When an OpenFOAM simulation runs in parallel, the data for decomposed fields and
mesh(es) has historically been stored in multiple files within separate
directories for each processor. Processor directories are named 'processorN',
where N is the processor number.
This commit introduces an alternative "collated" file format where the data for
each decomposed field (and mesh) is collated into a single file, which is
written and read on the master processor. The files are stored in a single
directory named 'processors'.
The new format produces significantly fewer files - one per field, instead of N
per field. For large parallel cases, this avoids the restriction on the number
of open files imposed by the operating system limits.
The file writing can be threaded allowing the simulation to continue running
while the data is being written to file. NFS (Network File System) is not
needed when using the the collated format and additionally, there is an option
to run without NFS with the original uncollated approach, known as
"masterUncollated".
The controls for the file handling are in the OptimisationSwitches of
etc/controlDict:
OptimisationSwitches
{
...
//- Parallel IO file handler
// uncollated (default), collated or masterUncollated
fileHandler uncollated;
//- collated: thread buffer size for queued file writes.
// If set to 0 or not sufficient for the file size threading is not used.
// Default: 2e9
maxThreadFileBufferSize 2e9;
//- masterUncollated: non-blocking buffer size.
// If the file exceeds this buffer size scheduled transfer is used.
// Default: 2e9
maxMasterFileBufferSize 2e9;
}
When using the collated file handling, memory is allocated for the data in the
thread. maxThreadFileBufferSize sets the maximum size of memory in bytes that
is allocated. If the data exceeds this size, the write does not use threading.
When using the masterUncollated file handling, non-blocking MPI communication
requires a sufficiently large memory buffer on the master node.
maxMasterFileBufferSize sets the maximum size in bytes of the buffer. If the
data exceeds this size, the system uses scheduled communication.
The installation defaults for the fileHandler choice, maxThreadFileBufferSize
and maxMasterFileBufferSize (set in etc/controlDict) can be over-ridden within
the case controlDict file, like other parameters. Additionally the fileHandler
can be set by:
- the "-fileHandler" command line argument;
- a FOAM_FILEHANDLER environment variable.
A foamFormatConvert utility allows users to convert files between the collated
and uncollated formats, e.g.
mpirun -np 2 foamFormatConvert -parallel -fileHandler uncollated
An example case demonstrating the file handling methods is provided in:
$FOAM_TUTORIALS/IO/fileHandling
The work was undertaken by Mattijs Janssens, in collaboration with Henry Weller.
724 lines
18 KiB
C
724 lines
18 KiB
C
/*---------------------------------------------------------------------------*\
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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\\ / O peration |
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\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
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\\/ M anipulation |
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-------------------------------------------------------------------------------
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License
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This file is part of OpenFOAM.
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OpenFOAM is free software: you can redistribute it and/or modify it
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under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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for more details.
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You should have received a copy of the GNU General Public License
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along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
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\*---------------------------------------------------------------------------*/
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#include "vtkPV3Foam.H"
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// OpenFOAM includes
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#include "cellSet.H"
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#include "faceSet.H"
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#include "pointSet.H"
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#include "IOobjectList.H"
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#include "IOPtrList.H"
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#include "polyBoundaryMeshEntries.H"
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#include "entry.H"
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#include "Cloud.H"
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#include "vtkPV3FoamReader.h"
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// local headers
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#include "vtkPV3FoamAddToSelection.H"
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#include "vtkPV3FoamUpdateInfoFields.H"
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// VTK includes
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#include "vtkDataArraySelection.h"
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// * * * * * * * * * * * * * * * Private Classes * * * * * * * * * * * * * * //
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namespace Foam
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{
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//- A class for reading zone information without requiring a mesh
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class zonesEntries
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:
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public regIOobject,
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public PtrList<entry>
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{
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public:
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// Constructors
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explicit zonesEntries(const IOobject& io)
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:
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regIOobject(io),
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PtrList<entry>(readStream(word("regIOobject")))
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{
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close();
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}
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// Member functions
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bool writeData(Ostream&) const
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{
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NotImplemented;
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return false;
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}
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};
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}
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// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
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template<class ZoneType>
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Foam::wordList Foam::vtkPV3Foam::getZoneNames
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(
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const ZoneMesh<ZoneType, polyMesh>& zmesh
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) const
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{
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wordList names(zmesh.size());
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label nZone = 0;
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forAll(zmesh, zoneI)
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{
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if (zmesh[zoneI].size())
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{
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names[nZone++] = zmesh[zoneI].name();
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}
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}
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names.setSize(nZone);
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return names;
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}
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Foam::wordList Foam::vtkPV3Foam::getZoneNames(const word& zoneType) const
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{
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wordList names;
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// mesh not loaded - read from file
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IOobject ioObj
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(
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zoneType,
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dbPtr_().findInstance
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(
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meshDir_,
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zoneType,
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IOobject::READ_IF_PRESENT
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),
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meshDir_,
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dbPtr_(),
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IOobject::READ_IF_PRESENT,
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IOobject::NO_WRITE,
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false
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);
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if (ioObj.typeHeaderOk<cellZoneMesh>(false))
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{
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zonesEntries zones(ioObj);
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names.setSize(zones.size());
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forAll(zones, zoneI)
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{
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names[zoneI] = zones[zoneI].keyword();
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}
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}
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return names;
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}
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void Foam::vtkPV3Foam::updateInfoInternalMesh
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(
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vtkDataArraySelection* arraySelection
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)
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{
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if (debug)
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{
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Info<< "<beg> Foam::vtkPV3Foam::updateInfoInternalMesh" << endl;
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}
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// Determine mesh parts (internalMesh, patches...)
