CKNGeometricUnitCell Class Reference

Class for Geometric unit cell. More...

#include "KNGeometricUnitCell.h"

Collaboration diagram for CKNGeometricUnitCell:

Public Member Functions
	CKNGeometricUnitCell ()
	~CKNGeometricUnitCell ()
CKNGeometricCoordination	GetCoordination ()
void	SetCoordination (CKNGeometricCoordination coordination)
	Get coordination of unit cell. More...
void	SetCoordination (double *pfCoordination)
	Set coordination of unit cell. More...
void	SetCoordination (double fXCoordination, double fYCoordination, double fZCoordination)
	Set coordination of unit cell. More...
void	SetID (double fID)
double	GetID ()
	Set unit cell ID. More...
void	ShiftID (double fShift)
	Get unit cell ID. More...
void	ArrangeAtom (CKNCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set atoms information(coordination, type) in unit cell. More...
unsigned int	NumberingSubElement (CKNGeometricCoordination ShapeCoordination, double fLength[3], int nShapeType, char *pszDomainMatName)
	Assign atom ID to sub element(atoms in unit cell) More...
void	SetSubDomainMaterial (CKNCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set atoms information(coordination, type) in unit cell. More...
double *	GetAssignedIndex ()
void	SetAssignIndex (double fXAssignIndex, double fYAssignIndex, double fZAssignIndex)
	Get Assign index. More...
void	CheckingNeighborCandiate (double fAssignedCount[3], bool bFrontFace, bool bBackEnd)
	Find neigbhor candidate for neighbor in atom. Maxium 26 unitcell index can be assigned. More...
int	GetSubElementSize ()
CKNGeometricAtom *	GetSubElementAt (double fIndex)
	Get atom count in unit cell. More...
CKNGeometricAtom *	GetSubElementByID (double fID)
	Return atom in unitcell by atom ID. More...
std::vector< double > *	GetNeighborCellID ()
void	ShiftAtomID (double fShift)
	Get neighbor unit cell ID. More...
void	SetUnitcellList (std::vector< CKNGeometricUnitCell > *pVect, std::vector< CKNGeometricUnitCell > *pVectPrev, std::vector< CKNGeometricUnitCell > *pVectNext)
	Set unit cell list of shape to each unit cell. More...
void	BuildNeighborInformation (double *pfAssignCount, std::vector< CKNGeometricAtom * > *pSurfaceList)
	Build neighbor information to each atom. More...
void	Serialize (double *pBuffer)
	Convert unit cell data to double buffer. More...
void	Deserialize (double *pBuffer)
	Convert double buffer to unit cell data. More...
void	SetPeriodic (bool bPeriodic, int periodicDirection)
	To mark unit cell is periodic condition. More...
bool	IsPeriodicUnitCell ()
	Check this unit cell is periodic condition or not. More...
void	CopyInnerAtomIndex (CKNGeometricUnitCell srcUnitCell)
	Copy atom id from source. This functino for periodic atom setting. More...

Static Public Member Functions
static void	SetLength (double fLength[3], double fOriginLength[3])
	Set unit cell length. More...
static double	GetLength (AXIS_DEFINE index)
static void	ResetSubElementID ()
	Get unit cell length. More...
static double	GetSubElementID ()
	Reset SubElement ID to Zero. More...
static double	CalculatingIndex (double fXAssignedIndex, double fYAssignedIndex, double fZAssignedIndex, double fAssignedCount[3])
	Calulating unit cell index. More...
static void	SetFullFillIndex (int nIndex)
	Changing Full fill neighbor index. More...

Static Public Attributes
static int	m_nFullFillIndex = 15
	Get SubElement ID. It means new atom id. More...

Private Member Functions
int	IsMachedNeighborRule (CKNGeometricAtom *pCompare1, CKNGeometricAtom *pCompare2, std::vector< CKNGeometricCoordination > *pNeighborRelation, int &nCheckFill)
	Checking neighbor with rule. More...
void	FinalSubElement ()
	Finalizing SubElement. More...
bool	FindingNeighborInUnitcell (CKNGeometricUnitCell *pUnitcell, CKNGeometricAtom *pCompare1, CKNGeometricAtom::ATOM_TYPE type1, std::vector< CKNGeometricCoordination > *pNeighborRelation, int &nCheckFill)
	Finding neighbor in same unit cell. More...
void	SetPeriodicDirection (int periodicDirection)
	Set periodic direction. More...
void	AddPeridoicDirection (CKNGeometricAtom::PERIODIC_DIRECTION periodicDirection)
	Adding periodic direction. More...

Private Attributes
double	m_fAssignedIndex [3]
	Assign index. More...
std::vector < CKNGeometricUnitCell > *	m_vectUnitCellInShape
	Unit cell list in shape. More...
std::vector < CKNGeometricUnitCell > *	m_vectUnitCellInPrev
	Front side unit cell list in shape. More...
std::vector < CKNGeometricUnitCell > *	m_vectUnitCellInNext
	Back side unit cell list in shape. More...
CKNGeometricCoordination	m_coordination
	Coordination of unit cell. More...
std::vector< CKNGeometricAtom >	m_vectIntenalAtom
	Atom in unit cell. More...
std::vector< double >	m_vectNeighborCellID
	Neighbor unit cell list. More...
double	m_fUnitCellID
	Unit cell ID. More...
bool	m_bPeriodicElement
	Periodic element flag. More...
int	m_periodicDirection
	Periodic direction information. More...

