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ENH: code improvements for vtkCloud function object (issue #926)

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- use parallel list writing, beginDataArray methods.

- use static_assert to restrict conversion of non-label integral types

- cache .vtp.series information by fileName instead of by cloud name.
  This issues if the output directory changes, and simplifies code.

ENH: emit TimeValue in files generated by vtkCloud

- additional information for passing to ParaView

ENH: vtkCloud output to postProcessing/ (issue #866)

- better alignment with other function objects, no collision with
  foamToVTK output.
This commit is contained in:
Mark Olesen
2018-09-17 09:36:00 +02:00
parent ed62ed1b19
commit 03eec4a5db
4 changed files with 226 additions and 265 deletions
Download Patch File Download Diff File Expand all files Collapse all files

278
src/functionObjects/lagrangian/vtkCloud/vtkCloud.C
View File

@ -44,36 +44,36 @@ namespace functionObjects
}
}
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
void Foam::functionObjects::vtkCloud::writeVerts
(
autoPtr<vtk::formatter>& format,
const label nParcels
const label nTotParcels
) const
{
if (Pstream::master())
{
format().tag(vtk::fileTag::VERTS);
// No collectives - can skip on slave processors
if (!format) return;
// Same payload throughout
const uint64_t payLoad = (nParcels * sizeof(label));
// Same payload for connectivity and offsets
const uint64_t payLoad = vtk::sizeofData<label>(nTotParcels);
format().tag(vtk::fileTag::VERTS);
//
// 'connectivity'
// = linear mapping onto points
//
{
format().openDataArray<label>(vtk::dataArrayAttr::CONNECTIVITY)
.closeTag();
format().beginDataArray<label>(vtk::dataArrayAttr::CONNECTIVITY);
format().writeSize(payLoad);
for (label i=0; i < nParcels; ++i)
for (label i=0; i < nTotParcels; ++i)
{
format().write(i);
}
format().flush();
format().endDataArray();
}
@ -82,27 +82,24 @@ void Foam::functionObjects::vtkCloud::writeVerts
// = linear mapping onto points (with 1 offset)
//
{
format().openDataArray<label>(vtk::dataArrayAttr::OFFSETS)
.closeTag();
format().beginDataArray<label>(vtk::dataArrayAttr::OFFSETS);
format().writeSize(payLoad);
for (label i=0; i < nParcels; ++i)
for (label i=0; i < nTotParcels; ++i)
{
format().write(i+1);
}
format().flush();
format().endDataArray();
}
format().endTag(vtk::fileTag::VERTS);
}
}
bool Foam::functionObjects::vtkCloud::writeCloud
(
const fileName& outputName,
const fileName& file,
const word& cloudName
)
{
@ -136,8 +133,8 @@ bool Foam::functionObjects::vtkCloud::writeCloud
}
// Total number of parcels on all processes
label nTotParcels = pointsPtr->size();
reduce(nTotParcels, sumOp<label>());
const label nTotParcels =
returnReduce(pointsPtr->size(), sumOp<label>());
if (pruneEmpty_ && !nTotParcels)
{
@ -147,89 +144,92 @@ bool Foam::functionObjects::vtkCloud::writeCloud
std::ofstream os;
autoPtr<vtk::formatter> format;
// Header
if (!file.hasExt("vtp"))
{
FatalErrorInFunction
<< type() << " File missing .vtp extension!" << nl << endl
<< exit(FatalError);
}
if (Pstream::master())
{
os.open(outputName);
mkDir(file.path());
os.open(file);
format = writeOpts_.newFormatter(os);
// beginFile()
// XML (inline)
format()
.xmlHeader()
.xmlComment
(
"cloud=" + cloudName
+ " time=" + time_.timeName()
+ " index=" + Foam::name(time_.timeIndex())
"case='" + time_.globalCaseName()
+ "' cloud='" + cloudName
+ "' time='" + time_.timeName()
+ "' index='" + Foam::name(time_.timeIndex())
+ "'"
)
.beginVTKFile(vtk::fileTag::POLY_DATA, "0.1");
.beginVTKFile<vtk::fileTag::POLY_DATA>();
// Begin piece
// FieldData with TimeValue
