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MRG: merged develop line back into integration branch

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This commit is contained in:
Andrew Heather
2017-05-18 11:11:12 +01:00
parent 8ff163713d 568570d2be
commit 2e9bead519
514 changed files with 12134 additions and 16093 deletions
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2
src/functionObjects/field/ddt2/ddt2.C
View File

@ -178,7 +178,7 @@ bool Foam::functionObjects::ddt2::execute()
{
results_.clear();
wordHashSet candidates = subsetStrings(selectFields_, mesh_.names());
wordHashSet candidates(subsetStrings(selectFields_, mesh_.names()));
DynamicList<word> missing(selectFields_.size());
DynamicList<word> ignored(selectFields_.size());

1
src/functionObjects/field/extractEulerianParticles/extractEulerianParticles/extractEulerianParticles.H
View File

@ -71,7 +71,6 @@ SourceFiles
#include "surfaceFieldsFwd.H"
#include "vectorList.H"
#include "globalIndex.H"
#include "cachedRandom.H"
#include "eulerianParticle.H"
#include "IOdictionary.H"
#include "injectedParticleCloud.H"

82
src/functionObjects/field/histogram/histogram.C
View File

@ -3,7 +3,7 @@
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2016 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd.
\\/ M anipulation | Copyright (C) 2016-2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
@ -45,23 +45,31 @@ void Foam::functionObjects::histogram::writeGraph
(
const coordSet& coords,
const word& fieldName,
const scalarField& values
const scalarField& normalizedValues,
const scalarField& absoluteValues
) const
{
const wordList fieldNames(1, fieldName);
fileName outputPath = baseTimeDir();
mkDir(outputPath);
OFstream graphFile
(
outputPath/formatterPtr_().getFileName(coords, fieldNames)
outputPath
/formatterPtr_().getFileName
(
coords,
wordList(1, fieldName)
)
);
Log << " Writing histogram of " << fieldName
<< " to " << graphFile.name() << endl;
List<const scalarField*> yPtrs(1);
yPtrs[0] = &values;
wordList fieldNames(2);
fieldNames[0] = fieldName;
fieldNames[1] = fieldName + "Count";
List<const scalarField*> yPtrs(2);
yPtrs[0] = &normalizedValues;
yPtrs[1] = &absoluteValues;
formatterPtr_().write(coords, fieldNames, yPtrs, graphFile);
}
@ -76,7 +84,9 @@ Foam::functionObjects::histogram::histogram
)
:
fvMeshFunctionObject(name, runTime, dict),
writeFile(obr_, name)
writeFile(obr_, name),
max_(-GREAT),
min_(GREAT)
{
read(dict);
}
@ -96,8 +106,9 @@ bool Foam::functionObjects::histogram::read(const dictionary& dict)
writeFile::read(dict);
dict.lookup("field") >> fieldName_;
dict.lookup("max") >> max_;
min_ = dict.lookupOrDefault<scalar>("min", 0);
max_ = dict.lookupOrDefault<scalar>("max", -GREAT);
min_ = dict.lookupOrDefault<scalar>("min", GREAT);
dict.lookup("nBins") >> nBins_;
word format(dict.lookup("setFormat"));
@ -149,38 +160,63 @@ bool Foam::functionObjects::histogram::write()
: obr_.lookupObject<volScalarField>(fieldName_)
);
scalar histMax = max_;
scalar histMin = min_;
if (max_ == -GREAT)
{
// Determine current min and max
histMax = max(field).value();
if (min_ == GREAT)
{
histMin = min(field).value();
}
Log << " Determined histogram bounds from field"
<< " min/max(" << fieldName_ << ") = "
<< histMin << ' ' << histMax << endl;
}
else if (min_ == GREAT)
{
histMin = 0;
}
// Calculate the mid-points of bins for the graph axis
pointField xBin(nBins_);
const scalar delta = (max_- min_)/nBins_;
const scalar delta = (histMax- histMin)/nBins_;
scalar x = min_ + 0.5*delta;
scalar x = histMin + 0.5*delta;
forAll(xBin, i)
{
xBin[i] = point(x, 0, 0);
x += delta;
}
scalarField data(nBins_, 0);
scalarField dataNormalized(nBins_, 0);
labelField dataCount(nBins_, 0);
const scalarField& V = mesh_.V();
forAll(field, celli)
{
const label bini = (field[celli] - min_)/delta;
const label bini = (field[celli] - histMin)/delta;
if (bini >= 0 && bini < nBins_)
{
data[bini] += V[celli];
dataNormalized[bini] += V[celli];
dataCount[bini]++;
}
}
Pstream::listCombineGather(data, plusEqOp<scalar>());
Pstream::listCombineGather(dataNormalized, plusEqOp<scalar>());
Pstream::listCombineGather(dataCount, plusEqOp<label>());
if (Pstream::master())
{
const scalar sumData = sum(data);
const scalar sumData = sum(dataNormalized);
if (sumData > SMALL)
{
data /= sumData;
dataNormalized /= sumData;
const coordSet coords
(
@ -190,7 +226,15 @@ bool Foam::functionObjects::histogram::write()
mag(xBin)
);
writeGraph(coords, fieldName_, data);
// Convert count field from labelField to scalarField
scalarField count(dataCount.size());
forAll(count, i)
{
count[i] = 1.0*dataCount[i];
}
writeGraph(coords, fieldName_, dataNormalized, count);
}
}

