initial conditions for the simulation of subaerial landslide generated tsunamis in GfsRiver.
  • GfsInitPyroclastic — Initial conditions for the simulation of pyroclastic flows.

• GfsOutput
  • GfsOutputInterfaceGrid — Outputs function that can be used to transport the characteristics of an interface generated in GfsSimulation 3D to GfsRiver.

Command-line programs

• gerris — The Gerris flow solver simulation engine
• gfsview-batch — Command-line description of GfsView (in batch and interactive mode)