Static Private Attributes
static double	m_fLength [3]
	Unit cell length. More...
static double	m_SubElementID = ATOM_DEFAULT_INDEX + 1
	Maxium atom ID in shape. More...

Detailed Description

Class for Geometric unit cell.

Date

03/Oct/2014

Author

Kyu Nam Cho(mysto.nosp@m.us@k.nosp@m.orea..nosp@m.ac.k.nosp@m.r), Hoon Ryu(elec1.nosp@m.020@.nosp@m.gmail.nosp@m..com)

Definition at line 20 of file KNGeometricUnitCell.h.

Constructor & Destructor Documentation

CKNGeometricUnitCell::CKNGeometricUnitCell

(

)

Definition at line 19 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, m_bPeriodicElement, m_fAssignedIndex, and m_fUnitCellID.

{
    m_fUnitCellID = -1;
    m_bPeriodicElement = false;
    
    m_fAssignedIndex[_X] = 0;
    m_fAssignedIndex[_Y] = 0;
    m_fAssignedIndex[_Z] = 0;
}

CKNGeometricUnitCell::~CKNGeometricUnitCell

(

)

Definition at line 29 of file KNGeometricUnitCell.cpp.

References FinalSubElement().

{
    FinalSubElement();
}

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Member Function Documentation

void CKNGeometricUnitCell::AddPeridoicDirection ( CKNGeometricAtom::PERIODIC_DIRECTION  periodicDirection )

private

Adding periodic direction.

Parameters

periodicDirection

Periodic direction

Definition at line 627 of file KNGeometricUnitCell.cpp.

References CKNGeometricAtomFactory::GetAtomCountInUnitcell(), and m_vectIntenalAtom.

{
    int             i, nSize = CKNGeometricAtomFactory::GetAtomCountInUnitcell();

    for (i = 0; i < nSize; ++i)
        m_vectIntenalAtom[i].AddPeridoicDirection(periodicDirection);
}

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void CKNGeometricUnitCell::ArrangeAtom

(

CKNCommandFileParser::LPINPUT_CMD_PARAM

lpParam

)

Set atoms information(coordination, type) in unit cell.

Parameters

lpParam

Input parameter parsing from command file

Definition at line 70 of file KNGeometricUnitCell.cpp.

References CKNGeometricAtom::A, CKNGeometricAtom::C, CKNGeometricAtomFactory::GetMaterialNumber(), m_coordination, CKNGeometricAtomFactory::m_vectAtomList_1, CKNGeometricAtomFactory::m_vectAtomList_2, m_vectIntenalAtom, CKNGeometricAtom::SetCoordination(), CKNGeometricAtom::SetDomainMaterial(), CKNGeometricCoordination::SetOffset(), CKNGeometricAtom::SetType(), and CKNCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    int                             i, nSize;

    nSize = CKNGeometricAtomFactory::m_vectAtomList_1.size();
    for (i = 0; i < nSize; ++i)
    {
        CKNGeometricCoordination    AtomCoordnation = CKNGeometricAtomFactory::m_vectAtomList_1[i].GetCoordination();
        CKNGeometricAtom            SubElement;

        AtomCoordnation.SetOffset(m_coordination);
        SubElement.SetType(CKNGeometricAtom::A, CKNGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0], CKNGeometricAtom::A));
        SubElement.SetDomainMaterial(CKNGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0]));
        SubElement.SetCoordination(AtomCoordnation);
        m_vectIntenalAtom.push_back(SubElement);
    }

    nSize = CKNGeometricAtomFactory::m_vectAtomList_2.size();
    for (i = 0; i < nSize; ++i)
    {
        CKNGeometricCoordination    AtomCoordnation = CKNGeometricAtomFactory::m_vectAtomList_2[i].GetCoordination();
        CKNGeometricAtom            SubElement;

        AtomCoordnation.SetOffset(m_coordination);
        SubElement.SetCoordination(AtomCoordnation);
        SubElement.SetType(CKNGeometricAtom::C, CKNGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0], CKNGeometricAtom::C));
        SubElement.SetDomainMaterial(CKNGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0]));
        m_vectIntenalAtom.push_back(SubElement);
    }
}

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void CKNGeometricUnitCell::BuildNeighborInformation	(	double *	pfAssignCount,
		std::vector< CKNGeometricAtom * > *	pSurfaceList
	)

Build neighbor information to each atom.

Parameters

pfAssignCount	Assign count of shape
pSurfaceList	Surface atom list

Finding internally first

Finding neighbor unitcell internal

Definition at line 348 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, CKNGeometricAtom::A, ATOM_DEFAULT_INDEX, FindingNeighborInUnitcell(), GetID(), CKNGeometricAtom::GetNeighborAtomID(), CKNGeometricAtom::GetNeighborCount(), CKNGeometricAtom::GetType(), IsMachedNeighborRule(), m_nFullFillIndex, m_vectIntenalAtom, m_vectNeighborCellID, CKNGeometricAtomFactory::m_vectNeighborRelation1To2, CKNGeometricAtomFactory::m_vectNeighborRelation2To1, m_vectUnitCellInNext, m_vectUnitCellInPrev, m_vectUnitCellInShape, and CKNGeometricAtom::SetNeighbor().

