CGeometricShape Class Reference

Class for Geometric shape. More...

#include "GeometricShape.h"

Collaboration diagram for CGeometricShape:

Public Member Functions
	CGeometricShape ()
	~CGeometricShape ()
void	SetOriginCoordination (double x, double y, double z)
	Building Geometric part. More...
void	SetDirection (double x_axis, double y_axis, double z_axis)
	Set direciton of shape. More...
void	SetLength (double lx, double ly, double lz)
	Set length of shape. More...
MATERIAL_INDEX	GetMaterialType ()
void	SetMaterialType (MATERIAL_INDEX type)
	Get maetrial typpe of shap. More...
void	SetMaterialType (char *pszType)
	Set maetrial type of shape. More...
unsigned int	GetShapeForm ()
void	SetShapeForm (unsigned int form)
	Get form type of shape. More...
void	SetShapeForm (char *pszForm)
	Get form type of shape. More...
bool	GetConsideringBoundaryCondition (AXIS_DEFINE direction)
void	SetConsideringBoundaryCondition (bool bConsider, AXIS_DEFINE direction)
	Get bondary condition of shape. More...
bool	FillUnitcell (CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set bondary condition of shape. More...
void	BuildNeighborInformation ()
	Find neighbor of each atom. More...
bool	IsFrontFace ()
void	SetFrontFace (bool bFrontFace)
	Check is this front face side in MPI running enviroment. More...
bool	IsBackendFace ()
	Set front face side mark to shape object. More...
void	SetBackendFace (bool bBackendFace)
	Check is this back end face side in MPI running enviroment. More...
bool	ConstructMapInfo (LPNEIGHBOR_MAP_INFO lpMapInfo, CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Extract atom information from runtime objects. More...
void	ShiftAtomID (double fShift)
	Shift atom id in MPI running enviroment. More...
void	PeriodicUnitCellNumbering (bool bXAxis=false)
	Numbering to periodic unitcell. More...
void	InitMapInfo (LPNEIGHBOR_MAP_INFO lpMapInfo)
	Intilize map info data. More...
bool	RefillPeriodicBinding (CMatrixOperation::CCSR *pResult, CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, unsigned int nRepeatIndex, double fKValue[3], unsigned int nBandSize, bool bRecover)
	Applying phase to Hamiltonian. More...
double	GetTotalAtomCount ()
void	SetTotalAtomCount (double fTotalAtomCountinMPI)
	Get total valid atom count in shape. More...
double	GetAtomStartID ()
	Set total valid atom count in shape. More...
void	ExchangeAtomInfoBetweenNode ()
	Get start index of atom in shape, using in MPI running enviroment. More...
void	FinalShape ()
	Finalize Shape variable. More...
std::vector< CGeometricAtom * > *	GetSurfaceAtomList ()
unsigned int	ConstructBasicGeometric (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, bool bMPI)
	Get Surface atom list. More...
void	SetupPEBoundaryCondition (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LP_CONTACT_GROUP_INFO *lpContactGroup)
	<Added by="" jhkang>=""> More...
bool	BuildPEHamiltonian (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, CMatrixOperation::CCSR *pCSRResult)
	Build PE Hamiltonian matrix from mapinfo data. More...
void	BuildPEBiasVector (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, LP_CONTACT_GROUP_INFO *lpContactGroup, CMatrixOperation::CVector *pVecResult)
void	BuildPEWaveVector (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, CMatrixOperation::CVector *pVecResult)
int	IsCoordinateMatched (double fa, double fb)
void	MapElecAtomOnPoissonGrid (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo)
void	ConstructContactRegionOnPoissonGrid (CCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, LP_CONTACT_GROUP_INFO *lpContactGroup)
bool	GetNeumannBoundaryCondition (AXIS_DEFINE direction)
void	SetNeumannBoundaryCondition (bool bConsider, AXIS_DEFINE direction)
	Get Neumann boundary condition of shape. More...
double *	GetUnitCellLength ()
void	SetShapeInformation (CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set shape information(Length, material, bondary condition and so on) More...
void	SetMatchingUnitcellCount (int nCount)

Static Public Member Functions
static bool	SetAtomAndNeighborInformation (CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set neighbor information to AtomFactory. More...
static void	FreeMapInfo (LPNEIGHBOR_MAP_INFO lpMapInfo)
	Release mapinfo data. More...

Public Attributes
unsigned int	m_nAtomFirstLayer
	<Added by="" jhkang="" end>=""> More...
unsigned int	m_nAtomLastLayer
	Last layer information for sending to next node. More...

Static Public Attributes
static CGeometricUnitCellInfo_zincblende	m_UnitCellInfo_zincblende
static CGeometricUnitCellInfo_cubic	m_UnitCellInfo_cubic
static IGeometricUnitCellInfo *	m_pUnitCellInfo
	Unitcell information pointer for using in class internal. More...
static CMatrixOperation::CDMatrix	m_rotationMatrix
	Rotation matrix for given direction. More...

Private Member Functions
bool	IsInBoundaryCondition (int x, int y, int z, int maxX, int maxY, int maxZ)
	<Added by="" jhkang="" end>=""> More...
void	FreeUnitCellList ()
	Relase unitcell list. More...
void	InitShape ()
	Initialize Shape variable. More...
void	RotateMatrix (CMatrixOperation::CDMatrix *pMatrixNbr, CMatrixOperation::CDMatrix *pMatrixResult, double fDegree[2])
	Rotate matrix with calculated degree. More...
CGeometricAtom *	GetAtomByIndex (double fID)
	Get atom instance by ID. More...
double	GetKPhaseSign (double fAtomPos, double fPeriodicAtomPos)
	Calculating Phase sign. More...
int	GetPeriodicDirection (int x, int y, int z, int maxX, int maxY, int maxZ)
	Get periodic direction information. More...
bool	CalculateUnitcellCount ()
	Calculating unitcell count in shape. More...
void	ArrangeUnitCell (CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Arranging unitcell into shape. More...
void	CheckingNeighborCandiate ()
	Checking neighbor unitcell by calculating index. More...
double *	Serialize (double fXLayer)
	Serialize unitcells with specific later index to double array. More...
void	Deserialize (std::vector< CGeometricUnitCell > *pVectUnitCell, double *pBuffer, bool bFrontSide)
	Deerialize unitcells from double array. More...
void	BuildGeoFileName (char *pszFileName, CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Make atom map naming. More...
bool	SetMapInfoSize (LPNEIGHBOR_MAP_INFO lpMapInfo, double fSize)
	Building Hamiltonian part. More...

Static Private Member Functions
static void	BuildRotationMatrix (double fDegree[2])
	Build rotation matrix for given direction. More...
static void	CalculateDegree (CCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Calculating degree from direction information. More...

Private Attributes
double	m_fLength [3]
	Building Geometric part. More...
double	m_fAssignedCount [3]
	Unitcell assigend count in shape for each direction. More...
unsigned int	m_ShapeForm
	Shape form. More...
bool	m_bConsiderBoundaryCondition [3]
	Bondary condition for each driection. More...
bool	m_bFrontFace
	Flag of front face or not. More...
bool	m_bBackendFace
	Flag of back end face or not. More...
double	m_fTotalAtomCountinMPI
	Total valid atom count in shape. More...
double	m_fAtomIDStartIndex
	Start atom index in current Shape. More...
MATERIAL_INDEX	m_MaterialType
	Material type of shape. More...
std::vector< CGeometricUnitCell >	m_vectUnitCell
	Array of unitcell in shape. More...
std::vector< CGeometricUnitCell >	m_vectPrevUnitCell
	Front edge unit cell that copy from previous side node. More...
std::vector< CGeometricUnitCell >	m_vectNextUnitCell
	Back end edge unit cell that copy from next side node. More...
std::vector< CGeometricAtom * >	m_vectSurfaceAtom
CGeometricCoordination	m_originCoordination
	Orign coordination of shape. More...
CGeometricDirection	m_shapDirection
int	m_nContactNumber
	<Added by="" jhkang>=""> More...
std::vector< double >	m_waveFunctionValue
bool	m_bNeumannBoundaryCondition [3]
int	m_nHandlingUnitcellCount
double	m_fUnitCellLength [3]

Detailed Description

Class for Geometric shape.

Date

03/Oct/2014

Definition at line 27 of file GeometricShape.h.

Constructor & Destructor Documentation

CGeometricShape::CGeometricShape

(

)

Definition at line 32 of file GeometricShape.cpp.

References InitShape().

{
    InitShape();
}

Here is the call graph for this function:

CGeometricShape::~CGeometricShape

(

)

Definition at line 37 of file GeometricShape.cpp.

References FinalShape().

{
    FinalShape();
}

Here is the call graph for this function:

Member Function Documentation

void CGeometricShape::ArrangeUnitCell ( CCommandFileParser::LPINPUT_CMD_PARAM  lpParam )

private

Arranging unitcell into shape.

Parameters

lpParam

Input parameters parsing from command file

Definition at line 403 of file GeometricShape.cpp.

References _X, _Y, _Z, CGeometricUnitCell::ArrangeAtom(), CGeometricCoordination::GetCoordination(), CGeometricCoordination::GetCoordinationAll(), CMPIManager::GetCurrentRank(), CGeometricUnitCell::GetLength(), GetPeriodicDirection(), CMPIManager::GetTotalNodeCount(), IsInBoundaryCondition(), m_bConsiderBoundaryCondition, m_bFrontFace, m_fAssignedCount, m_fLength, m_nAtomFirstLayer, m_nAtomLastLayer, m_originCoordination, m_vectNextUnitCell, m_vectPrevUnitCell, m_vectUnitCell, CGeometricAtom::NONE, CCommandFileParser::INPUT_CMD_PARAM::nShape, CGeometricUnitCell::NumberingSubElement(), CGeometricUnitCell::ResetSubElementID(), CGeometricUnitCell::SetAssignIndex(), CGeometricCoordination::SetCoordination(), CGeometricUnitCell::SetCoordination(), CGeometricUnitCell::SetID(), CGeometricCoordination::SetOffset(), CGeometricUnitCell::SetPeriodic(), CGeometricUnitCell::SetSubDomainMaterial(), CGeometricUnitCell::SetUnitcellList(), and CCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by FillUnitcell().

{
    int                         x, y, z, maxX, maxY, maxZ;
    CGeometricCoordination      currentPos, refPos;
    double                      fUnitcellLength[3];
    double                      fUnitcellID = 0;

    fUnitcellLength[_X] = CGeometricUnitCell::GetLength(_X);
    fUnitcellLength[_Y] = CGeometricUnitCell::GetLength(_Y);
    fUnitcellLength[_Z] = CGeometricUnitCell::GetLength(_Z);

    currentPos.SetCoordination(m_originCoordination.GetCoordinationAll());

    double          fOffset[3] = { 0, };

    if (m_bConsiderBoundaryCondition[_X])
    {
        if (m_bFrontFace)
            fOffset[_X] = -fUnitcellLength[_X];
    }

    if (m_bConsiderBoundaryCondition[_Y])
        fOffset[_Y] = -fUnitcellLength[_Y];
        
    if (m_bConsiderBoundaryCondition[_Z])
        fOffset[_Z] = -fUnitcellLength[_Z];

    currentPos.SetOffset(fOffset[_X], fOffset[_Y], fOffset[_Z]);
    refPos.SetCoordination(currentPos.GetCoordinationAll());

    maxX = (int)floor(m_fAssignedCount[_X]);
    maxY = (int)floor(m_fAssignedCount[_Y]);
    maxZ = (int)floor(m_fAssignedCount[_Z]);

    CGeometricUnitCell::ResetSubElementID();
    for (x = 0; x < maxX; ++x)
    {
        currentPos.SetCoordination(currentPos.GetCoordination(_X), refPos.GetCoordination(_Y), refPos.GetCoordination(_Z));
        for (y = 0; y < maxY; ++y)
        {
            currentPos.SetCoordination(currentPos.GetCoordination(_X), currentPos.GetCoordination(_Y), refPos.GetCoordination(_Z));
            for (z = 0; z < maxZ; ++z)
            {
                CGeometricUnitCell      UnitCell;
                
                UnitCell.SetCoordination(currentPos);
                UnitCell.SetID(fUnitcellID++);
                UnitCell.ArrangeAtom(lpParam);
        
                if (IsInBoundaryCondition(x, y, z, maxX, maxY, maxZ))
                {
                    //printf("[%03d] %10.10f, %10.10f, %10.10f\n", (int)(fUnitcellID - 1), currentPos.GetCoordination(CGeometricCoordination::X), currentPos.GetCoordination(CGeometricCoordination::Y), currentPos.GetCoordination(CGeometricCoordination::Z));
                    unsigned int nAtom = UnitCell.NumberingSubElement(m_originCoordination, m_fLength, lpParam->nShape[0], lpParam->szDomainMat[0]);
                    if (x == 0)
                        m_nAtomFirstLayer += nAtom;
                    if (x == 1 && m_bConsiderBoundaryCondition[_X])
                        m_nAtomFirstLayer += nAtom;
                    if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
                    {
                        if (x == maxX - 2)
                            m_nAtomLastLayer += nAtom;
                    }
                    else
                    {
                        if (x == maxX - 1)
                            m_nAtomLastLayer += nAtom;
                    }
                }
                else
                {
                    int     periodicDirection = CGeometricAtom::NONE;
                    
                    periodicDirection = GetPeriodicDirection(x, y, z, maxX, maxY, maxZ);
                    UnitCell.SetPeriodic(true, periodicDirection);
                }

                UnitCell.SetSubDomainMaterial(lpParam);         
                UnitCell.SetAssignIndex(x, y, z);
                UnitCell.SetUnitcellList(&m_vectUnitCell, &m_vectPrevUnitCell, &m_vectNextUnitCell);
                m_vectUnitCell.push_back(UnitCell);

                currentPos.SetOffset(0, 0, fUnitcellLength[_Z]);
            }
            currentPos.SetOffset(0, fUnitcellLength[_Y], 0);
        }
        currentPos.SetOffset(fUnitcellLength[_X], 0, 0);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::BuildGeoFileName ( char *  pszFileName, CCommandFileParser::LPINPUT_CMD_PARAM  lpParam  )

private

Make atom map naming.

Parameters

[out]	pszFileName	Geometric information file name
	lpParam	Input parameter parsing from command file

Definition at line 1343 of file GeometricShape.cpp.

References CCommandFileParser::INPUT_CMD_PARAM::bConsiderBoundaryCondition, CCommandFileParser::INPUT_CMD_PARAM::nDirectionSingle, CCommandFileParser::INPUT_CMD_PARAM::nSubDomainNumber, CCommandFileParser::INPUT_CMD_PARAM::szShape, and CCommandFileParser::INPUT_CMD_PARAM::szStructureType.

Referenced by ConstructMapInfo().

{
    char                szTemp[1024];
    unsigned int        i;


    sprintf(pszFileName, "Geo_%d_%d%d%d_%s_", lpParam->nDirectionSingle, lpParam->bConsiderBoundaryCondition[0] ? 1 : 0, lpParam->bConsiderBoundaryCondition[1] ? 1 : 0, lpParam->bConsiderBoundaryCondition[2] ? 1 : 0, lpParam->szStructureType);

    if (!strcmp(lpParam->szShape[0], "Box"))
        strcpy(szTemp, "B");
    else if (!strcmp(lpParam->szShape[0], "Cylinder"))
        strcpy(szTemp, "C");

    strcat(pszFileName, szTemp);

    for (i = 0; i < (unsigned int)lpParam->nSubDomainNumber; ++i)
    {
        if (!strcmp(lpParam->szShape[i + 1], "Box"))
            strcpy(szTemp, "B");
        else if (!strcmp(lpParam->szShape[i + 1], "Cylinder"))
            strcpy(szTemp, "C");

        strcat(pszFileName, szTemp);
    }
}

Here is the caller graph for this function:

void CGeometricShape::BuildNeighborInformation

(

)

Find neighbor of each atom.

Definition at line 116 of file GeometricShape.cpp.

References GetSurfaceAtomList(), m_fAssignedCount, and m_vectUnitCell.

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

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

    for (i = 0; i < nSize; ++i)
    {
        if( !m_vectUnitCell[i].IsPeriodicUnitCell() )
            m_vectUnitCell[i].BuildNeighborInformation(m_fAssignedCount, GetSurfaceAtomList());
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::BuildPEBiasVector	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		LP_CONTACT_GROUP_INFO *	lpContactGroup,
		CMatrixOperation::CVector *	pVecResult
	)

Definition at line 2187 of file GeometricShape.cpp.

