Class for Geometric shape. More...

#include "KNGeometricShape.h"

Collaboration diagram for CKNGeometricShape:

Public Member Functions
	CKNGeometricShape ()

	~CKNGeometricShape ()

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 (CKNCommandFileParser::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, CKNCommandFileParser::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 (CKNMatrixOperation::CKNCSR *pResult, CKNCommandFileParser::LPINPUT_CMD_PARAM lpParam, LPNEIGHBOR_MAP_INFO lpMapInfo, unsigned int nRepeatIndex, double fKValue[3])
	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< CKNGeometricAtom * > *	GetSurfaceAtomList ()

Static Public Member Functions
static void	SetShapeInformation (CKNGeometricShape &shape, CKNCommandFileParser::LPINPUT_CMD_PARAM lpParam)
	Set shape information(Length, material, bondary condition and so on) More...

static bool	SetAtomAndNeighborInformation (CKNCommandFileParser::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
	Get Surface atom list. More...

unsigned int	m_nAtomLastLayer
	Last layer information for sending to next node. More...

Static Public Attributes
static CKNGeometricUnitCellInfo_zincblende	m_UnitCellInfo_zincblende

static CKNGeometricUnitCellInfo_cubic	m_UnitCellInfo_cubic

static IKNGeometricUnitCellInfo *	m_pUnitCellInfo
	Unitcell information pointer for using in class internal. More...

static CKNMatrixOperation::CKNDMatrix	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)
	Check unitcell is in the bondary area or not. More...

void	FreeUnitCellList ()
	Relase unitcell list. More...

void	InitShape ()
	Initialize Shape variable. More...

void	RotateMatrix (CKNMatrixOperation::CKNDMatrix pMatrixNbr, CKNMatrixOperation::CKNDMatrix pMatrixResult, double fDegree[2])
	Rotate matrix with calculated degree. More...

CKNGeometricAtom *	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 (CKNCommandFileParser::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< CKNGeometricUnitCell > pVectUnitCell, double pBuffer, bool bFrontSide)
	Deerialize unitcells from double array. More...

void	BuildGeoFileName (char *pszFileName, CKNCommandFileParser::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 (CKNCommandFileParser::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< CKNGeometricUnitCell >	m_vectUnitCell
	Array of unitcell in shape. More...

std::vector< CKNGeometricUnitCell >	m_vectPrevUnitCell
	Front edge unit cell that copy from previous side node. More...

std::vector< CKNGeometricUnitCell >	m_vectNextUnitCell
	Back end edge unit cell that copy from next side node. More...

std::vector< CKNGeometricAtom * >	m_vectSurfaceAtom

CKNGeometricCoordination	m_originCoordination
	Orign coordination of shape. More...

CKNGeometricDirection	m_shapDirection
	Direction of shape. More...

Detailed Description

Class for Geometric shape.

Date: 03/Oct/2014

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

Definition at line 27 of file KNGeometricShape.h.

Constructor & Destructor Documentation

CKNGeometricShape::CKNGeometricShape ( )

Definition at line 33 of file KNGeometricShape.cpp.

References InitShape().

 {
     InitShape();
 }

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CKNGeometricShape::~CKNGeometricShape ( )

Definition at line 38 of file KNGeometricShape.cpp.

References FinalShape().

 {
     FinalShape();
 }

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Member Function Documentation

void CKNGeometricShape::ArrangeUnitCell ( CKNCommandFileParser::LPINPUT_CMD_PARAM lpParam )

private

Arranging unitcell into shape.

Parameters

lpParam Input parameters parsing from command file

Definition at line 393 of file KNGeometricShape.cpp.

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

Referenced by FillUnitcell().

 {
     int                         x, y, z, maxX, maxY, maxZ;
     CKNGeometricCoordination    currentPos, refPos;
     double                      fUnitcellLength[3];
     double                      fUnitcellID = 0;
 
     fUnitcellLength[_X] = CKNGeometricUnitCell::GetLength(_X);
     fUnitcellLength[_Y] = CKNGeometricUnitCell::GetLength(_Y);
     fUnitcellLength[_Z] = CKNGeometricUnitCell::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]);
 
     CKNGeometricUnitCell::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)
             {
                 CKNGeometricUnitCell        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(CKNGeometricCoordination::X), currentPos.GetCoordination(CKNGeometricCoordination::Y), currentPos.GetCoordination(CKNGeometricCoordination::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 (CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() - 1)
                     {
                         if (x == maxX - 2)
                             m_nAtomLastLayer += nAtom;
                     }
                     else
                     {
                         if (x == maxX - 1)
                             m_nAtomLastLayer += nAtom;
                     }
                 }
                 else
                 {
                     int     periodicDirection = CKNGeometricAtom::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);
     }
 }

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void CKNGeometricShape::BuildGeoFileName	(	char *	pszFileName,
		CKNCommandFileParser::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 1291 of file KNGeometricShape.cpp.

