From 03eec4a5dbbadcc7dcc1af7275e3061dc3b010ff Mon Sep 17 00:00:00 2001
From: Mark Olesen <Mark.Olesen@esi-group.com>
Date: Mon, 17 Sep 2018 09:36:00 +0200
Subject: [PATCH] ENH: code improvements for vtkCloud function object (issue
#926)
- 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.
---
.../lagrangian/vtkCloud/vtkCloud.C | 322 +++++++++---------
.../lagrangian/vtkCloud/vtkCloud.H | 40 +--
.../lagrangian/vtkCloud/vtkCloudTemplates.C | 113 ++----
.../simplifiedSiwek/system/vtkCloud | 2 +-
4 files changed, 219 insertions(+), 258 deletions(-)
diff --git a/src/functionObjects/lagrangian/vtkCloud/vtkCloud.C b/src/functionObjects/lagrangian/vtkCloud/vtkCloud.C
index c99faa34ce0..840e6da70c5 100644
--- a/src/functionObjects/lagrangian/vtkCloud/vtkCloud.C
+++ b/src/functionObjects/lagrangian/vtkCloud/vtkCloud.C
@@ -44,65 +44,62 @@ 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);
- //
- // 'connectivity'
- // = linear mapping onto points
- //
- {
- format().openDataArray<label>(vtk::dataArrayAttr::CONNECTIVITY)
- .closeTag();
-
- format().writeSize(payLoad);
- for (label i=0; i < nParcels; ++i)
- {
- format().write(i);
- }
- format().flush();
+ format().tag(vtk::fileTag::VERTS);
- format().endDataArray();
- }
+ //
+ // 'connectivity'
+ // = linear mapping onto points
+ //
+ {
+ format().beginDataArray<label>(vtk::dataArrayAttr::CONNECTIVITY);
+ format().writeSize(payLoad);
- //
- // 'offsets' (connectivity offsets)
- // = linear mapping onto points (with 1 offset)
- //
+ for (label i=0; i < nTotParcels; ++i)
{
- format().openDataArray<label>(vtk::dataArrayAttr::OFFSETS)
- .closeTag();
+ format().write(i);
+ }
+ format().flush();
+ format().endDataArray();
+ }
- format().writeSize(payLoad);
- for (label i=0; i < nParcels; ++i)
- {
- format().write(i+1);
- }
- format().flush();
+ //
+ // 'offsets' (connectivity offsets)
+ // = linear mapping onto points (with 1 offset)
+ //
+ {
+ format().beginDataArray<label>(vtk::dataArrayAttr::OFFSETS);
+ format().writeSize(payLoad);
- format().endDataArray();
+ for (label i=0; i < nTotParcels; ++i)
+ {
+ format().write(i+1);
}
-
- format().endTag(vtk::fileTag::VERTS);
+ 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>();
+
+
+ // FieldData with TimeValue
+ format()
+ .beginFieldData()
+ .writeTimeValue(time_.value())
+ .endFieldData();
+
- // Begin piece
+ // 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())
- {
- const uint64_t payLoad = (nTotParcels * 3 * sizeof(float));
+ // writePoints()
+ {
+ const uint64_t payLoad = vtk::sizeofData<float,3>(nTotParcels);
- format().tag(vtk::fileTag::POINTS)
- .openDataArray<float,3>(vtk::dataArrayAttr::POINTS)
- .closeTag();
+ format().tag(vtk::fileTag::POINTS)
+ .beginDataArray<float,3>(vtk::dataArrayAttr::POINTS);
- format().writeSize(payLoad);
+ 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::writeListParallel(format.ref(), *pointsPtr);
- vtk::writeList(format(), points);
- }
+ if (Pstream::master())
+ {
format().flush();
-
- format()
- .endDataArray()
- .endTag(vtk::fileTag::POINTS);
+ 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);
- }
-
- // Footer
- if (Pstream::master())
- {
- // slight cheat. </Piece> too
- format().endTag(vtk::fileTag::PIECE);
+ if (useVerts_)
+ {
+ format().endCellData();
+ }
+ else
+ {
+ format().endPointData();
+ }
+ 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);
}
}
}
diff --git a/src/functionObjects/lagrangian/vtkCloud/vtkCloud.H b/src/functionObjects/lagrangian/vtkCloud/vtkCloud.H
index ac4384b6edc..242d058d10e 100644
--- a/src/functionObjects/lagrangian/vtkCloud/vtkCloud.H
+++ b/src/functionObjects/lagrangian/vtkCloud/vtkCloud.H
@@ -53,14 +53,14 @@ Usage
type | Type name: vtkCloud | yes |
writeControl | Output control | recommended | timeStep
cloud | | no | defaultCloud
- clouds | wordRe list of clouds | no |
- fields | wordRe list of fields | no |
- cellData | Emit cellData instead of pointData | no | false
- directory | The output directory name | no | VTK
- 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
+ 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 | postProcessing/NAME
+ width | Padding width for file name | no | 8
+ 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>
diff --git a/src/functionObjects/lagrangian/vtkCloud/vtkCloudTemplates.C b/src/functionObjects/lagrangian/vtkCloud/vtkCloudTemplates.C
index b55d4d315c3..f68b666c9b1 100644
--- a/src/functionObjects/lagrangian/vtkCloud/vtkCloudTemplates.C
+++ b/src/functionObjects/lagrangian/vtkCloud/vtkCloudTemplates.C
@@ -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)
- {
- // 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);
- }
}
+ }
- format().flush();
+ vtk::writeListParallel(format.ref(), values);
- format()
- .endDataArray();
- }
- else
+ if (Pstream::master())
{
- // Slaves - send
-
- OPstream toMaster
- (
- Pstream::commsTypes::scheduled,
- Pstream::masterNo()
- );
+ // Non-legacy
+ format().flush();
- if (fldPtr)
- {
- toMaster
- << *fldPtr;
- }
- else
- {
- toMaster
- << Field<Type>();
- }
+ format().endDataArray();
}
}
diff --git a/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/vtkCloud b/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/vtkCloud
index d5c27965bb8..59d79860500 100644
--- a/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/vtkCloud
+++ b/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/vtkCloud
@@ -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
--
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