References ATOM_DEFAULT_INDEX, CCommandFileParser::INPUT_CMD_PARAM::bSaveContactBiasVector, CMaterialParam::BuildMaterialParam(), CONTACT_GROUP_INFO::ContactList, EPSILON0, CONTACT_GROUP_INFO::fContactBiasValue, GEO_PARAMETER::feips, NEIGHBOR_MAP_INFO::fItemCount, CCommandFileParser::INPUT_CMD_PARAM::fUnitcellLength, CMatrixOperation::CVector::GetAt(), CMPIManager::GetCurrentRank(), CGeometricAtomFactory::GetMaterialNumber(), CComplex::GetRealNumber(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_nContactNumber, CONTACT_GROUP_INFO::nContactDirection, NM, NMAXDOMAIN, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, NEIGHBOR_MAP_INFO::pMaterialNumber, CMPIManager::ReceiveDoubleBufferSync(), CMPIManager::SendDoubleBufferSync(), CMatrixOperation::CVector::SetAt(), CMatrixOperation::CVector::SetSize(), CUtility::ShowMsg(), and CCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by CSPLoop::ConstructionGeometric().

{
    unsigned int                                i, ia;
    int                                         nContactAtom, nContactDirection;
    double                                      *fBiasVectorGroup[6], fBiasSum;
    double                                      fGridSpacingSq[6];
    double                                      fEpsilon[NMAXDOMAIN];
    double                                      fNeighborEps;
    bool                                        bRtn;
    MATERIAL_INDEX                              nMaterialType;
    CMaterialParam                              materialParam;

    FILE                                        *out = NULL;
    char                                        szFileName[1024];
    char                                        szMsg[1024], szTemp[1024];

    for (i = 0; i < 6; i++)
    {
        fBiasVectorGroup[i] = (double*)malloc(sizeof(double)* (unsigned int)lpMapInfo->fItemCount);
        memset(fBiasVectorGroup[i], 0, sizeof(double)* (unsigned int)lpMapInfo->fItemCount);
    }

    for (i = 0; i < NMAXDOMAIN; i++)
    {
        nMaterialType = CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[i], CGeometricAtom::ATOM_TYPE::A);
        fEpsilon[nMaterialType] = materialParam.BuildMaterialParam(lpParam->szDomainMat[i], bRtn).feips * EPSILON0;
    }

    //  Grid spacing and material property
    fGridSpacingSq[0] = 1.0 / (lpParam->fUnitcellLength[0] * lpParam->fUnitcellLength[0]) / NM / NM;
    fGridSpacingSq[1] = fGridSpacingSq[0];
    fGridSpacingSq[2] = 1.0 / (lpParam->fUnitcellLength[1] * lpParam->fUnitcellLength[1]) / NM / NM;
    fGridSpacingSq[3] = fGridSpacingSq[2];
    fGridSpacingSq[4] = 1.0 / (lpParam->fUnitcellLength[2] * lpParam->fUnitcellLength[2]) / NM / NM;
    fGridSpacingSq[5] = fGridSpacingSq[4];

    for (i = 0; i < m_nContactNumber; i++)
    {
        for (ia = 0; ia < lpContactGroup[i]->ContactList.size(); ia++)
        {
            nContactAtom = lpContactGroup[i]->ContactList[ia];
            nContactDirection = lpContactGroup[i]->nContactDirection;

            if (lpContactGroup[i]->nContactDirection == 6)
            {
                if (lpMapInfo->pfNeighbor[2][nContactAtom] == ATOM_DEFAULT_INDEX)
                {
                    fBiasVectorGroup[2][nContactAtom] = lpContactGroup[i]->fContactBiasValue * fGridSpacingSq[2] * fEpsilon[(int)lpMapInfo->pMaterialNumber[nContactAtom]];
                }
                if (lpMapInfo->pfNeighbor[3][nContactAtom] == ATOM_DEFAULT_INDEX)
                {
                    fBiasVectorGroup[3][nContactAtom] = lpContactGroup[i]->fContactBiasValue * fGridSpacingSq[3] * fEpsilon[(int)lpMapInfo->pMaterialNumber[nContactAtom]];
                }
                if (lpMapInfo->pfNeighbor[4][nContactAtom] == ATOM_DEFAULT_INDEX)
                {
                    fBiasVectorGroup[4][nContactAtom] = lpContactGroup[i]->fContactBiasValue * fGridSpacingSq[4] * fEpsilon[(int)lpMapInfo->pMaterialNumber[nContactAtom]];
                }
                if (lpMapInfo->pfNeighbor[5][nContactAtom] == ATOM_DEFAULT_INDEX)
                {
                    fBiasVectorGroup[5][nContactAtom] = lpContactGroup[i]->fContactBiasValue * fGridSpacingSq[5] * fEpsilon[(int)lpMapInfo->pMaterialNumber[nContactAtom]];
                }
            }
            else
            {
                fBiasVectorGroup[nContactDirection][nContactAtom] = lpContactGroup[i]->fContactBiasValue * fGridSpacingSq[nContactDirection] * fEpsilon[(int)lpMapInfo->pMaterialNumber[nContactAtom]];
            }
        }
    }

    pVecResult->SetSize((unsigned int)lpMapInfo->fItemCount);

    for (ia = 0; ia < lpMapInfo->fItemCount; ia++)
    {
        fBiasSum = 0.0;
        for (i = 0; i < 6; i++)
        {
            fBiasSum += fBiasVectorGroup[i][ia];
        }
        pVecResult->SetAt(ia, fBiasSum, 0.0);
    }

    // Dump bias vector construction result
#ifndef DISABLE_MPI_ROUTINE
    MPI_Request         req;
    double              fTemp = 1;
#endif //DISABLE_MPI_ROUTINE

    if (true == lpParam->bSaveContactBiasVector)
    {
        strcpy(szTemp, "ContactBiasVector.dat");
#ifdef _WIN32
        sprintf(szFileName, "result\\%s", szTemp);
#else
        sprintf(szFileName, "result/%s", szTemp);
#endif

#ifdef DISABLE_MPI_ROUTINE
        out = fopen(szFileName, "wt");
#else //DISABLE_MPI_ROUTINE

        if (CMPIManager::IsRootRank())
        {
            CUtility::ShowMsg("-Save contact bias vector info. to file.\n");
            out = fopen(szFileName, "wt");
        }
        else
        {
            CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, &fTemp, 1, &req);
            out = fopen(szFileName, "at");
        }
#endif //DISABLE_MPI_ROUTINE
    }

    if (true == lpParam->bSaveContactBiasVector && NULL != out)
    {
        for (i = 0; i < lpMapInfo->fItemCount; i++)
        {
            sprintf(szMsg, "%6d (%11.8f %11.8f%11.8f )%12.3f %12.3f %12.3f %12.3f %12.3f %12.3f %12.3f\n", (int)lpMapInfo->pfID[i], lpMapInfo->pfX_Coordination[i], lpMapInfo->pfY_Coordination[i], lpMapInfo->pfZ_Coordination[i],
                fBiasVectorGroup[0][i], fBiasVectorGroup[1][i], fBiasVectorGroup[2][i], fBiasVectorGroup[3][i], fBiasVectorGroup[4][i], fBiasVectorGroup[5][i], pVecResult->GetAt(i).GetRealNumber());
            fputs(szMsg, out);
        }

        fclose(out);
#ifndef DISABLE_MPI_ROUTINE
        if (CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, &fTemp, 1, &req);
#endif //DISABLE_MPI_ROUTINE
    }
    for (i = 0; i < 6; i++)
        free(fBiasVectorGroup[i]);

}

Here is the call graph for this function:

Here is the caller graph for this function:

bool CGeometricShape::BuildPEHamiltonian	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		CMatrixOperation::CCSR *	pCSRResult
	)

Build PE Hamiltonian matrix from mapinfo data.

Definition at line 1480 of file GeometricShape.cpp.

References _X, _Y, _Z, ATOM_CONTACT_INDEX, ATOM_DEFAULT_INDEX, CCommandFileParser::INPUT_CMD_PARAM::bConsiderNeumannBoundaryCondition, CMaterialParam::BuildMaterialParam(), CMatrixOperation::CDMatrix::BuildMatrixFirst(), EPSILON0, GEO_PARAMETER::feips, CCommandFileParser::INPUT_CMD_PARAM::fUnitcellLength, CMPIManager::GetCurrentRank(), CGeometricAtomFactory::GetMaterialNumber(), CMatrixOperation::CCSR::GetRowCount(), CMPIManager::IsRootRank(), m_fAtomIDStartIndex, CMatrixOperation::FILL_MATRIX_DATA::nColumnIndex, NM, NMAXDOMAIN, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pMaterialNumber, CMatrixOperation::FILL_MATRIX_DATA::pMatrix, NEIGHBOR_MAP_INFO::pNeighborMaterial, CMatrixOperation::CCSR::PushMatrixConcurrentPE(), CMatrixOperation::CDMatrix::SetElement(), and CCommandFileParser::INPUT_CMD_PARAM::szDomainMat.

Referenced by CSPLoop::BuildHamiltonian().

{
    bool                                        bRtn = false;
    double                                      fNeighborEps;
    double                                      fGridSpacingSq[6];
    double                                      fOffDiagonalValue, fDiagonalValue;
    double                                      fEpsilon[NMAXDOMAIN];
    MATERIAL_INDEX                              nMaterialType;
    int                                         nCountNeumann = 0, nCountContact = 0, nCountZeroContact = 0, nCountNeumannSum = 0, nCountContactSum = 0, nCountZeroContactSum = 0;

    unsigned int                                i, j, nRowSize;
    CMatrixOperation::CDMatrix                  matrixOnSite;
    CMatrixOperation::CDMatrix                  matrixNbr[6];       //0: Xp, 1: Xm, 2: Yp, 3: Ym, 4: Zp, 5: Zm
    CMaterialParam                              materialParam;
    CMatrixOperation::FILL_MATRIX_DATA          elementData[7];

    //  Diagonal element setting arbitrarily
    matrixOnSite.BuildMatrixFirst(1, 1);

    //  Offdiagonal element setting arbitrarily
    for (i = 0; i < 6; i++)
    {
        matrixNbr[i].BuildMatrixFirst(1, 1);
    }

    //  Grid spacing and material property
    fGridSpacingSq[0] = 1.0 / (lpParam->fUnitcellLength[0] * lpParam->fUnitcellLength[0]) / NM / NM;
    fGridSpacingSq[1] = fGridSpacingSq[0];
    fGridSpacingSq[2] = 1.0 / (lpParam->fUnitcellLength[1] * lpParam->fUnitcellLength[1]) / NM / NM;
    fGridSpacingSq[3] = fGridSpacingSq[2];
    fGridSpacingSq[4] = 1.0 / (lpParam->fUnitcellLength[2] * lpParam->fUnitcellLength[2]) / NM / NM;
    fGridSpacingSq[5] = fGridSpacingSq[4];

    for (i = 0; i < NMAXDOMAIN; i++)
    {
        nMaterialType = CGeometricAtomFactory::GetMaterialNumber(lpParam->szDomainMat[i], CGeometricAtom::ATOM_TYPE::A);
        fEpsilon[nMaterialType] = materialParam.BuildMaterialParam(lpParam->szDomainMat[i], bRtn).feips * EPSILON0;
        if (CMPIManager::IsRootRank() && nMaterialType > 0)
        {
            printf("-material[%d] : nMaterialType = %d, episilon = %e, material name = %s\n", i, nMaterialType, fEpsilon[nMaterialType], lpParam->szDomainMat[i]);
        }
    }

    nRowSize = pCSRResult->GetRowCount();

    for (i = 0; i < nRowSize; i++)
    {
        fDiagonalValue = 0.0;

        for (j = 0; j < 6; j++)
        {

            if (ATOM_DEFAULT_INDEX == lpMapInfo->pfNeighbor[j][i])
            {
                fNeighborEps = -fEpsilon[(int)lpMapInfo->pMaterialNumber[i]];
                fOffDiagonalValue = fNeighborEps * fGridSpacingSq[j];
                fDiagonalValue += -fOffDiagonalValue;

                if (lpParam->bConsiderNeumannBoundaryCondition[_X] && (j / 2 == 0))
                {
                    fDiagonalValue += fOffDiagonalValue;
                    nCountNeumann++;
                }
                if (lpParam->bConsiderNeumannBoundaryCondition[_Y] && (j / 2 == 1))
                {
                    fDiagonalValue += fOffDiagonalValue;
                    nCountNeumann++;
                }
                if (lpParam->bConsiderNeumannBoundaryCondition[_Z] && (j / 2 == 2))
                {
                    fDiagonalValue += fOffDiagonalValue;
                    nCountNeumann++;
                }
                nCountZeroContact++;

                elementData[j + 1].nColumnIndex = ATOM_DEFAULT_INDEX;
                elementData[j + 1].pMatrix = NULL;
            }
            else if (ATOM_CONTACT_INDEX == lpMapInfo->pfNeighbor[j][i])
            {
                fNeighborEps = -fEpsilon[(int)lpMapInfo->pMaterialNumber[i]];
                fOffDiagonalValue = fNeighborEps * fGridSpacingSq[j];
                fDiagonalValue += -fOffDiagonalValue;

                elementData[j + 1].nColumnIndex = ATOM_DEFAULT_INDEX;
                elementData[j + 1].pMatrix = NULL;
                nCountContact++;
            }
            else
            {
                fNeighborEps = -fEpsilon[(int)lpMapInfo->pNeighborMaterial[j][i]];
                fOffDiagonalValue = fNeighborEps * fGridSpacingSq[j];
                fDiagonalValue += -fOffDiagonalValue;

                matrixNbr[j].SetElement(0, 0, fOffDiagonalValue, 0.0);
                elementData[j + 1].nColumnIndex = (int)lpMapInfo->pfNeighbor[j][i];
                elementData[j + 1].pMatrix = &matrixNbr[j];
            }
        }

        matrixOnSite.SetElement(0, 0, fDiagonalValue, 0.0);

        elementData[0].nColumnIndex = i + (unsigned int)m_fAtomIDStartIndex;
        elementData[0].pMatrix = &matrixOnSite;

        pCSRResult->PushMatrixConcurrentPE(i, &elementData[0], false);

    }
    nCountZeroContact -= nCountNeumann;
    printf("[Rank:%3d] Neumann atom = %d, Default Contact atom = %d, Contact group atom = %d \n", CMPIManager::GetCurrentRank(), nCountNeumann, nCountZeroContact, nCountContact);

    MPI_Reduce(&nCountNeumann, &nCountNeumannSum, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
    MPI_Reduce(&nCountZeroContact, &nCountZeroContactSum, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
    MPI_Reduce(&nCountContact, &nCountContactSum, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);

    if (CMPIManager::IsRootRank())
        printf("-Total Neumann atom = %d, Total contact atom = %d \n", nCountNeumannSum, nCountContactSum + nCountZeroContactSum);

    bRtn = true;
    return bRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::BuildPEWaveVector	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		CMatrixOperation::CVector *	pVecResult
	)

Definition at line 1751 of file GeometricShape.cpp.

References _X, _Y, _Z, ATOM_DEFAULT_INDEX, CCommandFileParser::INPUT_CMD_PARAM::bSaveWaveVector, NEIGHBOR_MAP_INFO::fItemCount, CCommandFileParser::INPUT_CMD_PARAM::fUnitcellLength, CMatrixOperation::CVector::GetAt(), CMPIManager::GetCurrentRank(), CComplex::GetRealNumber(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_waveFunctionValue, NM, NEIGHBOR_MAP_INFO::pfAtomOnGrid, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, Qo, CMPIManager::ReceiveDoubleBufferSync(), CMPIManager::SendDoubleBufferSync(), CMatrixOperation::CVector::SetAt(), CMatrixOperation::CVector::SetSize(), and CUtility::ShowMsg().

{
    unsigned int                                i, nCount = 0, nParamSize = 4;
    FILE                                        *waveIn = NULL, *out = NULL;
    char                                        szWaveFileName[1024];
    char                                        szOutFileName[1024], szMsg[1024], szTemp[1024];
    char                                        strSperate[] = " ";
    char                                        *token = NULL;
    double                                      fParam[4], ax, ay, az;

    pVecResult->SetSize((unsigned int)lpMapInfo->fItemCount);

    sprintf(szWaveFileName, "./testset/reference1_zb_rhs_unscaled_at_iter1.dat");
    waveIn = fopen(szWaveFileName, "rt");

    ax = lpParam->fUnitcellLength[_X] * NM;
    ay = lpParam->fUnitcellLength[_Y] * NM;
    az = lpParam->fUnitcellLength[_Z] * NM;

    while (fgets(szTemp, 1024, waveIn))
    {
        token = strtok(szTemp, strSperate);
        while (token)
        {
            fParam[nCount++] = atof(token);
            if (nParamSize == nCount)
                break;
            token = strtok(NULL, strSperate);
        }
        m_waveFunctionValue.push_back(fParam[3] / ax / ay / az * Qo);
        nCount = 0;
    }
    fclose(waveIn);

    for (i = 0; i < lpMapInfo->fItemCount; i++)
    {
        if ((int)lpMapInfo->pfAtomOnGrid[i] == ATOM_DEFAULT_INDEX)
            pVecResult->SetAt(i, 0.0, 0.0);
        else
            pVecResult->SetAt(i, m_waveFunctionValue[(int)lpMapInfo->pfAtomOnGrid[i]], 0.0);
    }

    // Dump wave vector construction result
#ifndef DISABLE_MPI_ROUTINE
    MPI_Request         req;
    double              fTemp = 1;
#endif //DISABLE_MPI_ROUTINE

    if (true == lpParam->bSaveWaveVector)
    {
        strcpy(szTemp, "WaveVector.dat");
#ifdef _WIN32
        sprintf(szOutFileName, "result\\%s", szTemp);
#else
        sprintf(szOutFileName, "result/%s", szTemp);
#endif

#ifdef DISABLE_MPI_ROUTINE
        out = fopen(szOutFileName, "wt");
#else //DISABLE_MPI_ROUTINE

        if (CMPIManager::IsRootRank())
        {
            CUtility::ShowMsg("-Save wave vector info. to file.\n");
            out = fopen(szOutFileName, "wt");
        }
        else
        {
            CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, &fTemp, 1, &req);
            out = fopen(szOutFileName, "at");
        }
#endif //DISABLE_MPI_ROUTINE
    }

    if (true == lpParam->bSaveWaveVector && NULL != out)
    {
        for (i = 0; i < lpMapInfo->fItemCount; i++)
        {
            sprintf(szMsg, "%6d %11.8f %11.8f%11.8f %18.12f\n", (int)lpMapInfo->pfID[i], lpMapInfo->pfX_Coordination[i], lpMapInfo->pfY_Coordination[i], lpMapInfo->pfZ_Coordination[i],
                pVecResult->GetAt(i).GetRealNumber());
            fputs(szMsg, out);
        }

        fclose(out);
#ifndef DISABLE_MPI_ROUTINE
        if (CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, &fTemp, 1, &req);
#endif //DISABLE_MPI_ROUTINE
    }
}

Here is the call graph for this function:

void CGeometricShape::BuildRotationMatrix ( double  fDegree[2] )

staticprivate

Build rotation matrix for given direction.

