CGeometricUnitCell Class Reference

Class for Geometric unit cell. More...

#include "GeometricUnitCell.h"

Collaboration diagram for CGeometricUnitCell:

Public Member Functions
	CGeometricUnitCell ()
	~CGeometricUnitCell ()
CGeometricCoordination	GetCoordination ()
void	SetCoordination (CGeometricCoordination 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 (CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set atoms information(coordination, type) in unit cell. More...
unsigned int	NumberingSubElement (CGeometricCoordination ShapeCoordination, double fLength[3], int nShapeType, char *pszDomainMatName)
	Assign atom ID to sub element(atoms in unit cell) More...
void	SetSubDomainMaterial (CCommandFileParser::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 ()
CGeometricAtom *	GetSubElementAt (double fIndex)
	Get atom count in unit cell. More...
CGeometricAtom *	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< CGeometricUnitCell > *pVect, std::vector< CGeometricUnitCell > *pVectPrev, std::vector< CGeometricUnitCell > *pVectNext)
	Set unit cell list of shape to each unit cell. More...
void	BuildNeighborInformation (double *pfAssignCount, std::vector< CGeometricAtom * > *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 (CGeometricUnitCell 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 (CGeometricAtom *pCompare1, CGeometricAtom *pCompare2, std::vector< CGeometricCoordination > *pNeighborRelation, int &nCheckFill)
	Checking neighbor with rule. More...
void	FinalSubElement ()
	Finalizing SubElement. More...
bool	FindingNeighborInUnitcell (CGeometricUnitCell *pUnitcell, CGeometricAtom *pCompare1, CGeometricAtom::ATOM_TYPE type1, std::vector< CGeometricCoordination > *pNeighborRelation, int &nCheckFill)
	Finding neighbor in same unit cell. More...
void	SetPeriodicDirection (int periodicDirection)
	Set periodic direction. More...
void	AddPeridoicDirection (CGeometricAtom::PERIODIC_DIRECTION periodicDirection)
	Adding periodic direction. More...

Private Attributes
double	m_fAssignedIndex [3]
	Assign index. More...
std::vector< CGeometricUnitCell > *	m_vectUnitCellInShape
	Unit cell list in shape. More...
std::vector< CGeometricUnitCell > *	m_vectUnitCellInPrev
	Front side unit cell list in shape. More...
std::vector< CGeometricUnitCell > *	m_vectUnitCellInNext
	Back side unit cell list in shape. More...
CGeometricCoordination	m_coordination
	Coordination of unit cell. More...
std::vector< CGeometricAtom >	m_vectInternalAtom
	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

Definition at line 18 of file GeometricUnitCell.h.

Constructor & Destructor Documentation

CGeometricUnitCell::CGeometricUnitCell

(

)

Definition at line 18 of file GeometricUnitCell.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;
}

CGeometricUnitCell::~CGeometricUnitCell

(

)

Definition at line 28 of file GeometricUnitCell.cpp.

References FinalSubElement().

{
    FinalSubElement();
}

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Member Function Documentation

void CGeometricUnitCell::AddPeridoicDirection ( CGeometricAtom::PERIODIC_DIRECTION  periodicDirection )

private

Adding periodic direction.

Parameters

periodicDirection

Periodic direction

Definition at line 629 of file GeometricUnitCell.cpp.

References CGeometricAtomFactory::GetAtomCountInUnitcell(), and m_vectInternalAtom.

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

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

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void CGeometricUnitCell::ArrangeAtom

(

CCommandFileParser::LPINPUT_CMD_PARAM

lpParam

)

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

Parameters

lpParam

Input parameter parsing from command file

Definition at line 69 of file GeometricUnitCell.cpp.

References CGeometricAtom::A, CGeometricAtom::C, CGeometricAtomFactory::GetMaterialNumber(), m_coordination, CGeometricAtomFactory::m_vectAtomList_1, CGeometricAtomFactory::m_vectAtomList_2, m_vectInternalAtom, CGeometricAtom::SetCoordination(), CGeometricAtom::SetDomainMaterial(), CGeometricAtom::SetDomainNumber(), CGeometricCoordination::SetOffset(), CGeometricAtom::SetType(), and CCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by CGeometricShape::ArrangeUnitCell().