{
    double                                      i, j, nSecondIndex, nSize;
    int                                         nCheckFill = 0;
    int                                         nMatchingIndex;
    CKNGeometricAtom                            *pCompare1, *pCompare2, *pAtom;
    CKNGeometricAtom::ATOM_TYPE                 type1, type2;
    std::vector<CKNGeometricCoordination>       *pNeighborRelation = NULL;
    bool                                        bFindAll = false;

    nSize = m_vectIntenalAtom.size();
    for (i = 0; i < nSize; ++i)
    {
        if (ATOM_DEFAULT_INDEX == m_vectIntenalAtom[(unsigned int)i].GetID())
            continue;

        pCompare1 = &m_vectIntenalAtom[(unsigned int)i];
        type1 = pCompare1->GetType();

        if (CKNGeometricAtom::A == type1)
            pNeighborRelation = &CKNGeometricAtomFactory::m_vectNeighborRelation1To2;
        else
            pNeighborRelation = &CKNGeometricAtomFactory::m_vectNeighborRelation2To1;
        
        bFindAll = false;
        nCheckFill = 0;
        nSecondIndex = -1;
        for (j = 0; j < nSize - 1; ++j)
        {
            nSecondIndex++;

            if (nSecondIndex == i)
                nSecondIndex++;

            pCompare2 = &m_vectIntenalAtom[(unsigned int)nSecondIndex];

            type2 = pCompare2->GetType();
            if (type1 == type2)
                continue;

            nMatchingIndex = IsMachedNeighborRule(pCompare1, pCompare2, pNeighborRelation, nCheckFill);

            if (-1 != nMatchingIndex)
            {
                pCompare1->SetNeighbor(nMatchingIndex, pCompare2);
                nCheckFill |= (int)(pow((double)2, (int)nMatchingIndex));
            }

            if (m_nFullFillIndex == nCheckFill)
            {
                bFindAll = true;
                break;
            }
        }
                
        if (bFindAll)
            continue;

        int     nNeighborUnitcellSize = m_vectNeighborCellID.size();

        for (j = 0; j < nNeighborUnitcellSize; ++j)
        {
            double                      fNeighborID = m_vectNeighborCellID[(unsigned int)j];
            CKNGeometricUnitCell        NeighborCell;

#ifndef DISABLE_MPI_ROUTINE
            if (fNeighborID < 0)
            {
                if( m_vectUnitCellInPrev->size() > 0 )
                {
                    NeighborCell = m_vectUnitCellInPrev->at((int)fNeighborID + (int)(floor(pfAssignCount[_Y]) * floor(pfAssignCount[_Z])));
                    bFindAll = FindingNeighborInUnitcell(&NeighborCell, pCompare1, type1, pNeighborRelation, nCheckFill);
                }
            }
            else if (fNeighborID >= m_vectUnitCellInShape->size())
            {
                if( m_vectUnitCellInNext->size() > 0 )
                {
                    NeighborCell = m_vectUnitCellInNext->at((int)fNeighborID - (int)(floor(pfAssignCount[_X]) * floor(pfAssignCount[_Y]) * floor(pfAssignCount[_Z])));
                    bFindAll = FindingNeighborInUnitcell(&NeighborCell, pCompare1, type1, pNeighborRelation, nCheckFill);
                }
            }
            else
#endif //DISABLE_MPI_ROUTINE
            {
                NeighborCell = m_vectUnitCellInShape->at((unsigned int)fNeighborID);
                bFindAll = FindingNeighborInUnitcell(&NeighborCell, pCompare1, type1, pNeighborRelation, nCheckFill);
            }

            if (bFindAll)
                break;
        }
                
        if (bFindAll)
            continue;
    }

    for (i = 0; i < nSize; ++i)
    {
        int         nNeighborSize;
        if (ATOM_DEFAULT_INDEX == m_vectIntenalAtom[(unsigned int)i].GetID())
            continue;

        pAtom = &m_vectIntenalAtom[(unsigned int)i];
        nNeighborSize = pAtom->GetNeighborCount();
        for (j = 0; j < nNeighborSize; ++j)
        {
            if (ATOM_DEFAULT_INDEX == pAtom->GetNeighborAtomID(j))
            {
                pSurfaceList->push_back(pAtom);
                break;
            }
        }
    }
}

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double CKNGeometricUnitCell::CalculatingIndex ( double  fXAssignedIndex, double  fYAssignedIndex, double  fZAssignedIndex, double  fAssignedCount[3]  )

static

Calulating unit cell index.

Parameters

fXAssignedIndex	x direction index
fYAssignedIndex	y direciton index
fZAssignedIndex	z direction index
fAssignedCount	Assigend count of shape

Returns

Unitcell index

Definition at line 306 of file KNGeometricUnitCell.cpp.

Referenced by CheckingNeighborCandiate(), and CKNGeometricShape::PeriodicUnitCellNumbering().

{
    return fXAssignedIndex * floor(fAssignedCount[1]) * floor(fAssignedCount[2]) + fYAssignedIndex * floor(fAssignedCount[2]) + fZAssignedIndex;
}

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void CKNGeometricUnitCell::CheckingNeighborCandiate	(	double	fAssignedCount[3],
		bool	bFrontFace,
		bool	bBackEnd
	)

Find neigbhor candidate for neighbor in atom. Maxium 26 unitcell index can be assigned.

Parameters

fAssignedCount	Assign index array
bFrontFace	Is this shape is front end face
bBackEnd	Is this shape is back end face

Definition at line 221 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, CalculatingIndex(), m_fAssignedIndex, and m_vectNeighborCellID.

