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foamChemistryReader: Added support for elements and specie composition

Browse Source 
Based on a patch contributed by Francesco Contino, Tommaso Lucchini,
Gianluca D’Errico, Hervé Jeanmart, Nicolas Bourgeois and Stéphane
Backaert.
This commit is contained in:
Henry Weller
2016-07-12 09:05:00 +01:00
parent d50bce000d
commit a6db20e3bb
12 changed files with 385 additions and 68 deletions
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4
applications/utilities/thermophysical/chemkinToFoam/chemkinToFoam.C
View File

@ -88,8 +88,8 @@ int main(int argc, char *argv[])
{
elementsDict.add
(
cr.specieComposition()[speciesList[si]][ei].elementName,
cr.specieComposition()[speciesList[si]][ei].nAtoms
cr.specieComposition()[speciesList[si]][ei].name(),
cr.specieComposition()[speciesList[si]][ei].nAtoms()
);
}

9
src/thermophysicalModels/reactionThermo/chemistryReaders/chemistryReader/chemistryReader.H
View File

@ -36,15 +36,19 @@ SourceFiles
#define chemistryReader_H
#include "typeInfo.H"
#include "runTimeSelectionTables.H"
#include "specieElement.H"
#include "Reaction.H"
#include "ReactionList.H"
#include "runTimeSelectionTables.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
typedef HashTable<List<specieElement>> speciesCompositionTable;
/*---------------------------------------------------------------------------*\
Class chemistryReader Declaration
\*---------------------------------------------------------------------------*/
@ -112,6 +116,9 @@ public:
//- Return access to the list of species
virtual const speciesTable& species() const = 0;
//- Table of species composition
virtual const speciesCompositionTable& specieComposition() const = 0;
//- Return access to the thermo packages
virtual const HashPtrTable<ThermoType>& speciesThermo() const = 0;

21
src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L
View File

@ -68,9 +68,6 @@ int yyFlexLexer::yywrap()
Foam::string foamSpecieString(const char* YYText)
{
Foam::string specieString(YYText);
// Transforming parentheses is no longer necessary
//specieString.replaceAll('(', '<');
//specieString.replaceAll(')', '>');
return specieString;
}
@ -483,9 +480,9 @@ bool finishReaction = false;
if (elementName.size() && nAtoms)
{
correctElementName(elementName);
currentSpecieComposition[nSpecieElements].elementName =
currentSpecieComposition[nSpecieElements].name() =
elementName;
currentSpecieComposition[nSpecieElements++].nAtoms = nAtoms;
currentSpecieComposition[nSpecieElements++].nAtoms() = nAtoms;
}
}
@ -540,24 +537,24 @@ bool finishReaction = false;
)
{
correctElementName(elementName);
currentSpecieComposition[nSpecieElements].elementName =
currentSpecieComposition[nSpecieElements].name() =
elementName;
currentSpecieComposition[nSpecieElements++].nAtoms = nAtoms;
currentSpecieComposition[nSpecieElements++].nAtoms() = nAtoms;
}
currentSpecieComposition.setSize(nSpecieElements);
HashTable<List<specieElement>>::iterator specieCompositionIter
speciesCompositionTable::iterator specieCompositionIter
(
specieComposition_.find(currentSpecieName)
speciesComposition_.find(currentSpecieName)
);
if (specieCompositionIter != specieComposition_.end())
if (specieCompositionIter != speciesComposition_.end())
{
specieComposition_.erase(specieCompositionIter);
speciesComposition_.erase(specieCompositionIter);
}
specieComposition_.insert
speciesComposition_.insert
(
currentSpecieName,
currentSpecieComposition