{
    int                             i, nSize;

    nSize = CGeometricAtomFactory::m_vectAtomList_1.size();
    for (i = 0; i < nSize; ++i)
    {
        CGeometricCoordination      AtomCoordnation = CGeometricAtomFactory::m_vectAtomList_1[i].GetCoordination();
        CGeometricAtom              SubElement;

        AtomCoordnation.SetOffset(m_coordination);
        SubElement.SetType(CGeometricAtom::A, CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0], CGeometricAtom::A));
        SubElement.SetDomainMaterial(CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0]));
        SubElement.SetCoordination(AtomCoordnation);
        SubElement.SetDomainNumber(1);
        m_vectInternalAtom.push_back(SubElement);
    }

    nSize = CGeometricAtomFactory::m_vectAtomList_2.size();
    for (i = 0; i < nSize; ++i)
    {
        CGeometricCoordination      AtomCoordnation = CGeometricAtomFactory::m_vectAtomList_2[i].GetCoordination();
        CGeometricAtom              SubElement;

        AtomCoordnation.SetOffset(m_coordination);
        SubElement.SetCoordination(AtomCoordnation);
        SubElement.SetType(CGeometricAtom::C, CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0], CGeometricAtom::C));
        SubElement.SetDomainMaterial(CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[0]));
        SubElement.SetDomainNumber(1);
        m_vectInternalAtom.push_back(SubElement);
    }
}

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void CGeometricUnitCell::BuildNeighborInformation	(	double *	pfAssignCount,
		std::vector< CGeometricAtom * > *	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 350 of file GeometricUnitCell.cpp.

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

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

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

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

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

            if (nSecondIndex == i)
                nSecondIndex++;

            pCompare2 = &m_vectInternalAtom[(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];
            CGeometricUnitCell          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_vectInternalAtom[(unsigned int)i].GetID())
            continue;

        pAtom = &m_vectInternalAtom[(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 CGeometricUnitCell::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 308 of file GeometricUnitCell.cpp.

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

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

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void CGeometricUnitCell::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 223 of file GeometricUnitCell.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 CGeometricUnitCell::CopyInnerAtomIndex

(

CGeometricUnitCell

srcUnitCell

)

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

Parameters

srcUnitCell

Source unit cell

Definition at line 316 of file GeometricUnitCell.cpp.

References CGeometricAtom::GetID(), GetSubElementAt(), GetSubElementSize(), m_vectInternalAtom, and SetID().

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

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void CGeometricUnitCell::Deserialize

(

double *

pBuffer

)

Convert double buffer to unit cell data.

Parameters

pBuffer

Source data buffer for serialization

Definition at line 559 of file GeometricUnitCell.cpp.

References CGeometricAtom::A, CGeometricAtom::C, CGeometricAtomFactory::GetAtomCountInUnitcell(), m_vectInternalAtom, CGeometricAtom::SetCoordination(), CGeometricAtom::SetID(), CGeometricAtom::SetPeriodic(), CGeometricAtom::SetPeriodicDirection(), and CGeometricAtom::SetType().

Referenced by CGeometricShape::Deserialize().

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

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

        atom.SetID(pBuffer[nPos++]);
        if( 0 == pBuffer[nPos++])
            atom.SetType(CGeometricAtom::A, (MATERIAL_INDEX)((int)pBuffer[nPos++]));
        else
            atom.SetType(CGeometricAtom::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_vectInternalAtom.push_back(atom);
    }
}

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void CGeometricUnitCell::FinalSubElement ( )

private

Finalizing SubElement.

Definition at line 296 of file GeometricUnitCell.cpp.

References m_vectInternalAtom.

Referenced by ~CGeometricUnitCell().