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//- Add internal mesh as first entry
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arrayRangeVolume_.reset(arraySelection->GetNumberOfArrays());
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arraySelection->AddArray
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(
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"internalMesh"
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);
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arrayRangeVolume_ += 1;
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if (debug)
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{
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// just for debug info
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getSelectedArrayEntries(arraySelection);
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Info<< "<end> Foam::vtkPV3Foam::updateInfoInternalMesh" << endl;
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}
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}
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void Foam::vtkPV3Foam::updateInfoLagrangian
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(
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vtkDataArraySelection* arraySelection
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)
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{
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if (debug)
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{
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Info<< "<beg> Foam::vtkPV3Foam::updateInfoLagrangian" << nl
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<< " " << dbPtr_->timePath()/cloud::prefix << endl;
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}
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// use the db directly since this might be called without a mesh,
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// but the region must get added back in
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fileName lagrangianPrefix(cloud::prefix);
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if (meshRegion_ != polyMesh::defaultRegion)
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{
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lagrangianPrefix = meshRegion_/cloud::prefix;
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}
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// Search for list of lagrangian objects for this time
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fileNameList cloudDirs
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(
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readDir(dbPtr_->timePath()/lagrangianPrefix, fileName::DIRECTORY)
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);
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arrayRangeLagrangian_.reset(arraySelection->GetNumberOfArrays());
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int nClouds = 0;
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forAll(cloudDirs, cloudI)
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{
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// Add cloud to GUI list
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arraySelection->AddArray
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(
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(cloudDirs[cloudI] + " - lagrangian").c_str()
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);
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++nClouds;
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}
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arrayRangeLagrangian_ += nClouds;
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if (debug)
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{
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// just for debug info
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getSelectedArrayEntries(arraySelection);
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Info<< "<end> Foam::vtkPV3Foam::updateInfoLagrangian" << endl;
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}
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}
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void Foam::vtkPV3Foam::updateInfoPatches
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(
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vtkDataArraySelection* arraySelection,
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stringList& enabledEntries
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)
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{
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if (debug)
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{
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Info<< "<beg> Foam::vtkPV3Foam::updateInfoPatches"
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<< " [meshPtr=" << (meshPtr_ ? "set" : "nullptr") << "]" << endl;
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}
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HashSet<string> enabledEntriesSet(enabledEntries);
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arrayRangePatches_.reset(arraySelection->GetNumberOfArrays());
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int nPatches = 0;
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if (meshPtr_)
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{
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const polyBoundaryMesh& patches = meshPtr_->boundaryMesh();
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const HashTable<labelList, word>& groups = patches.groupPatchIDs();
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const wordList allPatchNames = patches.names();
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// Add patch groups
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// ~~~~~~~~~~~~~~~~
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for
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(