Parameters

fDegree

Given degree of theta and phi

Definition at line 1320 of file GeometricShape.cpp.

References CMatrixOperation::CDMatrix::BuildMatrixFirst(), m_rotationMatrix, PHI_DEGREE, CMatrixOperation::CDMatrix::SetElement(), THETA_DEGREE, and CMatrixOperation::CDMatrix::TrnasPos().

Referenced by SetAtomAndNeighborInformation().

{
    m_rotationMatrix.BuildMatrixFirst(3, 3);

    m_rotationMatrix.SetElement(0, 0, cos(fDegree[THETA_DEGREE]) * cos(fDegree[PHI_DEGREE]), 0);
    m_rotationMatrix.SetElement(0, 1, -sin(fDegree[THETA_DEGREE]), 0);
    m_rotationMatrix.SetElement(0, 2, -cos(fDegree[THETA_DEGREE])*sin(fDegree[PHI_DEGREE]), 0);

    m_rotationMatrix.SetElement(1, 0, sin(fDegree[THETA_DEGREE]) * cos(fDegree[PHI_DEGREE]), 0);
    m_rotationMatrix.SetElement(1, 1, cos(fDegree[THETA_DEGREE]), 0);
    m_rotationMatrix.SetElement(1, 2, -sin(fDegree[THETA_DEGREE])*sin(fDegree[PHI_DEGREE]), 0);

    m_rotationMatrix.SetElement(2, 0, sin(fDegree[PHI_DEGREE]), 0);
    m_rotationMatrix.SetElement(2, 1, 0, 0);
    m_rotationMatrix.SetElement(2, 2, cos(fDegree[PHI_DEGREE]), 0);

    m_rotationMatrix.TrnasPos();
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::CalculateDegree ( CCommandFileParser::LPINPUT_CMD_PARAM  lpParam )

staticprivate

Calculating degree from direction information.

Parameters

lpParam

Input parameters parsing from command file

Definition at line 715 of file GeometricShape.cpp.

References CCommandFileParser::INPUT_CMD_PARAM::fDegree, CCommandFileParser::INPUT_CMD_PARAM::fDirection, PHI_DEGREE, PI_VALUE, and THETA_DEGREE.

Referenced by SetAtomAndNeighborInformation().

{
    /*TODO: changing input parameter sqrtf -> sqrt(from all source code)*/
    double          fR = sqrt(lpParam->fDirection[0] * lpParam->fDirection[0] + lpParam->fDirection[1] * lpParam->fDirection[1] + lpParam->fDirection[2] * lpParam->fDirection[2]);

    lpParam->fDegree[PHI_DEGREE] = PI_VALUE/2 - acos(lpParam->fDirection[2] / fR);
    lpParam->fDegree[THETA_DEGREE] = atan(lpParam->fDirection[1] / lpParam->fDirection[0]);
}

Here is the caller graph for this function:

bool CGeometricShape::CalculateUnitcellCount ( )

private

Calculating unitcell count in shape.

< Only for Show unitcell count

< Only for Show unitcell count

Definition at line 257 of file GeometricShape.cpp.

References _X, _Y, _Z, CMPIManager::AllReduceDouble(), CGeometricCoordination::GetCoordination(), CMPIManager::GetCurrentRank(), CGeometricUnitCell::GetLength(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_bBackendFace, m_bConsiderBoundaryCondition, m_bFrontFace, m_fAssignedCount, m_fLength, m_fUnitCellLength, m_nHandlingUnitcellCount, m_originCoordination, CGeometricCoordination::SetOffset(), and CUtility::ShowMsg().

Referenced by FillUnitcell().

{
    double              fXTotalCount;
    double              fXAssignCount, fYAssignCount, fZAssignCount;
    double              fUnitcellLength[3];
    bool                bRtn = false;
    bool                bPaddingUnitCell = false;
    char                szMsg[1024];
    
    fUnitcellLength[_X] = CGeometricUnitCell::GetLength(_X);
    fUnitcellLength[_Y] = CGeometricUnitCell::GetLength(_Y);
    fUnitcellLength[_Z] = CGeometricUnitCell::GetLength(_Z);

    m_fUnitCellLength[_X] = CGeometricUnitCell::GetLength(_X);
    m_fUnitCellLength[_Y] = CGeometricUnitCell::GetLength(_Y);
    m_fUnitCellLength[_Z] = CGeometricUnitCell::GetLength(_Z);

    fXTotalCount = floor(m_fLength[_X] / fUnitcellLength[_X]);
    if( !m_bConsiderBoundaryCondition[_X])
        bPaddingUnitCell = true;
    
    if( m_bConsiderBoundaryCondition[_Y])
        fYAssignCount = floor(m_fLength[_Y] / fUnitcellLength[_Y]) + 2;
    else
        fYAssignCount = ceil(m_fLength[_Y] / fUnitcellLength[_Y]);

    if( m_bConsiderBoundaryCondition[_Z])
        fZAssignCount = floor(m_fLength[_Z] / fUnitcellLength[_Z]) + 2;
    else
        fZAssignCount = ceil(m_fLength[_Z] / fUnitcellLength[_Z]);

#ifdef DISABLE_MPI_ROUTINE
    fXAssignCount = fXTotalCount;

    if (bPaddingUnitCell)
    {
        fXAssignCount++;
        fXTotalCount++;
    }

#else
    if( 1 == CMPIManager::GetTotalNodeCount() )
    {
        fXAssignCount = fXTotalCount;
        if (bPaddingUnitCell)
        {
            fXAssignCount++;
            fXTotalCount++;
        }
    }
    else
    {
        int             nNodeCount = CMPIManager::GetTotalNodeCount();
        unsigned int    nRank = (unsigned int)CMPIManager::GetCurrentRank();

        if( 1 > fXTotalCount / nNodeCount )
            return bRtn;

        unsigned int            nBaseCount, nRestCount;
        
        fXTotalCount /= m_nHandlingUnitcellCount;
        nBaseCount = (unsigned int)floor(fXTotalCount / nNodeCount);
        nRestCount = (unsigned int)floor(fXTotalCount) - nBaseCount * nNodeCount;

        fXAssignCount = nBaseCount;
        if( nRank < nRestCount )
            fXAssignCount += 1;

        if( true == bPaddingUnitCell && CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1 )
            fXAssignCount += 1;

        fXAssignCount *= m_nHandlingUnitcellCount;

        //m_fLength[LX] = fXAssignCount * fUnitcellLength[LX];

        unsigned int            nExtraAdding = 0;
#ifdef _WIN32
        nExtraAdding = min(nRestCount, nRank);
#else
        nExtraAdding = std::min(nRestCount, nRank);
#endif

        if (nRank > 0)
        {
            double          cx;

            cx = (nBaseCount * m_nHandlingUnitcellCount * nRank + nExtraAdding * m_nHandlingUnitcellCount) * fUnitcellLength[_X];
            m_originCoordination.SetOffset(cx, 0, 0);
        }

        if( fXAssignCount * fUnitcellLength[_X] + m_originCoordination.GetCoordination(_X) > m_fLength[_X] )
            m_fLength[_X] = m_fLength[_X] - m_originCoordination.GetCoordination(_X);
        else
            m_fLength[_X] = fXAssignCount * fUnitcellLength[_X];

#ifdef SHOW_DEBUG_STRING
    
        if( CMPIManager::IsRootRank())
        {
            sprintf(szMsg, "TotalAssignCount: %7f\n", fXTotalCount);
            CUtility::ShowMsg(szMsg);
        }

        sprintf(szMsg, "%d rank: Xoffset: %7f, LX: %7f, Assign Count: %7f\n", CMPIManager::GetCurrentRank(), m_originCoordination.GetCoordination(_X), m_fLength[_X], fXAssignCount);
        CUtility::ShowMsg(szMsg);

#endif //SHOW_DEBUG_STRING
    }
#endif //DISABLE_MPI_ROUTINE

    if (m_bConsiderBoundaryCondition[_X])
    {
        if (m_bFrontFace)
            fXAssignCount++;

        if (true == m_bBackendFace)
            fXAssignCount++;
    }
    
    m_fAssignedCount[_X] = fXAssignCount;
    m_fAssignedCount[_Y] = fYAssignCount;
    m_fAssignedCount[_Z] = fZAssignCount;




#ifndef _WIN32
    if( CMPIManager::IsRootRank())
    {
        fXAssignCount = CMPIManager::AllReduceDouble(fXAssignCount); 
#endif //_WIN32
        sprintf(szMsg, "-Unitcell counts: X-axis[%2.1f], Y-axis[%2.1f], Z-axis[%2.1f]\n", fXAssignCount, fYAssignCount, fZAssignCount);
        CUtility::ShowMsg(szMsg);
#ifndef _WIN32
    }
    else
        fXAssignCount = CMPIManager::AllReduceDouble(fXAssignCount); 
#endif //_WIN32

    bRtn = true;
    return bRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::CheckingNeighborCandiate ( )

private

Checking neighbor unitcell by calculating index.

Definition at line 754 of file GeometricShape.cpp.

References m_bBackendFace, m_bFrontFace, m_fAssignedCount, and m_vectUnitCell.

Referenced by FillUnitcell().

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

    for (i = 0; i < nSize; ++i)
    {
        m_vectUnitCell[i].CheckingNeighborCandiate(m_fAssignedCount, m_bFrontFace, m_bBackendFace);
    }
}

Here is the caller graph for this function:

unsigned int CGeometricShape::ConstructBasicGeometric	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		bool	bMPI
	)

Get Surface atom list.

< Setting shape parameters

< Setting unitcell parameters

< Arranging unitcell

< Numbering unitcell in periodic bonding layer

< Exchanging front and back side layer information between node

< Numbering unitcell in periodic bonding layer for exchanging layer

< Find Neighbor of each atom

< Make mapinfo runtime strcuture and writting into file

Definition at line 1369 of file GeometricShape.cpp.

References BuildNeighborInformation(), CALCULATION_SUCCESS, CAN_NOT_ALLOC_RANK, ConstructMapInfo(), ExchangeAtomInfoBetweenNode(), FillUnitcell(), FREE_MEM, PeriodicUnitCellNumbering(), SetAtomAndNeighborInformation(), SetShapeInformation(), and SHOW_SIMPLE_MSG.

Referenced by CSPLoop::ConstructionGeometric().

{
    unsigned int                nRtnCode = CALCULATION_SUCCESS;
    char                        szMsg[1024];

    SetShapeInformation(lpParam); 
    if (!CGeometricShape::SetAtomAndNeighborInformation(lpParam)) 
    {
        SHOW_SIMPLE_MSG("Terminated program. Direction information doesn't existed.\n");
        nRtnCode = CAN_NOT_ALLOC_RANK;
        FREE_MEM(lpParam);
        return nRtnCode;
    }
    if(!FillUnitcell(lpParam)) 
    {
        SHOW_SIMPLE_MSG("Terminated program. Node counts should be smaller than assigend unitcell count with X axis.\n");
        nRtnCode = CAN_NOT_ALLOC_RANK;
        FREE_MEM(lpParam);
        return nRtnCode;
    }

    PeriodicUnitCellNumbering(); 
    if (bMPI)
    {
        ExchangeAtomInfoBetweenNode(); 
        PeriodicUnitCellNumbering(true); 
    }
    BuildNeighborInformation(); 
    ConstructMapInfo(lpMapInfo, lpParam); 
    
    return nRtnCode;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::ConstructContactRegionOnPoissonGrid	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		LP_CONTACT_GROUP_INFO *	lpContactGroup
	)

Definition at line 1842 of file GeometricShape.cpp.

References _X, _Y, _Z, ATOM_CONTACT_INDEX, ATOM_DEFAULT_INDEX, BOX_CONTACT, BOX_SHAPE, CCommandFileParser::INPUT_CMD_PARAM::bSaveContactBiasVector, CIRCLE_CONTACT, CONTACT_GROUP_INFO::ContactList, CYLINDER_SHAPE, CCommandFileParser::INPUT_CMD_PARAM::fContactBias, CONTACT_GROUP_INFO::fContactBiasValue, CONTACT_GROUP_INFO::fContactLength, CCommandFileParser::INPUT_CMD_PARAM::fContactLength, CONTACT_GROUP_INFO::fContactOrigin, CCommandFileParser::INPUT_CMD_PARAM::fContactOrigin, NEIGHBOR_MAP_INFO::fItemCount, CGeometricCoordination::GetCoordination(), CMPIManager::GetCurrentRank(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_bBackendFace, m_bFrontFace, m_fLength, m_nContactNumber, m_originCoordination, m_ShapeForm, CONTACT_GROUP_INFO::nContactDirection, CCommandFileParser::INPUT_CMD_PARAM::nContactNumber, CONTACT_GROUP_INFO::nContactShape, CCommandFileParser::INPUT_CMD_PARAM::nContactShape, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, CMPIManager::ReceiveDoubleBufferSync(), CMPIManager::SendDoubleBufferSync(), CUtility::ShowMsg(), CCommandFileParser::INPUT_CMD_PARAM::szContactMaterial, and CCommandFileParser::INPUT_CMD_PARAM::szContactShape.

Referenced by CSPLoop::ConstructionGeometric().

