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ENH: read support for EnSight single-file transient (#3154)

Browse Source 
- the ensightReadFile init() now automatically sets up binary/ascii
  (for geometry files) and checks for the transient "BEGIN TIME STEP"
  marker. If found, will also populate the file offsets for each of
  the timesteps.  If no corresponding footer is found (which would be
  very inefficient), it simply pretends that there is only a single
  time step instead of performing a costly file scan.

- parsing of the ensight case file now also supports the use of

      filename numbers:

  as an alternative to

      filename start number:
      filename increment:

- improved parsing robustness of "time values:" entry.
  Can now also have contents on the same line as the introducer.

ENH: base-level adjustments for writing transient single-file

- beginGeometry() is now separated out from file creation.

- in append mode, ensightFile and ensightGeoFile will attempt to
  parse existing time-step information.
This commit is contained in:
Mark Olesen
2024-05-13 18:57:38 +02:00
committed by Kutalmış Berçin
parent ee895577ae
commit dfc9a8923a
43 changed files with 2135 additions and 875 deletions
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3
applications/test/ensightFile/Make/files
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@ -1,3 +0,0 @@
Test-ensightFile.C
EXE = $(FOAM_USER_APPBIN)/Test-ensightFile

8
applications/test/ensightFile/Make/options
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@ -1,8 +0,0 @@
EXE_INC = \
-I$(LIB_SRC)/fileFormats/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/conversion/lnInclude
EXE_LIBS = \
-lmeshTools \
-lconversion

3
applications/test/ensightFile1/Make/files Normal file
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@ -0,0 +1,3 @@
Test-ensightFile1.cxx
EXE = $(FOAM_USER_APPBIN)/Test-ensightFile1

5
applications/test/ensightFile1/Make/options Normal file
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@ -0,0 +1,5 @@
EXE_INC = \
-I$(LIB_SRC)/fileFormats/lnInclude
EXE_LIBS = \
-lfileFormats

137
applications/test/ensightFile1/Test-ensightFile1.cxx Normal file
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@ -0,0 +1,137 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-------------------------------------------------------------------------------
Copyright (C) 2024 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
Test-ensightFile
Description
check cleanup of ensight file and variable names
\*---------------------------------------------------------------------------*/
#include "argList.H"
#include "ensightFile.H"
#include "ensightGeoFile.H"
#include "Switch.H"
#include "IOstreams.H"
using namespace Foam;
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Main program:
int main(int argc, char *argv[])
{
argList::noBanner();
argList::noParallel();
argList::addBoolOption("ascii", "open as ascii instead of binary");
argList::addBoolOption("binary", "(default)");
argList::addBoolOption("clear", "force clear of time-steps");
argList::addBoolOption("no-end", "skip use of endTimeStep");
argList::addBoolOption("append", "open in append mode");
argList::addOption("geom", "geometry file");
argList::addOption("field", "field file");
#include "setRootCase.H"
const bool with_ascii = args.found("ascii") && !args.found("binary");
// const bool with_binary = args.found("binary");
const bool with_append = args.found("append");
const bool with_clear = args.found("clear");
const bool without_end = args.found("no-end");
const IOstreamOption::streamFormat fmt =
(
with_ascii
? IOstreamOption::ASCII
: IOstreamOption::BINARY
);
const IOstreamOption::appendType append =
(
with_append
? IOstreamOption::APPEND_ATE
: IOstreamOption::NO_APPEND
);
fileName file;
if (args.readIfPresent("geom", file))
{
Info<< "Open " << file << " as geometry "
<< " format:" << (with_ascii ? "ASCII" : "BINARY")
<< " append:" << Switch::name(with_append) << nl;
ensightGeoFile ensFile(append, file, fmt);
if (append)
{
ensFile.beginTimeStep();
// At the moment need to pair begin/end time-step calls
if (!without_end)
{
ensFile.endTimeStep();
}
}
if (with_clear)
{
ensFile.clearTimeSteps();
}
}
if (args.readIfPresent("field", file))
{
Info<< "Open " << file << " as field"
<< " format:" << (with_ascii ? "ASCII" : "BINARY")
<< " append:" << Switch::name(with_append) << nl;
ensightFile ensFile(append, file, fmt);
if (append)
{
ensFile.beginTimeStep();
// At the moment need to pair begin/end time-step calls
if (!without_end)
{
ensFile.endTimeStep();
}
}
if (with_clear)
{
ensFile.clearTimeSteps();
}
}
Info<< "\nEnd\n" << endl;
return 0;
}
// ************************************************************************* //