{
    double              cx[3], cy[3], cz[3];
    int                 cxCount = 1, cyCount = 1, czCount = 1;
    int                 x, y, z;

    cx[0] = m_fAssignedIndex[_X];
    cy[0] = m_fAssignedIndex[_Y];
    cz[0] = m_fAssignedIndex[_Z];

    if (cx[0] > 0 || (cx[0] == 0 && false == bFrontFace))
        cx[cxCount++] = cx[0] - 1;

    if (cy[0] > 0)
        cy[cyCount++] = cy[0] - 1;

    if (cz[0] > 0)
        cz[czCount++] = cz[0] - 1;

    if (cx[0] < fAssignedCount[_X] - 1 || (cx[0] == fAssignedCount[_X] - 1 && false == bBackEnd))
        cx[cxCount++] = cx[0] + 1;

    if (cy[0] < fAssignedCount[_Y] - 1)
        cy[cyCount++] = cy[0] + 1;

    if (cz[0] < fAssignedCount[_Z] - 1)
        cz[czCount++] = cz[0] + 1;

    for (x = 0; x < cxCount; ++x)
    {
        for (y = 0; y < cyCount; ++y)
        {
            for (z = 0; z < czCount; ++z)
            {
                if (0 == x && 0 == y && 0 == z)
                    continue;

                m_vectNeighborCellID.push_back(CalculatingIndex(cx[x], cy[y], cz[z], fAssignedCount));
            }
        }
    }
}

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void CKNGeometricUnitCell::CopyInnerAtomIndex

(

CKNGeometricUnitCell

srcUnitCell

)

Copy atom id from source. This functino for periodic atom setting.

Parameters

srcUnitCell

Source unit cell

Definition at line 314 of file KNGeometricUnitCell.cpp.

References CKNGeometricAtom::GetID(), GetSubElementAt(), GetSubElementSize(), m_vectIntenalAtom, and SetID().

{
    int             i, nSize = srcUnitCell.GetSubElementSize();
    for (i = 0; i < nSize; ++i)
        m_vectIntenalAtom[i].SetID(srcUnitCell.GetSubElementAt(i)->GetID());
}

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void CKNGeometricUnitCell::Deserialize

(

double *

pBuffer

)

Convert double buffer to unit cell data.

Parameters

pBuffer

Source data buffer for serialization

Definition at line 557 of file KNGeometricUnitCell.cpp.

References CKNGeometricAtom::A, CKNGeometricAtom::C, CKNGeometricAtomFactory::GetAtomCountInUnitcell(), m_vectIntenalAtom, CKNGeometricAtom::SetCoordination(), CKNGeometricAtom::SetID(), CKNGeometricAtom::SetPeriodic(), CKNGeometricAtom::SetPeriodicDirection(), and CKNGeometricAtom::SetType().

Referenced by CKNGeometricShape::Deserialize().

{
    int             i, nSize = CKNGeometricAtomFactory::GetAtomCountInUnitcell();
    int             nPos = 0;

    for( i = 0; i < nSize;++i)
    {
        CKNGeometricAtom        atom;

        atom.SetID(pBuffer[nPos++]);
        if( 0 == pBuffer[nPos++])
            atom.SetType(CKNGeometricAtom::A, (MATERIAL_INDEX)((int)pBuffer[nPos++]));
        else
            atom.SetType(CKNGeometricAtom::C, (MATERIAL_INDEX)((int)pBuffer[nPos++]));
        
        atom.SetPeriodic((bool)pBuffer[nPos++]);
        
        double      x = pBuffer[nPos++];
        double      y = pBuffer[nPos++];
        double      z = pBuffer[nPos++];
        atom.SetCoordination(x, y, z);
        atom.SetPeriodicDirection((int)pBuffer[nPos++]);
        m_vectIntenalAtom.push_back(atom);
    }
}

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void CKNGeometricUnitCell::FinalSubElement ( )

private

Finalizing SubElement.

Definition at line 294 of file KNGeometricUnitCell.cpp.

References m_vectIntenalAtom.

Referenced by ~CKNGeometricUnitCell().

{
    m_vectIntenalAtom.clear();
}

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bool CKNGeometricUnitCell::FindingNeighborInUnitcell ( CKNGeometricUnitCell *  pUnitcell, CKNGeometricAtom *  pCompare1, CKNGeometricAtom::ATOM_TYPE  type1, std::vector< CKNGeometricCoordination > *  pNeighborRelation, int &  nCheckFill  )

private

Finding neighbor in same unit cell.

Parameters

	pUnitcell	Searching target unit cell
	pCompare1	First comparing target atom
	type1	First compparing target atom type
	pNeighborRelation	Neighbor relation rule
[out]	nCheckFill	finding result of first comparing target atom's neighbor

Returns

Finding neighbor all or not yet

Definition at line 505 of file KNGeometricUnitCell.cpp.

References GetSubElementAt(), GetSubElementSize(), CKNGeometricAtom::GetType(), IsMachedNeighborRule(), and CKNGeometricAtom::SetNeighbor().

Referenced by BuildNeighborInformation().

{
    int                                         i, nSize = pUnitcell->GetSubElementSize();
    CKNGeometricAtom::ATOM_TYPE                 type2;
    int                                         nMatchingIndex;

    for (i = 0; i < nSize; ++i)
    {
        CKNGeometricAtom *pCompare2 = pUnitcell->GetSubElementAt(i);
        type2 = pCompare2->GetType();
        /*if (type1 == type2)
            continue;*/

        nMatchingIndex = IsMachedNeighborRule(pCompare1, pCompare2, pNeighborRelation, nCheckFill);

        if (-1 != nMatchingIndex)
        {
            pCompare1->SetNeighbor(nMatchingIndex, pCompare2);
            nCheckFill |= (int)(pow((double)2, (int)nMatchingIndex));
        }

        if (15 == nCheckFill)
            return true;
    }

    return false;
}

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double* CKNGeometricUnitCell::GetAssignedIndex ( )

inline

Definition at line 42 of file KNGeometricUnitCell.h.