18
src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.C
View File

@ -119,8 +119,8 @@ Foam::scalar Foam::chemkinReader::molecularWeight
forAll(specieComposition, i)
{
label nAtoms = specieComposition[i].nAtoms;
const word& elementName = specieComposition[i].elementName;
label nAtoms = specieComposition[i].nAtoms();
const word& elementName = specieComposition[i].name();
if (isotopeAtomicWts_.found(elementName))
{
@ -428,24 +428,26 @@ void Foam::chemkinReader::addReaction
forAll(lhs, i)
{
const List<specieElement>& specieComposition =
specieComposition_[speciesTable_[lhs[i].index]];
speciesComposition_[speciesTable_[lhs[i].index]];
forAll(specieComposition, j)
{
label elementi = elementIndices_[specieComposition[j].elementName];
nAtoms[elementi] += lhs[i].stoichCoeff*specieComposition[j].nAtoms;
label elementi = elementIndices_[specieComposition[j].name()];
nAtoms[elementi] +=
lhs[i].stoichCoeff*specieComposition[j].nAtoms();
}
}
forAll(rhs, i)
{
const List<specieElement>& specieComposition =
specieComposition_[speciesTable_[rhs[i].index]];
speciesComposition_[speciesTable_[rhs[i].index]];
forAll(specieComposition, j)
{
label elementi = elementIndices_[specieComposition[j].elementName];
nAtoms[elementi] -= rhs[i].stoichCoeff*specieComposition[j].nAtoms;
label elementi = elementIndices_[specieComposition[j].name()];
nAtoms[elementi] -=
rhs[i].stoichCoeff*specieComposition[j].nAtoms();
}
}

42
src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinReader.H
View File

@ -46,7 +46,6 @@ SourceFiles
#include "labelList.H"
#include "speciesTable.H"
#include "atomicWeights.H"
#include "reactionTypes.H"
#include <FlexLexer.h>
@ -77,33 +76,6 @@ public:
gas
};
//- species element
struct specieElement
{
word elementName;
label nAtoms;
bool operator==(const specieElement& se) const
{
return
(
nAtoms == se.nAtoms
&& elementName == se.elementName
);
}
bool operator!=(const specieElement& se) const
{
return !operator==(se);
}
friend Ostream& operator<<(Ostream& os, const specieElement& se)
{
os << se.nAtoms << token::SPACE << se.elementName;
return os;
}
};
private:
@ -203,7 +175,7 @@ private:
HashPtrTable<gasHThermoPhysics> speciesThermo_;
//- Table of species composition
HashTable<List<specieElement>> specieComposition_;
speciesCompositionTable speciesComposition_;
//- List of the reactions
ReactionList<gasHThermoPhysics> reactions_;
@ -369,6 +341,12 @@ public:
return speciesTable_;
}
//- Table of species composition
const speciesCompositionTable& specieComposition() const
{
return speciesComposition_;
}
//- Specie phase
const HashTable<phase>& speciePhase() const
{
@ -381,12 +359,6 @@ public:
return speciesThermo_;
}
//- Table of species composition
const HashTable<List<specieElement>>& specieComposition() const
{
return specieComposition_;
}
//- List of the reactions
const ReactionList<gasHThermoPhysics>& reactions() const
{

89
src/thermophysicalModels/reactionThermo/chemistryReaders/foamChemistryReader/foamChemistryReader.C
View File