{
    unsigned int                                i, j, ia;
    double                                      ax, ay, az;
    double                                      ox, oy, oz;
    double                                      lx, ly, lz;

    FILE                                        *out = NULL;
    char                                        szFileName[1024];
    char                                        szMsg[1024], szTemp[1024];

    m_nContactNumber = lpParam->nContactNumber;

    for (i = 0; i < m_nContactNumber; i++)
    {
        lpContactGroup[i]->nContactDirection = -1;

        lpContactGroup[i]->fContactOrigin[0] = lpParam->fContactOrigin[i][0];
        lpContactGroup[i]->fContactOrigin[1] = lpParam->fContactOrigin[i][1];
        lpContactGroup[i]->fContactOrigin[2] = lpParam->fContactOrigin[i][2];

        lpContactGroup[i]->fContactLength[0] = lpParam->fContactLength[i][0];
        lpContactGroup[i]->fContactLength[1] = lpParam->fContactLength[i][1];
        lpContactGroup[i]->fContactLength[2] = lpParam->fContactLength[i][2];

        lpContactGroup[i]->nContactShape = lpParam->nContactShape[i];

        lpContactGroup[i]->fContactBiasValue = lpParam->fContactBias[i];

        strcpy(lpContactGroup[i]->szContactMaterial, lpParam->szContactMaterial[i]);
        strcpy(lpContactGroup[i]->szContactShape, lpParam->szContactShape[i]);
    }

    if (m_ShapeForm == BOX_SHAPE)
    {
        for (i = 0; i < m_nContactNumber; i++)
        {
            if (lpContactGroup[i]->fContactLength[0] == 0.0)
            {
                if (m_bFrontFace)
                {
                    if (lpContactGroup[i]->fContactOrigin[0] == m_originCoordination.GetCoordination(_X))
                    {
                        lpContactGroup[i]->nContactDirection = 1;
                        if (CMPIManager::IsRootRank())
                            printf("-Contact group[%3d] is on X left end\n", i + 1);
                    }
                }

                if (m_bBackendFace)
                {
                    if (lpContactGroup[i]->fContactOrigin[0] == m_fLength[0] + m_originCoordination.GetCoordination(_X))
                    {
                        lpContactGroup[i]->nContactDirection = 0;
                        if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
                            printf("-Contact group[%3d] is on X right end\n", i + 1);
                    }
                }
            }
            else if (lpContactGroup[i]->fContactLength[1] == 0.0)
            {
                if (lpContactGroup[i]->fContactOrigin[1] == m_originCoordination.GetCoordination(_Y))
                {
                    lpContactGroup[i]->nContactDirection = 3;
                    if (CMPIManager::IsRootRank())
                        printf("-Contact group[%3d] is on Y left end\n", i + 1);
                }
                else if (lpContactGroup[i]->fContactOrigin[1] == m_fLength[1] + m_originCoordination.GetCoordination(_Y))
                {
                    lpContactGroup[i]->nContactDirection = 2;
                    if (CMPIManager::IsRootRank())
                        printf("-Contact group[%3d] is on Y right end\n", i + 1);
                }
                else
                {
                    printf("-Error: Contact group[%3d] origin in y-direction does not match to one of the boundaries.\n", i + 1);
                    exit(1);
                }
            }
            else if (lpContactGroup[i]->fContactLength[2] == 0.0)
            {
                if (lpContactGroup[i]->fContactOrigin[2] == m_originCoordination.GetCoordination(_Z))
                {
                    lpContactGroup[i]->nContactDirection = 5;
                    if (CMPIManager::IsRootRank())
                        printf("-Contact group[%3d] is on Z left end\n", i + 1);
                }
                else if (lpContactGroup[i]->fContactOrigin[2] == m_fLength[2] + m_originCoordination.GetCoordination(_Z))
                {
                    lpContactGroup[i]->nContactDirection = 4;
                    if (CMPIManager::IsRootRank())
                        printf("-Contact group[%3d] is on Z right end\n", i + 1);
                }
                else
                {
                    printf("-Error: Contact group[%3d] origin in z-direction does not match to one of the boundaries.\n", i + 1);
                    exit(1);
                }
            }
            else
            {
                printf("-Error: Contact size in an direction should be zero for box shape.\n");
            }
        }

        for (ia = 0; ia < lpMapInfo->fItemCount; ia++)
        {
            ax = lpMapInfo->pfX_Coordination[ia];
            ay = lpMapInfo->pfY_Coordination[ia];
            az = lpMapInfo->pfZ_Coordination[ia];

            for (i = 0; i < m_nContactNumber; i++)
            {
                ox = lpContactGroup[i]->fContactOrigin[0];
                oy = lpContactGroup[i]->fContactOrigin[1];
                oz = lpContactGroup[i]->fContactOrigin[2];

                lx = lpContactGroup[i]->fContactLength[0];
                ly = lpContactGroup[i]->fContactLength[1];
                lz = lpContactGroup[i]->fContactLength[2];

                if (lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] == ATOM_DEFAULT_INDEX)
                {
                    switch ((int)(lpContactGroup[i]->nContactDirection / 2))
                    {
                    case 0:
                        switch (lpContactGroup[i]->nContactShape)
                        {
                        case BOX_CONTACT:
                            if (((ay > oy) && (ay < oy + ly)) && ((az > oz) && (az < oz + lz)))
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        case CIRCLE_CONTACT:
                            if ((ay - oy - ly / 2)*(ay - oy - ly / 2) / (ly / 2) / (ly / 2) + (az - oz - lz / 2)*(az - oz - lz / 2) / (lz / 2) / (lz / 2) < 1.0)
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        }
                        break;
                    case 1:
                        switch (lpContactGroup[i]->nContactShape)
                        {
                        case BOX_CONTACT:
                            if (((ax > ox) && (ax < ox + lx)) && ((az > oz) && (az < oz + lz)))
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        case CIRCLE_CONTACT:
                            if ((ax - ox - lx / 2)*(ax - ox - lx / 2) / (lx / 2) / (lx / 2) + (az - oz - lz / 2)*(az - oz - lz / 2) / (lz / 2) / (lz / 2) < 1.0)
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        }
                        break;
                    case 2:
                        switch (lpContactGroup[i]->nContactShape)
                        {
                        case BOX_CONTACT:
                            if (((ax > ox) && (ax < ox + lx)) && ((ay > oy) && (ay < oy + ly)))
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        case CIRCLE_CONTACT:
                            if ((ax - ox - lx / 2)*(ax - ox - lx / 2) / (lx / 2) / (lx / 2) + (ay - oy - ly / 2)*(ay - oy - ly / 2) / (ly / 2) / (ly / 2) < 1.0)
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                            break;
                        }
                    }
                }
            }
        }
    }

    if (m_ShapeForm == CYLINDER_SHAPE)
    {
        for (i = 0; i < m_nContactNumber; i++)
        {
            if (lpContactGroup[i]->fContactLength[0] == 0.0)
            {
                if (m_bFrontFace)
                {
                    if (lpContactGroup[i]->fContactOrigin[0] == m_originCoordination.GetCoordination(_X))
                    {
                        lpContactGroup[i]->nContactDirection = 1;
                        if (CMPIManager::IsRootRank())
                            printf("-Contact group[%3d] is on X left end for cylinder shape\n", i + 1);
                    }
                }

                if (m_bBackendFace)
                {
                    if (lpContactGroup[i]->fContactOrigin[0] == m_fLength[0] + m_originCoordination.GetCoordination(_X))
                    {
                        lpContactGroup[i]->nContactDirection = 0;
                        if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
                            printf("-Contact group[%3d] is on X right end for cylinder shape\n", i + 1);
                    }
                }
            }
            else if (lpContactGroup[i]->fContactLength[0] > 0.0)
            {
                lpContactGroup[i]->nContactDirection = 6;
                if (CMPIManager::IsRootRank())
                    printf("-Contact group[%3d] is on cylinderical surface\n", i + 1);
            }
            else
            {
                printf("-Error: Contact size in x-direction should be greater than or equal to zero.\n");
            }
        }

        for (ia = 0; ia < lpMapInfo->fItemCount; ia++)
        {
            ax = lpMapInfo->pfX_Coordination[ia];
            ay = lpMapInfo->pfY_Coordination[ia];
            az = lpMapInfo->pfZ_Coordination[ia];

            for (i = 0; i < m_nContactNumber; i++)
            {
                ox = lpContactGroup[i]->fContactOrigin[0];
                oy = lpContactGroup[i]->fContactOrigin[1];
                oz = lpContactGroup[i]->fContactOrigin[2];

                lx = lpContactGroup[i]->fContactLength[0];
                ly = lpContactGroup[i]->fContactLength[1];
                lz = lpContactGroup[i]->fContactLength[2];

                switch ((int)(lpContactGroup[i]->nContactDirection / 2))
                {
                case 0:
                    if (lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] == ATOM_DEFAULT_INDEX)
                    {
                        switch (lpContactGroup[i]->nContactShape)
                        {
                        case BOX_CONTACT:
                            if (((ay > oy) && (ay < oy + ly)) && ((az > oz) && (az < oz + lz)))
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        case CIRCLE_CONTACT:
                            if ((ay - oy - ly / 2)*(ay - oy - ly / 2) / (ly / 2) / (ly / 2) + (az - oz - lz / 2)*(az - oz - lz / 2) / (lz / 2) / (lz / 2) < 1.0)
                            {
                                lpContactGroup[i]->ContactList.push_back(ia);
                                lpMapInfo->pfNeighbor[lpContactGroup[i]->nContactDirection][ia] = ATOM_CONTACT_INDEX;
                            }
                            break;
                        }
                    }
                    break;

                case 3:
                    for (j = 2; j < 6; j++)
                    {
                        if ((lpMapInfo->pfNeighbor[j][ia] == ATOM_DEFAULT_INDEX))
                        {
                            switch (lpContactGroup[i]->nContactShape)
                            {
                            case BOX_CONTACT:
                                if ((ax > ox) && (ax < ox + lx))
                                {
                                    lpContactGroup[i]->ContactList.push_back(ia);
                                    lpMapInfo->pfNeighbor[j][ia] = ATOM_CONTACT_INDEX;
                                }
                                break;
                            }
                        }
                    }
                    break;
                }
            }
        }
    }

    // Dump contact group info
#ifndef DISABLE_MPI_ROUTINE
    MPI_Request         req;
    double              fTemp = 1;
#endif //DISABLE_MPI_ROUTINE

    if (true == lpParam->bSaveContactBiasVector)
    {
        strcpy(szTemp, "ContactGroupInfo.dat");
#ifdef _WIN32
        sprintf(szFileName, "result\\%s", szTemp);
#else
        sprintf(szFileName, "result/%s", szTemp);
#endif

#ifdef DISABLE_MPI_ROUTINE
        out = fopen(szFileName, "wt");
#else //DISABLE_MPI_ROUTINE

        if (CMPIManager::IsRootRank())
        {
            CUtility::ShowMsg("-Save contact group info. to file.\n");
            out = fopen(szFileName, "wt");
        }
        else
        {
            CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, &fTemp, 1, &req);
            out = fopen(szFileName, "at");
        }
#endif //DISABLE_MPI_ROUTINE
    }

    if (true == lpParam->bSaveContactBiasVector && NULL != out)
    {
        for (i = 0; i < m_nContactNumber; i++)
        {
            for (j = 0; j < lpContactGroup[i]->ContactList.size(); j++)
            {
                ia = lpContactGroup[i]->ContactList[j];
                sprintf(szMsg, "Contact group [ %3d ] %3d %5s %5.3f, atom[ %6d ] (%11.8f, %11.8f, %11.8f) \n",
                    i + 1, lpContactGroup[i]->nContactDirection, lpContactGroup[i]->szContactShape, lpContactGroup[i]->fContactBiasValue,
                    (int)lpMapInfo->pfID[ia], lpMapInfo->pfX_Coordination[ia], lpMapInfo->pfY_Coordination[ia], lpMapInfo->pfZ_Coordination[ia]);

                fputs(szMsg, out);
            }
        }

        fclose(out);
#ifndef DISABLE_MPI_ROUTINE
        if (CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, &fTemp, 1, &req);
#endif //DISABLE_MPI_ROUTINE
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool CGeometricShape::ConstructMapInfo	(	LPNEIGHBOR_MAP_INFO	lpMapInfo,
		CCommandFileParser::LPINPUT_CMD_PARAM	lpParam
	)

Extract atom information from runtime objects.

Parameters

lpMapInfo	Atom map information
bFileWrite	Option for save file or not

Returns

Operation success return true, else return false

Definition at line 769 of file GeometricShape.cpp.

References _X, _Y, _Z, ATOM_DEFAULT_INDEX, CCommandFileParser::INPUT_CMD_PARAM::bSaveMapFile, BuildGeoFileName(), NEIGHBOR_MAP_INFO::fItemCount, FreeMapInfo(), CGeometricCoordination::GetCoordination(), CGeometricAtom::GetCoordination(), CMPIManager::GetCurrentRank(), CGeometricAtom::GetDomainMaterialNumber(), CGeometricAtom::GetDomainNumber(), CGeometricAtom::GetID(), CGeometricAtom::GetMaterialMaterialNumber(), CGeometricAtom::GetMaterialNumber(), CGeometricAtom::GetNeighborAtomID(), CGeometricAtom::GetNeighborCount(), CGeometricUnitCell::GetSubElementID(), CMPIManager::GetTotalNodeCount(), CGeometricAtom::GetType(), InitMapInfo(), CMPIManager::IsDeflationRoot(), CGeometricAtom::IsPeriodicAtom(), CGeometricAtom::IsPeriodicCoupling(), CMPIManager::IsRootRank(), m_vectUnitCell, NEIGHBOR_MAP_INFO::pAtomType, NEIGHBOR_MAP_INFO::pbPeriodicCondition, NEIGHBOR_MAP_INFO::pDomainMaterialNumber, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, NEIGHBOR_MAP_INFO::pMaterialNumber, NEIGHBOR_MAP_INFO::pnDomainNumber, NEIGHBOR_MAP_INFO::pNeighborMaterial, CMPIManager::ReceiveDoubleBufferSync(), CMPIManager::SendDoubleBufferSync(), SetMapInfoSize(), and CUtility::ShowMsg().

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{
    bool                bRtn = false;
    char                szMsg[1024], szAdditional[1024];
    unsigned int        i, j, k, nSize, nAtomSize, nNeighborSize, nMapIndex = 0;;
    FILE                *out = NULL;
    char                szFileName[1024];
    double              fNeighborAtomID = ATOM_DEFAULT_INDEX;
    bool                bPeriodic = false;
    char                szTemp[1024], szMaterial[1024], szTemp2[1024], szOpt[1024];
#ifndef DISABLE_MPI_ROUTINE
    MPI_Request         req;
    double              fTemp = 1;
#endif //DISABLE_MPI_ROUTINE

    BuildGeoFileName(szTemp, lpParam);
        
    InitMapInfo(lpMapInfo);

    //printf("Save ConstructMapInfo: %s\n", lpParam->bSaveMapFile ? "true" : "false");
    if (true == lpParam->bSaveMapFile && CMPIManager::IsDeflationRoot())
    {
#ifdef _WIN32
        _mkdir("result");
        sprintf(szFileName, "result\\%s", szTemp);
#else
        mkdir("result", 0777);
        sprintf(szFileName, "result/%s", szTemp);
#endif
        

#ifdef DISABLE_MPI_ROUTINE
        out = fopen(szFileName, "wt");
#else //DISABLE_MPI_ROUTINE

        if( CMPIManager::IsRootRank() )
        {
            CUtility::ShowMsg("-Save atom map to file.\n");
            out = fopen(szFileName, "wt");
        }
        else
        {
            CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank()-1, &fTemp, 1, &req);
            out = fopen(szFileName, "at");
        }
#endif //DISABLE_MPI_ROUTINE
    }
    
    nSize = m_vectUnitCell.size();

    if (!SetMapInfoSize(lpMapInfo, CGeometricUnitCell::GetSubElementID()))
    {
        if (NULL != out)
            fclose(out);
        CGeometricShape::FreeMapInfo(lpMapInfo);
        return bRtn;
    }
        
#ifdef SHOW_ATOM_MAP_RESULT_ON_SCREEN
    CUtility::ShowMsg("\n");
    CUtility::ShowMsg("Atom list--------------------------------------\n");
#endif //SHOW_ATOM_MAP_RESULT_ON_SCREEN
    for (i = 0; i < nSize; ++i)
    {
        double      fIDForDebug;
        nAtomSize = m_vectUnitCell[i].GetSubElementSize();

        for (j = 0; j < nAtomSize; ++j)
        {
            CGeometricAtom                  *pAtom = m_vectUnitCell[i].GetSubElementAt(j);
            if (ATOM_DEFAULT_INDEX == pAtom->GetID() || true == pAtom->IsPeriodicAtom())
                continue;

            CGeometricCoordination          coord = pAtom->GetCoordination();
            fIDForDebug = pAtom->GetID();

            sprintf(szAdditional, "");
            sprintf(szMaterial, "");
            sprintf(szOpt, "");
            nNeighborSize = pAtom->GetNeighborCount();
            for (k = 0; k < nNeighborSize; ++k)
            {
                fNeighborAtomID = pAtom->GetNeighborAtomID(k);

                if (ATOM_DEFAULT_INDEX == fNeighborAtomID)
                    bPeriodic = false;
                else
                    bPeriodic = pAtom->IsPeriodicCoupling(k);

#ifdef NOSHOW_MINORS_ONE
                if (ATOM_DEFAULT_INDEX == pAtom->GetNeighborAtom(k))
                {   
                    sprintf(szTemp, "\t");
                    sprintf(szTemp2, "\t", (int)pAtom->GetMaterialMaterialNumber(k));
                }
                else
#endif //NOSHOW_MINORS_ONE
                {
                    sprintf(szTemp, "\t%7.0f", fNeighborAtomID);
                    if (-1 == fNeighborAtomID)
                        sprintf(szTemp2, "\t%7.0d", -1);
                    else
                        sprintf(szTemp2, "\t%7.0d", (int)pAtom->GetMaterialMaterialNumber(k));
                }
                strcat(szAdditional, szTemp);
                strcat(szMaterial, szTemp2);
                sprintf(szOpt, "\t%7d", pAtom->GetDomainNumber());

                lpMapInfo->pfNeighbor[k][nMapIndex] = fNeighborAtomID;
                lpMapInfo->pbPeriodicCondition[k][nMapIndex] = bPeriodic;
                lpMapInfo->pNeighborMaterial[k][nMapIndex] = pAtom->GetMaterialMaterialNumber(k);
            }

            sprintf(szMsg, "%-7.0f\t%d\t%d\t%15.6f\t%15.6f\t%15.6f%s%s%s\n", pAtom->GetID(), (int)pAtom->GetType(), (int)pAtom->GetMaterialNumber(),
                                                        coord.GetCoordination(_X),
                                                        coord.GetCoordination(_Y),
                                                        coord.GetCoordination(_Z),
                                                        szAdditional, szMaterial, szOpt);
            //printf("%s", szMsg);
                        
            lpMapInfo->fItemCount++;
            lpMapInfo->pAtomType[nMapIndex] = pAtom->GetType();
            lpMapInfo->pMaterialNumber[nMapIndex] = pAtom->GetMaterialNumber();
            lpMapInfo->pDomainMaterialNumber[nMapIndex] = pAtom->GetDomainMaterialNumber();
            lpMapInfo->pnDomainNumber[nMapIndex] = pAtom->GetDomainNumber();
            lpMapInfo->pfID[nMapIndex] = pAtom->GetID();
            lpMapInfo->pfX_Coordination[nMapIndex] = coord.GetCoordination(_X);
            lpMapInfo->pfY_Coordination[nMapIndex] = coord.GetCoordination(_Y);
            lpMapInfo->pfZ_Coordination[nMapIndex] = coord.GetCoordination(_Z);
            nMapIndex++;

            if (true == lpParam->bSaveMapFile && NULL != out)
                fputs(szMsg, out);
#ifdef SHOW_ATOM_MAP_RESULT_ON_SCREEN
            CUtility::ShowMsg(szMsg);
#endif //SHOW_ATOM_MAP_RESULT_ON_SCREEN

        }
    }
    
    if (true == lpParam->bSaveMapFile && NULL != out)
    {
        fclose(out);
#ifndef DISABLE_MPI_ROUTINE
        if( CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank()+1, &fTemp, 1, &req);
#endif //DISABLE_MPI_ROUTINE
    }
        
    bRtn = true;
    return bRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::Deserialize ( std::vector< CGeometricUnitCell > *  pVectUnitCell, double *  pBuffer, bool  bFrontSide  )

private

Deerialize unitcells from double array.