7
src/functionObjects/field/histogram/histogram.H
View File

@ -3,7 +3,7 @@
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2016 OpenFOAM Foundation
\\/ M anipulation |
\\/ M anipulation | Copyright (C) 2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
@ -53,7 +53,7 @@ Usage
type | type name: histogram | yes |
field | Field to analyse | yes |
nBins | Number of bins for the histogram | yes|
max | Maximum value sampled | yes |
max | Maximum value sampled | no | field max
min | minimum value sampled | no | 0
setFormat | Output format | yes |
\endtable
@ -115,7 +115,8 @@ class histogram
(
const coordSet& coords,
const word& valueName,
const scalarField& values
const scalarField& normalizedValues,
const scalarField& absoluteValues
) const;
//- Disallow default bitwise copy construct

2
src/functionObjects/field/particleDistribution/particleDistribution.C
View File

@ -61,7 +61,7 @@ Foam::functionObjects::particleDistribution::particleDistribution
cloudName_("unknown-cloudName"),
nameVsBinWidth_(),
tagFieldName_("none"),
rndGen_(1234, -1),
rndGen_(),
writerPtr_(nullptr)
{
read(dict);

4
src/functionObjects/field/particleDistribution/particleDistribution.H
View File

@ -73,7 +73,7 @@ SourceFiles
#include "fvMeshFunctionObject.H"
#include "writeFile.H"
#include "scalarField.H"
#include "cachedRandom.H"
#include "Random.H"
#include "Tuple2.H"
#include "writer.H"
@ -107,7 +107,7 @@ protected:
word tagFieldName_;
//- Random number generator - used by distribution models
cachedRandom rndGen_;
Random rndGen_;
//- Writer
autoPtr<writer<scalar>> writerPtr_;

2
src/functionObjects/field/randomise/randomiseTemplates.C
View File

@ -47,7 +47,7 @@ bool Foam::functionObjects::randomise::calcRandomised()
forAll(field, celli)
{
Type rndPert;
rand.randomise(rndPert);
rand.randomise01(rndPert);
rndPert = 2.0*rndPert - pTraits<Type>::one;
rndPert /= mag(rndPert);
rfield[celli] += magPerturbation_*rndPert;

11
src/functionObjects/field/readFields/readFields.C
View File

@ -3,7 +3,7 @@
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\/ M anipulation |
\\/ M anipulation | Copyright (C) 2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
@ -50,9 +50,15 @@ Foam::functionObjects::readFields::readFields
)
:
fvMeshFunctionObject(name, runTime, dict),
fieldSet_()
fieldSet_(),
readOnStart_(true)
{
read(dict);
if (readOnStart_)
{
execute();
}
}
@ -69,6 +75,7 @@ bool Foam::functionObjects::readFields::read(const dictionary& dict)
fvMeshFunctionObject::read(dict);
dict.lookup("fields") >> fieldSet_;
dict.readIfPresent("readOnStart", readOnStart_);
return true;
}

6
src/functionObjects/field/readFields/readFields.H
View File

@ -3,7 +3,7 @@
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2015-2016 OpenCFD Ltd.
\\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
@ -48,6 +48,7 @@ Usage
Property | Description | Required | Default value
type | type name: readFields | yes |
fields | list of fields to read | no |
readOnStart | flag to start reading on start-up | no | yes
log | Log to standard output | no | yes
\endtable
@ -88,6 +89,9 @@ protected:
//- Fields to load
wordList fieldSet_;
//- Flag to read on construction
bool readOnStart_;
// Protected Member Functions

2
src/functionObjects/field/zeroGradient/zeroGradient.C
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@ -135,7 +135,7 @@ bool Foam::functionObjects::zeroGradient::execute()
{
results_.clear();
wordHashSet candidates = subsetStrings(selectFields_, mesh_.names());
wordHashSet candidates(subsetStrings(selectFields_, mesh_.names()));
DynamicList<word> missing(selectFields_.size());
DynamicList<word> ignored(selectFields_.size());

1
src/functionObjects/graphics/runTimePostProcessing/CMakeLists-Common.txt
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@ -21,7 +21,6 @@ include_directories(
link_directories(
$ENV{FOAM_LIBBIN}
$ENV{FOAM_EXT_LIBBIN}
)
add_definitions(