@ -42,6 +42,85 @@ Foam::speciesTable& Foam::foamChemistryReader<ThermoType>::setSpecies
}
template<class ThermoType>
void Foam::foamChemistryReader<ThermoType>::readSpeciesComposition()
{
if (!chemDict_.found("elements"))
{
Info<< " elements not defined in " << chemDict_.name() << endl;
return;
}
wordList e(chemDict_.lookup("elements"));
label currentElementIndex(0);
DynamicList<word> elementNames_;
HashTable<label> elementIndices_;
forAll(e, ei)
{
if (!elementIndices_.found(e[ei]))
{
elementIndices_.insert(e[ei], currentElementIndex++);
elementNames_.append(e[ei]);
}
else
{
IOWarningInFunction(chemDict_)
<< "element " << e[ei] << " already in table." << endl;
}
}
// Loop through all species in thermoDict to retrieve
// the species composition
forAll(speciesTable_, si)
{
if (thermoDict_.subDict(speciesTable_[si]).isDict("elements"))
{
dictionary currentElements
(
thermoDict_.subDict(speciesTable_[si]).subDict("elements")
);
wordList currentElementsName(currentElements.toc());
List<specieElement> currentComposition(currentElementsName.size());
forAll(currentElementsName, eni)
{
currentComposition[eni].name() = currentElementsName[eni];
currentComposition[eni].nAtoms() =
currentElements.lookupOrDefault
(
currentElementsName[eni],
0
);
}
// Add current specie composition to the hash table
speciesCompositionTable::iterator specieCompositionIter
(
speciesComposition_.find(speciesTable_[si])
);
if (specieCompositionIter != speciesComposition_.end())
{
speciesComposition_.erase(specieCompositionIter);
}
speciesComposition_.insert(speciesTable_[si], currentComposition);
}
else
{
FatalIOErrorInFunction(thermoDict_)
<< "Specie " << speciesTable_[si]
<< " does not contain element description."
<< exit(FatalIOError);
}
}
}
// * * * * * * * * * * * * * * * * Constructor * * * * * * * * * * * * * * * //
template<class ThermoType>
@ -70,7 +149,9 @@ Foam::foamChemistryReader<ThermoType>::foamChemistryReader
speciesTable_(setSpecies(chemDict_, species)),
speciesThermo_(thermoDict_),
reactions_(speciesTable_, speciesThermo_, chemDict_)
{}
{
readSpeciesComposition();
}
template<class ThermoType>
@ -95,10 +176,12 @@ Foam::foamChemistryReader<ThermoType>::foamChemistryReader
fileName(thermoDict.lookup("foamChemistryThermoFile")).expand()
)()
),
speciesThermo_(thermoDict_),
speciesTable_(setSpecies(chemDict_, species)),
speciesThermo_(thermoDict_),
reactions_(speciesTable_, speciesThermo_, chemDict_)
{}
{
readSpeciesComposition();
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

34
src/thermophysicalModels/reactionThermo/chemistryReaders/foamChemistryReader/foamChemistryReader.H
View File

@ -63,12 +63,21 @@ class foamChemistryReader
//- Thermo properties dictionary
dictionary thermoDict_;
//- Table of the thermodynamic data given in the foamChemistry file
HashPtrTable<ThermoType> speciesThermo_;
//- List of elements
DynamicList<word> elementNames_;
//- Element indices
HashTable<label> elementIndices_;
//- Table of species
speciesTable& speciesTable_;
//- Table of species composition
speciesCompositionTable speciesComposition_;
//- Table of the thermodynamic data given in the foamChemistry file
HashPtrTable<ThermoType> speciesThermo_;
//- List of the reactions
ReactionList<ThermoType> reactions_;
@ -78,6 +87,9 @@ class foamChemistryReader
//- Set the species list
speciesTable& setSpecies(const dictionary& dict, speciesTable& species);
//- Read the species composition
void readSpeciesComposition();
//- Disallow default bitwise copy construct
foamChemistryReader(const foamChemistryReader&);
@ -117,12 +129,30 @@ public:
// Member functions
//- List of elements
const wordList& elementNames() const
{
return elementNames_;
}
//- Element indices
const HashTable<label>& elementIndices() const
{
return elementIndices_;
}
//- Table of species
const speciesTable& species() const
{
return speciesTable_;
}
//- Table of species composition
const speciesCompositionTable& specieComposition() const
{
return speciesComposition_;
}
//- Table of the thermodynamic data given in the foamChemistry file
const HashPtrTable<ThermoType>& speciesThermo() const
{

121
src/thermophysicalModels/specie/specieElement/specieElement.H Normal file
View File