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HashTable<labelList, word>::const_iterator iter = groups.begin();
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iter != groups.end();
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++iter
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)
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{
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const word& groupName = iter.key();
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const labelList& patchIDs = iter();
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label nFaces = 0;
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forAll(patchIDs, i)
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{
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nFaces += patches[patchIDs[i]].size();
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}
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// Valid patch if nFace > 0 - add patch to GUI list
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if (nFaces)
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{
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string vtkGrpName = groupName + " - group";
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arraySelection->AddArray(vtkGrpName.c_str());
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++nPatches;
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if (enabledEntriesSet.found(vtkGrpName))
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{
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if (!reader_->GetShowGroupsOnly())
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{
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enabledEntriesSet.erase(vtkGrpName);
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forAll(patchIDs, i)
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{
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const polyPatch& pp = patches[patchIDs[i]];
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if (pp.size())
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{
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string vtkPatchName = pp.name() + " - patch";
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enabledEntriesSet.insert(vtkPatchName);
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}
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}
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}
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}
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}
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}
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// Add patches
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// ~~~~~~~~~~~
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if (!reader_->GetShowGroupsOnly())
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{
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forAll(patches, patchi)
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{
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const polyPatch& pp = patches[patchi];
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if (pp.size())
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{
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// Add patch to GUI list
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arraySelection->AddArray
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(
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(pp.name() + " - patch").c_str()
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);
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++nPatches;
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}
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}
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}
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}
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else
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{
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// mesh not loaded - read from file
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// but this could fail if we've supplied a bad region name
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IOobject ioObj
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(
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"boundary",
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dbPtr_().findInstance
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(
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meshDir_,
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|
"boundary",
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IOobject::READ_IF_PRESENT
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),
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meshDir_,
|
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dbPtr_(),
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IOobject::READ_IF_PRESENT,
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IOobject::NO_WRITE,
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false
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);
|
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|
|
// this should only ever fail if the mesh region doesn't exist
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if (ioObj.typeHeaderOk<polyBoundaryMesh>(true))
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{
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polyBoundaryMeshEntries patchEntries(ioObj);
|
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|
|
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// Read patches and determine sizes
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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wordList names(patchEntries.size());
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labelList sizes(patchEntries.size());
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forAll(patchEntries, patchi)
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{