21
src/functionObjects/graphics/runTimePostProcessing/scene.C
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@ -131,6 +131,21 @@ void Foam::functionObjects::runTimePostPro::scene::readColours
}
void Foam::functionObjects::runTimePostPro::scene::setActorVisibility
(
vtkRenderer* renderer,
const bool visible
) const
{
vtkActorCollection *actors = renderer->GetActors();
for (int i = 0; i < actors->GetNumberOfItems(); ++i)
{
vtkActor *actor = vtkActor::SafeDownCast(actors->GetItemAsObject(i));
actor->SetVisibility(visible);
}
}
void Foam::functionObjects::runTimePostPro::scene::initialise
(
vtkRenderer* renderer,
@ -239,9 +254,13 @@ void Foam::functionObjects::runTimePostPro::scene::setCamera
// to be done once on initialisation
if (!clipBox_.empty())
{
// Call ResetCamera() to fit clip box in view
setActorVisibility(renderer, false);
clipBoxActor_->VisibilityOn();
// Call ResetCamera() to fit clip box in view
renderer->ResetCamera();
setActorVisibility(renderer, true);
clipBoxActor_->VisibilityOff();
}

9
src/functionObjects/graphics/runTimePostProcessing/scene.H
View File

@ -3,7 +3,7 @@
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2015 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd.
\\/ M anipulation | Copyright (C) 2016-2017 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
@ -105,6 +105,13 @@ class scene
//- Read colour properties
void readColours(const dictionary& dict);
//- Set visibility of all actors on/off
void setActorVisibility
(
vtkRenderer* renderer,
const bool visible
) const;
//- Disallow default bitwise copy construct
scene(const scene&);

2
src/functionObjects/utilities/ensightWrite/ensightWrite.C
View File

@ -246,7 +246,7 @@ bool Foam::functionObjects::ensightWrite::write()
ensCase().setTime(t.value(), t.timeIndex());
}
wordHashSet candidates = subsetStrings(selectFields_, mesh_.names());
wordHashSet candidates(subsetStrings(selectFields_, mesh_.names()));
DynamicList<word> missing(selectFields_.size());
DynamicList<word> ignored(selectFields_.size());

40
src/functionObjects/utilities/timeActivatedFileUpdate/timeActivatedFileUpdate.C
View File

@ -48,11 +48,10 @@ namespace functionObjects
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
void Foam::functionObjects::timeActivatedFileUpdate::updateFile
(
const bool checkFiles
)
void Foam::functionObjects::timeActivatedFileUpdate::updateFile()
{
modified_ = false;
label i = lastIndex_;
while
(
@ -68,19 +67,15 @@ void Foam::functionObjects::timeActivatedFileUpdate::updateFile
Log << nl << type() << ": copying file" << nl << timeVsFile_[i].second()
<< nl << "to:" << nl << fileToUpdate_ << nl << endl;
fileName destFile(fileToUpdate_ + Foam::name(pid()));
cp(timeVsFile_[i].second(), destFile);
mv(destFile, fileToUpdate_);
lastIndex_ = i;
if (checkFiles)
if (Pstream::master() || time_.distributed())
{
// Do an early check to avoid an additional iteration before
// any changes are picked up (see Time::run : does readModified
// before executing FOs). Note we have to protect the read
// constructor of *this from triggering this behaviour.
const_cast<Time&>(time_).Time::readModifiedObjects();
// Slaves do not copy if running non-distributed
fileName destFile(fileToUpdate_ + Foam::name(pid()));
cp(timeVsFile_[i].second(), destFile);
mv(destFile, fileToUpdate_);
}
lastIndex_ = i;
modified_ = true;
}
}
@ -98,7 +93,8 @@ Foam::functionObjects::timeActivatedFileUpdate::timeActivatedFileUpdate
time_(runTime),
fileToUpdate_("unknown-fileToUpdate"),
timeVsFile_(),
lastIndex_(-1)
lastIndex_(-1),
modified_(false)
{
read(dict);
}
@ -142,8 +138,8 @@ bool Foam::functionObjects::timeActivatedFileUpdate::read
<< timeVsFile_[i].second() << endl;
}
// Copy starting files. Avoid recursion by not checking for modified files.
updateFile(false);
// Copy starting files
updateFile();
return true;
}
@ -151,7 +147,7 @@ bool Foam::functionObjects::timeActivatedFileUpdate::read
bool Foam::functionObjects::timeActivatedFileUpdate::execute()
{
updateFile(true);
updateFile();
return true;
}
@ -163,4 +159,10 @@ bool Foam::functionObjects::timeActivatedFileUpdate::write()
}
bool Foam::functionObjects::timeActivatedFileUpdate::filesModified() const
{
return modified_;
}
// ************************************************************************* //

8
src/functionObjects/utilities/timeActivatedFileUpdate/timeActivatedFileUpdate.H
View File

@ -106,11 +106,14 @@ class timeActivatedFileUpdate
//- Index of last file copied
label lastIndex_;
//- Has anything been copied?
bool modified_;
// Private Member Functions
//- Update file
void updateFile(const bool checkFiles);
void updateFile();
//- Disallow default bitwise copy construct
timeActivatedFileUpdate(const timeActivatedFileUpdate&);
@ -150,6 +153,9 @@ public:
//- Do nothing
virtual bool write();
//- Did any file get changed during execution?
virtual bool filesModified() const;
};