format()
.beginFieldData()
.writeTimeValue(time_.value())
.endFieldData();
// writeGeometry()
// beginPiece()
if (useVerts_)
{
format()
.openTag(vtk::fileTag::PIECE)
.xmlAttr(vtk::fileAttr::NUMBER_OF_POINTS, nTotParcels)
.xmlAttr(vtk::fileAttr::NUMBER_OF_VERTS, nTotParcels)
.closeTag();
.tag
(
vtk::fileTag::PIECE,
vtk::fileAttr::NUMBER_OF_POINTS, nTotParcels,
vtk::fileAttr::NUMBER_OF_VERTS, nTotParcels
);
}
else
{
format()
.openTag(vtk::fileTag::PIECE)
.xmlAttr(vtk::fileAttr::NUMBER_OF_POINTS, nTotParcels)
.closeTag();
}
.tag
(
vtk::fileTag::PIECE,
vtk::fileAttr::NUMBER_OF_POINTS, nTotParcels
);
}
// Points
if (Pstream::master())
// writePoints()
{
const uint64_t payLoad = (nTotParcels * 3 * sizeof(float));
const uint64_t payLoad = vtk::sizeofData<float,3>(nTotParcels);
format().tag(vtk::fileTag::POINTS)
.openDataArray<float,3>(vtk::dataArrayAttr::POINTS)
.closeTag();
.beginDataArray<float,3>(vtk::dataArrayAttr::POINTS);
format().writeSize(payLoad);
// Master
vtk::writeList(format(), *pointsPtr);
// Slaves - recv
for (int slave=1; slave<Pstream::nProcs(); ++slave)
{
IPstream fromSlave(Pstream::commsTypes::scheduled, slave);
pointList points(fromSlave);
vtk::writeList(format(), points);
}
}
format().flush();
format()
.endDataArray()
.endTag(vtk::fileTag::POINTS);
vtk::writeListParallel(format.ref(), *pointsPtr);
if (Pstream::master())
{
format().flush();
format().endDataArray();
format().endTag(vtk::fileTag::POINTS);
if (useVerts_)
{
writeVerts(format, nTotParcels);
}
}
else
{
// Slaves - send
OPstream toMaster
(
Pstream::commsTypes::scheduled,
Pstream::masterNo()
);
toMaster
<< *pointsPtr;
}
// Prevent any possible conversion of positions as a field
@ -237,8 +237,7 @@ bool Foam::functionObjects::vtkCloud::writeCloud
(
[](const word& k)
{
return k.startsWith("position")
|| k.startsWith("coordinate");
return k.startsWith("position") || k.startsWith("coordinate");
},
true // prune
);
@ -251,16 +250,17 @@ bool Foam::functionObjects::vtkCloud::writeCloud
// Write fields
const vtk::fileTag dataType =
(
useVerts_
? vtk::fileTag::CELL_DATA
: vtk::fileTag::POINT_DATA
);
if (Pstream::master())
{
format().tag(dataType);
if (useVerts_)
{
format().beginCellData();
}
else
{
format().beginPointData();
}
}
DynamicList<word> written(obrTmp.size());
@ -271,15 +271,16 @@ bool Foam::functionObjects::vtkCloud::writeCloud
if (Pstream::master())
{
format().endTag(dataType);
if (useVerts_)
{
format().endCellData();
}
else
{
format().endPointData();
}
// Footer
if (Pstream::master())
{
// slight cheat. </Piece> too
format().endTag(vtk::fileTag::PIECE);
format().endPiece();
format().endTag(vtk::fileTag::POLY_DATA)
.endVTKFile();
}
@ -291,7 +292,7 @@ bool Foam::functionObjects::vtkCloud::writeCloud
// {
// cloudName
// {
// file "<case>/VTK/cloud1_000.vtp";
// file "<case>/postProcessing/name/cloud1_0001.vtp";
// fields (U T rho);
// }
// }
@ -299,9 +300,9 @@ bool Foam::functionObjects::vtkCloud::writeCloud
dictionary propsDict;
// Use case-local filename and "<case>" shortcut for readable output
// and possibly relocation of files
// and for possibly relocation of files
fileName fName(outputName.relative(stringOps::expand("<case>")));
fileName fName(file.relative(time_.globalPath()));
if (fName.isAbsolute())
{
propsDict.add("file", fName);
@ -334,17 +335,18 @@ Foam::functionObjects::vtkCloud::vtkCloud
pruneEmpty_(false),
selectClouds_(),
selectFields_(),
dirName_("VTK"),
directory_(),
series_()
{
if (postProcess)
{
// Disable for post-process mode.
// Emit as FatalError for the try/catch in the caller.
FatalError
<< type() << " disabled in post-process mode"
<< exit(FatalError);
}
// May still want this? (OCT-2018)