3
applications/test/ensightFileName/Make/files Normal file
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@ -0,0 +1,3 @@
Test-ensightFileName.cxx
EXE = $(FOAM_USER_APPBIN)/Test-ensightFileName

5
applications/test/ensightFileName/Make/options Normal file
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@ -0,0 +1,5 @@
EXE_INC = \
-I$(LIB_SRC)/fileFormats/lnInclude
EXE_LIBS = \
-lfileFormats

4
applications/test/ensightFile/Test-ensightFile.C → applications/test/ensightFileName/Test-ensightFileName.cxx
View File

@ -24,10 +24,10 @@ License
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
Application
Test-ensightFile
Test-ensightFileName
Description
check cleanup of ensight file and variable names
Check cleanup of ensight file and variable names
\*---------------------------------------------------------------------------*/

399
applications/utilities/mesh/conversion/ensightToFoam/ensightMeshReader.C
View File

@ -5,7 +5,7 @@
\\ / A nd | www.openfoam.com
\\/ M anipulation |
-------------------------------------------------------------------------------
Copyright (C) 2022-2023 OpenCFD Ltd.
Copyright (C) 2022-2024 OpenCFD Ltd.
-------------------------------------------------------------------------------
License
This file is part of OpenFOAM.
@ -93,29 +93,34 @@ void Foam::fileFormats::ensightMeshReader::readIDs
(
ensightReadFile& is,
const bool doRead,
const label nShapes,
const label elemCount,
labelList& foamToElem,
Map<label>& elemToFoam
) const
{
const label sz = foamToElem.size();
foamToElem.resize(sz+nShapes);
const label begElem = foamToElem.size();
const label endElem = begElem + elemCount;
foamToElem.resize(foamToElem.size()+elemCount);
if (doRead)
{
elemToFoam.reserve(elemToFoam.size()+nShapes);
for (label shapei = 0; shapei < nShapes; shapei++)
elemToFoam.reserve(elemToFoam.size()+elemCount);
for (label elemi = begElem; elemi < endElem; ++elemi)
{
label elemi;
is.read(elemi);
foamToElem[sz+shapei] = elemi;
elemToFoam.insert(elemi, sz+shapei);
label id;
is.read(id);
foamToElem[elemi] = id;
elemToFoam.insert(id, elemi);
}
}
else
{
for (label shapei = 0; shapei < nShapes; shapei++)
// identity
for (label elemi = begElem; elemi < endElem; ++elemi)
{
foamToElem[sz+shapei] = sz+shapei;
foamToElem[elemi] = elemi;
}
}
}
@ -209,37 +214,54 @@ bool Foam::fileFormats::ensightMeshReader::readGoldPart
// Work
DynamicList<label> verts;
string line;
string buffer;
while (is.good())
{
do
{
is.readKeyword(line);
// Get entire line/string
is.read(buffer);
}
while (line.empty() && is.good());
while (buffer.empty() && is.good());
const auto split = stringOps::splitSpace(line);
if (!is.good())
{
break;
}
else if (buffer.contains("BEGIN TIME STEP"))
{
// Graciously handle a miscued start
continue;
}
else if (buffer.contains("END TIME STEP"))
{
// END TIME STEP is a valid means to terminate input
break;
}
const auto split = stringOps::splitSpace(buffer);
if (split.size() == 0)
if (split.empty())
{
continue;
}
if (split[0] == "part")
const auto keyword(split[0].str());
if (keyword == "part")
{
return false;
}
else if (split[0] == "node_ids")
else if (keyword == "node_ids")
{
const label nPoints = points.size();
// Ignore for now
for (label i = 0; i < nPoints; i++)
// Ignore point ids
for (label pointi = 0; pointi < nPoints; ++pointi)
{
label index;
is.read(index);
label id;
is.read(id);
}
}
else if (split[0] == "coordinates")
else if (keyword == "coordinates")
{
label nPoints;
is.read(nPoints);
@ -257,207 +279,205 @@ bool Foam::fileFormats::ensightMeshReader::readGoldPart
nodeIdToPoints
);
points.setSize(nPoints);
for (label pointi = 0; pointi < nPoints; pointi++)
{
is.read(points[pointi].x());
}
for (label pointi = 0; pointi < nPoints; pointi++)
{
is.read(points[pointi].y());
}
for (label pointi = 0; pointi < nPoints; pointi++)
{
is.read(points[pointi].z());
}
is.readPoints(nPoints, points);
}
else if (split[0] == "tetra4")
