Files
openfoam/applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C
Andrew Heather 2defba00a9 ENH: Lagrangian - provided backwards compatibility for cases using the
old "positions" file form

The change to barycentric-based tracking changed the contents of the
cloud "positions" file to a new format comprising the barycentric
co-ordinates and other cell position-based info.  This broke
backwards compatibility, providing no option to restart old cases
(v1706 and earlier), and caused difficulties for dependent code, e.g.
for post-processing utilities that could only infer the contents only
after reading.

The barycentric position info is now written to a file called
"coordinates" with provision to restart old cases for which only the
"positions" file is available. Related utilities, e.g. for parallel
running and data conversion have been updated to be able to support both
file types.

To write the "positions" file by default, use set the following option
in the InfoSwitches section of the controlDict:

    writeLagrangianPositions 1;
2017-09-13 13:13:36 +01:00

1114 lines
36 KiB
C

/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
\\/ M anipulation | Copyright (C) 2015 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
OpenFOAM is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.
You should have received a copy of the GNU General Public License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
Application
reconstructPar
Group
grpParallelUtilities
Description
Reconstructs fields of a case that is decomposed for parallel
execution of OpenFOAM.
\*---------------------------------------------------------------------------*/
#include "argList.H"
#include "timeSelector.H"
#include "fvCFD.H"
#include "IOobjectList.H"
#include "processorMeshes.H"
#include "regionProperties.H"
#include "fvFieldReconstructor.H"
#include "pointFieldReconstructor.H"
#include "reconstructLagrangian.H"
#include "cellSet.H"
#include "faceSet.H"
#include "pointSet.H"
#include "hexRef8Data.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
bool haveAllTimes
(
const HashSet<word>& masterTimeDirSet,
const instantList& timeDirs
)
{
// Loop over all times
forAll(timeDirs, timei)
{
if (!masterTimeDirSet.found(timeDirs[timei].name()))
{
return false;
}
}
return true;
}
int main(int argc, char *argv[])
{
argList::addNote
(
"Reconstruct fields of a parallel case"
);
// Enable -constant ... if someone really wants it
// Enable -withZero to prevent accidentally trashing the initial fields
timeSelector::addOptions(true, true);
argList::noParallel();
#include "addRegionOption.H"
argList::addBoolOption
(
"allRegions",
"operate on all regions in regionProperties"
);
argList::addOption
(
"fields",
"list",
"specify a list of fields to be reconstructed. Eg, '(U T p)' - "
"regular expressions not currently supported"
);
argList::addBoolOption
(
"noFields",
"skip reconstructing fields"
);
argList::addOption
(
"lagrangianFields",
"list",
"specify a list of lagrangian fields to be reconstructed. Eg, '(U d)' -"
"regular expressions not currently supported, "
"positions always included."
);
argList::addBoolOption
(
"noLagrangian",
"skip reconstructing lagrangian positions and fields"
);
argList::addBoolOption
(
"noSets",
"skip reconstructing cellSets, faceSets, pointSets"
);
argList::addBoolOption
(
"newTimes",
"only reconstruct new times (i.e. that do not exist already)"
);
#include "setRootCase.H"
#include "createTime.H"
HashSet<word> selectedFields;
if (args.optionFound("fields"))
{
args.optionLookup("fields")() >> selectedFields;
}
const bool noFields = args.optionFound("noFields");
if (noFields)
{
Info<< "Skipping reconstructing fields"
<< nl << endl;
}
const bool noLagrangian = args.optionFound("noLagrangian");
if (noLagrangian)
{
Info<< "Skipping reconstructing lagrangian positions and fields"
<< nl << endl;
}
const bool noReconstructSets = args.optionFound("noSets");
if (noReconstructSets)
{
Info<< "Skipping reconstructing cellSets, faceSets and pointSets"
<< nl << endl;
}
HashSet<word> selectedLagrangianFields;
if (args.optionFound("lagrangianFields"))
{
if (noLagrangian)
{
FatalErrorInFunction
<< "Cannot specify noLagrangian and lagrangianFields "
<< "options together."
