Commit 1b37b869 authored by Thomas Fetzer's avatar Thomas Fetzer
Browse files

[doxygen]

The parameters are now listed using the mark down support of doxygen for
creating tables. The parameter spreadsheet and html are now superfluous.
The script for checking new/old parameters has been updated.

reviewed by bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15394 2fb0f335-1f38-0410-981e-8018bf24f1b0
parent d66fc0e6
......@@ -40,39 +40,44 @@ sed -i 's/,/, /g' new_parameters.csv
sort -u new_parameters.csv -o new_parameters.csv
# remove lines containing no parameter names
sed -i '/, , /d' new_parameters.csv
#adapt to doxygen format
sed -i 's/^/ * | /' new_parameters.csv
sed -i 's/, / | /g' new_parameters.csv
# 2. obtain a list old_parameters.csv of all old parameters
# convert the spreadsheet to csv
if ! unoconv --format=csv -e FilterOptions=44,34,0,3,1/1/2/1/3/1/4/9/5/9 -o tmp.csv doc/doxygen/extradoc/parameters.ods; then
echo "Failed to convert parameters.ods. Be sure that it is not opened somewhere."
rm -f new_parameters.csv tmp.csv
exit 1
fi
unoconv --format=csv -i FilterOptions=44,34,0,3,1/1/2/1/3/1/4/9/5/9 -o old_parameters.csv tmp.csv
rm tmp.csv
cp -v doc/doxygen/extradoc/parameterlist.txt old_parameters.csv
# truncate the test from file
sed -i -e '1,12d' old_parameters.csv
# remove lines containing no parameter names
sed -i '/,,/d' old_parameters.csv
sed -i '/| | | /d' old_parameters.csv
# remove bold format for parameter groups
sed -i 's/ \\b / /g' old_parameters.csv
# loop over all lines, add group name if necessary
word=""
while read line; do
word=$(echo "$line" | awk '{print $1;}')
word=$(echo "$line" | awk '{print $3;}')
#echo "$word"
firstletter=$(echo $word | head -c 1)
if [ $firstletter != "," ]; then
if [ "$firstletter" != "|" ]; then
group=$word
fi
if [ $group = "" ]; then
echo "No group found in line $line. Abort."
if [ "$group" = "" ]; then
echo "No group found in line $line."
fi
linewithoutgroup=$(echo "$line" | cut -d " " -f2-)
echo "$group $linewithoutgroup" >>tmp.csv
done <old_parameters.csv
mv tmp.csv old_parameters.csv
# format in the same way as new_parameters.csv
sed -i 's/ //g' old_parameters.csv
sed -i 's/,/, /g' old_parameters.csv
sort -u old_parameters.csv -o old_parameters.csv
# truncate the default and description information
cat old_parameters.csv | while read line
do
TEMP=`echo "${line% |*}"`
echo "${TEMP% |*}" >> tmp.csv
done
mv tmp.csv old_parameters.csv
#adapt to doxygen format
sed -i 's/| | /| /g' old_parameters.csv
sed -i 's/^/ * | /' old_parameters.csv
# 3. compare lists of old and new parameters
# treat additions
......@@ -81,8 +86,10 @@ if [[ -s added.csv ]]; then
echo ""
echo "Compared to parameters.ods, the following parameters have been _added_:"
echo ""
echo "Group, Parameter, Type:"
echo "Group | Parameter | Type:"
echo "-------------------------"
sed -i 's/+//g' added.csv
sed -i 's/ \* | //g' added.csv
cat added.csv
echo ""
echo "Search for those parameters and their default values. If default values"
......@@ -96,8 +103,11 @@ if [[ -s deleted.csv ]]; then
echo ""
echo "Compared to parameters.ods, the following parameters have been _deleted_:"
echo ""
echo "Group, Parameter, Type:"
echo "Group | Parameter | Type:"
echo "-------------------------"
sed -i 's/-//g' deleted.csv
sed -i 's/ \* | //g' deleted.csv
sed -i '/^\*/d' deleted.csv
cat deleted.csv
echo ""
echo "Check whether those parameters really don't exist anymore by grepping for"
......