else if (keyword == "tetra4")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent<< "tetra4 " << nShapes
Pout<< indent<< "tetra4 " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label celli = cells.size();
cells.resize(celli+nShapes);
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
cellToElemIds,
elemIdToCells
);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
cells.resize(startElemi+elemCount);
faceListList::subList myElements = cells.slice(startElemi);
const auto& model = cellModel::ref(cellModel::TET);
for (label shapei = 0; shapei < nShapes; shapei++)
for (auto& cellFaces : myElements)
{
readVerts(is, 4, nodeIdToPoints, verts);
if (setHandedness_)
{
setHandedness(model, verts, points);
}
const cellShape cellVerts(model, verts);
cells[celli+shapei] = cellVerts.faces();
cellFaces = cellShape(model, verts).faces();
}
}
else if (split[0] == "pyramid5")
else if (keyword == "pyramid5")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent<< "pyramid5 " << nShapes
Pout<< indent<< "pyramid5 " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label celli = cells.size();
cells.resize(celli+nShapes);
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
cellToElemIds,
elemIdToCells
);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
cells.resize(startElemi+elemCount);
faceListList::subList myElements = cells.slice(startElemi);
const auto& model = cellModel::ref(cellModel::PYR);
for (label shapei = 0; shapei < nShapes; shapei++)
for (auto& cellFaces : myElements)
{
readVerts(is, 5, nodeIdToPoints, verts);
if (setHandedness_)
{
setHandedness(model, verts, points);
}
const cellShape cellVerts(model, verts);
cells[celli+shapei] = cellVerts.faces();
cellFaces = cellShape(model, verts).faces();
}
}
else if (split[0] == "penta6")
else if (keyword == "penta6")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent<< "penta6 " << nShapes
Pout<< indent<< "penta6 " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label celli = cells.size();
cells.resize(celli+nShapes);
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
cellToElemIds,
elemIdToCells
);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
cells.resize(startElemi+elemCount);
faceListList::subList myElements = cells.slice(startElemi);
const auto& model = cellModel::ref(cellModel::PRISM);
for (label shapei = 0; shapei < nShapes; shapei++)
for (auto& cellFaces : myElements)
{
readVerts(is, 6, nodeIdToPoints, verts);
if (setHandedness_)
{
setHandedness(model, verts, points);
}
const cellShape cellVerts(model, verts);
cells[celli+shapei] = cellVerts.faces();
cellFaces = cellShape(model, verts).faces();
}
}
else if (split[0] == "hexa8")
else if (keyword == "hexa8")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent<< "hexa8 " << nShapes
Pout<< indent<< "hexa8 " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label celli = cells.size();
cells.resize(celli+nShapes);
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
cellToElemIds,
elemIdToCells
);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
cells.resize(startElemi+elemCount);
faceListList::subList myElements = cells.slice(startElemi);
const auto& model = cellModel::ref(cellModel::HEX);
for (label shapei = 0; shapei < nShapes; shapei++)
for (auto& cellFaces : myElements)
{
readVerts(is, 8, nodeIdToPoints, verts);
if (setHandedness_)
{
setHandedness(model, verts, points);
}
const cellShape cellVerts(model, verts);
cells[celli+shapei] = cellVerts.faces();
cellFaces = cellShape(model, verts).faces();
}
}
else if (split[0] == "nfaced")
else if (keyword == "nfaced")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent<< "nfaced " << nShapes
Pout<< indent<< "nfaced " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label celli = cells.size();
cells.resize(celli+nShapes);
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
cellToElemIds,
elemIdToCells
);
for (label shapei = 0; shapei < nShapes; shapei++)