Parameters

[out]	pVectUnitCell	Buffer for saving deserializing result
	pBuffer	Source data buffer
	bFrontSide	Option is fornt side or not

Definition at line 1293 of file GeometricShape.cpp.

References _Y, _Z, CGeometricUnitCell::Deserialize(), CGeometricAtomFactory::GetAtomCountInUnitcell(), m_fAssignedCount, m_vectUnitCell, CGeometricUnitCell::SetID(), and UNITCELL_WRITING_BLOCK_SIZE.

Referenced by ExchangeAtomInfoBetweenNode().

{
    double              fReceivingCount = floor(m_fAssignedCount[_Y]) * floor(m_fAssignedCount[_Z]);
    int                 i, nSize = m_vectUnitCell.size();
    int                 fPos = 0;
    int                 nAtomCountInCell = CGeometricAtomFactory::GetAtomCountInUnitcell();
    double              fID;

    if( bFrontSide )
        fID = -fReceivingCount;
    else
        fID = m_vectUnitCell[m_vectUnitCell.size()-1].GetID() + 1;

    for (i = 0 ; i < floor(fReceivingCount); ++i)
    {
        CGeometricUnitCell          unitcell;

        unitcell.SetID(fID++);
        unitcell.Deserialize(pBuffer + fPos);
        pVectUnitCell->push_back(unitcell);
        fPos += nAtomCountInCell*UNITCELL_WRITING_BLOCK_SIZE;
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::ExchangeAtomInfoBetweenNode

(

)

Get start index of atom in shape, using in MPI running enviroment.

Exchange edge information between MPI nodes

< Exchange bondary atom layer to back side

< Exchange bondary atom layer to front side

Definition at line 1148 of file GeometricShape.cpp.

References _X, _Y, _Z, CMPIManager::BroadcastDouble(), Deserialize(), FREE_MEM, CGeometricAtomFactory::GetAtomCountInUnitcell(), CMPIManager::GetCurrentRank(), CGeometricUnitCell::GetSubElementID(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_bConsiderBoundaryCondition, m_fAssignedCount, m_fAtomIDStartIndex, m_fTotalAtomCountinMPI, m_vectNextUnitCell, m_vectPrevUnitCell, m_vectUnitCell, CMPIManager::ReceiveDoubleBufferSync(), CMPIManager::SendDoubleBufferSync(), Serialize(), ShiftAtomID(), and UNITCELL_WRITING_BLOCK_SIZE.

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{
    double              fShift = CMPIManager::GetCurrentRank() * floor(m_fAssignedCount[0]) * floor(m_fAssignedCount[1]) * floor(m_fAssignedCount[2]);
    int                 i, nSize = m_vectUnitCell.size();
    double              fSendingCount = floor(m_fAssignedCount[_Y]) * floor(m_fAssignedCount[_Z]);
    double              *pSendBuffer = NULL;
    int                 nAtomCountInCell = CGeometricAtomFactory::GetAtomCountInUnitcell();
    double              *pReceiveBuffer = (double*)malloc(sizeof(double)*(fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell));
    MPI_Request         req[2];
    double              fAtomID = 0;

    if (1 == CMPIManager::GetTotalNodeCount())
    {
        m_fTotalAtomCountinMPI = CGeometricUnitCell::GetSubElementID();
        FREE_MEM(pReceiveBuffer);
        return;
    }

    
    if (CMPIManager::IsRootRank())
    {
        fAtomID = CGeometricUnitCell::GetSubElementID();
        CMPIManager::SendDoubleBufferSync(1, &fAtomID, 1, &req[0]);
    }
    else
    {
        CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, &fAtomID, 1, &req[1]);
        m_fAtomIDStartIndex = fAtomID;
        for (i = 0; i < nSize; ++i)
            m_vectUnitCell[i].ShiftAtomID(fAtomID);

        if (CMPIManager::GetCurrentRank() > 0 && CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
        {
            fAtomID += CGeometricUnitCell::GetSubElementID();
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, &fAtomID, 1, &req[0]);
        }
        else if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
        {
            fAtomID += CGeometricUnitCell::GetSubElementID();
            m_fTotalAtomCountinMPI = fAtomID;
        }
    }

    CMPIManager::BroadcastDouble(&m_fTotalAtomCountinMPI, 1, CMPIManager::GetTotalNodeCount() - 1);

    
    if (CMPIManager::IsRootRank())
    {
        pSendBuffer = Serialize(floor(m_fAssignedCount[_X])-1);
        CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
    }
    else
    {
        CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
        Deserialize(&m_vectPrevUnitCell, pReceiveBuffer, true);

        if (CMPIManager::GetCurrentRank() != CMPIManager::GetTotalNodeCount() - 1)
        {
            pSendBuffer = Serialize(floor(m_fAssignedCount[_X])-1);
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
        }
        else
        {   
            if( m_bConsiderBoundaryCondition[_X])
            {
                pSendBuffer = Serialize(floor(m_fAssignedCount[_X])-2);
                CMPIManager::SendDoubleBufferSync(0, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
            }
        }
    }

    if (m_bConsiderBoundaryCondition[_X] && CMPIManager::IsRootRank())
    {
        CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetTotalNodeCount() - 1, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
        Deserialize(&m_vectPrevUnitCell, pReceiveBuffer, true);
    }
    FREE_MEM(pSendBuffer);

    if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
    {
        pSendBuffer = Serialize(0);
        CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
    }
    else
    {
        CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
        Deserialize(&m_vectNextUnitCell, pReceiveBuffer, false);

        if (!CMPIManager::IsRootRank())
        {
            pSendBuffer = Serialize(0);
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
        }
        else
        {
            if( m_bConsiderBoundaryCondition[_X])
            {
                pSendBuffer = Serialize(1);
                CMPIManager::SendDoubleBufferSync(CMPIManager::GetTotalNodeCount() - 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
            }
        }
    }

    if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1 && m_bConsiderBoundaryCondition[_X])
    {
        CMPIManager::ReceiveDoubleBufferSync(0, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
        Deserialize(&m_vectNextUnitCell, pReceiveBuffer, false);
    }

    FREE_MEM(pSendBuffer);
    FREE_MEM(pReceiveBuffer);
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool CGeometricShape::FillUnitcell

(

CCommandFileParser::LPINPUT_CMD_PARAM

lpParam

)

Set bondary condition of shape.

Spreading atom into shape

Parameters

lpParam

Input parameter parsing from command file

Returns

Function working success or not

Definition at line 102 of file GeometricShape.cpp.

References ArrangeUnitCell(), CalculateUnitcellCount(), and CheckingNeighborCandiate().

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{
    bool            bRtn;
    
    bRtn = CalculateUnitcellCount();
    if( !bRtn )
        return bRtn;
    
    ArrangeUnitCell(lpParam);
    CheckingNeighborCandiate();

    return bRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::FinalShape

(

)

Finalize Shape variable.

Definition at line 252 of file GeometricShape.cpp.

References FreeUnitCellList().

Referenced by CTBMS_Solver::Launching_TBMS_Solver(), and ~CGeometricShape().

{
    FreeUnitCellList();
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::FreeMapInfo ( LPNEIGHBOR_MAP_INFO  lpMapInfo )

static

Release mapinfo data.

Parameters

lpMapInfo

Atom map information

<Added by="" jhkang>="">

<Added by="" jhkang="" end>="">

Definition at line 1086 of file GeometricShape.cpp.

References FREE_MEM, MAX_NEIGHBOR, NEIGHBOR_MAP_INFO::pAtomType, NEIGHBOR_MAP_INFO::pbPeriodicCondition, NEIGHBOR_MAP_INFO::pDomainMaterialNumber, NEIGHBOR_MAP_INFO::pfAtomOnGrid, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, NEIGHBOR_MAP_INFO::pMaterialNumber, NEIGHBOR_MAP_INFO::pnDomainNumber, and NEIGHBOR_MAP_INFO::pNeighborMaterial.

Referenced by ConstructMapInfo(), CTBMS_Solver::FinalEvn(), and CSPLoop::Finalize().

{
    unsigned int        i;

    FREE_MEM(lpMapInfo->pfID);
    FREE_MEM(lpMapInfo->pAtomType);
    FREE_MEM(lpMapInfo->pMaterialNumber);
    FREE_MEM(lpMapInfo->pDomainMaterialNumber);
    FREE_MEM(lpMapInfo->pnDomainNumber);
    FREE_MEM(lpMapInfo->pfX_Coordination);
    FREE_MEM(lpMapInfo->pfY_Coordination);
    FREE_MEM(lpMapInfo->pfZ_Coordination);
    
    for (i = 0; i < MAX_NEIGHBOR; ++i)
    {
        FREE_MEM(lpMapInfo->pfNeighbor[i]);
        FREE_MEM(lpMapInfo->pbPeriodicCondition[i]);
        FREE_MEM(lpMapInfo->pNeighborMaterial[i]);
    }

    FREE_MEM(lpMapInfo->pfAtomOnGrid);
}

Here is the caller graph for this function:

void CGeometricShape::FreeUnitCellList ( )

private

Relase unitcell list.

Definition at line 219 of file GeometricShape.cpp.

References m_vectNextUnitCell, m_vectPrevUnitCell, m_vectSurfaceAtom, and m_vectUnitCell.

Referenced by FinalShape().

{
    m_vectUnitCell.clear();
    m_vectPrevUnitCell.clear();
    m_vectNextUnitCell.clear();
    m_vectSurfaceAtom.clear();
}

Here is the caller graph for this function:

CGeometricAtom * CGeometricShape::GetAtomByIndex ( double  fID )

private

Get atom instance by ID.

Parameters

fID

Atom ID

Returns

Atom instance pointer

Definition at line 696 of file GeometricShape.cpp.

References CGeometricAtom::IsPeriodicAtom(), and m_vectUnitCell.

Referenced by RefillPeriodicBinding().

{
    CGeometricAtom                      *pRtn = NULL;
    int                                 nSize, i;

    nSize = m_vectUnitCell.size();
    for( i = 0; i < nSize ; ++ i)
    {
        pRtn = m_vectUnitCell[i].GetSubElementByID(fID);
        if( NULL != pRtn && false == pRtn->IsPeriodicAtom())
            return pRtn;
    }

    return pRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

double CGeometricShape::GetAtomStartID ( )

inline

Set total valid atom count in shape.

Definition at line 57 of file GeometricShape.h.

References m_fAtomIDStartIndex.

Referenced by CTBMS_Solver::AllocateCSR(), CSPLoop::AllocateCSR(), CSPLoop::BuildHamiltonian(), and CTBMS_Solver::Launching_TBMS_Solver().

{ return m_fAtomIDStartIndex; }; 

Here is the caller graph for this function:

bool CGeometricShape::GetConsideringBoundaryCondition ( AXIS_DEFINE  direction )

inline

Definition at line 42 of file GeometricShape.h.

References m_bConsiderBoundaryCondition.

{ return m_bConsiderBoundaryCondition[direction]; }; 

double CGeometricShape::GetKPhaseSign ( double  fAtomPos, double  fPeriodicAtomPos  )

private

Calculating Phase sign.

Parameters

fAtomPos	Atom coordination
fPeriodicAtomPos	Periodic atom coordination

Returns

sign of Phase

Definition at line 682 of file GeometricShape.cpp.

Referenced by RefillPeriodicBinding().

{
    double          fRtn = 1.;
    
    if( fPeriodicAtomPos - fAtomPos > 0 ) 
        fRtn = -1.;

    return fRtn;
}

Here is the caller graph for this function:

MATERIAL_INDEX CGeometricShape::GetMaterialType ( )

inline

Definition at line 36 of file GeometricShape.h.

References m_MaterialType.

{ return m_MaterialType; }; 

bool CGeometricShape::GetNeumannBoundaryCondition ( AXIS_DEFINE  direction )

inline

Definition at line 70 of file GeometricShape.h.

References m_bNeumannBoundaryCondition.

{ return m_bNeumannBoundaryCondition[direction]; }; 

int CGeometricShape::GetPeriodicDirection ( int  x, int  y, int  z, int  maxX, int  maxY, int  maxZ  )

private

Get periodic direction information.

Parameters

x	x direction unitcell index
y	y direction unitcall index
z	z direction unitcell index
maxX	x direction max index of unitcell
maxY	y direction max index of unitcell
maxZ	z direction max index of unitcell

Definition at line 135 of file GeometricShape.cpp.

References _X, _Y, _Z, CMPIManager::GetCurrentRank(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_bConsiderBoundaryCondition, CGeometricAtom::NONE, CGeometricAtom::X_DIRECTION, CGeometricAtom::Y_DIRECTION, and CGeometricAtom::Z_DIRECTION.

Referenced by ArrangeUnitCell().

{
    int                 nRtn = CGeometricAtom::NONE;

    if (0 == x && true == m_bConsiderBoundaryCondition[_X])
#ifndef DISABLE_MPI_ROUTINE
    if( CMPIManager::IsRootRank() )
            nRtn |= CGeometricAtom::X_DIRECTION;
#else //DISABLE_MPI_ROUTINE
        nRtn |= CGeometricAtom::X_DIRECTION;
#endif //DISABLE_MPI_ROUTINE

    if (0 == y && true == m_bConsiderBoundaryCondition[_Y])
        nRtn |= CGeometricAtom::Y_DIRECTION;

    if (0 == z && true == m_bConsiderBoundaryCondition[_Z])
        nRtn |= CGeometricAtom::Z_DIRECTION;

    if (maxX - 1 == x && true == m_bConsiderBoundaryCondition[_X])
#ifndef DISABLE_MPI_ROUTINE
    if( CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() -1 )
            nRtn |= CGeometricAtom::X_DIRECTION;
#else //DISABLE_MPI_ROUTINE
        nRtn |= CGeometricAtom::X_DIRECTION;
#endif //DISABLE_MPI_ROUTINE

    if (maxY - 1 == y && true == m_bConsiderBoundaryCondition[_Y])
        nRtn |= CGeometricAtom::Y_DIRECTION;

    if (maxZ - 1 == z && true == m_bConsiderBoundaryCondition[_Z])
        nRtn |= CGeometricAtom::Z_DIRECTION;

    return nRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

unsigned int CGeometricShape::GetShapeForm ( )

inline

Definition at line 39 of file GeometricShape.h.

References m_ShapeForm.

{ return m_ShapeForm; }; 

std::vector<CGeometricAtom*>* CGeometricShape::GetSurfaceAtomList ( )

inline

Definition at line 60 of file GeometricShape.h.

References m_vectSurfaceAtom.

Referenced by BuildNeighborInformation(), CSPLoop::ConstructionGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{ return &m_vectSurfaceAtom; }; 

Here is the caller graph for this function:

double CGeometricShape::GetTotalAtomCount ( )

inline

Definition at line 55 of file GeometricShape.h.

References m_fTotalAtomCountinMPI.

Referenced by CTBMS_Solver::AllocateCSR(), and CSPLoop::AllocateCSR().

{ return m_fTotalAtomCountinMPI;}; 

Here is the caller graph for this function:

double* CGeometricShape::GetUnitCellLength ( )

inline

Definition at line 77 of file GeometricShape.h.

Referenced by CSPLoop::executeSPLoop().

{ return m_fUnitCellLength; };

Here is the caller graph for this function:

void CGeometricShape::InitMapInfo

(

LPNEIGHBOR_MAP_INFO

lpMapInfo

)

Intilize map info data.

Parameters

lpMapInfo

Atom map information

<Added by="" jhkang>="">

<Added by="" jhkang="" end>="">

Definition at line 1114 of file GeometricShape.cpp.

References NEIGHBOR_MAP_INFO::fItemCount, MAX_NEIGHBOR, NEIGHBOR_MAP_INFO::pAtomType, NEIGHBOR_MAP_INFO::pbPeriodicCondition, NEIGHBOR_MAP_INFO::pfAtomOnGrid, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, and NEIGHBOR_MAP_INFO::pNeighborMaterial.