......@@ -7,5 +7,127 @@
* The listed run-time parameters are in general available,
* but we point out that a certain model might not be able
* to use every parameter!
* \htmlinclude parameters.html
*
* | Group | Parameter | Type | Default Value | Explanation
* | :- | :- | :- | :- | :-
* | - | ParameterFile | std::string | executable.input | The name of the parameter file
* | \b FreeFlow | BoundaryLayerModel | int | 0 | 0 for none, 1 Blasius, 2 and 3 turbulent BL, 9 constant thickness
* | | BoundaryLayerOffset | Scalar | - | virtual run-up distance for BL models
* | | ConstThickness | Scalar | - | constant BL thickness (BL model 9)
* | | ExponentMTC | Scalar | - | Mass transfer coefficient for S^MTC
* | | MassTransferModel | int | 0 | 0 for none, 1 power law, 2 Schluender model
* | | RefMassfrac | Scalar | - | Free stream water mass fraction
* | | VxMax | Scalar | - | Free stream velocity
* | \b Grid | File | std::string | - | The name of the grid file, if DGF should be used
* | | NumberOfCellsX | int | - | The number of cells in x direction, if GridCreator should be used
* | | NumberOfCellsY | int | - | The number of cells in y direction, if GridCreator should be used
* | | NumberOfCellsZ | int | - | The number of cells in z direction, if GridCreator should be used
* | | UpperRightX | Scalar | - | The x-coordinate of the upper back right corner, if GridCreator should be used
* | | UpperRightY | Scalar | - | The y-coordinate of the upper back right corner, if GridCreator should be used
* | | UpperRightZ | Scalar | - | The z-coordinate of the upper back right corner, if GridCreator should be used
* | \b GridAdapt | AdaptionInterval | int | 1 | Time step interval for adaption
* | | CoarsenPercentileFlux | Scalar | 0.2 | Percentile of cells coarsened because of flux criterion
* | | CoarsenPercentileSat | Scalar | 0.2 | Percentile of cells coarsened because of saturation criterion
* | | CoarsenThresholdFlux | Scalar | 0.2 | Flux threshold for coarsening cells
* | | CoarsenThresholdSat | Scalar | 0.2 | Saturation threshold for coarsening cells
* | | CoarsenTolerance | Scalar | 0.001 | Tolerance for coarsening
* | | EnableInitializationIndicator | bool | FALSE | Switch the use of initial grid adaption on/off
* | | EnableMultiPointFluxApproximation | bool | TRUE | HangingNode: Two-point flux approximation (false) or MPFA (true)
* | | MaxInteractionVolumes | int | 4 | Maximum number of interaction regions used
* | | MaxLevel | int | 1 | Maximum allowed level
* | | MinLevel | int | 0 | Mimimum allowed level
* | | RefineAtDirichletBC | bool | FALSE | Switch for refinement at Dirichlet BC's -> not used by all indicators!
* | | RefineAtFluxBC | bool | FALSE | Switch for refinement at Neumann BC's -> not used by all indicators!
* | | RefineAtSource | bool | FALSE | Switch for refinement at sources -> not used by all indicators!