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const dictionary& patchDict = patchEntries[patchi].dict();
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sizes[patchi] = readLabel(patchDict.lookup("nFaces"));
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names[patchi] = patchEntries[patchi].keyword();
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}
|
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|
|
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// Add (non-zero) patch groups to the list of mesh parts
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// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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HashTable<labelList, word> groups(patchEntries.size());
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forAll(patchEntries, patchi)
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{
|
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const dictionary& patchDict = patchEntries[patchi].dict();
|
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|
|
wordList groupNames;
|
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patchDict.readIfPresent("inGroups", groupNames);
|
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|
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forAll(groupNames, groupI)
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{
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HashTable<labelList, word>::iterator iter = groups.find
|
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(
|
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groupNames[groupI]
|
|
);
|
|
if (iter != groups.end())
|
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{
|
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iter().append(patchi);
|
|
}
|
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else
|
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{
|
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groups.insert(groupNames[groupI], labelList(1, patchi));
|
|
}
|
|
}
|
|
}
|
|
|
|
for
|
|
(
|
|
HashTable<labelList, word>::const_iterator iter =
|
|
groups.begin();
|
|
iter != groups.end();
|
|
++iter
|
|
)
|
|
{
|
|
const word& groupName = iter.key();
|
|
const labelList& patchIDs = iter();
|
|
|
|
label nFaces = 0;
|
|
forAll(patchIDs, i)
|
|
{
|
|
nFaces += sizes[patchIDs[i]];
|
|
}
|
|
|
|
// Valid patch if nFace > 0 - add patch to GUI list
|
|
if (nFaces)
|
|
{
|
|
string vtkGrpName = groupName + " - group";
|
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arraySelection->AddArray(vtkGrpName.c_str());
|
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|
|
++nPatches;
|
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|
|
if (enabledEntriesSet.found(vtkGrpName))
|
|
{
|
|
if (!reader_->GetShowGroupsOnly())
|
|
{
|
|
enabledEntriesSet.erase(vtkGrpName);
|
|
forAll(patchIDs, i)
|
|
{
|
|
if (sizes[patchIDs[i]])
|
|
{
|
|
string vtkPatchName =
|
|
names[patchIDs[i]] + " - patch";
|
|
enabledEntriesSet.insert(vtkPatchName);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
// Add (non-zero) patches to the list of mesh parts
|
|
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
if (!reader_->GetShowGroupsOnly())
|
|
{
|
|
forAll(names, patchi)
|
|
{
|
|
// Valid patch if nFace > 0 - add patch to GUI list
|
|
if (sizes[patchi])
|
|
{
|
|
arraySelection->AddArray
|
|
(
|
|
(names[patchi] + " - patch").c_str()
|
|
);
|
|
|
|
++nPatches;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
arrayRangePatches_ += nPatches;
|
|
|
|
// Update enabled entries in case of group selection
|
|
enabledEntries = enabledEntriesSet.toc();
|
|
|
|
if (debug)
|
|
{
|
|
// just for debug info
|
|
getSelectedArrayEntries(arraySelection);
|
|
|
|
Info<< "<end> Foam::vtkPV3Foam::updateInfoPatches" << endl;
|
|
}
|
|
}
|
|
|
|
|
|
void Foam::vtkPV3Foam::updateInfoZones
|
|
(
|
|
vtkDataArraySelection* arraySelection
|
|
)
|
|
{
|
|
if (!reader_->GetIncludeZones())
|
|
{
|
|
return;
|
|
}
|
|
|
|
if (debug)
|
|
{
|
|
Info<< "<beg> Foam::vtkPV3Foam::updateInfoZones"
|
|
<< " [meshPtr=" << (meshPtr_ ? "set" : "nullptr") << "]" << endl;
|
|
}
|
|
|
|
wordList namesLst;
|
|
|
|
//
|
|
// cellZones information
|
|
// ~~~~~~~~~~~~~~~~~~~~~
|
|
if (meshPtr_)
|
|
{
|
|
namesLst = getZoneNames(meshPtr_->cellZones());
|
|
}
|
|
else
|
|
{
|
|
namesLst = getZoneNames("cellZones");
|
|
}
|
|
|
|
arrayRangeCellZones_.reset(arraySelection->GetNumberOfArrays());
|
|
forAll(namesLst, elemI)
|
|
{
|
|
arraySelection->AddArray
|
|
(
|
|
(namesLst[elemI] + " - cellZone").c_str()
|
|
);
|
|
}
|
|
arrayRangeCellZones_ += namesLst.size();
|
|
|
|
|
|
//
|
|
// faceZones information
|
|
// ~~~~~~~~~~~~~~~~~~~~~
|
|
if (meshPtr_)
|
|
{
|
|
namesLst = getZoneNames(meshPtr_->faceZones());
|
|
}
|
|
else
|
|
{
|
|
namesLst = getZoneNames("faceZones");
|
|
}
|
|
|
|
arrayRangeFaceZones_.reset(arraySelection->GetNumberOfArrays());
|
|
forAll(namesLst, elemI)
|
|
{
|
|
arraySelection->AddArray
|
|
(
|
|
(namesLst[elemI] + " - faceZone").c_str()
|
|
);
|
|
}
|
|
arrayRangeFaceZones_ += namesLst.size();
|
|
|
|
|
|
//
|
|
// pointZones information
|
|
// ~~~~~~~~~~~~~~~~~~~~~~
|
|
if (meshPtr_)
|
|
{
|
|
namesLst = getZoneNames(meshPtr_->pointZones());
|
|
}
|
|
else
|
|
{
|
|
namesLst = getZoneNames("pointZones");
|
|
}
|
|
|
|
arrayRangePointZones_.reset(arraySelection->GetNumberOfArrays());
|
|
forAll(namesLst, elemI)
|
|
{
|
|
arraySelection->AddArray
|
|
(
|
|
(namesLst[elemI] + " - pointZone").c_str()
|
|
);
|
|
}
|
|
arrayRangePointZones_ += namesLst.size();
|
|
|
|
if (debug)
|
|
{
|
|
// just for debug info
|
|
getSelectedArrayEntries(arraySelection);
|
|
|
|
Info<< "<end> Foam::vtkPV3Foam::updateInfoZones" << endl;
|
|
}
|
|
}
|
|
|
|
|
|
void Foam::vtkPV3Foam::updateInfoSets
|
|
(
|
|
vtkDataArraySelection* arraySelection
|
|
)
|
|
{
|
|
if (!reader_->GetIncludeSets())
|
|
{
|
|
return;
|
|
}
|
|
|
|
if (debug)
|
|
{
|
|
Info<< "<beg> Foam::vtkPV3Foam::updateInfoSets" << endl;
|
|
}
|
|
|
|
// Add names of sets. Search for last time directory with a sets
|
|
// subdirectory. Take care not to search beyond the last mesh.