References m_fAssignedIndex.

{ return m_fAssignedIndex; }; 

CKNGeometricCoordination CKNGeometricUnitCell::GetCoordination ( )

inline

Definition at line 32 of file KNGeometricUnitCell.h.

References m_coordination.

{ return m_coordination; }; 

double CKNGeometricUnitCell::GetID ( )

inline

Set unit cell ID.

Definition at line 37 of file KNGeometricUnitCell.h.

References m_fUnitCellID.

Referenced by BuildNeighborInformation(), and GetSubElementByID().

{ return m_fUnitCellID; }; 

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static double CKNGeometricUnitCell::GetLength ( AXIS_DEFINE  index )

inlinestatic

Definition at line 27 of file KNGeometricUnitCell.h.

References m_fLength.

Referenced by CKNGeometricShape::ArrangeUnitCell(), and CKNGeometricShape::CalculateUnitcellCount().

{ return m_fLength[index]; }; 

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std::vector<double>* CKNGeometricUnitCell::GetNeighborCellID ( )

inline

Definition at line 48 of file KNGeometricUnitCell.h.

References m_vectNeighborCellID.

{ return &m_vectNeighborCellID; }; 

CKNGeometricAtom * CKNGeometricUnitCell::GetSubElementAt

(

double

fIndex

)

Get atom count in unit cell.

Return atom in unitcell by sequence

Parameters

fIndex

Index of atom

Returns

Pointer of atom instance

Definition at line 268 of file KNGeometricUnitCell.cpp.

References m_vectIntenalAtom.

Referenced by CopyInnerAtomIndex(), and FindingNeighborInUnitcell().

{
    if (fIndex >= m_vectIntenalAtom.size())
        return NULL;

    return &m_vectIntenalAtom[(int)floor(fIndex)];
}

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CKNGeometricAtom * CKNGeometricUnitCell::GetSubElementByID

(

double

fID

)

Return atom in unitcell by atom ID.

Parameters

fID	Index of atom

Returns

Pointer of atom instance

Definition at line 280 of file KNGeometricUnitCell.cpp.

References GetID(), and m_vectIntenalAtom.

{
    int                         nSize, i;

    nSize = m_vectIntenalAtom.size();
    for( i = 0 ;i < nSize ; ++ i )
    {
        if( fID == m_vectIntenalAtom[i].GetID() )
            return &m_vectIntenalAtom[i];
    }

    return NULL;
}

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static double CKNGeometricUnitCell::GetSubElementID ( )

inlinestatic

Reset SubElement ID to Zero.

Definition at line 29 of file KNGeometricUnitCell.h.

Referenced by CKNGeometricShape::ConstructMapInfo(), and CKNGeometricShape::ExchangeAtomInfoBetweenNode().

{ return m_SubElementID;}; 

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int CKNGeometricUnitCell::GetSubElementSize ( )

inline

Definition at line 45 of file KNGeometricUnitCell.h.

References m_vectIntenalAtom.

Referenced by CopyInnerAtomIndex(), and FindingNeighborInUnitcell().

{ return m_vectIntenalAtom.size(); }; 

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int CKNGeometricUnitCell::IsMachedNeighborRule ( CKNGeometricAtom *  pCompare1, CKNGeometricAtom *  pCompare2, std::vector< CKNGeometricCoordination > *  pNeighborRelation, int &  nCheckFill  )

private

Checking neighbor with rule.

Parameters

	pCompare1	First comparing target atom
	pCompare2	Second comparing target atom
	pNeighborRelation	Neighbor relation rule
[out]	nCheckFill	finding result of first comparing target atom's neighbor

Returns

Neighbor index

Definition at line 474 of file KNGeometricUnitCell.cpp.

References ATOM_DEFAULT_INDEX, CKNGeometricAtom::GetCoordination(), CKNGeometricAtom::GetNeighborAtomID(), and CKNGeometricCoordination::SetOffset().

Referenced by BuildNeighborInformation(), and FindingNeighborInUnitcell().

{
    int                         i, nSize;
    CKNGeometricCoordination    coordination1;
    CKNGeometricCoordination    coordination2 = pCompare2->GetCoordination();
    
    nSize = pNeighborRelation->size();
    for (i = 0; i < nSize; ++i)
    {
        double      fNeighbor = pCompare1->GetNeighborAtomID(i);
        if (ATOM_DEFAULT_INDEX != fNeighbor)
            continue;

        coordination1 = pCompare1->GetCoordination();
        coordination1.SetOffset(pNeighborRelation->at(i));
        
        if (coordination2 == coordination1)
            return i;
    }

    return -1;
}

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bool CKNGeometricUnitCell::IsPeriodicUnitCell ( )

inline

Check this unit cell is periodic condition or not.

Definition at line 55 of file KNGeometricUnitCell.h.