// Extend and fill the new trailing portion
const label startElemi = cells.size();
cells.resize(startElemi+elemCount);
faceListList::subList myElements = cells.slice(startElemi);
for (auto& cellFaces : myElements)
{
label nFaces;
is.read(nFaces);
faceList& cellFaces = cells[celli+shapei];
cellFaces.setSize(nFaces);
cellFaces.resize(nFaces);
}
for (label shapei = 0; shapei < nShapes; shapei++)
for (auto& cellFaces : myElements)
{
faceList& cellFaces = cells[celli+shapei];
forAll(cellFaces, cellFacei)
for (face& f : cellFaces)
{
label nVerts;
is.read(nVerts);
cellFaces[cellFacei].setSize(nVerts);
f.resize(nVerts);
}
}
for (label shapei = 0; shapei < nShapes; shapei++)
for (faceList& cellFaces : myElements)
{
faceList& cellFaces = cells[celli+shapei];
forAll(cellFaces, cellFacei)
for (face& f : cellFaces)
{
face& f = cellFaces[cellFacei];
readVerts(is, f.size(), nodeIdToPoints, verts);
f.labelList::operator=(verts);
}
}
forAll(f, fp)
// Full check
forAll(myElements, elemi)
{
for (const face& f : myElements[elemi])
{
for (label pointi : f)
{
if (f[fp] < 0 || f[fp] >= points.size())
if (pointi < 0 || pointi >= points.size())
{
FatalErrorInFunction<< "Face:" << shapei
FatalErrorInFunction
<< "Face:" << elemi
<< " verts:" << f
<< " indexes outside points:" << points.size()
<< exit(FatalError);
@ -466,107 +486,104 @@ bool Foam::fileFormats::ensightMeshReader::readGoldPart
}
}
}
else if (split[0] == "tria3")
else if (keyword == "tria3")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent << "tria3 " << nShapes
Pout<< indent << "tria3 " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label facei = faces.size();
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
faceToElemIDs,
elemIdToFaces
);
faces.setSize(facei+nShapes);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
faces.resize(startElemi+elemCount, face(3)); // <- tria3
faceList::subList myElements = faces.slice(startElemi);
for (label shapei = 0; shapei < nShapes; shapei++)
for (face& f : myElements)
{
auto& f = faces[facei+shapei];
f.setSize(3);
readVerts(is, f.size(), nodeIdToPoints, verts);
f.labelList::operator=(verts);
}
}
else if (split[0] == "quad4")
else if (keyword == "quad4")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent << "quad4 " << nShapes
Pout<< indent << "quad4 " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label facei = faces.size();
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
faceToElemIDs,
elemIdToFaces
);
faces.setSize(facei+nShapes);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
faces.resize(startElemi+elemCount, face(4)); // <- quad4
faceList::subList myElements = faces.slice(startElemi);
for (label shapei = 0; shapei < nShapes; shapei++)
for (face& f : myElements)
{
auto& f = faces[facei+shapei];
f.setSize(4);
readVerts(is, f.size(), nodeIdToPoints, verts);
f.labelList::operator=(verts);
}
}
else if (split[0] == "nsided")
else if (keyword == "nsided")
{
label nShapes;
is.read(nShapes);
label elemCount;
is.read(elemCount);
Pout<< indent << "nsided " << nShapes
Pout<< indent << "nsided " << elemCount
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
const label facei = faces.size();
readIDs
(
is,
read_elem_ids,
nShapes,
elemCount,
faceToElemIDs,
elemIdToFaces
);
faces.setSize(facei+nShapes);
// Extend and fill the new trailing portion
const label startElemi = cells.size();
faces.resize(startElemi+elemCount);
faceList::subList myElements = faces.slice(startElemi);
for (label shapei = 0; shapei < nShapes; shapei++)
for (face& f : myElements)
{
auto& f = faces[facei+shapei];
label nVerts;
is.read(nVerts);
f.setSize(nVerts);
f.resize(nVerts);
}
for (label shapei = 0; shapei < nShapes; shapei++)
for (face& f : myElements)
{
auto& f = faces[facei+shapei];
readVerts(is, f.size(), nodeIdToPoints, verts);
f.labelList::operator=(verts);
}
}
else
{
WarningInFunction << "Unhandled key " << string(split[0])
<< " from line " << line