Referenced by ConstructMapInfo().

{
    unsigned int        i;

    lpMapInfo->pfID = NULL;
    lpMapInfo->pAtomType = NULL;
    lpMapInfo->pfX_Coordination = NULL;
    lpMapInfo->pfY_Coordination = NULL;
    lpMapInfo->pfZ_Coordination = NULL;
    lpMapInfo->fItemCount = 0;
    
    for (i = 0; i < MAX_NEIGHBOR; ++i)
    {
        lpMapInfo->pfNeighbor[i] = NULL;
        lpMapInfo->pbPeriodicCondition[i] = NULL;
        lpMapInfo->pNeighborMaterial[i] = NULL;
    }

    lpMapInfo->pfAtomOnGrid = NULL;
}

Here is the caller graph for this function:

void CGeometricShape::InitShape ( )

private

Initialize Shape variable.

Definition at line 227 of file GeometricShape.cpp.

References _X, _Y, _Z, BOX_SHAPE, m_bBackendFace, m_bConsiderBoundaryCondition, m_bFrontFace, m_fAtomIDStartIndex, m_fLength, m_fTotalAtomCountinMPI, m_fUnitCellLength, m_MaterialType, m_nAtomFirstLayer, m_nAtomLastLayer, m_nHandlingUnitcellCount, m_originCoordination, m_pUnitCellInfo, m_shapDirection, m_ShapeForm, CGeometricCoordination::SetCoordination(), CGeometricDirection::SetDirection(), and Si.

Referenced by CGeometricShape().

{
    m_originCoordination.SetCoordination(0.0, 0.0, 0.0);
    m_shapDirection.SetDirection(1, 0, 0);
    m_fLength[_X] = 0;
    m_fLength[_Y] = 0;
    m_fLength[_Z] = 0;
    m_MaterialType = Si;
    m_ShapeForm = BOX_SHAPE;
    m_bConsiderBoundaryCondition[_X] = false;
    m_bConsiderBoundaryCondition[_Y] = false;
    m_bConsiderBoundaryCondition[_Z] = false;
    m_bFrontFace = false;
    m_bBackendFace = false;
    m_fTotalAtomCountinMPI= 0;
    m_fAtomIDStartIndex = 0;
    m_pUnitCellInfo = NULL;
    m_nAtomFirstLayer = 0;
    m_nAtomLastLayer = 0;
    m_fUnitCellLength[_X] = 0;
    m_fUnitCellLength[_Y] = 0;
    m_fUnitCellLength[_Z] = 0;
    m_nHandlingUnitcellCount = 1;
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool CGeometricShape::IsBackendFace ( )

inline

Set front face side mark to shape object.

Definition at line 48 of file GeometricShape.h.

References m_bBackendFace.

{ return m_bBackendFace; }; 

int CGeometricShape::IsCoordinateMatched	(	double	fa,
		double	fb
	)

Definition at line 1602 of file GeometricShape.cpp.

Referenced by MapElecAtomOnPoissonGrid().

{
    double criteria = 0.001, criteria2 = criteria * criteria;

    if ((fa - fb)*(fa - fb) < criteria2)
        return (1);
    else return(0);
}

Here is the caller graph for this function:

bool CGeometricShape::IsFrontFace ( )

inline

Definition at line 46 of file GeometricShape.h.

References m_bFrontFace.

{ return m_bFrontFace; }; 

bool CGeometricShape::IsInBoundaryCondition ( int  x, int  y, int  z, int  maxX, int  maxY, int  maxZ  )

private

<Added by="" jhkang="" end>="">

Check unitcell is in the bondary area or not

Parameters

x	x direction unitcell index
y	y direction unitcall index
z	z direction unitcell index
maxX	x direction max index of unitcell
maxY	y direction max index of unitcell
maxZ	z direction max index of unitcell

Returns

If it is in bondary condition return true, else return false

Definition at line 179 of file GeometricShape.cpp.

References _X, _Y, _Z, CMPIManager::GetCurrentRank(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), and m_bConsiderBoundaryCondition.

Referenced by ArrangeUnitCell().

{
    bool            bRtn = false;

    if (0 == x && true == m_bConsiderBoundaryCondition[_X])
#ifndef DISABLE_MPI_ROUTINE
    {
        if( CMPIManager::IsRootRank() )
            return bRtn;
    }
#else //DISABLE_MPI_ROUTINE
        return bRtn;
#endif //DISABLE_MPI_ROUTINE

    if (0 == y && true == m_bConsiderBoundaryCondition[_Y])
        return bRtn;

    if (0 == z && true == m_bConsiderBoundaryCondition[_Z])
        return bRtn;

    if (maxX - 1 == x && true == m_bConsiderBoundaryCondition[_X])
#ifndef DISABLE_MPI_ROUTINE
    {
        if( CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() -1 )
            return bRtn;
    }
#else //DISABLE_MPI_ROUTINE
        return bRtn;
#endif //DISABLE_MPI_ROUTINE

    if (maxY - 1 == y && true == m_bConsiderBoundaryCondition[_Y])
        return bRtn;

    if (maxZ - 1 == z && true == m_bConsiderBoundaryCondition[_Z])
        return bRtn;

    bRtn = true;
    return bRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::MapElecAtomOnPoissonGrid	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo
	)

Definition at line 1611 of file GeometricShape.cpp.

References _X, ATOM_DEFAULT_INDEX, CCommandFileParser::INPUT_CMD_PARAM::bSaveContactBiasVector, CCommandFileParser::INPUT_CMD_PARAM::bSaveWaveVector, NEIGHBOR_MAP_INFO::fItemCount, CGeometricCoordination::GetCoordination(), CMPIManager::GetCurrentRank(), CMPIManager::GetTotalNodeCount(), IGeometricUnitCellInfo::GetUnitcCellSize(), IsCoordinateMatched(), CMPIManager::IsRootRank(), m_fLength, m_originCoordination, m_pUnitCellInfo, NEIGHBOR_MAP_INFO::pfAtomOnGrid, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, CMPIManager::ReceiveDoubleBufferSync(), CMPIManager::SendDoubleBufferSync(), and CUtility::ShowMsg().

{
    unsigned int        i;
    int                 nCount = 0, nElecAtomID = 0, nParamSize = 4, nPoissonGridID = -1, nMatchedGrid = 0, nMatchedGridSum = 0;
    bool                bMappingError = 0;
    double              fParam[4], fPoissonGridID;
    double              *fUnitcellLength;
    char                szAtomFileName[1024];
    char                szOutFileName[1024], szMsg[1024], szTemp[1024];
    FILE                *atomIn = NULL, *out = NULL;
    char                *token = NULL;
    char                strSperate[] = " ";
    double              tol = 1.0e-6;

    for (i = 0; i < lpMapInfo->fItemCount; i++)
        lpMapInfo->pfAtomOnGrid[i] = ATOM_DEFAULT_INDEX;

    sprintf(szAtomFileName, "./testset/reference1_zb_rhs_unscaled_at_iter1.dat");

#ifdef DISABLE_MPI_ROUTINE
    out = fopen(szOutFileName, "wt");
#else //DISABLE_MPI_ROUTINE
    MPI_Request         req;
    double              fTemp = 1.0;
    MPI_Status status;

    if (CMPIManager::IsRootRank())
    {
        atomIn = fopen(szAtomFileName, "rt");
    }
    else
    {
        CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, &fTemp, 1, &req);
        atomIn = fopen(szAtomFileName, "rt");
    }
#endif //DISABLE_MPI_ROUTINE

    fUnitcellLength = m_pUnitCellInfo->GetUnitcCellSize();

    while (fgets(szTemp, 1024, atomIn))
    {
        token = strtok(szTemp, strSperate);

        while (token)
        {
            fParam[nCount++] = atof(token);
            if (nParamSize == nCount)
                break;
            token = strtok(NULL, strSperate);
        }

        if ((fParam[0] > m_originCoordination.GetCoordination(_X) + tol) && (fParam[0] <= m_fLength[0] + m_originCoordination.GetCoordination(_X) + tol))
        {
            for (i = 0; i < lpMapInfo->fItemCount; i++)
            {
                if (IsCoordinateMatched(fParam[0], lpMapInfo->pfX_Coordination[i]))
                if (IsCoordinateMatched(fParam[1], lpMapInfo->pfY_Coordination[i]))
                if (IsCoordinateMatched(fParam[2], lpMapInfo->pfZ_Coordination[i]))
                {
                    nPoissonGridID = i;
                    nMatchedGrid++;
                }
            }

            if (nPoissonGridID >= 0 && nPoissonGridID < lpMapInfo->fItemCount)
                lpMapInfo->pfAtomOnGrid[nPoissonGridID] = nElecAtomID;
            else
            {
                printf("[Rank:%3d] Error: Elec grid cannot be mapped to Poisson grid, Elec grid = %d, Poisson grid = %d, ( %15.12f %15.12f %15.12f )\n", CMPIManager::GetCurrentRank(), nElecAtomID, nPoissonGridID, fParam[0], fParam[1], fParam[2]);
                bMappingError = 1;
            }

            nPoissonGridID = ATOM_DEFAULT_INDEX;
        }
        nElecAtomID++;
        nCount = 0;
    }

    fclose(atomIn);
#ifndef DISABLE_MPI_ROUTINE
    if (CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
        CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, &fTemp, 1, &req);

#endif //DISABLE_MPI_ROUTINE

    if (bMappingError)
        exit(1);
    else
    {
        printf("[Rank:%3d] Number of elec atoms matched to Poisson grid  = %5d \n", CMPIManager::GetCurrentRank(), nMatchedGrid);

        MPI_Reduce(&nMatchedGrid, &nMatchedGridSum, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD);
        if (CMPIManager::IsRootRank())
            printf("-Total number of elec atoms matched to Poisson grid  = %5d \n", nMatchedGridSum);
    }

    //  Dump zb to cb mapping result
    if (true == lpParam->bSaveWaveVector)
    {
        strcpy(szTemp, "PEGrid_ElecGrid_Map.dat");
#ifdef _WIN32
        sprintf(szOutFileName, "result\\%s", szTemp);
#else
        sprintf(szOutFileName, "result/%s", szTemp);
#endif

#ifdef DISABLE_MPI_ROUTINE
        out = fopen(szOutFileName, "wt");
#else //DISABLE_MPI_ROUTINE

        if (CMPIManager::IsRootRank())
        {
            CUtility::ShowMsg("-Save wave vector info. to file.\n");
            out = fopen(szOutFileName, "wt");
        }
        else
        {
            CMPIManager::ReceiveDoubleBufferSync(CMPIManager::GetCurrentRank() - 1, &fTemp, 1, &req);
            out = fopen(szOutFileName, "at");
        }
#endif //DISABLE_MPI_ROUTINE
    }

    if (true == lpParam->bSaveContactBiasVector && NULL != out)
    {
        for (unsigned int i = 0; i < lpMapInfo->fItemCount; i++)
        {
            sprintf(szMsg, "Grid ID = %10.0f, Elec. atom ID on Grid = %10.0f\n", lpMapInfo->pfID[i], lpMapInfo->pfAtomOnGrid[i]);
            fputs(szMsg, out);
        }

        fclose(out);
#ifndef DISABLE_MPI_ROUTINE
        if (CMPIManager::GetCurrentRank() < CMPIManager::GetTotalNodeCount() - 1)
            CMPIManager::SendDoubleBufferSync(CMPIManager::GetCurrentRank() + 1, &fTemp, 1, &req);
#endif //DISABLE_MPI_ROUTINE
    }

}

Here is the call graph for this function:

void CGeometricShape::PeriodicUnitCellNumbering

(

bool

bXAxis = false

)

Numbering to periodic unitcell.

Parameters

bXAxis

Do operation to x axis or not

Definition at line 508 of file GeometricShape.cpp.

References _X, _Y, _Z, CGeometricUnitCell::CalculatingIndex(), FIND_TARGET_INDEX, CMPIManager::GetCurrentRank(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), m_bConsiderBoundaryCondition, m_fAssignedCount, m_vectNextUnitCell, m_vectPrevUnitCell, and m_vectUnitCell.

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{
    int             i, nSize = m_vectUnitCell.size();
    int             maxX, maxY, maxZ;
    double          targetCx, targetCy, targetCz;
    double          *pfAssignIndex = NULL;
    double          fCopyIndex = -1;

    if (true != m_bConsiderBoundaryCondition[_X] && true != m_bConsiderBoundaryCondition[_Y] && true != m_bConsiderBoundaryCondition[_Z])
        return;

    maxX = (int)floor(m_fAssignedCount[_X]);
    maxY = (int)floor(m_fAssignedCount[_Y]);
    maxZ = (int)floor(m_fAssignedCount[_Z]);

    for (i = 0; i < nSize; ++i)
    {
        if (m_vectUnitCell[i].IsPeriodicUnitCell())
        {
            pfAssignIndex = m_vectUnitCell[i].GetAssignedIndex();
            targetCx = pfAssignIndex[_X];
            targetCy = pfAssignIndex[_Y];
            targetCz = pfAssignIndex[_Z];

            FIND_TARGET_INDEX(targetCy, pfAssignIndex, m_fAssignedCount, _Y);
            FIND_TARGET_INDEX(targetCz, pfAssignIndex, m_fAssignedCount, _Z);

            if (m_bConsiderBoundaryCondition[_X])
            {
#ifdef DISABLE_MPI_ROUTINE
                FIND_TARGET_INDEX(targetCx, pfAssignIndex, m_fAssignedCount, _X);
#else //DISABLE_MPI_ROUTINE 
                if( 1 == CMPIManager::GetTotalNodeCount() )
                {
                    FIND_TARGET_INDEX(targetCx, pfAssignIndex, m_fAssignedCount, _X);
                }
                else
                {
                    if( 0 == pfAssignIndex[_X] && CMPIManager::IsRootRank())
                    {
                        targetCx = -1;
                        if( false == bXAxis)
                            continue;
                    }
                    else if (m_fAssignedCount[_X] - 1 == pfAssignIndex[_X] 
                        && CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
                    {
                        targetCx = pfAssignIndex[_X]+1;
                        if( false == bXAxis)
                            continue;
                    }
                }
#endif //DISABLE_MPI_ROUTINE
            }

            fCopyIndex = CGeometricUnitCell::CalculatingIndex(targetCx, targetCy, targetCz, m_fAssignedCount);
#ifndef DISABLE_MPI_ROUTINE
            if( 1 == CMPIManager::GetTotalNodeCount() )
            {
                if( false == bXAxis )
                    m_vectUnitCell[i].CopyInnerAtomIndex(m_vectUnitCell[(unsigned int)fCopyIndex]);
            }
            else
            {
                if (fCopyIndex < 0 && m_vectPrevUnitCell.size() > 0)
                {
                    m_vectUnitCell[i].CopyInnerAtomIndex(m_vectPrevUnitCell[(unsigned int)(fCopyIndex + m_fAssignedCount[_Y] * m_fAssignedCount[_Z])]);
                }
                else if (fCopyIndex >= maxX * maxY * maxZ && m_vectNextUnitCell.size() > 0)
                {
                    m_vectUnitCell[i].CopyInnerAtomIndex(m_vectNextUnitCell[(unsigned int)(fCopyIndex - m_fAssignedCount[_X] * m_fAssignedCount[_Y] * m_fAssignedCount[_Z])]);
                }
                else
                {
                    if( false == bXAxis )
                        m_vectUnitCell[i].CopyInnerAtomIndex(m_vectUnitCell[(unsigned int)fCopyIndex]);
                }
            }
#else //DISABLE_MPI_ROUTINE
            {
                if( false == bXAxis )
                    m_vectUnitCell[i].CopyInnerAtomIndex(m_vectUnitCell[(unsigned int)fCopyIndex]);
            }
#endif //DISABLE_MPI_ROUTINE
        }
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool CGeometricShape::RefillPeriodicBinding	(	CMatrixOperation::CCSR *	pResult,
		CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		unsigned int	nRepeatIndex,
		double	fKValue[3],
		unsigned int	nBandSize,
		bool	bRecover
	)

Applying phase to Hamiltonian.

Parameters

[out]	CMatrixOperation	CSR instance
	lpParam	Input parameters parsing from command file
	lpMapInfo	Atom map information
	nRepeatIndex	Repeat index, means k points
	fKValue	k value for x, y, z direction
	nBandSize	Band Size

Returns

Operatoin success return true, else return false

Definition at line 607 of file GeometricShape.cpp.

References CMatrixOperation::CCSR::AreaScalarMultiple(), ATOM_DEFAULT_INDEX, NEIGHBOR_MAP_INFO::fItemCount, GetAtomByIndex(), CGeometricCoordination::GetCoordination(), CGeometricAtom::GetCoordination(), CGeometricDirection::GetDirectionAll(), CComplex::GetImaginaryNumber(), GetKPhaseSign(), CGeometricAtom::GetNeighborCoordination(), CGeometricAtom::GetNeighborPeriodicDirection(), CComplex::GetRealNumber(), CGeometricAtom::IsPeriodicCoupling(), m_shapDirection, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, PI_VALUE, and CComplex::SetComplexNumber().