<< exit(FatalError);
}
args.optionLookup("lagrangianFields")() >> selectedLagrangianFields;
}
const bool newTimes = args.optionFound("newTimes");
const bool allRegions = args.optionFound("allRegions");
wordList regionNames;
wordList regionDirs;
if (allRegions)
{
Info<< "Reconstructing for all regions in regionProperties" << nl
<< endl;
regionProperties rp(runTime);
forAllConstIter(HashTable<wordList>, rp, iter)
{
const wordList& regions = iter();
forAll(regions, i)
{
if (findIndex(regionNames, regions[i]) == -1)
{
regionNames.append(regions[i]);
}
}
}
regionDirs = regionNames;
}
else
{
word regionName;
if (args.optionReadIfPresent("region", regionName))
{
regionNames = wordList(1, regionName);
regionDirs = regionNames;
}
else
{
regionNames = wordList(1, fvMesh::defaultRegion);
regionDirs = wordList(1, word::null);
}
}
// Determine the processor count
label nProcs = fileHandler().nProcs(args.path(), regionDirs[0]);
if (!nProcs)
{
FatalErrorInFunction
<< "No processor* directories found"
<< exit(FatalError);
}
// Create the processor databases
PtrList<Time> databases(nProcs);
forAll(databases, proci)
{
databases.set
(
proci,
new Time
(
Time::controlDictName,
args.rootPath(),
args.caseName()/fileName(word("processor") + name(proci))
)
);
}
// Use the times list from the master processor
// and select a subset based on the command-line options
instantList timeDirs = timeSelector::select
(
databases[0].times(),
args
);
// Note that we do not set the runTime time so it is still the
// one set through the controlDict. The -time option
// only affects the selected set of times from processor0.
// - can be illogical
// + any point motion handled through mesh.readUpdate
if (timeDirs.empty())
{
WarningInFunction << "No times selected";
exit(1);
}
// Get current times if -newTimes
instantList masterTimeDirs;
if (newTimes)
{
masterTimeDirs = runTime.times();
}
HashSet<word> masterTimeDirSet(2*masterTimeDirs.size());
forAll(masterTimeDirs, i)
{
masterTimeDirSet.insert(masterTimeDirs[i].name());
}
// Set all times on processor meshes equal to reconstructed mesh
forAll(databases, proci)
{
databases[proci].setTime(runTime);
}
forAll(regionNames, regioni)
{
const word& regionName = regionNames[regioni];
const word& regionDir = regionDirs[regioni];
Info<< "\n\nReconstructing fields for mesh " << regionName << nl
<< endl;
if
(
newTimes
&& regionNames.size() == 1
&& regionDirs[0].empty()
&& haveAllTimes(masterTimeDirSet, timeDirs)
)
{
Info<< "Skipping region " << regionName
<< " since already have all times"
<< endl << endl;
continue;
}
fvMesh mesh
(
IOobject
(
regionName,
runTime.timeName(),
runTime,
Foam::IOobject::MUST_READ
)
);
// Read all meshes and addressing to reconstructed mesh
processorMeshes procMeshes(databases, regionName);
// Check face addressing for meshes that have been decomposed
// with a very old foam version
#include "checkFaceAddressingComp.H"
// Loop over all times
forAll(timeDirs, timei)
{
if (newTimes && masterTimeDirSet.found(timeDirs[timei].name()))
{
Info<< "Skipping time " << timeDirs[timei].name()
<< endl << endl;
continue;
}
// Set time for global database
runTime.setTime(timeDirs[timei], timei);
Info<< "Time = " << runTime.timeName() << endl << endl;
// Set time for all databases
forAll(databases, proci)
{
databases[proci].setTime(timeDirs[timei], timei);
}
// Check if any new meshes need to be read.
fvMesh::readUpdateState meshStat = mesh.readUpdate();
fvMesh::readUpdateState procStat = procMeshes.readUpdate();
if (procStat == fvMesh::POINTS_MOVED)
{
// Reconstruct the points for moving mesh cases and write
// them out
procMeshes.reconstructPoints(mesh);
}
else if (meshStat != procStat)
{
WarningInFunction
<< "readUpdate for the reconstructed mesh:"
<< meshStat << nl
<< "readUpdate for the processor meshes :"
<< procStat << nl
<< "These should be equal or your addressing"
<< " might be incorrect."