References m_bPeriodicElement.

unsigned int CKNGeometricUnitCell::NumberingSubElement	(	CKNGeometricCoordination	ShapeCoordination,
		double	fLength[3],
		int	nShapeType,
		char *	pszDomainMatName
	)

Assign atom ID to sub element(atoms in unit cell)

Parameters

ShapeCoordination	Coordination of shape
fLength	Length of shape
szShape	Form of shape

Returns

Atom count

Definition at line 153 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, BOX_SHAPE, CYLINDER_SHAPE, GENERAL_TOLERANCE, CKNGeometricCoordination::GetCoordination(), CKNGeometricAtomFactory::GetMaterialNumber(), m_SubElementID, and m_vectIntenalAtom.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    double              cx, cy, cz;
    int                 i, nSize = m_vectIntenalAtom.size();
    unsigned int        count = 0;

    for (i = 0; i < nSize; ++i)
    {
        CKNGeometricCoordination coordination = m_vectIntenalAtom[i].GetCoordination();
        
        cx = coordination.GetCoordination(_X);
        cy = coordination.GetCoordination(_Y);
        cz = coordination.GetCoordination(_Z);
                
        if (cx < 0 || cx > ShapeCoordination.GetCoordination(_X) + fLength[_X])
        {
            if( fabs(cx - (ShapeCoordination.GetCoordination(_X) + fLength[_X])) > GENERAL_TOLERANCE)
            {
                //printf("cx: %10.10f, cy: %10.10f, cz %10.10f\n", cx, cy, cz);
                continue;
            }
        }
        
        switch (nShapeType)
        {
        case BOX_SHAPE:
            if (cy < 0 || cy > ShapeCoordination.GetCoordination(_Y) + fLength[_Y])
                continue;

            if (cz < 0 || cz > ShapeCoordination.GetCoordination(_Z) + fLength[_Z])
                continue;
            break;
        case CYLINDER_SHAPE:
            if ((pow((cy - (fLength[_Y] / 2)), 2) / pow(fLength[_Y] / 2, 2)) +
                pow((cz - (fLength[_Z] / 2)), 2) / pow(fLength[_Z] / 2, 2) > 1)
                continue;
            break;
        }

        count++;

        MATERIAL_INDEX  nMaterialType;

        nMaterialType = CKNGeometricAtomFactory::GetMaterialNumber(pszDomainMatName, m_vectIntenalAtom[i].GetType());
        m_vectIntenalAtom[i].SetMaterial(nMaterialType);
        m_vectIntenalAtom[i].SetID(m_SubElementID++);
    }

    return count;
}

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static void CKNGeometricUnitCell::ResetSubElementID ( )

inlinestatic

Get unit cell length.

Definition at line 28 of file KNGeometricUnitCell.h.

References m_SubElementID.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{ m_SubElementID = 0; }; 

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void CKNGeometricUnitCell::Serialize

(

double *

pBuffer

)

Convert unit cell data to double buffer.

Parameters

[out]

pBuffer

Data buffer to save serialization result

Definition at line 536 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, and m_vectIntenalAtom.

{
    int             i, nSize = m_vectIntenalAtom.size();
    int             nPos = 0;

    for( i = 0; i < nSize;++i)
    {
        pBuffer[nPos++] = m_vectIntenalAtom[i].GetID();
        pBuffer[nPos++] = (double)m_vectIntenalAtom[i].GetType();
        pBuffer[nPos++] = (double)m_vectIntenalAtom[i].GetMaterialNumber();
        pBuffer[nPos++] = (double)m_vectIntenalAtom[i].IsPeriodicAtom();
        pBuffer[nPos++] = m_vectIntenalAtom[i].GetCoordination().GetCoordination(_X);
        pBuffer[nPos++] = m_vectIntenalAtom[i].GetCoordination().GetCoordination(_Y);
        pBuffer[nPos++] = m_vectIntenalAtom[i].GetCoordination().GetCoordination(_Z);
        pBuffer[nPos++] = (double)m_vectIntenalAtom[i].GetPeriodicDirection();
    }
}

void CKNGeometricUnitCell::SetAssignIndex	(	double	fXAssignIndex,
		double	fYAssignIndex,
		double	fZAssignIndex
	)

Get Assign index.

Assign index set to unit cell. This index will be used for boundary check, neighbor unit cell finding

Parameters

fXAssignIndex	Assign index of x
fYAssignIndex	Assign index of y
fZAssignIndex	Assign index of z

Definition at line 209 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, and m_fAssignedIndex.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    m_fAssignedIndex[_X] = floor(fXAssignIndex);
    m_fAssignedIndex[_Y] = floor(fYAssignIndex);
    m_fAssignedIndex[_Z] = floor(fZAssignIndex);
}

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void CKNGeometricUnitCell::SetCoordination

(

CKNGeometricCoordination

coordination

)

Get coordination of unit cell.

Set coordination of unit cell

Parameters

coordination

Coordination

Definition at line 44 of file KNGeometricUnitCell.cpp.

References CKNGeometricCoordination::GetCoordinationAll(), m_coordination, and CKNGeometricCoordination::SetCoordination().

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    m_coordination.SetCoordination(coordination.GetCoordinationAll());
}

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void CKNGeometricUnitCell::SetCoordination

(

double *

pfCoordination

)

Set coordination of unit cell.

Parameters

pfCoordination

Coordination buffer

Definition at line 52 of file KNGeometricUnitCell.cpp.

References m_coordination, and CKNGeometricCoordination::SetCoordination().

{
    m_coordination.SetCoordination(pfCoordination);
}

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void CKNGeometricUnitCell::SetCoordination	(	double	fXCoordination,
		double	fYCoordination,
		double	fZCoordination
	)

Set coordination of unit cell.

Parameters

fXCoordination	x Coordination
fYCoordination	y Coordination
fZCoordination	z Coordination

Definition at line 62 of file KNGeometricUnitCell.cpp.

References m_coordination, and CKNGeometricCoordination::SetCoordination().