Referenced by CTBMS_Solver::Launching_TBMS_Solver(), and CSPLoop::SolveSchroedinger().

{
    unsigned int                        i, j, k;
    double                              *pDirection = m_shapDirection.GetDirectionAll();
    double                              kTotal = 0;
    CComplex                            calcuResult;
    double                              fNeighborIndex[4];
    bool                                bRtn = false;
    
    if( 0 == fKValue[0] && 0 == fKValue[1] && 0 == fKValue[2] )
    {
        bRtn = true;
        return bRtn;
    }
        
    for (i = 0; i < lpMapInfo->fItemCount; ++i)
    {
        int                     nMatrixIndex = 0;
        double                  kkTotal = kTotal;
        CGeometricAtom*         pCurrentAtom = GetAtomByIndex(lpMapInfo->pfID[i]);

        for (j = 0; j < 4; ++j)
            fNeighborIndex[j] = lpMapInfo->pfNeighbor[j][i];
        //fNeighborIndex[0] = lpMapInfo->pfNeighbor_1[i]; fNeighborIndex[1] = lpMapInfo->pfNeighbor_2[i]; fNeighborIndex[2] = lpMapInfo->pfNeighbor_3[i]; fNeighborIndex[3] = lpMapInfo->pfNeighbor_4[i];
                
    /*  if (CGeometricAtom::C == lpMapInfo->pAtomType[i])
            nMatrixIndex = 4;*/

        for (j = 0; j < 4; j++)
        {
            double                              kTotal = 0;

            if (ATOM_DEFAULT_INDEX != fNeighborIndex[j] && true == pCurrentAtom->IsPeriodicCoupling(j))
            {
                CGeometricCoordination      coupleCoordination = pCurrentAtom->GetNeighborCoordination(j);
                int                         periodicDirection = pCurrentAtom->GetNeighborPeriodicDirection(j);

                if (coupleCoordination == pCurrentAtom->GetCoordination())
                    continue;

                for (k = 0; k < 3; k++)
                {
                    int         nPeriodic = periodicDirection & (int)pow((double)2, (int)k);

                    if (0 != nPeriodic)
                    {
                        double      fPhase = GetKPhaseSign(pCurrentAtom->GetCoordination().GetCoordination((AXIS_DEFINE)k),
                            coupleCoordination.GetCoordination((AXIS_DEFINE)k));
                        kTotal += (fPhase * fKValue[k] * PI_VALUE);
                    }
                }
                calcuResult.SetComplexNumber(cos(kTotal), sin(kTotal));

                if( bRecover )
                {
                    double      fReal = calcuResult.GetRealNumber(), fImaginary = calcuResult.GetImaginaryNumber();
                    double      fTemp = fReal * fReal  + fImaginary * fImaginary;

                    calcuResult.SetComplexNumber(fReal / fTemp, -1 * (fImaginary/fTemp));
                }

                pResult->AreaScalarMultiple(i * nBandSize, nBandSize, (unsigned int)fNeighborIndex[j] * nBandSize, nBandSize, calcuResult);
            }
        }
    }

    bRtn = true;
    return bRtn;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::RotateMatrix ( CMatrixOperation::CDMatrix *  pMatrixNbr, CMatrixOperation::CDMatrix *  pMatrixResult, double  fDegree[2]  )

private

Rotate matrix with calculated degree.

Parameters

pMatrixNbr	Source matrix
pMatrixResult	Rotated matrix
paramter	Geometric parameters

Definition at line 729 of file GeometricShape.cpp.

References CMatrixOperation::CDMatrix::BuildMatrixFirst(), CMatrixOperation::MMMul(), PHI_DEGREE, CMatrixOperation::CDMatrix::SetElement(), THETA_DEGREE, and CMatrixOperation::CDMatrix::TrnasPos().

{
    CMatrixOperation::CDMatrix      matrixRotate;

    matrixRotate.BuildMatrixFirst(3, 3);

    matrixRotate.SetElement(0, 0, cos(fDegree[THETA_DEGREE]) * cos(fDegree[PHI_DEGREE]), 0);
    matrixRotate.SetElement(0, 1, -sin(fDegree[THETA_DEGREE]), 0);
    matrixRotate.SetElement(0, 2, -cos(fDegree[THETA_DEGREE])*sin(fDegree[PHI_DEGREE]), 0);

    matrixRotate.SetElement(1, 0, sin(fDegree[THETA_DEGREE]) * cos(fDegree[PHI_DEGREE]), 0);
    matrixRotate.SetElement(1, 1, cos(fDegree[THETA_DEGREE]), 0);
    matrixRotate.SetElement(1, 2, -sin(fDegree[THETA_DEGREE])*sin(fDegree[PHI_DEGREE]), 0);

    matrixRotate.SetElement(2, 0, sin(fDegree[PHI_DEGREE]), 0);
    matrixRotate.SetElement(2, 1, 0, 0);
    matrixRotate.SetElement(2, 2, cos(fDegree[PHI_DEGREE]), 0);
    
    matrixRotate.TrnasPos();
    
    pMatrixNbr->TrnasPos();
    CMatrixOperation::MMMul(&matrixRotate, pMatrixNbr, pMatrixResult);
    pMatrixResult->TrnasPos();
}

Here is the call graph for this function:

double * CGeometricShape::Serialize ( double  fXLayer )

private

Serialize unitcells with specific later index to double array.

Parameters

fXLayer

Target x layer index

Definition at line 1268 of file GeometricShape.cpp.

References _Y, _Z, CGeometricAtomFactory::GetAtomCountInUnitcell(), m_fAssignedCount, m_vectUnitCell, and UNITCELL_WRITING_BLOCK_SIZE.

Referenced by ExchangeAtomInfoBetweenNode().

{
    double              *pBuffer = NULL;
    double              fSendingCount = floor(m_fAssignedCount[_Y]) * floor(m_fAssignedCount[_Z]);
    int                 i, nSize = m_vectUnitCell.size();
    int                 fPos = 0;
    int                 nAtomCountInCell = CGeometricAtomFactory::GetAtomCountInUnitcell();

    pBuffer = (double*)malloc(sizeof(double)*(fSendingCount*nAtomCountInCell*UNITCELL_WRITING_BLOCK_SIZE));

    for (i = (int)(fXLayer * floor(fSendingCount)); i < fXLayer * fSendingCount + floor(fSendingCount); ++i)
    {
        
        m_vectUnitCell[i].Serialize(pBuffer + fPos);
        fPos += nAtomCountInCell*UNITCELL_WRITING_BLOCK_SIZE;
    }

    return pBuffer;
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool CGeometricShape::SetAtomAndNeighborInformation ( CCommandFileParser::LPINPUT_CMD_PARAM  lpParam )

static

Set neighbor information to AtomFactory.

Parameters

lpParam

Input parameters parsing from command file

Returns

Success or fail

Definition at line 952 of file GeometricShape.cpp.

References _X, _Y, _Z, CGeometricAtom::A, CGeometricAtom::A2C, CCommandFileParser::INPUT_CMD_PARAM::bNeedRotate, BuildRotationMatrix(), CGeometricAtom::C, CGeometricAtom::C2A, CalculateDegree(), CUBIC, CCommandFileParser::INPUT_CMD_PARAM::fDegree, CCommandFileParser::INPUT_CMD_PARAM::fUnitcellLength, IGeometricUnitCellInfo::GetA2CNeighborCount(), IGeometricUnitCellInfo::GetAnionCount(), IGeometricUnitCellInfo::GetAtomCoordination(), IGeometricUnitCellInfo::GetC2ANeighborCount(), IGeometricUnitCellInfo::GetCationCount(), CGeometricCoordination::GetCoordination(), IGeometricUnitCellInfo::GetNeighborCoordination(), IGeometricUnitCellInfo::GetUnitcCellSize(), CGeometricAtomFactory::InitAtomList(), IGeometricUnitCellInfo::InitCoordination(), CGeometricAtomFactory::InitNeighborList(), m_pUnitCellInfo, m_UnitCellInfo_cubic, m_UnitCellInfo_zincblende, CCommandFileParser::INPUT_CMD_PARAM::nDirectionSingle, IGeometricUnitCellInfo::RotateNeighbor(), IGeometricUnitCellInfo::SetAtomCoordination(), CGeometricAtomFactory::SetAtomCoordination(), CGeometricUnitCellInfo_zincblende::SetDireciton(), CGeometricUnitCell::SetLength(), IGeometricUnitCellInfo::SetNeighborCoordination(), CGeometricAtomFactory::SetNeighborCoordination(), CGeometricAtom::SetNeighborNumber(), IGeometricUnitCellInfo::SetUnitCellSize(), CCommandFileParser::INPUT_CMD_PARAM::szStructureType, and ZB.

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{
    unsigned int                    i;
    CGeometricCoordination          coordination;

    CGeometricAtomFactory::InitAtomList();
    CGeometricAtomFactory::InitNeighborList();

    
    if (!strcmp(lpParam->szStructureType, CUBIC))
    {
        m_pUnitCellInfo = &m_UnitCellInfo_cubic;
        CGeometricAtom::SetNeighborNumber(6);
        lpParam->bNeedRotate = false;
        switch( lpParam->nDirectionSingle )
        {
        case 100:
            lpParam->fUnitcellLength[0] /= 4;
            lpParam->fUnitcellLength[1] /= 4;
            lpParam->fUnitcellLength[2] /= 4;
            break;
        case 110:
            break;
        case 111:
            break;
        }
    }
    else if (!strcmp(lpParam->szStructureType, ZB))
    {
        lpParam->bNeedRotate = true;
        m_pUnitCellInfo = &m_UnitCellInfo_zincblende;
        m_UnitCellInfo_zincblende.SetDireciton(lpParam->nDirectionSingle);
        CGeometricAtom::SetNeighborNumber(4);

        if (100 == lpParam->nDirectionSingle)
            lpParam->bNeedRotate = false;
    }

    if (NULL != m_pUnitCellInfo)
    {
        m_pUnitCellInfo->InitCoordination();
        m_pUnitCellInfo->SetUnitCellSize(lpParam->fUnitcellLength);
        m_pUnitCellInfo->SetAtomCoordination();
        m_pUnitCellInfo->SetNeighborCoordination();
        
        if (lpParam->bNeedRotate)
        {
            CalculateDegree(lpParam);
            BuildRotationMatrix(lpParam->fDegree);
            m_pUnitCellInfo->RotateNeighbor(&CGeometricShape::m_rotationMatrix);
        }
    }
    else
        return false;

    for (i = 0; i < m_pUnitCellInfo->GetAnionCount(); ++i)
    {
        coordination = m_pUnitCellInfo->GetAtomCoordination(CGeometricAtom::A, i);
        CGeometricAtomFactory::SetAtomCoordination(CGeometricAtom::A,
            coordination.GetCoordination(_X),
            coordination.GetCoordination(_Y),
            coordination.GetCoordination(_Z));
    }

    for (i = 0; i < m_pUnitCellInfo->GetCationCount(); ++i)
    {
        coordination = m_pUnitCellInfo->GetAtomCoordination(CGeometricAtom::C, i);
        CGeometricAtomFactory::SetAtomCoordination(CGeometricAtom::C,
            coordination.GetCoordination(_X),
            coordination.GetCoordination(_Y),
            coordination.GetCoordination(_Z));
    }

    for (i = 0; i < (unsigned int)m_pUnitCellInfo->GetA2CNeighborCount(); ++i)
    {
        coordination = m_pUnitCellInfo->GetNeighborCoordination(CGeometricAtom::A2C, i);
        CGeometricAtomFactory::SetNeighborCoordination(CGeometricAtom::A2C,
            coordination.GetCoordination(_X),
            coordination.GetCoordination(_Y),
            coordination.GetCoordination(_Z));

    }
    
    for (i = 0; i < (unsigned int)m_pUnitCellInfo->GetC2ANeighborCount(); i++)
    {
        coordination = m_pUnitCellInfo->GetNeighborCoordination(CGeometricAtom::C2A, i);
        CGeometricAtomFactory::SetNeighborCoordination(CGeometricAtom::C2A,
            coordination.GetCoordination(_X),
            coordination.GetCoordination(_Y),
            coordination.GetCoordination(_Z));
    }

    CGeometricUnitCell::SetLength(lpParam->fUnitcellLength, m_pUnitCellInfo->GetUnitcCellSize());
    
    return true;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::SetBackendFace ( bool  bBackendFace )

inline

Check is this back end face side in MPI running enviroment.

Set back end side mark to shape object

Definition at line 49 of file GeometricShape.h.

References m_bBackendFace.

Referenced by SetShapeInformation().

Here is the caller graph for this function:

void CGeometricShape::SetConsideringBoundaryCondition ( bool  bConsider, AXIS_DEFINE  direction  )

inline

Get bondary condition of shape.

Definition at line 43 of file GeometricShape.h.

References m_bConsiderBoundaryCondition.

Referenced by SetShapeInformation().

{ m_bConsiderBoundaryCondition[direction] = bConsider; }; 

Here is the caller graph for this function:

void CGeometricShape::SetDirection	(	double	x_axis,
		double	y_axis,
		double	z_axis
	)

Set direciton of shape.

Parameters

x_axis	x direction information
y_axis	y direction information
z_axis	z direction information

Definition at line 57 of file GeometricShape.cpp.

References m_shapDirection, and CGeometricDirection::SetDirection().

Referenced by SetShapeInformation().

{
    m_shapDirection.SetDirection(x_axis, y_axis, z_axis);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::SetFrontFace ( bool  bFrontFace )

inline

Check is this front face side in MPI running enviroment.

Definition at line 47 of file GeometricShape.h.

References m_bFrontFace.

Referenced by SetShapeInformation().

{ m_bFrontFace = bFrontFace; }; 

Here is the caller graph for this function:

void CGeometricShape::SetLength	(	double	lx,
		double	ly,
		double	lz
	)

Set length of shape.

Parameters

lx	x direction length
ly	y direction length
lz	z direction length

Definition at line 67 of file GeometricShape.cpp.

References _X, _Y, _Z, and m_fLength.

Referenced by SetShapeInformation().

{
    m_fLength[_X] = lx;
    m_fLength[_Y] = ly;
    m_fLength[_Z] = lz;
}

Here is the caller graph for this function:

bool CGeometricShape::SetMapInfoSize ( LPNEIGHBOR_MAP_INFO  lpMapInfo, double  fSize  )

private

Building Hamiltonian part.

Set map info size, size that means aton count in map info

Parameters

lpMapInfo	Atom map information
fSize	Size of map

<Added by="" jhkang>="">

<Added by="" jhkang="" end>="">

Definition at line 1053 of file GeometricShape.cpp.

References ALLOC_WITH_NULL_INIT, MAX_NEIGHBOR, NEIGHBOR_MAP_INFO::pAtomType, NEIGHBOR_MAP_INFO::pbPeriodicCondition, NEIGHBOR_MAP_INFO::pDomainMaterialNumber, NEIGHBOR_MAP_INFO::pfAtomOnGrid, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, NEIGHBOR_MAP_INFO::pfX_Coordination, NEIGHBOR_MAP_INFO::pfY_Coordination, NEIGHBOR_MAP_INFO::pfZ_Coordination, NEIGHBOR_MAP_INFO::pMaterialNumber, NEIGHBOR_MAP_INFO::pnDomainNumber, and NEIGHBOR_MAP_INFO::pNeighborMaterial.

Referenced by ConstructMapInfo().

{
    bool                bRtn = false;
    unsigned int        i;

    ALLOC_WITH_NULL_INIT(lpMapInfo->pfID, double, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pAtomType, CGeometricAtom::ATOM_TYPE, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pMaterialNumber, MATERIAL_INDEX, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pDomainMaterialNumber, MATERIAL_INDEX, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pnDomainNumber, unsigned int, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pfX_Coordination, double, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pfY_Coordination, double, (size_t)fSize);
    ALLOC_WITH_NULL_INIT(lpMapInfo->pfZ_Coordination, double, (size_t)fSize);
    
    for (i = 0; i < MAX_NEIGHBOR; ++i)
    {
        ALLOC_WITH_NULL_INIT(lpMapInfo->pfNeighbor[i], double, (size_t)fSize);
        ALLOC_WITH_NULL_INIT(lpMapInfo->pbPeriodicCondition[i], bool, (size_t)fSize);
        ALLOC_WITH_NULL_INIT(lpMapInfo->pNeighborMaterial[i], MATERIAL_INDEX, (size_t)fSize);
    }

    ALLOC_WITH_NULL_INIT(lpMapInfo->pfAtomOnGrid, double, (size_t)fSize);


    bRtn = true;
    return bRtn;
}

Here is the caller graph for this function:

void CGeometricShape::SetMatchingUnitcellCount ( int  nCount )

inline

Definition at line 128 of file GeometricShape.h.

References m_nHandlingUnitcellCount.

Referenced by CSPLoop::ConstructionGeometric().