@ -0,0 +1,121 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2016 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
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/>.
Class
Foam::specieElement
Description
SourceFiles
specieElementI.H
\*---------------------------------------------------------------------------*/
#ifndef specieElement_H
#define specieElement_H
#include "word.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
// Forward declaration of friend functions and operators
class specieElement;
Ostream& operator<<(Ostream&, const specieElement&);
/*---------------------------------------------------------------------------*\
Class specieElement Declaration
\*---------------------------------------------------------------------------*/
class specieElement
{
// Private data
//- Name of the element
word name_;
//- Number of atoms of this element in the specie
label nAtoms_;
public:
// Constructors
//- Construct null
inline specieElement();
//- Construct from components
inline specieElement(const word& name, const label nAtoms);
//- Construct from Istream
inline specieElement(Istream&);
// Member Functions
//- Return the name of the element
inline const word& name() const;
//- Return non-const access to the name of the element
inline word& name();
//- Return the number of atoms of this element in the specie
inline label nAtoms() const;
//- Return non-const access to the number of atoms of this element
// in the specie
inline label& nAtoms();
// Member Operators
//- Equality comparison
inline bool operator==(const specieElement&) const;
//- Inequality comparison
inline bool operator!=(const specieElement&) const;
// IOstream Operators
inline friend Ostream& operator<<(Ostream&, const specieElement&);
};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#include "specieElementI.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
#endif
// ************************************************************************* //

101
src/thermophysicalModels/specie/specieElement/specieElementI.H Normal file
View File

@ -0,0 +1,101 @@
/*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
\\ / A nd | Copyright (C) 2016 OpenFOAM Foundation
\\/ M anipulation |
-------------------------------------------------------------------------------
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/>.
\*---------------------------------------------------------------------------*/
#include "token.H"
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
inline Foam::specieElement::specieElement()
{}
inline Foam::specieElement::specieElement(const word& name, const label nAtoms)
:
name_(name),
nAtoms_(nAtoms)
{}
inline Foam::specieElement::specieElement(Istream& is)
:
name_(is),
nAtoms_(readLabel(is))
{}
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::word& Foam::specieElement::name() const
{
return name_;
}
inline Foam::word& Foam::specieElement::name()
{
return name_;
}
inline Foam::label Foam::specieElement::nAtoms() const
{
return nAtoms_;
}
inline Foam::label& Foam::specieElement::nAtoms()
{
return nAtoms_;
}
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
inline bool Foam::specieElement::operator==(const specieElement& se) const
{
return
(
nAtoms_ == se.nAtoms_
&& name_ == se.name_
);
}
inline bool Foam::specieElement::operator!=(const specieElement& se) const
{
return !operator==(se);
}
// * * * * * * * * * * * * * * * Ostream Operator * * * * * * * * * * * * * //
inline Foam::Ostream& Foam::operator<<(Ostream& os, const specieElement& se)
{
os << se.name() << token::SPACE << se.nAtoms();
return os;
}
// ************************************************************************* //

4
tutorials/combustion/chemFoam/gri/Allclean
View File

@ -6,7 +6,7 @@ cd ${0%/*} || exit 1 # Run from this directory
cleanCase
rm -rf 0 chemFoam.out validation/OF_vs_CHEMKINII.eps validation/chemkinII
rm -rf 0 chemFoam.out constant/reactions constant/thermo \
validation/OF_vs_CHEMKINII.eps validation/chemkinII
#------------------------------------------------------------------------------

4
tutorials/combustion/chemFoam/gri/Allrun
View File

@ -7,6 +7,10 @@ cd ${0%/*} || exit 1 # Run from this directory
# Set application name
application=`getApplication`
runApplication chemkinToFoam \
chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
constant/reactions constant/thermo
runApplication $application
(cd validation && ./Allrun $*)

6
tutorials/combustion/chemFoam/gri/constant/thermophysicalProperties
View File

@ -26,8 +26,8 @@ thermoType
specie specie;
}
CHEMKINFile "$FOAM_CASE/chemkin/chem.inp";
CHEMKINThermoFile "$FOAM_CASE/chemkin/therm.dat";
CHEMKINTransportFile "$FOAM_CASE/chemkin/transportProperties";
chemistryReader foamChemistryReader;
foamChemistryFile "$FOAM_CASE/constant/reactions";
foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
// ************************************************************************* //