<< " Please check your time directories for any "
<< "mesh directories." << endl;
}
// Get list of objects from processor0 database
IOobjectList objects
(
procMeshes.meshes()[0],
databases[0].timeName()
);
if (!noFields)
{
// If there are any FV fields, reconstruct them
Info<< "Reconstructing FV fields" << nl << endl;
fvFieldReconstructor fvReconstructor
(
mesh,
procMeshes.meshes(),
procMeshes.faceProcAddressing(),
procMeshes.cellProcAddressing(),
procMeshes.boundaryProcAddressing()
);
fvReconstructor.reconstructFvVolumeInternalFields<scalar>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeInternalFields<vector>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeInternalFields
<sphericalTensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeInternalFields<symmTensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeInternalFields<tensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeFields<scalar>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeFields<vector>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeFields<sphericalTensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeFields<symmTensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvVolumeFields<tensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvSurfaceFields<scalar>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvSurfaceFields<vector>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvSurfaceFields<sphericalTensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvSurfaceFields<symmTensor>
(
objects,
selectedFields
);
fvReconstructor.reconstructFvSurfaceFields<tensor>
(
objects,
selectedFields
);
if (fvReconstructor.nReconstructed() == 0)
{
Info<< "No FV fields" << nl << endl;
}
}
if (!noFields)
{
Info<< "Reconstructing point fields" << nl << endl;
const pointMesh& pMesh = pointMesh::New(mesh);
PtrList<pointMesh> pMeshes(procMeshes.meshes().size());
forAll(pMeshes, proci)
{
pMeshes.set
(
proci,
new pointMesh(procMeshes.meshes()[proci])
);
}
pointFieldReconstructor pointReconstructor
(
pMesh,
pMeshes,
procMeshes.pointProcAddressing(),
procMeshes.boundaryProcAddressing()
);
pointReconstructor.reconstructFields<scalar>
(
objects,
selectedFields
);
pointReconstructor.reconstructFields<vector>
(
objects,
selectedFields
);
pointReconstructor.reconstructFields<sphericalTensor>
(
objects,
selectedFields
);
pointReconstructor.reconstructFields<symmTensor>
(
objects,
selectedFields
);
pointReconstructor.reconstructFields<tensor>
(
objects,
selectedFields
);
if (pointReconstructor.nReconstructed() == 0)
{
Info<< "No point fields" << nl << endl;
}
}
// If there are any clouds, reconstruct them.
// The problem is that a cloud of size zero will not get written so
// in pass 1 we determine the cloud names and per cloud name the
// fields. Note that the fields are stored as IOobjectList from
// the first processor that has them. They are in pass2 only used
// for name and type (scalar, vector etc).
if (!noLagrangian)
{
HashTable<IOobjectList> cloudObjects;
forAll(databases, proci)
{
fileName lagrangianDir
(
fileHandler().filePath
(
databases[proci].timePath()
/ regionDir
/ cloud::prefix
)
);
fileNameList cloudDirs;
if (!lagrangianDir.empty())
{
cloudDirs = fileHandler().readDir
(
lagrangianDir,
fileName::DIRECTORY
);
}
forAll(cloudDirs, i)
{
// Check if we already have cloud objects for this
// cloudname
HashTable<IOobjectList>::const_iterator iter =
cloudObjects.find(cloudDirs[i]);
if (iter == cloudObjects.end())
{
// Do local scan for valid cloud objects
IOobjectList sprayObjs
(
procMeshes.meshes()[proci],
databases[proci].timeName(),
cloud::prefix/cloudDirs[i]
);
IOobject* positionsPtr =
sprayObjs.lookup(word("positions"));
IOobject* coordsPtr =
sprayObjs.lookup(word("coordinates"));
if (coordsPtr || positionsPtr)
{
cloudObjects.insert(cloudDirs[i], sprayObjs);
}
}
}
}
if (cloudObjects.size())
{
// Pass2: reconstruct the cloud
forAllConstIter(HashTable<IOobjectList>, cloudObjects, iter)
{
const word cloudName = word::validate(iter.key());
// Objects (on arbitrary processor)
const IOobjectList& sprayObjs = iter();
Info<< "Reconstructing lagrangian fields for cloud "
<< cloudName << nl << endl;
reconstructLagrangianPositions
(
mesh,
cloudName,
procMeshes.meshes(),
procMeshes.faceProcAddressing(),
procMeshes.cellProcAddressing()
);
reconstructLagrangianFields<label>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFieldFields<label>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFields<scalar>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFieldFields<scalar>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFields<vector>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFieldFields<vector>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFields<sphericalTensor>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFieldFields<sphericalTensor>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFields<symmTensor>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFieldFields<symmTensor>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFields<tensor>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
reconstructLagrangianFieldFields<tensor>
(
cloudName,
mesh,
procMeshes.meshes(),
sprayObjs,
selectedLagrangianFields
);
}
}
else
{
Info<< "No lagrangian fields" << nl << endl;
}
}
if (!noReconstructSets)
{
// Scan to find all sets
HashTable<label> cSetNames;
HashTable<label> fSetNames;
HashTable<label> pSetNames;
forAll(procMeshes.meshes(), proci)
{
const fvMesh& procMesh = procMeshes.meshes()[proci];
// Note: look at sets in current time only or between
// mesh and current time?. For now current time. This will
// miss out on sets in intermediate times that have not
// been reconstructed.