{
    m_vectInternalAtom.clear();
}

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bool CGeometricUnitCell::FindingNeighborInUnitcell ( CGeometricUnitCell *  pUnitcell, CGeometricAtom *  pCompare1, CGeometricAtom::ATOM_TYPE  type1, std::vector< CGeometricCoordination > *  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 507 of file GeometricUnitCell.cpp.

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

Referenced by BuildNeighborInformation().

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

    for (i = 0; i < nSize; ++i)
    {
        CGeometricAtom *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* CGeometricUnitCell::GetAssignedIndex ( )

inline

Definition at line 40 of file GeometricUnitCell.h.

References m_fAssignedIndex.

{ return m_fAssignedIndex; }; 

CGeometricCoordination CGeometricUnitCell::GetCoordination ( )

inline

Definition at line 30 of file GeometricUnitCell.h.

References m_coordination.

{ return m_coordination; }; 

double CGeometricUnitCell::GetID ( )

inline

Set unit cell ID.

Definition at line 35 of file GeometricUnitCell.h.

References m_fUnitCellID.

Referenced by BuildNeighborInformation(), and GetSubElementByID().

{ return m_fUnitCellID; }; 

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static double CGeometricUnitCell::GetLength ( AXIS_DEFINE  index )

inlinestatic

Definition at line 25 of file GeometricUnitCell.h.

References m_fLength.

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

{ return m_fLength[index]; }; 

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

inline

Definition at line 46 of file GeometricUnitCell.h.

References m_vectNeighborCellID.

{ return &m_vectNeighborCellID; }; 

CGeometricAtom * CGeometricUnitCell::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 270 of file GeometricUnitCell.cpp.

References m_vectInternalAtom.

Referenced by CopyInnerAtomIndex(), and FindingNeighborInUnitcell().

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

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

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CGeometricAtom * CGeometricUnitCell::GetSubElementByID

(

double

fID

)

Return atom in unitcell by atom ID.

Parameters

fID	Index of atom

Returns

Pointer of atom instance

Definition at line 282 of file GeometricUnitCell.cpp.

References GetID(), and m_vectInternalAtom.

{
    int                         nSize, i;

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

    return NULL;
}

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static double CGeometricUnitCell::GetSubElementID ( )

inlinestatic

Reset SubElement ID to Zero.

Definition at line 27 of file GeometricUnitCell.h.

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

{ return m_SubElementID;}; 

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int CGeometricUnitCell::GetSubElementSize ( )

inline

Definition at line 43 of file GeometricUnitCell.h.

References m_vectInternalAtom.

Referenced by CopyInnerAtomIndex(), and FindingNeighborInUnitcell().

{ return m_vectInternalAtom.size(); }; 

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int CGeometricUnitCell::IsMachedNeighborRule ( CGeometricAtom *  pCompare1, CGeometricAtom *  pCompare2, std::vector< CGeometricCoordination > *  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 476 of file GeometricUnitCell.cpp.

References ATOM_DEFAULT_INDEX, CGeometricAtom::GetCoordination(), CGeometricAtom::GetNeighborAtomID(), and CGeometricCoordination::SetOffset().

Referenced by BuildNeighborInformation(), and FindingNeighborInUnitcell().

{
    int                         i, nSize;
    CGeometricCoordination      coordination1;
    CGeometricCoordination      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 CGeometricUnitCell::IsPeriodicUnitCell ( )

inline

Check this unit cell is periodic condition or not.

Definition at line 53 of file GeometricUnitCell.h.

References m_bPeriodicElement.

unsigned int CGeometricUnitCell::NumberingSubElement	(	CGeometricCoordination	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 155 of file GeometricUnitCell.cpp.

References _X, _Y, _Z, BOX_SHAPE, CYLINDER_SHAPE, GENERAL_TOLERANCE, CGeometricCoordination::GetCoordination(), CGeometricAtomFactory::GetMaterialNumber(), m_SubElementID, and m_vectInternalAtom.

Referenced by CGeometricShape::ArrangeUnitCell().