References CKNCommandFileParser::INPUT_CMD_PARAM::bConsiderBoundaryCondition, CKNCommandFileParser::INPUT_CMD_PARAM::nDirectionSingle, CKNCommandFileParser::INPUT_CMD_PARAM::nSubDomainNumber, and CKNCommandFileParser::INPUT_CMD_PARAM::szShape.

Referenced by ConstructMapInfo().

 {
     char                szTemp[1024];
     unsigned int        i;
 
 
     sprintf(pszFileName, "Geo_%d_%d%d%d_", lpParam->nDirectionSingle, lpParam->bConsiderBoundaryCondition[0] ? 1 : 0, lpParam->bConsiderBoundaryCondition[1] ? 1 : 0, lpParam->bConsiderBoundaryCondition[2] ? 1 : 0);
 
     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);
     }
 }

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void CKNGeometricShape::BuildNeighborInformation ( )

Find neighbor of each atom.

Definition at line 117 of file KNGeometricShape.cpp.

References GetSurfaceAtomList(), m_fAssignedCount, and m_vectUnitCell.

Referenced by CKNTBMS_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());
     }
 }

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

staticprivate

Build rotation matrix for given direction.

Parameters

fDegree Given degree of theta and phi

Definition at line 1268 of file KNGeometricShape.cpp.

References CKNMatrixOperation::CKNDMatrix::BuildMatrixFirst(), m_rotationMatrix, PHI_DEGREE, CKNMatrixOperation::CKNDMatrix::SetElement(), THETA_DEGREE, and CKNMatrixOperation::CKNDMatrix::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();
 }

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void CKNGeometricShape::CalculateDegree ( CKNCommandFileParser::LPINPUT_CMD_PARAM lpParam )

staticprivate

Calculating degree from direction information.

Parameters

lpParam Input parameters parsing from command file

Definition at line 696 of file KNGeometricShape.cpp.

References CKNCommandFileParser::INPUT_CMD_PARAM::fDegree, CKNCommandFileParser::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]);
 }

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bool CKNGeometricShape::CalculateUnitcellCount ( )

private

Calculating unitcell count in shape.

< Only for Show unitcell count

Definition at line 254 of file KNGeometricShape.cpp.

References _X, _Y, _Z, CKNMPIManager::AllReduceDouble(), CKNGeometricCoordination::GetCoordination(), CKNMPIManager::GetCurrentRank(), CKNGeometricUnitCell::GetLength(), CKNMPIManager::GetTotalNodeCount(), CKNMPIManager::IsRootRank(), m_bBackendFace, m_bConsiderBoundaryCondition, m_bFrontFace, m_fAssignedCount, m_fLength, m_originCoordination, CKNGeometricCoordination::SetOffset(), and CKNIPCCUtility::ShowMsg().

Referenced by FillUnitcell().

 {
     double              fXTotalCount;
     double              fXAssignCount, fYAssignCount, fZAssignCount;
     double              fUnitcellLength[3];
     bool                bRtn = false;
     bool                bPaddingUnitCell = false;
     char                szMsg[1024];
     
     fUnitcellLength[_X] = CKNGeometricUnitCell::GetLength(_X);
     fUnitcellLength[_Y] = CKNGeometricUnitCell::GetLength(_Y);
     fUnitcellLength[_Z] = CKNGeometricUnitCell::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 == CKNMPIManager::GetTotalNodeCount() )
     {
         fXAssignCount = fXTotalCount;
         if (bPaddingUnitCell)
         {
             fXAssignCount++;
             fXTotalCount++;
         }
     }
     else
     {
         int             nNodeCount = CKNMPIManager::GetTotalNodeCount();
         unsigned int    nRank = (unsigned int)CKNMPIManager::GetCurrentRank();
 
         if( 1 > fXTotalCount / nNodeCount )
             return bRtn;
 
         unsigned int            nBaseCount, nRestCount;
         
         nBaseCount = (unsigned int)floor(fXTotalCount / nNodeCount);
         nRestCount = (unsigned int)floor(fXTotalCount) - nBaseCount * nNodeCount;
 
         fXAssignCount = nBaseCount;
         if( nRank < nRestCount )
             fXAssignCount += 1;
 
         if( true == bPaddingUnitCell && CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() - 1 )
             fXAssignCount += 1;
 