WarningInFunction << "Unhandled key " << keyword
<< " from line " << buffer
<< " starting at line " << is.lineNumber()
<< " position " << is.stdStream().tellg() << endl;
}
@ -584,16 +601,21 @@ bool Foam::fileFormats::ensightMeshReader::readGeometry
const scalar scaleFactor
)
{
// Auto-detect ascii/binary format,
// skips any initial "BEGIN TIME STEP"
ensightReadFile is(geometryFile_);
// Skip 'binary' tag
is.readBinaryHeader();
string header;
is.read(header);
Info<< "Ensight : " << header << endl;
is.read(header);
Info<< "Ensight : " << header << endl;
string buffer;
// Ensight Geometry File
is.read(buffer);
Info<< "Ensight : " << buffer << nl;
// Description - 1
is.read(buffer);
Info<< "Ensight : " << buffer << nl;
bool read_node_ids = false;
@ -623,61 +645,72 @@ bool Foam::fileFormats::ensightMeshReader::readGeometry
// Parse all
string line;
SubStrings<string> split;
while (is.good())
{
do
{
is.readKeyword(line);
// Get entire line/string
is.read(buffer);
}
while (line.empty() && is.good());
const auto split = stringOps::splitSpace(line);
while (buffer.empty() && is.good());
if (buffer.contains("END TIME STEP"))
{
// END TIME STEP is a valid means to terminate input
break;
}
split = stringOps::splitSpace(buffer);
if (split[0] == "extents")
if (split.empty())
{
point min;
point max;
is.read(min.x());
is.read(max.x());
is.read(min.y());
is.read(max.y());
is.read(min.z());
is.read(max.z());
Pout<< indent
<< "Read extents " << boundBox(min, max)
<< endl;
continue;
}
else if (split[0] == "node")
const auto keyword(split[0].str());
if (keyword == "extents")
{
word id(split[1]);
word op(split[2]);
// Optional extents (xmin, xmax, ymin, ymax, zmin, zmax)
boundBox bb;
point& min = bb.min();
point& max = bb.max();
is.read(min.x()); is.read(max.x());
is.read(min.y()); is.read(max.y());
is.read(min.z()); is.read(max.z());
Pout<< indent << "Read extents " << bb << endl;
}
else if (keyword == "node")
{
// "node id (off|assign|given|ignore)"
std::string op(split[2]);
if (op == "given" || op == "ignore")
{
Pout<< indent << "Reading node ids" << endl;
read_node_ids = true;
}
}
else if (split[0] == "element")
else if (keyword == "element")
{
word id(split[1]);
word op(split[2]);
// "element id (off|assign|given|ignore)"
std::string op(split[2]);
if (op == "given" || op == "ignore")
{
Pout<< indent << "Reading element ids" << endl;
read_elem_ids = true;
}
}
else if (split[0] == "part")
else if (keyword == "part")
{
bool finished = false;
do
{
// Make space
partIDs.emplace_back();
is.read(partIDs.back());
partNames.emplace_back();
is.read(partNames.back());
// Read part id and name
is.read(partIDs.emplace_back());
is.read(partNames.emplace_back());
Pout<< indent
<< "Reading part " << partIDs.back()
@ -954,7 +987,7 @@ bool Foam::fileFormats::ensightMeshReader::readGeometry
const face& f = rotateFace(cFaces[cFacei], rotatedFace);
const auto fFnd = vertsToCell.find(f);
if (fFnd)
if (fFnd.good())
{
// Already inserted. Internal face.
vertsToCell.erase(fFnd);
@ -1026,7 +1059,12 @@ bool Foam::fileFormats::ensightMeshReader::readGeometry
)
);
if (!cAndF)
if (cAndF.good())
{
partCellAndFace[patchFacei++] = cAndF.val();
vertsToCell.erase(cAndF);
}
else
{
//WarningInFunction
// << "Did not find face " << facei
@ -1036,11 +1074,6 @@ bool Foam::fileFormats::ensightMeshReader::readGeometry
// << " in part " << parti
// << endl;
}
else
{
partCellAndFace[patchFacei++] = cAndF();
vertsToCell.erase(cAndF);
}
}
partCellAndFace.setSize(patchFacei);
}

6
applications/utilities/postProcessing/dataConversion/foamToEnsight/foamToEnsight.C
View File

@ -554,7 +554,8 @@ int main(int argc, char *argv[])
{
autoPtr<ensightGeoFile> os =
ensCase.newGeometry(hasMovingMesh);
ensMesh.write(os);
ensMesh.write(os.ref());
}
// finite-area
@ -562,7 +563,8 @@ int main(int argc, char *argv[])
{
autoPtr<ensightGeoFile> os =
ensFaCasePtr->newGeometry(hasMovingMesh);
ensFaMeshPtr->write(os);
ensFaMeshPtr->write(os.ref());
}
}