// if (postProcess)
// {
// // Disable for post-process mode.
// // Emit as FatalError for the try/catch in the caller.
// FatalError
// << type() << " disabled in post-process mode"
// << exit(FatalError);
// }
read(dict);
}
@ -356,8 +358,11 @@ bool Foam::functionObjects::vtkCloud::read(const dictionary& dict)
{
fvMeshFunctionObject::read(dict);
// We probably cannot trust old information after a reread
series_.clear();
//
// writer options - default is xml base64. Legacy is not desired.
// Default format is xml base64. Legacy is not desired.
//
writeOpts_ = vtk::formatType::INLINE_BASE64;
@ -374,7 +379,7 @@ bool Foam::functionObjects::vtkCloud::read(const dictionary& dict)
(
dict.lookupOrDefault
(
"writePrecision",
"precision",
IOstream::defaultPrecision()
)
);
@ -382,7 +387,7 @@ bool Foam::functionObjects::vtkCloud::read(const dictionary& dict)
// Info<< type() << " " << name() << " output-format: "
// << writeOpts_.description() << nl;
int padWidth = dict.lookupOrDefault<int>("width", 8);
const int padWidth = dict.lookupOrDefault<int>("width", 8);
// Appropriate printf format - Enforce min/max sanity limits
if (padWidth < 1 || padWidth > 31)
@ -400,11 +405,6 @@ bool Foam::functionObjects::vtkCloud::read(const dictionary& dict)
pruneEmpty_ = dict.lookupOrDefault<bool>("prune", false);
//
// other options
//
dict.readIfPresent("directory", dirName_);
selectClouds_.clear();
dict.readIfPresent("clouds", selectClouds_);
@ -418,6 +418,28 @@ bool Foam::functionObjects::vtkCloud::read(const dictionary& dict)
selectFields_.clear();
dict.readIfPresent("fields", selectFields_);
// Output directory
directory_.clear();
dict.readIfPresent("directory", directory_);
if (directory_.size())
{
// User-defined output directory
directory_.expand();
if (!directory_.isAbsolute())
{
directory_ = time_.globalPath()/directory_;
}
}
else
{
// Standard postProcessing/ naming
directory_ = time_.globalPath()/functionObject::outputPrefix/name();
}
directory_.clean();
return true;
}
@ -437,30 +459,15 @@ bool Foam::functionObjects::vtkCloud::write()
return true; // skip - not available
}
// const word timeDesc =
// (
// useTimeName_
// ? time_.timeName()
// : printf_.empty()
// ? Foam::name(time_.timeIndex())
// : word::printf(printf_, time_.timeIndex())
// );
const scalar timeValue = time_.value();
const word timeDesc =
const word timeDesc = "_" +
(
printf_.empty()
? Foam::name(time_.timeIndex())
: word::printf(printf_, time_.timeIndex())
);
fileName vtkDir(dirName_);
vtkDir.expand();
if (!vtkDir.isAbsolute())
{
vtkDir = stringOps::expand("<case>")/vtkDir;
}
mkDir(vtkDir);
Log << name() << " output Time: " << time_.timeName() << nl;
// Each cloud separately
@ -470,26 +477,33 @@ bool Foam::functionObjects::vtkCloud::write()
const fileName outputName
(
vtkDir/cloudName + "_" + timeDesc + ".vtp"
directory_/cloudName + timeDesc + ".vtp"
);
// writeCloud() includes mkDir (on master)
if (writeCloud(outputName, cloudName))
{
Log << " cloud : " << outputName << endl;
Log << " cloud : "
<< outputName.relative(time_.globalPath()) << endl;
if (Pstream::master())
{
// Add to file-series and emit as JSON
// - misbehaves if vtkDir changes during the run,
// but that causes other issues too.
fileName seriesName(vtk::seriesWriter::base(outputName));
series_(cloudName).append({time_.value(), timeDesc});
vtk::seriesWriter& series = series_(seriesName);
vtk::seriesWrite
(
vtkDir/cloudName + ".vtp",
series_[cloudName]
);
// First time?
// Load from file, verify against filesystem,
// prune time >= currentTime
if (series.empty())
{
series.load(seriesName, true, timeValue);
}
series.append(timeValue, outputName);
series.write(seriesName);
}
}
}