         //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 * nRank + nExtraAdding) * 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( CKNMPIManager::IsRootRank())
         {
             sprintf(szMsg, "TotalAssignCount: %7f\n", fXTotalCount);
             CKNIPCCUtility::ShowMsg(szMsg);
         }
 
         sprintf(szMsg, "%d rank: Xoffset: %7f, LX: %7f, Assign Count: %7f\n", CKNMPIManager::GetCurrentRank(), m_originCoordination.GetCoordination(_X), m_fLength[_X], fXAssignCount);
         CKNIPCCUtility::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( CKNMPIManager::IsRootRank())
     {
         fXAssignCount = CKNMPIManager::AllReduceDouble(fXAssignCount); 
 #endif //_WIN32
         sprintf(szMsg, "-Unitcell counts: X-axis[%2.1f], Y-axis[%2.1f], Z-axis[%2.1f]\n", fXAssignCount, fYAssignCount, fZAssignCount);
         CKNIPCCUtility::ShowMsg(szMsg);
 #ifndef _WIN32
     }
     else
         fXAssignCount = CKNMPIManager::AllReduceDouble(fXAssignCount); 
 #endif //_WIN32
 
     bRtn = true;
     return bRtn;
 }

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void CKNGeometricShape::CheckingNeighborCandiate ( )

private

Checking neighbor unitcell by calculating index.

Definition at line 735 of file KNGeometricShape.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);
     }
 }

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bool CKNGeometricShape::ConstructMapInfo	(	LPNEIGHBOR_MAP_INFO	lpMapInfo,
		CKNCommandFileParser::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 750 of file KNGeometricShape.cpp.

Referenced by CKNTBMS_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];
 #ifndef DISABLE_MPI_ROUTINE
     MPI_Request         req;
     double              fTemp = 1;
 #endif //DISABLE_MPI_ROUTINE
 
     BuildGeoFileName(szTemp, lpParam);
         
     InitMapInfo(lpMapInfo);
     if (true == lpParam->bSaveMapFile)
     {
 #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( CKNMPIManager::IsRootRank() &&  CKNMPIManager::IsDeflationRoot() )
         {
             CKNIPCCUtility::ShowMsg("-Save atom map to file.\n");
             out = fopen(szFileName, "wt");
         }
         else
         {
             CKNMPIManager::ReceiveDoubleBufferSync(CKNMPIManager::GetCurrentRank()-1, &fTemp, 1, &req);
             out = fopen(szFileName, "at");
         }
 #endif //DISABLE_MPI_ROUTINE
     }
     
     nSize = m_vectUnitCell.size();
 
     if (!SetMapInfoSize(lpMapInfo, CKNGeometricUnitCell::GetSubElementID()))
     {
         if (NULL != out)
             fclose(out);
         CKNGeometricShape::FreeMapInfo(lpMapInfo);
         return bRtn;
     }
         
 #ifdef SHOW_ATOM_MAP_RESULT_ON_SCREEN
     CKNIPCCUtility::ShowMsg("\n");
     CKNIPCCUtility::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)
         {
             CKNGeometricAtom                *pAtom = m_vectUnitCell[i].GetSubElementAt(j);
             if (ATOM_DEFAULT_INDEX == pAtom->GetID() || true == pAtom->IsPeriodicAtom())
                 continue;
 
             CKNGeometricCoordination        coord = pAtom->GetCoordination();
             fIDForDebug = pAtom->GetID();
 
             sprintf(szAdditional, "");
             sprintf(szMaterial, "");
             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);
 
                 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\n", pAtom->GetID(), (int)pAtom->GetType(), (int)pAtom->GetMaterialNumber(),
                                                         coord.GetCoordination(_X),
                                                         coord.GetCoordination(_Y),
                                                         coord.GetCoordination(_Z),
                                                         szAdditional, szMaterial);
                         
             lpMapInfo->fItemCount++;
             lpMapInfo->pAtomType[nMapIndex] = pAtom->GetType();
             lpMapInfo->pMaterialNumber[nMapIndex] = pAtom->GetMaterialNumber();
             lpMapInfo->pDomainMaterialNumber[nMapIndex] = pAtom->GetDomainMaterialNumber();
             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
             CKNIPCCUtility::ShowMsg(szMsg);
 #endif //SHOW_ATOM_MAP_RESULT_ON_SCREEN
 