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

    for (i = 0; i < nSize; ++i)
    {
        CGeometricCoordination   coordination = m_vectInternalAtom[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 = CGeometricAtomFactory::GetMaterialNumber(pszDomainMatName, m_vectInternalAtom[i].GetType());
        m_vectInternalAtom[i].SetMaterial(nMaterialType);
        m_vectInternalAtom[i].SetID(m_SubElementID++);
    }

    return count;
}

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static void CGeometricUnitCell::ResetSubElementID ( )

inlinestatic

Get unit cell length.

Definition at line 26 of file GeometricUnitCell.h.

References m_SubElementID.

Referenced by CGeometricShape::ArrangeUnitCell().

{ m_SubElementID = 0; }; 

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void CGeometricUnitCell::Serialize

(

double *

pBuffer

)

Convert unit cell data to double buffer.

Parameters

[out]

pBuffer

Data buffer to save serialization result

Definition at line 538 of file GeometricUnitCell.cpp.

References _X, _Y, _Z, and m_vectInternalAtom.

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

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

void CGeometricUnitCell::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 211 of file GeometricUnitCell.cpp.

References _X, _Y, _Z, and m_fAssignedIndex.

Referenced by CGeometricShape::ArrangeUnitCell().

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

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void CGeometricUnitCell::SetCoordination

(

CGeometricCoordination

coordination

)

Get coordination of unit cell.

Set coordination of unit cell

Parameters

coordination

Coordination

Definition at line 43 of file GeometricUnitCell.cpp.

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

Referenced by CGeometricShape::ArrangeUnitCell().

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

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void CGeometricUnitCell::SetCoordination

(

double *

pfCoordination

)

Set coordination of unit cell.

Parameters

pfCoordination

Coordination buffer

Definition at line 51 of file GeometricUnitCell.cpp.

References m_coordination, and CGeometricCoordination::SetCoordination().

{
    m_coordination.SetCoordination(pfCoordination);
}

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void CGeometricUnitCell::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 61 of file GeometricUnitCell.cpp.

References m_coordination, and CGeometricCoordination::SetCoordination().

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

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static void CGeometricUnitCell::SetFullFillIndex ( int  nIndex )

inlinestatic

Changing Full fill neighbor index.

Definition at line 56 of file GeometricUnitCell.h.

References m_nFullFillIndex.

void CGeometricUnitCell::SetID ( double  fID )

inline

Definition at line 34 of file GeometricUnitCell.h.

References m_fUnitCellID.

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

{ m_fUnitCellID = fID; }; 

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

static

Set unit cell length.

Definition at line 33 of file GeometricUnitCell.cpp.

References _X, _Y, _Z, and m_fLength.

Referenced by CGeometricShape::SetAtomAndNeighborInformation().

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

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

To mark unit cell is periodic condition.

Parameters

bPeriodic	Periodic flag
periodicDirection	Periodic direction

Definition at line 589 of file GeometricUnitCell.cpp.

References CGeometricAtomFactory::GetAtomCountInUnitcell(), m_bPeriodicElement, m_periodicDirection, and m_vectInternalAtom.

Referenced by CGeometricShape::ArrangeUnitCell().

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

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

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void CGeometricUnitCell::SetPeriodicDirection ( int  periodicDirection )

private

Set periodic direction.

Parameters

periodicDirection

Periodic direction

Definition at line 618 of file GeometricUnitCell.cpp.

References CGeometricAtomFactory::GetAtomCountInUnitcell(), and m_vectInternalAtom.

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

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

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void CGeometricUnitCell::SetSubDomainMaterial

(

CCommandFileParser::LPINPUT_CMD_PARAM

lpParam

)

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

Parameters

lpParam

Input parameter parsing from command file

Definition at line 105 of file GeometricUnitCell.cpp.

References _X, _Y, _Z, BOX_SHAPE, CYLINDER_SHAPE, CCommandFileParser::INPUT_CMD_PARAM::fOrigin, CCommandFileParser::INPUT_CMD_PARAM::fShapeLength, CGeometricCoordination::GetCoordination(), CGeometricAtomFactory::GetMaterialNumber(), m_vectInternalAtom, CCommandFileParser::INPUT_CMD_PARAM::nShape, CCommandFileParser::INPUT_CMD_PARAM::nSubDomainNumber, and CCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by CGeometricShape::ArrangeUnitCell().