{ m_nHandlingUnitcellCount = nCount; }

Here is the caller graph for this function:

void CGeometricShape::SetMaterialType ( MATERIAL_INDEX  type )

inline

Get maetrial typpe of shap.

Definition at line 37 of file GeometricShape.h.

References m_MaterialType.

Referenced by SetMaterialType(), and SetShapeInformation().

{ m_MaterialType = type; }; 

Here is the caller graph for this function:

void CGeometricShape::SetMaterialType

(

char *

pszType

)

Set maetrial type of shape.

Set maetrial type of shape

Parameters

pszType

Material type information

Definition at line 77 of file GeometricShape.cpp.

References GaAs, InAs, SetMaterialType(), and Si.

{
    if (!strcmp(pszType, "Si"))
        SetMaterialType(Si);
    else if (!strcmp(pszType, "GaAs"))
        SetMaterialType(GaAs);
    else if (!strcmp(pszType, "InAs"))
        SetMaterialType(InAs);
}

Here is the call graph for this function:

void CGeometricShape::SetNeumannBoundaryCondition ( bool  bConsider, AXIS_DEFINE  direction  )

inline

Get Neumann boundary condition of shape.

Definition at line 71 of file GeometricShape.h.

References m_bNeumannBoundaryCondition.

{ m_bNeumannBoundaryCondition[direction] = bConsider; }; 

void CGeometricShape::SetOriginCoordination	(	double	x,
		double	y,
		double	z
	)

Building Geometric part.

Set origin coordination of shape

Parameters

x	x coordination
y	y coordination
z	z coordination

Definition at line 47 of file GeometricShape.cpp.

References m_originCoordination, and CGeometricCoordination::SetCoordination().

Referenced by SetShapeInformation().

{
    m_originCoordination.SetCoordination(x, y, z);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::SetShapeForm ( unsigned int  form )

inline

Get form type of shape.

Definition at line 40 of file GeometricShape.h.

References m_ShapeForm.

Referenced by SetShapeForm(), and SetShapeInformation().

{ m_ShapeForm = form; }; 

Here is the caller graph for this function:

void CGeometricShape::SetShapeForm

(

char *

pszForm

)

Get form type of shape.

Get form type of shape

Parameters

pszForm

Shape form

Definition at line 90 of file GeometricShape.cpp.

References BOX_SHAPE, CYLINDER_SHAPE, and SetShapeForm().

{
    if (!strcmp(pszForm, "Box"))
        SetShapeForm(BOX_SHAPE);
    else if (!strcmp(pszForm, "Cylinder"))
        SetShapeForm(CYLINDER_SHAPE);
}

Here is the call graph for this function:

void CGeometricShape::SetShapeInformation

(

CCommandFileParser::LPINPUT_CMD_PARAM

lpParam

)

Set shape information(Length, material, bondary condition and so on)

Parameters

shape	Geometric Shape
lpParam	Input parameters parsing from command file

Definition at line 926 of file GeometricShape.cpp.

References _X, _Y, _Z, CCommandFileParser::INPUT_CMD_PARAM::bConsiderBoundaryCondition, CCommandFileParser::INPUT_CMD_PARAM::fOrigin, CCommandFileParser::INPUT_CMD_PARAM::fShapeLength, CMPIManager::GetCurrentRank(), CMPIManager::GetTotalNodeCount(), CMPIManager::IsRootRank(), SetBackendFace(), SetConsideringBoundaryCondition(), SetDirection(), SetFrontFace(), SetLength(), SetMaterialType(), SetOriginCoordination(), SetShapeForm(), CCommandFileParser::INPUT_CMD_PARAM::szDomainMat, and CCommandFileParser::INPUT_CMD_PARAM::szShape.

Referenced by ConstructBasicGeometric(), and CTBMS_Solver::Launching_TBMS_Solver().

{

    SetDirection(1, 0, 0);
    SetLength(lpParam->fShapeLength[0][_X], lpParam->fShapeLength[0][_Y], lpParam->fShapeLength[0][_Z]);
    SetOriginCoordination(lpParam->fOrigin[0][_X], lpParam->fOrigin[0][_Y], lpParam->fOrigin[0][_Z]);
    SetMaterialType(lpParam->szDomainMat[0]);
    SetShapeForm(lpParam->szShape[0]);
    SetConsideringBoundaryCondition(lpParam->bConsiderBoundaryCondition[_X], _X);
    SetConsideringBoundaryCondition(lpParam->bConsiderBoundaryCondition[_Y], _Y);
    SetConsideringBoundaryCondition(lpParam->bConsiderBoundaryCondition[_Z], _Z);
#ifdef DISABLE_MPI_ROUTINE
    SetFrontFace(true);
    SetBackendFace(true);
#else //DISABLE_MPI_ROUTINE
    if (CMPIManager::IsRootRank())
        SetFrontFace(true);
    if (CMPIManager::GetCurrentRank() == CMPIManager::GetTotalNodeCount() - 1)
        SetBackendFace(true);
#endif //DISABLE_MPI_ROUTINE
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::SetTotalAtomCount ( double  fTotalAtomCountinMPI )

inline

Get total valid atom count in shape.

Definition at line 56 of file GeometricShape.h.

References m_fTotalAtomCountinMPI.

{ m_fTotalAtomCountinMPI = fTotalAtomCountinMPI;}; 

void CGeometricShape::SetupPEBoundaryCondition	(	CCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LP_CONTACT_GROUP_INFO *	lpContactGroup
	)

<Added by="" jhkang>="">

<Added by jhkang, Poisson equation hamiltonian construct>

Definition at line 1403 of file GeometricShape.cpp.

References _X, _Y, _Z, CCommandFileParser::INPUT_CMD_PARAM::bConsiderNeumannBoundaryCondition, BOX_SHAPE, CYLINDER_SHAPE, CMPIManager::IsRootRank(), m_bConsiderBoundaryCondition, m_bNeumannBoundaryCondition, m_ShapeForm, and CCommandFileParser::INPUT_CMD_PARAM::nContactNumber.

Referenced by CSPLoop::ConstructionGeometric().

{
    unsigned int                            i;
    bool                                    bErrorCheck = 0;

    m_bNeumannBoundaryCondition[_X] = lpParam->bConsiderNeumannBoundaryCondition[_X];
    m_bNeumannBoundaryCondition[_Y] = lpParam->bConsiderNeumannBoundaryCondition[_Y];
    m_bNeumannBoundaryCondition[_Z] = lpParam->bConsiderNeumannBoundaryCondition[_Z];

    if (m_bNeumannBoundaryCondition[_X] == 1 && m_bNeumannBoundaryCondition[_Y] == 1 && m_bNeumannBoundaryCondition[_Z] == 1)
    {
        if (CMPIManager::IsRootRank())
        {
            printf("-Error: Applying neumann BC to all directions makes A matrix singular! Program terminated!\n");
            exit(1);
        }
    }

    if (m_bConsiderBoundaryCondition[_X] == 1 && m_bConsiderBoundaryCondition[_Y] == 1 && m_bConsiderBoundaryCondition[_Z] == 1)
    {
        if (CMPIManager::IsRootRank())
        {
            printf("-Error: Applying periodic BC to all directions makes A matrix singular! Program terminated!\n");
            exit(1);
        }
    }

    if ((m_bNeumannBoundaryCondition[_X] == 1 && m_bConsiderBoundaryCondition[_X] == 1) ||
        (m_bNeumannBoundaryCondition[_Y] == 1 && m_bConsiderBoundaryCondition[_Y] == 1) ||
        (m_bNeumannBoundaryCondition[_Z] == 1 && m_bConsiderBoundaryCondition[_Z] == 1))
    {
        if (CMPIManager::IsRootRank())
        {
            printf("-Error: Applying neumann BC with periodic BC to same direction is not allowed! Program terminated!\n");
            exit(1);
        }
    }

    if (lpContactGroup == NULL && CMPIManager::IsRootRank())
    {
        printf("-No contact boundary condition \n");
    }
    else
    {
        for (i = 0; i < lpParam->nContactNumber; i++)
        {
            if ((lpContactGroup[i]->nContactDirection == 0 || lpContactGroup[i]->nContactDirection == 1) && m_bConsiderBoundaryCondition[0])
            {
                printf("-Error: Applying periodic BC with contact group[%3d] boundary in same x-direction is not allowed. Program terminated!\n", i + 1);
                bErrorCheck = 1;
            }
            if (m_ShapeForm == BOX_SHAPE)
            {
                if ((lpContactGroup[i]->nContactDirection == 2 || lpContactGroup[i]->nContactDirection == 3) && m_bConsiderBoundaryCondition[1])
                {
                    printf("-Error: Applying periodic BC with contact group[%3d] boundary in same y-direction is not allowed. Program terminated!\n", i + 1);
                    bErrorCheck = 1;
                }
                if ((lpContactGroup[i]->nContactDirection == 4 || lpContactGroup[i]->nContactDirection == 5) && m_bConsiderBoundaryCondition[2])
                {
                    printf("-Error: Applying periodic BC with contact group[%3d] boundary in same z-direction is not allowed. Program terminated!\n", i + 1);
                    bErrorCheck = 1;
                }
            }
            if (m_ShapeForm == CYLINDER_SHAPE)
            {
                if (lpContactGroup[i]->nContactDirection == 6 && (m_bConsiderBoundaryCondition[1] == 1 || m_bConsiderBoundaryCondition[2] == 1))
                {
                    printf("-Error: Applying periodic BC in cylinder shape with contact group[%3d] boundary is not allowed. Program terminated!\n", i + 1);
                    bErrorCheck = 1;
                }
            }
        }
        if (bErrorCheck) exit(1);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void CGeometricShape::ShiftAtomID

(

double

fShift

)

Shift atom id in MPI running enviroment.

Parameters

fShift

Increasing count of ID

Definition at line 1140 of file GeometricShape.cpp.

References m_vectUnitCell.

Referenced by ExchangeAtomInfoBetweenNode().

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

    for (i = 0; i < nSize; ++i)
        m_vectUnitCell[i].ShiftAtomID(fShift);
}

Here is the caller graph for this function:

Member Data Documentation

bool CGeometricShape::m_bBackendFace

private

Flag of back end face or not.

Definition at line 87 of file GeometricShape.h.

Referenced by CalculateUnitcellCount(), CheckingNeighborCandiate(), ConstructContactRegionOnPoissonGrid(), InitShape(), IsBackendFace(), and SetBackendFace().

bool CGeometricShape::m_bConsiderBoundaryCondition[3]

private

Bondary condition for each driection.

Definition at line 85 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), CalculateUnitcellCount(), ExchangeAtomInfoBetweenNode(), GetConsideringBoundaryCondition(), GetPeriodicDirection(), InitShape(), IsInBoundaryCondition(), PeriodicUnitCellNumbering(), SetConsideringBoundaryCondition(), and SetupPEBoundaryCondition().

bool CGeometricShape::m_bFrontFace

private

Flag of front face or not.

Definition at line 86 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), CalculateUnitcellCount(), CheckingNeighborCandiate(), ConstructContactRegionOnPoissonGrid(), InitShape(), IsFrontFace(), and SetFrontFace().

bool CGeometricShape::m_bNeumannBoundaryCondition[3]

private

Neumann bondary condition for each driection

Definition at line 100 of file GeometricShape.h.

Referenced by GetNeumannBoundaryCondition(), SetNeumannBoundaryCondition(), and SetupPEBoundaryCondition().

double CGeometricShape::m_fAssignedCount[3]

private

Unitcell assigend count in shape for each direction.

Definition at line 83 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), BuildNeighborInformation(), CalculateUnitcellCount(), CheckingNeighborCandiate(), Deserialize(), ExchangeAtomInfoBetweenNode(), PeriodicUnitCellNumbering(), and Serialize().

double CGeometricShape::m_fAtomIDStartIndex

private

Start atom index in current Shape.

Definition at line 89 of file GeometricShape.h.

Referenced by BuildPEHamiltonian(), ExchangeAtomInfoBetweenNode(), GetAtomStartID(), and InitShape().

double CGeometricShape::m_fLength[3]

private

Building Geometric part.

Length of shape

Definition at line 77 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), CalculateUnitcellCount(), ConstructContactRegionOnPoissonGrid(), InitShape(), MapElecAtomOnPoissonGrid(), and SetLength().

double CGeometricShape::m_fTotalAtomCountinMPI

private

Total valid atom count in shape.

Definition at line 88 of file GeometricShape.h.

Referenced by ExchangeAtomInfoBetweenNode(), GetTotalAtomCount(), InitShape(), and SetTotalAtomCount().

double CGeometricShape::m_fUnitCellLength[3]

private

Definition at line 134 of file GeometricShape.h.

Referenced by CalculateUnitcellCount(), and InitShape().

MATERIAL_INDEX CGeometricShape::m_MaterialType

private

Material type of shape.

Definition at line 90 of file GeometricShape.h.

Referenced by GetMaterialType(), InitShape(), and SetMaterialType().

unsigned int CGeometricShape::m_nAtomFirstLayer

<Added by="" jhkang="" end>="">

Set Neumann boundary condition of shapeBuilding Hamiltonian part First layer information for sending to previous node

Definition at line 71 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), CSPLoop::BuildHamiltonian(), InitShape(), and CTBMS_Solver::Launching_TBMS_Solver().

unsigned int CGeometricShape::m_nAtomLastLayer

Last layer information for sending to next node.

Definition at line 76 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), CSPLoop::BuildHamiltonian(), InitShape(), and CTBMS_Solver::Launching_TBMS_Solver().

int CGeometricShape::m_nContactNumber

private

<Added by="" jhkang>="">

Definition at line 98 of file GeometricShape.h.

Referenced by BuildPEBiasVector(), and ConstructContactRegionOnPoissonGrid().

int CGeometricShape::m_nHandlingUnitcellCount

private

Definition at line 133 of file GeometricShape.h.

Referenced by CalculateUnitcellCount(), InitShape(), and SetMatchingUnitcellCount().

CGeometricCoordination CGeometricShape::m_originCoordination

private

Orign coordination of shape.

Definition at line 95 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), CalculateUnitcellCount(), ConstructContactRegionOnPoissonGrid(), InitShape(), MapElecAtomOnPoissonGrid(), and SetOriginCoordination().

IGeometricUnitCellInfo * CGeometricShape::m_pUnitCellInfo

static

Unitcell information pointer for using in class internal.

Definition at line 126 of file GeometricShape.h.

Referenced by InitShape(), MapElecAtomOnPoissonGrid(), and SetAtomAndNeighborInformation().

CMatrixOperation::CDMatrix CGeometricShape::m_rotationMatrix

static

Rotation matrix for given direction.

Definition at line 127 of file GeometricShape.h.

Referenced by CHamiltonianBuilder::BuildACCANeighborFor10Band(), BuildRotationMatrix(), and CHamiltonianBuilder::RotateTransMatrixFor10Band().

CGeometricDirection CGeometricShape::m_shapDirection

private

Direction of shape

Definition at line 96 of file GeometricShape.h.

Referenced by InitShape(), RefillPeriodicBinding(), and SetDirection().

unsigned int CGeometricShape::m_ShapeForm

private

Shape form.

Definition at line 84 of file GeometricShape.h.

Referenced by ConstructContactRegionOnPoissonGrid(), GetShapeForm(), InitShape(), SetShapeForm(), and SetupPEBoundaryCondition().

CGeometricUnitCellInfo_cubic CGeometricShape::m_UnitCellInfo_cubic

static

Definition at line 125 of file GeometricShape.h.

Referenced by SetAtomAndNeighborInformation().

CGeometricUnitCellInfo_zincblende CGeometricShape::m_UnitCellInfo_zincblende

static

Definition at line 124 of file GeometricShape.h.

Referenced by SetAtomAndNeighborInformation().

std::vector<CGeometricUnitCell> CGeometricShape::m_vectNextUnitCell

private

Back end edge unit cell that copy from next side node.

Definition at line 93 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), ExchangeAtomInfoBetweenNode(), FreeUnitCellList(), and PeriodicUnitCellNumbering().

std::vector<CGeometricUnitCell> CGeometricShape::m_vectPrevUnitCell

private

Front edge unit cell that copy from previous side node.

Definition at line 92 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), ExchangeAtomInfoBetweenNode(), FreeUnitCellList(), and PeriodicUnitCellNumbering().

std::vector<CGeometricAtom*> CGeometricShape::m_vectSurfaceAtom

private

Definition at line 94 of file GeometricShape.h.

Referenced by FreeUnitCellList(), and GetSurfaceAtomList().

std::vector<CGeometricUnitCell> CGeometricShape::m_vectUnitCell

private

Array of unitcell in shape.

Definition at line 91 of file GeometricShape.h.

Referenced by ArrangeUnitCell(), BuildNeighborInformation(), CheckingNeighborCandiate(), ConstructMapInfo(), Deserialize(), ExchangeAtomInfoBetweenNode(), FreeUnitCellList(), GetAtomByIndex(), PeriodicUnitCellNumbering(), Serialize(), and ShiftAtomID().

std::vector<double> CGeometricShape::m_waveFunctionValue

private

Definition at line 99 of file GeometricShape.h.

Referenced by BuildPEWaveVector().

---

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

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