         }
     }
     
     if (true == lpParam->bSaveMapFile && NULL != out)
     {
         fclose(out);
 #ifndef DISABLE_MPI_ROUTINE
         if( CKNMPIManager::GetCurrentRank() < CKNMPIManager::GetTotalNodeCount() - 1)
             CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetCurrentRank()+1, &fTemp, 1, &req);
 #endif //DISABLE_MPI_ROUTINE
     }
         
     bRtn = true;
     return bRtn;
 }

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void CKNGeometricShape::Deserialize	(	std::vector< CKNGeometricUnitCell > *	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 1241 of file KNGeometricShape.cpp.

References _Y, _Z, CKNGeometricUnitCell::Deserialize(), CKNGeometricAtomFactory::GetAtomCountInUnitcell(), m_fAssignedCount, m_vectUnitCell, CKNGeometricUnitCell::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 = CKNGeometricAtomFactory::GetAtomCountInUnitcell();
     double              fID;
 
     if( bFrontSide )
         fID = -fReceivingCount;
     else
         fID = m_vectUnitCell[m_vectUnitCell.size()-1].GetID() + 1;
 
     for (i = 0 ; i < floor(fReceivingCount); ++i)
     {
         CKNGeometricUnitCell            unitcell;
 
         unitcell.SetID(fID++);
         unitcell.Deserialize(pBuffer + fPos);
         pVectUnitCell->push_back(unitcell);
         fPos += nAtomCountInCell*UNITCELL_WRITING_BLOCK_SIZE;
     }
 }

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void CKNGeometricShape::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 1096 of file KNGeometricShape.cpp.

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

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver(), and CKNGeometricConstructionLaunch::LaunchingGeometricConstructionMPI().

 {
     double              fShift = CKNMPIManager::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 = CKNGeometricAtomFactory::GetAtomCountInUnitcell();
     double              *pReceiveBuffer = (double*)malloc(sizeof(double)*(fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell));
     MPI_Request         req[2];
     double              fAtomID = 0;
 
     if( 1 == CKNMPIManager::GetTotalNodeCount() )
     {
         m_fTotalAtomCountinMPI = CKNGeometricUnitCell::GetSubElementID();
         FREE_MEM(pReceiveBuffer);
         return;
     }
 
     
     if( CKNMPIManager::IsRootRank())
     {
         fAtomID = CKNGeometricUnitCell::GetSubElementID();
         CKNMPIManager::SendDoubleBufferSync(1, &fAtomID, 1, &req[0]);
     }
     else
     {
         CKNMPIManager::ReceiveDoubleBufferSync(CKNMPIManager::GetCurrentRank()-1, &fAtomID, 1, &req[1]);
         m_fAtomIDStartIndex = fAtomID;
         for (i = 0; i < nSize; ++i)
             m_vectUnitCell[i].ShiftAtomID(fAtomID);
 
         if( CKNMPIManager::GetCurrentRank() > 0 && CKNMPIManager::GetCurrentRank() < CKNMPIManager::GetTotalNodeCount() - 1)
         {
             fAtomID += CKNGeometricUnitCell::GetSubElementID();
             CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetCurrentRank()+1, &fAtomID, 1, &req[0]);
         }
         else if(CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() - 1)
         {
             fAtomID += CKNGeometricUnitCell::GetSubElementID();
             m_fTotalAtomCountinMPI = fAtomID;
         }
     }
 
     CKNMPIManager::BroadcastDouble(&m_fTotalAtomCountinMPI, 1, CKNMPIManager::GetTotalNodeCount() - 1);
 
     
     if( CKNMPIManager::IsRootRank() )
     {
         pSendBuffer = Serialize(floor(m_fAssignedCount[_X])-1);
         CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetCurrentRank() + 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
     }
     else
     {
         CKNMPIManager::ReceiveDoubleBufferSync(CKNMPIManager::GetCurrentRank() -1, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
         Deserialize(&m_vectPrevUnitCell, pReceiveBuffer, true);
 
         if(  CKNMPIManager::GetCurrentRank() != CKNMPIManager::GetTotalNodeCount() - 1)
         {
             pSendBuffer = Serialize(floor(m_fAssignedCount[_X])-1);
             CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetCurrentRank() + 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
         }
         else
         {   
             if( m_bConsiderBoundaryCondition[_X])
             {
                 pSendBuffer = Serialize(floor(m_fAssignedCount[_X])-2);
                 CKNMPIManager::SendDoubleBufferSync(0, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
             }
         }
     }
 