IOobjectList objects
(
procMesh,
databases[0].timeName(), //procMesh.facesInstance()
polyMesh::meshSubDir/"sets"
);
IOobjectList cSets(objects.lookupClass(cellSet::typeName));
forAllConstIter(IOobjectList, cSets, iter)
{
cSetNames.insert(iter.key(), cSetNames.size());
}
IOobjectList fSets(objects.lookupClass(faceSet::typeName));
forAllConstIter(IOobjectList, fSets, iter)
{
fSetNames.insert(iter.key(), fSetNames.size());
}
IOobjectList pSets(objects.lookupClass(pointSet::typeName));
forAllConstIter(IOobjectList, pSets, iter)
{
pSetNames.insert(iter.key(), pSetNames.size());
}
}
if (cSetNames.size() || fSetNames.size() || pSetNames.size())
{
// Construct all sets
PtrList<cellSet> cellSets(cSetNames.size());
PtrList<faceSet> faceSets(fSetNames.size());
PtrList<pointSet> pointSets(pSetNames.size());
Info<< "Reconstructing sets:" << endl;
if (cSetNames.size())
{
Info<< " cellSets "
<< cSetNames.sortedToc() << endl;
}
if (fSetNames.size())
{
Info<< " faceSets "
<< fSetNames.sortedToc() << endl;
}
if (pSetNames.size())
{
Info<< " pointSets "
<< pSetNames.sortedToc() << endl;
}
// Load sets
forAll(procMeshes.meshes(), proci)
{
const fvMesh& procMesh = procMeshes.meshes()[proci];
IOobjectList objects
(
procMesh,
databases[0].timeName(),
polyMesh::meshSubDir/"sets"
);
// cellSets
const labelList& cellMap =
procMeshes.cellProcAddressing()[proci];
IOobjectList cSets
(
objects.lookupClass(cellSet::typeName)
);
forAllConstIter(IOobjectList, cSets, iter)
{
// Load cellSet
const cellSet procSet(*iter());
label setI = cSetNames[iter.key()];
if (!cellSets.set(setI))
{
cellSets.set
(
setI,
new cellSet
(
mesh,
iter.key(),
procSet.size()
)
);
}
cellSet& cSet = cellSets[setI];
cSet.instance() = runTime.timeName();
forAllConstIter(cellSet, procSet, iter)
{
cSet.insert(cellMap[iter.key()]);
}
}
// faceSets
const labelList& faceMap =
procMeshes.faceProcAddressing()[proci];
IOobjectList fSets
(
objects.lookupClass(faceSet::typeName)
);
forAllConstIter(IOobjectList, fSets, iter)
{
// Load faceSet
const faceSet procSet(*iter());
label setI = fSetNames[iter.key()];
if (!faceSets.set(setI))
{
faceSets.set
(
setI,
new faceSet
(
mesh,
iter.key(),
procSet.size()
)
);
}
faceSet& fSet = faceSets[setI];
fSet.instance() = runTime.timeName();
forAllConstIter(faceSet, procSet, iter)
{
fSet.insert(mag(faceMap[iter.key()])-1);
}
}
// pointSets
const labelList& pointMap =
procMeshes.pointProcAddressing()[proci];
IOobjectList pSets
(
objects.lookupClass(pointSet::typeName)
);
forAllConstIter(IOobjectList, pSets, iter)
{
// Load pointSet
const pointSet propSet(*iter());
label setI = pSetNames[iter.key()];
if (!pointSets.set(setI))
{
pointSets.set
(
setI,
new pointSet
(
mesh,
iter.key(),
propSet.size()
)
);
}
pointSet& pSet = pointSets[setI];
pSet.instance() = runTime.timeName();
forAllConstIter(pointSet, propSet, iter)
{
pSet.insert(pointMap[iter.key()]);
}
}
}
// Write sets
forAll(cellSets, i)
{
cellSets[i].write();
}
forAll(faceSets, i)
{
faceSets[i].write();