{
    m_coordination.SetCoordination(fXCoordination, fYCoordination, fZCoordination);
}

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static void CKNGeometricUnitCell::SetFullFillIndex ( int  nIndex )

inlinestatic

Changing Full fill neighbor index.

Definition at line 58 of file KNGeometricUnitCell.h.

References m_nFullFillIndex.

void CKNGeometricUnitCell::SetID ( double  fID )

inline

Definition at line 36 of file KNGeometricUnitCell.h.

References m_fUnitCellID.

Referenced by CKNGeometricShape::ArrangeUnitCell(), CopyInnerAtomIndex(), and CKNGeometricShape::Deserialize().

{ m_fUnitCellID = fID; }; 

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void CKNGeometricUnitCell::SetLength ( double  fLength[3], double  fOriginLength[3]  )

static

Set unit cell length.

Definition at line 34 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, and m_fLength.

Referenced by CKNGeometricShape::SetAtomAndNeighborInformation(), and CKNGeometricConstructionLaunch::SetUnitCellInformation().

{ 
    m_fLength[_X] = fOriginLength[_X];
    m_fLength[_Y] = fOriginLength[_Y];
    m_fLength[_Z] = fOriginLength[_Z];
}

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void CKNGeometricUnitCell::SetPeriodic	(	bool	bPeriodic,
		int	periodicDirection
	)

To mark unit cell is periodic condition.

Parameters

bPeriodic	Periodic flag
periodicDirection	Periodic direction

Definition at line 587 of file KNGeometricUnitCell.cpp.

References CKNGeometricAtomFactory::GetAtomCountInUnitcell(), m_bPeriodicElement, m_periodicDirection, and m_vectIntenalAtom.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    int             i, nSize = CKNGeometricAtomFactory::GetAtomCountInUnitcell();
    int             nPos = 0;

    m_bPeriodicElement = bPeriodic;
    m_periodicDirection = periodicDirection;
    for (i = 0; i < nSize; ++i)
    {
        m_vectIntenalAtom[i].SetPeriodic(bPeriodic);
        m_vectIntenalAtom[i].SetPeriodicDirection(periodicDirection);
    }
}

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void CKNGeometricUnitCell::SetPeriodicDirection ( int  periodicDirection )

private

Set periodic direction.

Parameters

periodicDirection

Periodic direction

Definition at line 616 of file KNGeometricUnitCell.cpp.

References CKNGeometricAtomFactory::GetAtomCountInUnitcell(), and m_vectIntenalAtom.

{
    int             i, nSize = CKNGeometricAtomFactory::GetAtomCountInUnitcell();

    for (i = 0; i < nSize; ++i)
        m_vectIntenalAtom[i].SetPeriodicDirection(periodicDirection);
}

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void CKNGeometricUnitCell::SetSubDomainMaterial

(

CKNCommandFileParser::LPINPUT_CMD_PARAM

lpParam

)

Set atoms information(coordination, type) in unit cell.

Parameters

lpParam

Input parameter parsing from command file

Definition at line 104 of file KNGeometricUnitCell.cpp.

References _X, _Y, _Z, BOX_SHAPE, CYLINDER_SHAPE, CKNCommandFileParser::INPUT_CMD_PARAM::fOrigin, CKNCommandFileParser::INPUT_CMD_PARAM::fShapeLength, CKNGeometricCoordination::GetCoordination(), CKNGeometricAtomFactory::GetMaterialNumber(), m_vectIntenalAtom, CKNCommandFileParser::INPUT_CMD_PARAM::nShape, CKNCommandFileParser::INPUT_CMD_PARAM::nSubDomainNumber, and CKNCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    double              cx, cy, cz;
    int                 i, j, nSize = m_vectIntenalAtom.size();

    for (j = 0; j < lpParam->nSubDomainNumber; ++j)
    {
            for (i = 0; i < nSize; ++i)
            {
                CKNGeometricCoordination coordination = m_vectIntenalAtom[i].GetCoordination();
        
                cx = coordination.GetCoordination(_X);
                cy = coordination.GetCoordination(_Y);
                cz = coordination.GetCoordination(_Z);
                
                if (cx < lpParam->fOrigin[j+1][0] || cx > (lpParam->fOrigin[j+1][0] + lpParam->fShapeLength[j+1][0]))
                    continue;
        
                switch (lpParam->nShape[j + 1])
                {
                case BOX_SHAPE:
                    if (cy < lpParam->fOrigin[j + 1][1] || cy >(lpParam->fOrigin[j + 1][1] + lpParam->fShapeLength[j + 1][1]))
                        continue;

                    if (cz < lpParam->fOrigin[j + 1][2] || cz >(lpParam->fOrigin[j + 1][2] + lpParam->fShapeLength[j + 1][2]))
                        continue;
                    break;
                case CYLINDER_SHAPE:
                    if ((pow(((cy - lpParam->fOrigin[j + 1][_Y]) - (lpParam->fShapeLength[j + 1][_Y] / 2)), 2) / pow(lpParam->fShapeLength[j + 1][_Y] / 2, 2)) +
                        pow(((cz - lpParam->fOrigin[j + 1][_Z]) - (lpParam->fShapeLength[j + 1][_Z] / 2)), 2) / pow(lpParam->fShapeLength[j + 1][_Z] / 2, 2) > 1)
                        continue;
                    break;
                }

                MATERIAL_INDEX  nMaterialType;

                nMaterialType = CKNGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[j+1], m_vectIntenalAtom[i].GetType());
                m_vectIntenalAtom[i].SetMaterial(nMaterialType);
            }
    }

}

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void CKNGeometricUnitCell::SetUnitcellList	(	std::vector< CKNGeometricUnitCell > *	pVect,
		std::vector< CKNGeometricUnitCell > *	pVectPrev,
		std::vector< CKNGeometricUnitCell > *	pVectNext
	)

Set unit cell list of shape to each unit cell.