     if( m_bConsiderBoundaryCondition[_X] && CKNMPIManager::IsRootRank())
     {
         CKNMPIManager::ReceiveDoubleBufferSync(CKNMPIManager::GetTotalNodeCount() - 1, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
         Deserialize(&m_vectPrevUnitCell, pReceiveBuffer, true);
     }
     FREE_MEM(pSendBuffer);
 
     if(  CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() - 1 )
     {
         pSendBuffer = Serialize(0);
         CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetCurrentRank() - 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
     }
     else
     {
         CKNMPIManager::ReceiveDoubleBufferSync(CKNMPIManager::GetCurrentRank() + 1, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
         Deserialize(&m_vectNextUnitCell, pReceiveBuffer, false);
 
         if( !CKNMPIManager::IsRootRank())
         {
             pSendBuffer = Serialize(0);
             CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetCurrentRank() - 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
         }
         else
         {
             if( m_bConsiderBoundaryCondition[_X])
             {
                 pSendBuffer = Serialize(1);
                 CKNMPIManager::SendDoubleBufferSync(CKNMPIManager::GetTotalNodeCount() - 1, pSendBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[1]);
             }
         }
     }
 
     if(  CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() - 1 && m_bConsiderBoundaryCondition[_X])
     {
         CKNMPIManager::ReceiveDoubleBufferSync(0, pReceiveBuffer, (int)fSendingCount*UNITCELL_WRITING_BLOCK_SIZE*nAtomCountInCell, &req[0]);
         Deserialize(&m_vectNextUnitCell, pReceiveBuffer, false);
     }
 
     FREE_MEM(pSendBuffer);
     FREE_MEM(pReceiveBuffer);
 }

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bool CKNGeometricShape::FillUnitcell ( CKNCommandFileParser::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 103 of file KNGeometricShape.cpp.

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

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver(), CKNGeometricConstructionLaunch::LaunchingGeometricConstruction(), and CKNGeometricConstructionLaunch::LaunchingGeometricConstructionMPI().

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

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void CKNGeometricShape::FinalShape ( )

Finalize Shape variable.

Definition at line 249 of file KNGeometricShape.cpp.

References FreeUnitCellList().

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver(), and ~CKNGeometricShape().

 {
     FreeUnitCellList();
 }

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void CKNGeometricShape::FreeMapInfo ( LPNEIGHBOR_MAP_INFO lpMapInfo )

static

Release mapinfo data.

Parameters

lpMapInfo Atom map information

Definition at line 1043 of file KNGeometricShape.cpp.

References FREE_MEM, MAX_NEIGHBOR, 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, and NEIGHBOR_MAP_INFO::pNeighborMaterial.

Referenced by ConstructMapInfo(), CKNTBMS_Solver::FinalEvn(), and CKNGeometricConstructionLaunch::LaunchingGeometricConstruction().

 {
     unsigned int        i;
 
     FREE_MEM(lpMapInfo->pfID);
     FREE_MEM(lpMapInfo->pAtomType);
     FREE_MEM(lpMapInfo->pMaterialNumber);
     FREE_MEM(lpMapInfo->pDomainMaterialNumber);
     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]);
     }
 }

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void CKNGeometricShape::FreeUnitCellList ( )

private

Relase unitcell list.

Definition at line 220 of file KNGeometricShape.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();
 }

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CKNGeometricAtom * CKNGeometricShape::GetAtomByIndex ( double fID )

private

Get atom instance by ID.

Parameters

fID Atom ID

Returns: Atom instance pointer

Definition at line 677 of file KNGeometricShape.cpp.

References CKNGeometricAtom::IsPeriodicAtom(), and m_vectUnitCell.

Referenced by RefillPeriodicBinding().

 {
     CKNGeometricAtom                    *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;
 }

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double CKNGeometricShape::GetAtomStartID ( )

inline

Set total valid atom count in shape.

Definition at line 57 of file KNGeometricShape.h.

References m_fAtomIDStartIndex.

Referenced by CKNTBMS_Solver::AllocateCSR(), and CKNTBMS_Solver::Launching_TBMS_Solver().

57 { return m_fAtomIDStartIndex; };

CKNGeometricShape::m_fAtomIDStartIndex

double m_fAtomIDStartIndex

Start atom index in current Shape.

Definition: KNGeometricShape.h:76

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bool CKNGeometricShape::GetConsideringBoundaryCondition ( AXIS_DEFINE direction )

inline

Definition at line 42 of file KNGeometricShape.h.