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

    for (j = 0; j < lpParam->nSubDomainNumber; ++j)
    {
            for (i = 0; i < nSize; ++i)
            {
                CGeometricCoordination   coordination = m_vectInternalAtom[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 = CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[j + 1], m_vectInternalAtom[i].GetType());
                m_vectInternalAtom[i].SetMaterial(nMaterialType);
                m_vectInternalAtom[i].SetDomainNumber(j+2);
            }
    }

}

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void CGeometricUnitCell::SetUnitcellList	(	std::vector< CGeometricUnitCell > *	pVect,
		std::vector< CGeometricUnitCell > *	pVectPrev,
		std::vector< CGeometricUnitCell > *	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 608 of file GeometricUnitCell.cpp.

References m_vectUnitCellInNext, m_vectUnitCellInPrev, and m_vectUnitCellInShape.

Referenced by CGeometricShape::ArrangeUnitCell().

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

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void CGeometricUnitCell::ShiftAtomID

(

double

fShift

)

Get neighbor unit cell ID.

Shift atom ID by given fShift value

Parameters

fShift

Shift value

Definition at line 326 of file GeometricUnitCell.cpp.

References m_vectInternalAtom, and ShiftID().

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

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

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void CGeometricUnitCell::ShiftID

(

double

fShift

)

Get unit cell ID.

Shift subelement(atom) ID

Parameters

fShift

Shift value

Definition at line 337 of file GeometricUnitCell.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 CGeometricUnitCell::m_bPeriodicElement

private

Periodic element flag.

Definition at line 75 of file GeometricUnitCell.h.

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

CGeometricCoordination CGeometricUnitCell::m_coordination

private

Coordination of unit cell.

Definition at line 71 of file GeometricUnitCell.h.

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

double CGeometricUnitCell::m_fAssignedIndex[3]

private

Assign index.

Definition at line 67 of file GeometricUnitCell.h.

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

double CGeometricUnitCell::m_fLength

staticprivate

Unit cell length.

Definition at line 65 of file GeometricUnitCell.h.

Referenced by GetLength(), and SetLength().

double CGeometricUnitCell::m_fUnitCellID

private

Unit cell ID.

Definition at line 74 of file GeometricUnitCell.h.

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

int CGeometricUnitCell::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 27 of file GeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetFullFillIndex().

int CGeometricUnitCell::m_periodicDirection

private

Periodic direction information.

Definition at line 76 of file GeometricUnitCell.h.

Referenced by SetPeriodic().

double CGeometricUnitCell::m_SubElementID = ATOM_DEFAULT_INDEX + 1

staticprivate

Maxium atom ID in shape.

Definition at line 66 of file GeometricUnitCell.h.

Referenced by NumberingSubElement(), and ResetSubElementID().

std::vector<CGeometricAtom> CGeometricUnitCell::m_vectInternalAtom

private

Atom in unit cell.

Definition at line 72 of file GeometricUnitCell.h.

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

std::vector<double> CGeometricUnitCell::m_vectNeighborCellID

private

Neighbor unit cell list.

Definition at line 73 of file GeometricUnitCell.h.

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

std::vector<CGeometricUnitCell>* CGeometricUnitCell::m_vectUnitCellInNext

private

Back side unit cell list in shape.

Definition at line 70 of file GeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetUnitcellList().

std::vector<CGeometricUnitCell>* CGeometricUnitCell::m_vectUnitCellInPrev

private

Front side unit cell list in shape.

Definition at line 69 of file GeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetUnitcellList().

std::vector<CGeometricUnitCell>* CGeometricUnitCell::m_vectUnitCellInShape

private

Unit cell list in shape.

Definition at line 68 of file GeometricUnitCell.h.

Referenced by BuildNeighborInformation(), and SetUnitcellList().

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

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