}
forAll(pointSets, i)
{
pointSets[i].write();
}
}
// Reconstruct refinement data
{
PtrList<hexRef8Data> procData(procMeshes.meshes().size());
forAll(procMeshes.meshes(), procI)
{
const fvMesh& procMesh = procMeshes.meshes()[procI];
procData.set
(
procI,
new hexRef8Data
(
IOobject
(
"dummy",
procMesh.time().timeName(),
polyMesh::meshSubDir,
procMesh,
IOobject::READ_IF_PRESENT,
IOobject::NO_WRITE,
false
)
)
);
}
// Combine individual parts
const PtrList<labelIOList>& cellAddr =
procMeshes.cellProcAddressing();
UPtrList<const labelList> cellMaps(cellAddr.size());
forAll(cellAddr, i)
{
cellMaps.set(i, &cellAddr[i]);
}
const PtrList<labelIOList>& pointAddr =
procMeshes.pointProcAddressing();
UPtrList<const labelList> pointMaps(pointAddr.size());
forAll(pointAddr, i)
{
pointMaps.set(i, &pointAddr[i]);
}
UPtrList<const hexRef8Data> procRefs(procData.size());
forAll(procData, i)
{
procRefs.set(i, &procData[i]);
}
hexRef8Data
(
IOobject
(
"dummy",
mesh.time().timeName(),
polyMesh::meshSubDir,
mesh,
IOobject::NO_READ,
IOobject::NO_WRITE,
false
),
cellMaps,
pointMaps,
procRefs
).write();
}
}
// Reconstruct refinement data
{
PtrList<hexRef8Data> procData(procMeshes.meshes().size());
forAll(procMeshes.meshes(), procI)
{
const fvMesh& procMesh = procMeshes.meshes()[procI];
procData.set
(
procI,
new hexRef8Data
(
IOobject
(
"dummy",
procMesh.time().timeName(),
polyMesh::meshSubDir,
procMesh,
IOobject::READ_IF_PRESENT,
IOobject::NO_WRITE,
false
)
)
);
}
// Combine individual parts
const PtrList<labelIOList>& cellAddr =
procMeshes.cellProcAddressing();
UPtrList<const labelList> cellMaps(cellAddr.size());
forAll(cellAddr, i)
{
cellMaps.set(i, &cellAddr[i]);
}
const PtrList<labelIOList>& pointAddr =
procMeshes.pointProcAddressing();
UPtrList<const labelList> pointMaps(pointAddr.size());
forAll(pointAddr, i)
{
pointMaps.set(i, &pointAddr[i]);
}
UPtrList<const hexRef8Data> procRefs(procData.size());
forAll(procData, i)
{
procRefs.set(i, &procData[i]);
}
hexRef8Data
(
IOobject
(
"dummy",
mesh.time().timeName(),
polyMesh::meshSubDir,
mesh,
IOobject::NO_READ,
IOobject::NO_WRITE,
false
),
cellMaps,
pointMaps,
procRefs
).write();
}
// If there is a "uniform" directory in the time region
// directory copy from the master processor
{
fileName uniformDir0
(
fileHandler().filePath
(
databases[0].timePath()/regionDir/"uniform"
)
);
if (!uniformDir0.empty() && fileHandler().isDir(uniformDir0))
{
fileHandler().cp(uniformDir0, runTime.timePath()/regionDir);
}
}
// For the first region of a multi-region case additionally
// copy the "uniform" directory in the time directory
if (regioni == 0 && regionDir != word::null)
{
fileName uniformDir0
(
fileHandler().filePath
(
databases[0].timePath()/"uniform"
)
);
if (!uniformDir0.empty() && fileHandler().isDir(uniformDir0))
{
fileHandler().cp(uniformDir0, runTime.timePath());
}
}
}
}
Info<< "\nEnd\n" << endl;
return 0;
}
// ************************************************************************* //