molecule.H

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/*---------------------------------------------------------------------------*\
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  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
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    \\  /    A nd           | www.openfoam.com
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-------------------------------------------------------------------------------
    Copyright (C) 2011-2017 OpenFOAM Foundation
    Copyright (C) 2016 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/>.
 
Class
    Foam::molecule
 
Description
    Foam::molecule
 
SourceFiles
    moleculeI.H
    molecule.C
    moleculeIO.C
 
\*---------------------------------------------------------------------------*/
 
#ifndef molecule_H
#define molecule_H
 
#include "particle.H"
#include "IOstream.H"
#include "autoPtr.H"
#include "diagTensor.H"
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
namespace Foam
{
 
// Class forward declarations
class moleculeCloud;
 
 
// Forward declaration of friend functions and operators
 
class molecule;
 
Ostream& operator<<(Ostream&, const molecule&);
 
 
/*---------------------------------------------------------------------------*\
                           Class molecule Declaration
\*---------------------------------------------------------------------------*/
 
class molecule
:
    public particle
{
public:
 
    //- Size in bytes of the fields
    static const std::size_t sizeofFields;
 
 
    // Values of special that are less than zero are for built-in functionality.
    // Values greater than zero are user specifiable/expandable
    // (i.e. test special_ >= SPECIAL_USER)
 
    enum specialTypes
    {
        SPECIAL_TETHERED = -1,
        SPECIAL_FROZEN   = -2,
        NOT_SPECIAL      = 0,
        SPECIAL_USER     = 1
    };
 
 
    //- Class to hold molecule constant properties
    class constantProperties
    {
        // Private data
 
            Field<vector> siteReferencePositions_;
 
            List<scalar> siteMasses_;
 
            List<scalar> siteCharges_;
 
            List<label> siteIds_;
 
            List<bool> pairPotentialSites_;
 
            List<bool> electrostaticSites_;
 
            diagTensor momentOfInertia_;
 
            scalar mass_;
 
 
        // Private Member Functions
 
            void checkSiteListSizes() const;
 
            void setInteracionSiteBools
            (
                const List<word>& siteIds,
                const List<word>& pairPotSiteIds
            );
 
            bool linearMoleculeTest() const;
 
 
    public:
 
        inline constantProperties();
 
        //- Construct from dictionary
        inline constantProperties(const dictionary& dict);
 
        // Member functions
 
        inline const Field<vector>& siteReferencePositions() const;
 
        inline const List<scalar>& siteMasses() const;
 
        inline const List<scalar>& siteCharges() const;
 
        inline const List<label>& siteIds() const;
 
        inline List<label>& siteIds();
 
        inline const List<bool>& pairPotentialSites() const;
 
        inline bool pairPotentialSite(label sId) const;
 
        inline const List<bool>& electrostaticSites() const;
 
        inline bool electrostaticSite(label sId) const;
 
        inline const diagTensor& momentOfInertia() const;
 
        inline bool linearMolecule() const;
 
        inline bool pointMolecule() const;
 
        inline label degreesOfFreedom() const;
 
        inline scalar mass() const;
 
        inline label nSites() const;
    };
 
 
    //- Class used to pass tracking data to the trackToFace function
    class trackingData
    :
        public particle::trackingData
    {
        // label specifying which part of the integration algorithm is taking
        label part_;
 
 
    public:
 
        // Constructors
 
            trackingData(moleculeCloud& cloud, label part)
            :
                particle::trackingData(cloud),
                part_(part)
            {}
 
        // Member functions
 
            inline label part() const
            {
                return part_;
            }
    };
 
 
private:
 
    // Private data
 
        tensor Q_;
 
        vector v_;
 
        vector a_;
 
        vector pi_;
 
        vector tau_;
 
        vector specialPosition_;
 
        scalar potentialEnergy_;
 
        // - r_ij f_ij, stress dyad
        tensor rf_;
 
        label special_;
 
        label id_;
 