|
|
|
|
word facesInstance = dbPtr_().findInstance
|
|
(
|
|
meshDir_,
|
|
"faces",
|
|
IOobject::READ_IF_PRESENT
|
|
);
|
|
|
|
word setsInstance = dbPtr_().findInstance
|
|
(
|
|
meshDir_/"sets",
|
|
word::null,
|
|
IOobject::READ_IF_PRESENT,
|
|
facesInstance
|
|
);
|
|
|
|
IOobjectList objects(dbPtr_(), setsInstance, meshDir_/"sets");
|
|
|
|
if (debug)
|
|
{
|
|
Info<< " Foam::vtkPV3Foam::updateInfoSets read "
|
|
<< objects.names() << " from " << setsInstance << endl;
|
|
}
|
|
|
|
|
|
arrayRangeCellSets_.reset(arraySelection->GetNumberOfArrays());
|
|
arrayRangeCellSets_ += addToSelection<cellSet>
|
|
(
|
|
arraySelection,
|
|
objects,
|
|
" - cellSet"
|
|
);
|
|
|
|
arrayRangeFaceSets_.reset(arraySelection->GetNumberOfArrays());
|
|
arrayRangeFaceSets_ += addToSelection<faceSet>
|
|
(
|
|
arraySelection,
|
|
objects,
|
|
" - faceSet"
|
|
);
|
|
|
|
arrayRangePointSets_.reset(arraySelection->GetNumberOfArrays());
|
|
arrayRangePointSets_ += addToSelection<pointSet>
|
|
(
|
|
arraySelection,
|
|
objects,
|
|
" - pointSet"
|
|
);
|
|
|
|
if (debug)
|
|
{
|
|
// just for debug info
|
|
getSelectedArrayEntries(arraySelection);
|
|
|
|
Info<< "<end> Foam::vtkPV3Foam::updateInfoSets" << endl;
|
|
}
|
|
}
|
|
|
|
|
|
void Foam::vtkPV3Foam::updateInfoLagrangianFields()
|
|
{
|
|
if (debug)
|
|
{
|
|
Info<< "<beg> Foam::vtkPV3Foam::updateInfoLagrangianFields"
|
|
<< endl;
|
|
}
|
|
|
|
vtkDataArraySelection* fieldSelection =
|
|
reader_->GetLagrangianFieldSelection();
|
|
|
|
// preserve the enabled selections
|
|
stringList enabledEntries = getSelectedArrayEntries(fieldSelection);
|
|
fieldSelection->RemoveAllArrays();
|
|
|
|
// TODO - currently only get fields from ONE cloud
|
|
// have to decide if the second set of fields get mixed in
|
|
// or dealt with separately
|
|
|
|
const arrayRange& range = arrayRangeLagrangian_;
|
|
if (range.empty())
|
|
{
|
|
return;
|
|
}
|
|
|
|
int partId = range.start();
|
|
word cloudName = getPartName(partId);
|
|
|
|
// use the db directly since this might be called without a mesh,
|
|
// but the region must get added back in
|
|
fileName lagrangianPrefix(cloud::prefix);
|
|
if (meshRegion_ != polyMesh::defaultRegion)
|
|
{
|
|
lagrangianPrefix = meshRegion_/cloud::prefix;
|
|
}
|
|
|
|
IOobjectList objects
|
|
(
|
|
dbPtr_(),
|
|
dbPtr_().timeName(),
|
|
lagrangianPrefix/cloudName
|
|
);
|
|
|
|
addToSelection<IOField<label>>
|
|
(
|
|
fieldSelection,
|
|
objects
|
|
);
|
|
addToSelection<IOField<scalar>>
|
|
(
|
|
fieldSelection,
|
|
objects
|
|
);
|
|
addToSelection<IOField<vector>>
|
|
(
|
|
fieldSelection,
|
|
objects
|
|
);
|
|
addToSelection<IOField<sphericalTensor>>
|
|
(
|
|
fieldSelection,
|
|
|
|
objects
|
|
);
|
|
addToSelection<IOField<symmTensor>>
|
|
(
|
|
fieldSelection,
|
|
objects
|
|
);
|
|
addToSelection<IOField<tensor>>
|
|
(
|
|
fieldSelection,
|
|
objects
|
|
);
|
|
|
|
// restore the enabled selections
|
|
setSelectedArrayEntries(fieldSelection, enabledEntries);
|
|
|
|
if (debug)
|
|
{
|
|
Info<< "<end> Foam::vtkPV3Foam::updateInfoLagrangianFields - "
|
|
<< "lagrangian objects.size() = " << objects.size() << endl;
|
|
}
|
|
}
|
|
|
|
|
|
// ************************************************************************* //
|