moleculeCloud.H

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/*---------------------------------------------------------------------------*\
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  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     |
    \\  /    A nd           | www.openfoam.com
     \\/     M anipulation  |
-------------------------------------------------------------------------------
    Copyright (C) 2011-2017 OpenFOAM Foundation
    Copyright (C) 2019 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::moleculeCloud
 
Description
 
SourceFiles
    moleculeCloudI.H
    moleculeCloud.C
 
\*---------------------------------------------------------------------------*/
 
#ifndef moleculeCloud_H
#define moleculeCloud_H
 
#include "Cloud.H"
#include "molecule.H"
#include "IOdictionary.H"
#include "potential.H"
#include "InteractionLists.H"
#include "labelVector.H"
#include "Random.H"
#include "fileName.H"
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
namespace Foam
{
 
/*---------------------------------------------------------------------------*\
                       Class moleculeCloud Declaration
\*---------------------------------------------------------------------------*/
 
class moleculeCloud
:
    public Cloud<molecule>
{
    // Private Data
 
        const polyMesh& mesh_;
 
        const potential& pot_;
 
        List<DynamicList<molecule*>> cellOccupancy_;
 
        InteractionLists<molecule> il_;
 
        List<molecule::constantProperties> constPropList_;
 
        Random rndGen_;
 
 
    // Private Member Functions
 
        void buildConstProps();
 
        void setSiteSizesAndPositions();
 
        //- Determine which molecules are in which cells
        void buildCellOccupancy();
 
        void calculatePairForce();
 
        inline void evaluatePair
        (
            molecule& molI,
            molecule& molJ
        );
 
        inline bool evaluatePotentialLimit
        (
            molecule& molI,
            molecule& molJ
        ) const;
 
        void calculateTetherForce();
 
        void calculateExternalForce();
 
        void removeHighEnergyOverlaps();
 
        void initialiseMolecules
        (
            const IOdictionary& mdInitialiseDict
        );
 
        void createMolecule
        (
            const point& position,
            label cell,
            label id,
            bool tethered,
            scalar temperature,
            const vector& bulkVelocity
        );
 
        label nSites() const;
 
        inline vector equipartitionLinearVelocity
        (
            scalar temperature,
            scalar mass
        );
 
        inline vector equipartitionAngularMomentum
        (
            scalar temperature,
            const molecule::constantProperties& cP
        );
 
        //- No copy construct
        moleculeCloud(const moleculeCloud&) = delete;
 
        //- No copy assignment
        void operator=(const moleculeCloud&) = delete;
 
 
public:
 
    // Constructors
 
        //- Construct given mesh and potential references
        moleculeCloud
        (
            const polyMesh& mesh,
            const potential& pot,
            bool readFields = true
        );
 
        //- Construct given mesh, potential and mdInitialiseDict
        moleculeCloud
        (
            const polyMesh& mesh,
            const potential& pot,
            const IOdictionary& mdInitialiseDict,
            bool readFields = true
        );
 
 
    // Member Functions
 
        //- Evolve the molecules (move, calculate forces, control state etc)
        void evolve();
 
        void calculateForce();
 
        void applyConstraintsAndThermostats
        (
            const scalar targetTemperature,
            const scalar measuredTemperature
        );
 
 
    // Access
 
        inline const polyMesh& mesh() const;
 
        inline const potential& pot() const;
 
        inline const List<DynamicList<molecule*>>& cellOccupancy() const;
 
        inline const InteractionLists<molecule>& il() const;
 
        inline const List<molecule::constantProperties> constProps() const;
 
        inline const molecule::constantProperties& constProps(label id) const;
 
        inline Random& rndGen();
 
 
    // Member Operators
 
        //- Write molecule sites in XYZ format
        void writeXYZ(const fileName& fName) const;
};
 
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
} // End namespace Foam
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
#include "moleculeCloudI.H"
 
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
#endif
 
// ************************************************************************* //