Parameters

pVect	vector of unit cell
pVectPrev	vector of previous unit cell
pVectNext	vector of next unit cell

Definition at line 606 of file KNGeometricUnitCell.cpp.

References m_vectUnitCellInNext, m_vectUnitCellInPrev, and m_vectUnitCellInShape.

Referenced by CKNGeometricShape::ArrangeUnitCell().

{
    m_vectUnitCellInShape = pVect; 
    m_vectUnitCellInPrev = pVectPrev;
    m_vectUnitCellInNext = pVectNext;
}

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void CKNGeometricUnitCell::ShiftAtomID

(

double

fShift

)

Get neighbor unit cell ID.

Shift atom ID by given fShift value

Parameters

fShift

Shift value

Definition at line 324 of file KNGeometricUnitCell.cpp.

References m_vectIntenalAtom, and ShiftID().

{
    int             i, nSize = m_vectIntenalAtom.size();

    for (i = 0; i < nSize; ++i)
        m_vectIntenalAtom[i].ShiftID(fShift);
}

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void CKNGeometricUnitCell::ShiftID

(

double

fShift

)

Get unit cell ID.

Shift subelement(atom) ID

Parameters

fShift

Shift value

Definition at line 335 of file KNGeometricUnitCell.cpp.

References m_fUnitCellID, and m_vectNeighborCellID.

Referenced by ShiftAtomID().

{
    int             i, nSize = m_vectNeighborCellID.size();

    m_fUnitCellID += fShift; 
    for (i = 0; i < nSize; ++i)
        m_vectNeighborCellID[i] += fShift;
}

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Member Data Documentation

bool CKNGeometricUnitCell::m_bPeriodicElement

private

Periodic element flag.

Definition at line 77 of file KNGeometricUnitCell.h.

Referenced by CKNGeometricUnitCell(), IsPeriodicUnitCell(), and SetPeriodic().

CKNGeometricCoordination CKNGeometricUnitCell::m_coordination

private

Coordination of unit cell.

Definition at line 73 of file KNGeometricUnitCell.h.

Referenced by ArrangeAtom(), GetCoordination(), and SetCoordination().

double CKNGeometricUnitCell::m_fAssignedIndex[3]

private

Assign index.

Definition at line 69 of file KNGeometricUnitCell.h.

Referenced by CheckingNeighborCandiate(), CKNGeometricUnitCell(), GetAssignedIndex(), and SetAssignIndex().

double CKNGeometricUnitCell::m_fLength

staticprivate

Unit cell length.

Definition at line 67 of file KNGeometricUnitCell.h.

Referenced by GetLength(), and SetLength().

double CKNGeometricUnitCell::m_fUnitCellID

private

Unit cell ID.

Definition at line 76 of file KNGeometricUnitCell.h.

Referenced by CKNGeometricUnitCell(), GetID(), SetID(), and ShiftID().

int CKNGeometricUnitCell::m_nFullFillIndex = 15

static

Get SubElement ID. It means new atom id.

Check Neighbor relation check index 15 = 4 neighbors, 63 = 6 neighbors

Definition at line 29 of file KNGeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetFullFillIndex().

int CKNGeometricUnitCell::m_periodicDirection

private

Periodic direction information.

Definition at line 78 of file KNGeometricUnitCell.h.

Referenced by SetPeriodic().

double CKNGeometricUnitCell::m_SubElementID = ATOM_DEFAULT_INDEX + 1

staticprivate

Maxium atom ID in shape.

Definition at line 68 of file KNGeometricUnitCell.h.

Referenced by NumberingSubElement(), and ResetSubElementID().

std::vector<CKNGeometricAtom> CKNGeometricUnitCell::m_vectIntenalAtom

private

Atom in unit cell.

Definition at line 74 of file KNGeometricUnitCell.h.

Referenced by AddPeridoicDirection(), ArrangeAtom(), BuildNeighborInformation(), CopyInnerAtomIndex(), Deserialize(), FinalSubElement(), GetSubElementAt(), GetSubElementByID(), GetSubElementSize(), NumberingSubElement(), Serialize(), SetPeriodic(), SetPeriodicDirection(), SetSubDomainMaterial(), and ShiftAtomID().

std::vector<double> CKNGeometricUnitCell::m_vectNeighborCellID

private

Neighbor unit cell list.

Definition at line 75 of file KNGeometricUnitCell.h.

Referenced by BuildNeighborInformation(), CheckingNeighborCandiate(), GetNeighborCellID(), and ShiftID().

std::vector<CKNGeometricUnitCell>* CKNGeometricUnitCell::m_vectUnitCellInNext

private

Back side unit cell list in shape.

Definition at line 72 of file KNGeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetUnitcellList().

std::vector<CKNGeometricUnitCell>* CKNGeometricUnitCell::m_vectUnitCellInPrev

private

Front side unit cell list in shape.

Definition at line 71 of file KNGeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetUnitcellList().

std::vector<CKNGeometricUnitCell>* CKNGeometricUnitCell::m_vectUnitCellInShape

private

Unit cell list in shape.

Definition at line 70 of file KNGeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetUnitcellList().

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The documentation for this class was generated from the following files:

• D:/For Doxygen/KNGeometricUnitCell.h
• D:/For Doxygen/KNGeometricUnitCell.cpp