References m_bConsiderBoundaryCondition.

42 { return m_bConsiderBoundaryCondition[direction]; };

CKNGeometricShape::m_bConsiderBoundaryCondition

bool m_bConsiderBoundaryCondition[3]

Bondary condition for each driection.

Definition: KNGeometricShape.h:72

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

private

Calculating Phase sign.

Parameters

fAtomPos	Atom coordination
fPeriodicAtomPos	Periodic atom coordination

Returns: sign of Phase

Definition at line 663 of file KNGeometricShape.cpp.

Referenced by RefillPeriodicBinding().

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

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MATERIAL_INDEX CKNGeometricShape::GetMaterialType ( )

inline

Definition at line 36 of file KNGeometricShape.h.

References m_MaterialType.

36 { return m_MaterialType; };

CKNGeometricShape::m_MaterialType

MATERIAL_INDEX m_MaterialType

Material type of shape.

Definition: KNGeometricShape.h:77

int CKNGeometricShape::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 136 of file KNGeometricShape.cpp.

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

Referenced by ArrangeUnitCell().

 {
     int                 nRtn = CKNGeometricAtom::NONE;
 
     if (0 == x && true == m_bConsiderBoundaryCondition[_X])
 #ifndef DISABLE_MPI_ROUTINE
         if( CKNMPIManager::IsRootRank() )
             nRtn |= CKNGeometricAtom::X_DIRECTION;
 #else //DISABLE_MPI_ROUTINE
         nRtn |= CKNGeometricAtom::X_DIRECTION;
 #endif //DISABLE_MPI_ROUTINE
 
     if (0 == y && true == m_bConsiderBoundaryCondition[_Y])
         nRtn |= CKNGeometricAtom::Y_DIRECTION;
 
     if (0 == z && true == m_bConsiderBoundaryCondition[_Z])
         nRtn |= CKNGeometricAtom::Z_DIRECTION;
 
     if (maxX - 1 == x && true == m_bConsiderBoundaryCondition[_X])
 #ifndef DISABLE_MPI_ROUTINE
         if( CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() -1 )
             nRtn |= CKNGeometricAtom::X_DIRECTION;
 #else //DISABLE_MPI_ROUTINE
         nRtn |= CKNGeometricAtom::X_DIRECTION;
 #endif //DISABLE_MPI_ROUTINE
 
     if (maxY - 1 == y && true == m_bConsiderBoundaryCondition[_Y])
         nRtn |= CKNGeometricAtom::Y_DIRECTION;
 
     if (maxZ - 1 == z && true == m_bConsiderBoundaryCondition[_Z])
         nRtn |= CKNGeometricAtom::Z_DIRECTION;
 
     return nRtn;
 }

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unsigned int CKNGeometricShape::GetShapeForm ( )

inline

Definition at line 39 of file KNGeometricShape.h.

References m_ShapeForm.

39 { return m_ShapeForm; };

CKNGeometricShape::m_ShapeForm

unsigned int m_ShapeForm

Shape form.

Definition: KNGeometricShape.h:71

std::vector<CKNGeometricAtom*>* CKNGeometricShape::GetSurfaceAtomList ( )

inline

Definition at line 60 of file KNGeometricShape.h.

Referenced by BuildNeighborInformation(), and CKNTBMS_Solver::Launching_TBMS_Solver().

60 { return &m_vectSurfaceAtom; };

CKNGeometricShape::m_vectSurfaceAtom

std::vector< CKNGeometricAtom * > m_vectSurfaceAtom

Definition: KNGeometricShape.h:81

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double CKNGeometricShape::GetTotalAtomCount ( )

inline

Definition at line 55 of file KNGeometricShape.h.

References m_fTotalAtomCountinMPI.

Referenced by CKNTBMS_Solver::AllocateCSR().

55 { return m_fTotalAtomCountinMPI;};

CKNGeometricShape::m_fTotalAtomCountinMPI

double m_fTotalAtomCountinMPI

Total valid atom count in shape.

Definition: KNGeometricShape.h:75

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void CKNGeometricShape::InitMapInfo ( LPNEIGHBOR_MAP_INFO lpMapInfo )

Intilize map info data.

Parameters

lpMapInfo Atom map information

Definition at line 1066 of file KNGeometricShape.cpp.

References NEIGHBOR_MAP_INFO::fItemCount, MAX_NEIGHBOR, NEIGHBOR_MAP_INFO::pAtomType, NEIGHBOR_MAP_INFO::pbPeriodicCondition, 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;
     }
 }

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void CKNGeometricShape::InitShape ( )

private

Initialize Shape variable.