32
src/functionObjects/lagrangian/vtkCloud/vtkCloud.H
View File

@ -55,12 +55,12 @@ Usage
cloud | | no | defaultCloud
clouds | wordRe list of clouds | no |
fields | wordRe list of fields | no |
prune | Suppress writing of empty clouds | no | false
cellData | Emit cellData instead of pointData | no | false
directory | The output directory name | no | VTK
directory | The output directory name | no | postProcessing/NAME
width | Padding width for file name | no | 8
format | ascii or binary format | no | binary
prune | suppress writing of empty clouds | no | false
writePrecision | write precision in ascii | no | same as IOstream
format | Format as ascii or binary | no | binary
precision | Write precision in ascii | no | same as IOstream
\endtable
The output filename and fields are added to the functionObjectProperties
@ -94,12 +94,10 @@ SourceFiles
#include "fvMeshFunctionObject.H"
#include "foamVtkOutputOptions.H"
#include "foamVtkSeriesWriter.H"
#include "wordRes.H"
#include "instant.H"
#include "DynamicList.H"
#include "HashTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
@ -135,27 +133,25 @@ class vtkCloud
//- Subset of cloud fields to process
wordRes selectFields_;
//- Output directory name
fileName dirName_;
//- Output directory
fileName directory_;
//- Per cloud output for file series
HashTable<DynamicList<instant>> series_;
HashTable<vtk::seriesWriter, fileName> series_;
// Private Member Functions
//- Write a cloud to disk, and record on the cloud OutputProperties
bool writeCloud
(
const fileName& outputName,
const word& cloudName
);
//- Write a cloud to disk (creates parent directory),
//- and record on the cloud OutputProperties.
// \param file is the output file name, with extension.
bool writeCloud(const fileName& file, const word& cloudName);
//- Write VERTS connectivity
//- Write vertex (cells) - callable on master only
void writeVerts
(
autoPtr<vtk::formatter>& format,
const label nParcels
const label nTotParcels
) const;
//- Write fields of IOField<Type>