* | | RefinePercentileFlux | Scalar | 0.8 | Percentile of cells refined because of flux criterion
* | | RefinePercentileSat | Scalar | 0.8 | Percentile of cells refined because of saturation criterion
* | | RefineThresholdFlux | Scalar | 0.8 | Flux threshold for refining cells
* | | RefineThresholdSat | Scalar | 0.8 | Saturation threshold for refining cells
* | | RefineTolerance | Scalar | 0.05 | Tolerance for refinement
* | \b Impet | CFLFactor | Scalar | 1 | Scalar factor for additional scaling of the time step
* | | DtVariationRestrictionFactor | Scalar | std::numeric_limits<double>::max() | |
* | | EnableVolumeIntegral | bool | TRUE | Enables volume integral in the pressure equation (volume balance formulation)
* | | ErrorTermFactor | Scalar | 0.5 | Scaling factor for the error term
* | | ErrorTermLowerBound | Scalar | 0.1 (2p), 0.2 (2p2c) | Lower threshold used for the error term evaluation
* | | ErrorTermUpperBound | Scalar | 0.9 | Upper threshold used for the error term evaluation
* | | IterationFlag | int | 0 | 0 = no iterations, 1 = iterate IterationNumber iterations, 2 = iterate until converged or IterationNumber is reached
* | | IterationNumber | int | 2 | Number of iterations if IMPET iterations are enabled by the IterationFlags
* | | MaximumDefect | Scalar | 1.00E-005 | Maximum Defect if IMPET iterations are enabled by the IterationFlags
* | | PorosityThreshold | Scalar | 1e-6 | |
* | | RelaxationFactor | Scalar | 1 | 1 = new solution is new solution, 0 = old solution is new solution
* | | RestrictFluxInTransport | int | 0 | Restrict flux if direction reverses after pressure equation
* | | SubCFLFactor | Scalar | 1 | CFL factor for local time-stepping
* | | SwitchNormals | bool | FALSE | |
* | \b Implicit | EnableHints | bool | FALSE | use the already calculated solutions as starting values of the volume variables
* | | EnableJacobianRecycling | bool | FALSE | Specify whether the jacobian matrix of the last iteration of a time step should be reused
* | | EnablePartialReassemble | bool | FALSE | Specify whether the jacobian matrix should be only reassembled for elements where at least one vertex is above the specified tolerance
* | | EnableSmoothUpwinding | bool | FALSE | Use the smooth upwinding method (MPNC only)
* | | MassUpwindWeight | Scalar | 1 (0.5 for 1p) | The value of the weight of the upwind direction in the mass conservation equations
* | | MaxTimeStepDivisions | int | 10 | |
* | | MobilityUpwindWeight | Scalar | 1 (0.5 for 1p) | Weight for the upwind mobility in the velocity calculation
* | | NumericDifferenceMethod | int | 1 | which kind of method should be used to numerically calculate the partial derivatives of the residual (1: forward, 0: central, -1: backward)
* | | UseTwoPointFlux | bool | FALSE | indicates whether two-point flux should be used
* | | WithStabilization | bool | TRUE | |
* | \b LinearSolver | GMResRestart | int | 10 | restart parameter for GMRes
* | | MaxIterations | double | 250 (imp), 500 (dec) | maximum number of iterations of solver
* | | PreconditionerIterations | int | 1 | number of preconditioner iterations per solver iteration
* | | PreconditionerRelaxation | double | 1 | relaxation parameter for the preconditioner
* | | ResidualReduction | double | 1e-6 (imp), 1e-13 (dec) | target reduction of the initial residual
* | | Verbosity | int | 0 | Specifies the verbosity of the linear solver
* | \b MPFA | CalcVelocityInTransport | bool | FALSE | Enable facewise velocity calculation in the transport step (less efficient!)