Definition at line 228 of file KNGeometricShape.cpp.

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

Referenced by CKNGeometricShape().

 {
     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;
 }

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bool CKNGeometricShape::IsBackendFace ( )

inline

Set front face side mark to shape object.

Definition at line 48 of file KNGeometricShape.h.

References m_bBackendFace.

48 { return m_bBackendFace; };

CKNGeometricShape::m_bBackendFace

bool m_bBackendFace

Flag of back end face or not.

Definition: KNGeometricShape.h:74

bool CKNGeometricShape::IsFrontFace ( )

inline

Definition at line 46 of file KNGeometricShape.h.

References m_bFrontFace.

46 { return m_bFrontFace; };

CKNGeometricShape::m_bFrontFace

bool m_bFrontFace

Flag of front face or not.

Definition: KNGeometricShape.h:73

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

private

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 180 of file KNGeometricShape.cpp.

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

Referenced by ArrangeUnitCell().

 {
     bool            bRtn = false;
 
     if (0 == x && true == m_bConsiderBoundaryCondition[_X])
 #ifndef DISABLE_MPI_ROUTINE
     {
         if( CKNMPIManager::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( CKNMPIManager::GetCurrentRank() == CKNMPIManager::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;
 }

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void CKNGeometricShape::PeriodicUnitCellNumbering ( bool bXAxis = false )

Numbering to periodic unitcell.

Parameters

bXAxis Do operation to x axis or not

Definition at line 498 of file KNGeometricShape.cpp.

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

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver(), CKNGeometricConstructionLaunch::LaunchingGeometricConstruction(), and CKNGeometricConstructionLaunch::LaunchingGeometricConstructionMPI().

 {
     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 == CKNMPIManager::GetTotalNodeCount() )
                 {
                     FIND_TARGET_INDEX(targetCx, pfAssignIndex, m_fAssignedCount, _X);
                 }
                 else
                 {
                     if( 0 == pfAssignIndex[_X] && CKNMPIManager::IsRootRank())
                     {
                         targetCx = -1;
                         if( false == bXAxis)
                             continue;
                     }
                     else if (m_fAssignedCount[_X] - 1 == pfAssignIndex[_X] 
                     && CKNMPIManager::GetCurrentRank() == CKNMPIManager::GetTotalNodeCount() - 1)
                     {
                         targetCx = pfAssignIndex[_X]+1;
                         if( false == bXAxis)
                             continue;
                     }
                 }
 #endif //DISABLE_MPI_ROUTINE
             }
 
             fCopyIndex = CKNGeometricUnitCell::CalculatingIndex(targetCx, targetCy, targetCz, m_fAssignedCount);
 #ifndef DISABLE_MPI_ROUTINE
             if( 1 == CKNMPIManager::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
         }
     }
 }

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bool CKNGeometricShape::RefillPeriodicBinding	(	CKNMatrixOperation::CKNCSR *	pResult,
		CKNCommandFileParser::LPINPUT_CMD_PARAM	lpParam,
		LPNEIGHBOR_MAP_INFO	lpMapInfo,
		unsigned int	nRepeatIndex,
		double	fKValue[3]
	)

Applying phase to Hamiltonian.

Parameters

[out]	CKNMatrixOperation	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

Returns: Operatoin success return true, else return false

Definition at line 596 of file KNGeometricShape.cpp.

References CKNMatrixOperation::CKNCSR::AreaScalarMultiple(), ATOM_DEFAULT_INDEX, NEIGHBOR_MAP_INFO::fItemCount, GetAtomByIndex(), CKNGeometricCoordination::GetCoordination(), CKNGeometricAtom::GetCoordination(), CKNGeometricDirection::GetDirectionAll(), GetKPhaseSign(), CKNGeometricAtom::GetNeighborCoordination(), CKNGeometricAtom::GetNeighborPeriodicDirection(), CKNGeometricAtom::IsPeriodicCoupling(), m_shapDirection, ORBITALS, NEIGHBOR_MAP_INFO::pfID, NEIGHBOR_MAP_INFO::pfNeighbor, PI_VALUE, and CKNComplex::SetComplexNumber().

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver().