        List<vector> siteForces_;
 
        List<vector> sitePositions_;
 
 
    // Private Member Functions
 
        tensor rotationTensorX(scalar deltaT) const;
 
        tensor rotationTensorY(scalar deltaT) const;
 
        tensor rotationTensorZ(scalar deltaT) const;
 
 
public:
 
    friend class Cloud<molecule>;
 
    // Constructors
 
        //- Construct from components
        inline molecule
        (
            const polyMesh& mesh,
            const barycentric& coordinates,
            const label celli,
            const label tetFacei,
            const label tetPti,
            const tensor& Q,
            const vector& v,
            const vector& a,
            const vector& pi,
            const vector& tau,
            const vector& specialPosition,
            const constantProperties& constProps,
            const label special,
            const label id
        );
 
        //- Construct from a position and a cell, searching for the rest of the
        //  required topology
        inline molecule
        (
            const polyMesh& mesh,
            const vector& position,
            const label celli,
            const tensor& Q,
            const vector& v,
            const vector& a,
            const vector& pi,
            const vector& tau,
            const vector& specialPosition,
            const constantProperties& constProps,
            const label special,
            const label id
        );
 
        //- Construct from Istream
        molecule
        (
            const polyMesh& mesh,
            Istream& is,
            bool readFields = true,
            bool newFormat = true
        );
 
        //- Construct and return a clone
        autoPtr<particle> clone() const
        {
            return autoPtr<particle>(new molecule(*this));
        }
 
        //- Factory class to read-construct particles used for
        //  parallel transfer
        class iNew
        {
            const polyMesh& mesh_;
 
        public:
 
            iNew(const polyMesh& mesh)
            :
                mesh_(mesh)
            {}
 
            autoPtr<molecule> operator()(Istream& is) const
            {
                return autoPtr<molecule>::New(mesh_, is, true);
            }
        };
 
 
    // Member Functions
 
        // Tracking
 
            bool move(moleculeCloud&, trackingData&, const scalar trackTime);
 
            virtual void transformProperties(const tensor& T);
 
            virtual void transformProperties(const vector& separation);
 
            void setSitePositions(const constantProperties& constProps);
 
            void setSiteSizes(label size);
 
 
        // Access
 
            inline const tensor& Q() const;
            inline tensor& Q();
 
            inline const vector& v() const;
            inline vector& v();
 
            inline const vector& a() const;
            inline vector& a();
 
            inline const vector& pi() const;
            inline vector& pi();
 
            inline const vector& tau() const;
            inline vector& tau();
 
            inline const List<vector>& siteForces() const;
            inline List<vector>& siteForces();
 
            inline const List<vector>& sitePositions() const;
            inline List<vector>& sitePositions();
 
            inline const vector& specialPosition() const;
            inline vector& specialPosition();
 
            inline scalar potentialEnergy() const;
            inline scalar& potentialEnergy();
 
            inline const tensor& rf() const;
            inline tensor& rf();
 
            inline label special() const;
 
            inline bool tethered() const;
 
            inline label id() const;
 
 
    // Member Operators
 
        //- Overridable function to handle the particle hitting a patch
        //  Executed before other patch-hitting functions
        bool hitPatch(moleculeCloud& cloud, trackingData& td);
 
        //- Overridable function to handle the particle hitting a processorPatch
        void hitProcessorPatch(moleculeCloud& cloud, trackingData& td);
 
        //- Overridable function to handle the particle hitting a wallPatch
        void hitWallPatch(moleculeCloud& cloud, trackingData& td);
 
 
    // I-O
 
        static void readFields(Cloud<molecule>& mC);
 
        static void writeFields(const Cloud<molecule>& mC);
 
 
    // IOstream Operators
 
        friend Ostream& operator<<(Ostream&, const molecule&);
};
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
} // End namespace Foam
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
#include "moleculeI.H"
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
#endif
 
// ************************************************************************* //