* | | EnableComplexLStencil | bool | TRUE | Enable use of the two more complex (non-centered) L-shapes (3-d)
* | | EnableSimpleLStencil | bool | TRUE | Enable use of the two simpler (centered) L-shapes (3-d)
* | | EnableTPFA | bool | FALSE | Enable use of TPFA (3-d) if neighboring cells are of the same grid level
* | | TransmissibilityCriterion | int | 0 | 0 = default criterion, 1 = accumulative criterion
* | | TransmissibilityCriterionThreshold | Scalar | 1e-8 | Threshold for transmissibility choice
* | \b Newton | AbsTolerance | Scalar | 1.00E-005 | the value for the absolute error reduction below which convergence is declared
* | | EnableAbsoluteCriterion | bool | FALSE | indicate whether the absolute error should be used
* | | EnableChop | bool | TRUE | Chop the Newton update at the beginning of the non-linear solver (MPNC only)
* | | EnableRelativeCriterion | bool | TRUE | indicate whether the relative error should be used
* | | EnableResidualCriterion | bool | FALSE | Enable absolute criterion
* | | EnableShiftCriterion | bool | TRUE | Enable relative criterion for convergence
* | | MaxRelativeShift | Scalar | 1e-8 | Set relative tolerance
* | | MaxSteps | int | 18 | Number of maximum iterations for the Newton method
* | | MaxTimeStepDivisions | int | 10 | |
* | | RelTolerance | Scalar | 1.00E-008 | the value for the relative error below which convergence is declared
* | | ResidualReduction | Scalar | 1e-5 | factor for reduction of error for iterative linear solvers
* | | SatisfyAbsAndRel | bool | FALSE | indicate whether both of the criteria should be satisfied to declare convergence
* | | SatisfyResidualAndShiftCriterion | bool | FALSE | Use absolute and relative criteria
* | | TargetSteps | int | 10 | The number of iterations at which the Newton method should aim at
* | | UseLineSearch | bool | FALSE | Specifies whether the update should be done using line search
* | | WriteConvergence | bool | FALSE | specifies whether the convergence rate and the global residual gets written out to disk for every Newton iteration
* | \b Pardiso | NumProcessors | int | - | |
* | \b PorousMedium | CharPoreDiameter | Scalar | - | Parameter for Schluender mass-transfer model
* | \b Problem | EnableGravity | bool | TRUE | Returns whether gravity is considered in the problem
* | | Salinity | Scalar | 1e-3 | |
* | \b SpatialParams | ForchCoeff | Scalar | 0.55 | Property for the forchheimer coefficient
* | \b Stokes | StabilizationAlpha | Scalar | 0 | The parameter for the stabilization
* | | StabilizationBeta | Scalar | 0 | The parameter for the stabilization at boundaries
* | \b TimeManager | DtInitial | Scalar | - | The initial time step size
* | | MaxTimeStepSize | Scalar | 1.00E+100 | maximum time step size
* | | PrintParameters | bool | TRUE | print used and unused parameters and their values at the end of the simulation
* | | PrintProperties | bool | FALSE | print used properties and their values at the end of the simulation
* | | Restart | Scalar | FALSE | use the restart mechanism
* | | SubTimestepVerbosity | int | 0 | |
* | | TEnd | Scalar | - | the final time until the simulation should run
* | \b Vtk | AddAverageMolarMass | bool | FALSE | add average molar mass to output (MPNC only)
* | | AddBoundaryTypes | bool | FALSE | add boundary types to output (MPNC only)
* | | AddDeltaP | bool | FALSE | Output of pressure minus a fixed value
* | | AddDensities | bool | TRUE | add densities to output (MPNC only)
* | | AddEnthalpies | bool | TRUE | add enthalpies to output (MPNC only)
* | | AddFugacities | bool | FALSE | add fugacities to output (MPNC only)
* | | AddInternalEnergies | bool | FALSE | add internal energies to output (MPNC only)
* | | AddMassFractions | bool | FALSE | add mass fractions to output (MPNC only)
* | | AddMobilities | bool | TRUE | add mobilities to output (MPNC only)
* | | AddMolarities | bool | FALSE | add molarities to output (MPNC only)
* | | AddMoleFractions | bool | TRUE | add mole fractions to output (MPNC only)
* | | AddPermeability | bool | FALSE | |
* | | AddPorosity | bool | TRUE | add porosity to output (MPNC only)
* | | AddPressures | bool | TRUE | add pressures to output (MPNC only)
* | | AddSaturations | bool | TRUE | add saturations to output (MPNC only)
* | | AddTemperatures | bool | FALSE | add temperatures to output (MPNC only)
* | | AddVelocities | bool | FALSE | add velocities to output (MPNC only)
* | | AddVelocity | bool | FALSE | add velocity to output (2p(ni) and 2p2c(ni) only)
* | | OutputLevel | int | 0 (2 for 2p2c) | Vtk output verbosity (0: only primary variables, >0 more depending on the model)
* | | RockMechanicsSignConvention | bool | TRUE | Compressive stress has positive sign
*/
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