115
src/functionObjects/lagrangian/vtkCloud/vtkCloudTemplates.C
View File

@ -35,10 +35,23 @@ Foam::wordList Foam::functionObjects::vtkCloud::writeFields
const label nTotParcels
) const
{
const int nCmpt(pTraits<Type>::nComponents);
const direction nCmpt(pTraits<Type>::nComponents);
static_assert
(
(
std::is_same<typename pTraits<Type>::cmptType,label>::value
|| std::is_floating_point<typename pTraits<Type>::cmptType>::value
),
"Label and Floating-point vector space only"
);
const bool isLabel =
std::is_same<typename pTraits<Type>::cmptType,label>::value;
// Other integral types (eg, bool etc) would need cast/convert to label.
// Similarly for labelVector etc.
const bool useIntField =
std::is_integral<typename pTraits<Type>::cmptType>();
// Fields are not always on all processors (eg, multi-component parcels).
// Thus need to resolve names between all processors.
@ -47,104 +60,42 @@ Foam::wordList Foam::functionObjects::vtkCloud::writeFields
Pstream::combineGather(fieldNames, ListOps::uniqueEqOp<word>());
Pstream::combineScatter(fieldNames);
// Sort to get identical order of fields on all processors
// Consistent order on all processors
Foam::sort(fieldNames);
for (const word& fieldName : fieldNames)
{
const auto* fldPtr = obrTmp.findObject<IOField<Type>>(fieldName);
const List<Type>* fldPtr = obrTmp.findObject<IOField<Type>>(fieldName);
const List<Type>& values = (fldPtr ? *fldPtr : List<Type>());
if (Pstream::master())
{
if (useIntField)
if (isLabel)
{
const uint64_t payLoad(nTotParcels * nCmpt * sizeof(label));
format().openDataArray<label, nCmpt>(fieldName)
.closeTag();
const uint64_t payLoad =
vtk::sizeofData<label, nCmpt>(nTotParcels);
format().beginDataArray<label, nCmpt>(fieldName);
format().writeSize(payLoad);
if (fldPtr)
{
// Data on master
const auto& fld = *fldPtr;
// Ensure consistent output width
for (const Type& val : fld)
{
for (int cmpt=0; cmpt < nCmpt; ++cmpt)
{
format().write(label(component(val, cmpt)));
}
}
}
// Slaves - recv
for (int slave=1; slave<Pstream::nProcs(); ++slave)
{
IPstream fromSlave(Pstream::commsTypes::scheduled, slave);
Field<Type> recv(fromSlave);
for (const Type& val : recv)
{
for (int cmpt=0; cmpt < nCmpt; ++cmpt)
{
format().write(label(component(val, cmpt)));
}
}
}
}
else
{
const uint64_t payLoad(nTotParcels * nCmpt * sizeof(float));
format().openDataArray<float, nCmpt>(fieldName)
.closeTag();
const uint64_t payLoad =
vtk::sizeofData<float, nCmpt>(nTotParcels);
format().beginDataArray<float, nCmpt>(fieldName);
format().writeSize(payLoad);
}
}
if (fldPtr)
vtk::writeListParallel(format.ref(), values);
if (Pstream::master())
{
// Data on master
vtk::writeList(format(), *fldPtr);
}
// Slaves - recv
for (int slave=1; slave<Pstream::nProcs(); ++slave)
{
IPstream fromSlave(Pstream::commsTypes::scheduled, slave);
Field<Type> recv(fromSlave);
vtk::writeList(format(), recv);
}
}
// Non-legacy
format().flush();
format()
.endDataArray();
}
else
{
// Slaves - send
OPstream toMaster
(
Pstream::commsTypes::scheduled,
Pstream::masterNo()
);
if (fldPtr)
{
toMaster
<< *fldPtr;
}
else
{
toMaster
<< Field<Type>();
}
format().endDataArray();
}
}

2
tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/vtkCloud
View File

@ -19,7 +19,7 @@ cloudWrite1
// format ascii;
// writePrecision 12;
//- Output directory name - Default="VTK"
//- Output directory name - Default postProcessing
// directory "VTK";
//- Write more frequent than fields