 {
     unsigned int                        i, j, k;
     double                              *pDirection = m_shapDirection.GetDirectionAll();
     double                              kTotal = 0;
     CKNComplex                          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;
         CKNGeometricAtom*       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 (CKNGeometricAtom::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))
             {
                 CKNGeometricCoordination    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));
 
                 pResult->AreaScalarMultiple(i * ORBITALS, ORBITALS, (unsigned int)fNeighborIndex[j] * ORBITALS, ORBITALS, calcuResult);
             }
         }
     }
 
     bRtn = true;
     return bRtn;
 }

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void CKNGeometricShape::RotateMatrix	(	CKNMatrixOperation::CKNDMatrix *	pMatrixNbr,
		CKNMatrixOperation::CKNDMatrix *	pMatrixResult,
		double	fDegree[2]
	)

private

Rotate matrix with calculated degree.

Parameters

pMatrixNbr	Source matrix
pMatrixResult	Rotated matrix
paramter	Geometric parameters

Definition at line 710 of file KNGeometricShape.cpp.

References CKNMatrixOperation::CKNDMatrix::BuildMatrixFirst(), CKNMatrixOperation::MMMul(), PHI_DEGREE, CKNMatrixOperation::CKNDMatrix::SetElement(), THETA_DEGREE, and CKNMatrixOperation::CKNDMatrix::TrnasPos().

 {
     CKNMatrixOperation::CKNDMatrix      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();
     CKNMatrixOperation::MMMul(&matrixRotate, pMatrixNbr, pMatrixResult);
     pMatrixResult->TrnasPos();
 }

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double * CKNGeometricShape::Serialize ( double fXLayer )

private

Serialize unitcells with specific later index to double array.

Parameters

fXLayer Target x layer index

Definition at line 1216 of file KNGeometricShape.cpp.

References _Y, _Z, CKNGeometricAtomFactory::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 = CKNGeometricAtomFactory::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;
 }

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bool CKNGeometricShape::SetAtomAndNeighborInformation ( CKNCommandFileParser::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 927 of file KNGeometricShape.cpp.

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver().

 {
     unsigned int                    i;
     CKNGeometricCoordination        coordination;
 
     CKNGeometricAtomFactory::InitAtomList();
     CKNGeometricAtomFactory::InitNeighborList();
 
     
     if (!strcmp(lpParam->szStructureType, CUBIC))
     {
         m_pUnitCellInfo = &m_UnitCellInfo_cubic;
         CKNGeometricAtom::SetNeighborNumber(6);
         lpParam->bNeedRotate = false;
     }
     else if (!strcmp(lpParam->szStructureType, ZB))
     {
         lpParam->bNeedRotate = true;
         m_pUnitCellInfo = &m_UnitCellInfo_zincblende;
         m_UnitCellInfo_zincblende.SetDireciton(lpParam->nDirectionSingle);
         CKNGeometricAtom::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(&CKNGeometricShape::m_rotationMatrix);
         }
     }
     else
         return false;
 
     for (i = 0; i < m_pUnitCellInfo->GetAnionCount(); ++i)
     {
         coordination = m_pUnitCellInfo->GetAtomCoordination(CKNGeometricAtom::A, i);
         CKNGeometricAtomFactory::SetAtomCoordination(CKNGeometricAtom::A,
             coordination.GetCoordination(_X),
             coordination.GetCoordination(_Y),
             coordination.GetCoordination(_Z));
     }
 
     for (i = 0; i < m_pUnitCellInfo->GetCationCount(); ++i)
     {
         coordination = m_pUnitCellInfo->GetAtomCoordination(CKNGeometricAtom::C, i);
         CKNGeometricAtomFactory::SetAtomCoordination(CKNGeometricAtom::C,
             coordination.GetCoordination(_X),
             coordination.GetCoordination(_Y),
             coordination.GetCoordination(_Z));
     }
 
     for (i = 0; i < (unsigned int)m_pUnitCellInfo->GetA2CNeighborCount(); ++i)
     {
         coordination = m_pUnitCellInfo->GetNeighborCoordination(CKNGeometricAtom::A2C, i);
         CKNGeometricAtomFactory::SetNeighborCoordination(CKNGeometricAtom::A2C,
             coordination.GetCoordination(_X),
             coordination.GetCoordination(_Y),
             coordination.GetCoordination(_Z));
 
     }
     
     for (i = 0; i < (unsigned int)m_pUnitCellInfo->GetC2ANeighborCount(); i++)
     {
         coordination = m_pUnitCellInfo->GetNeighborCoordination(CKNGeometricAtom::C2A, i);
         CKNGeometricAtomFactory::SetNeighborCoordination(CKNGeometricAtom::C2A,
             coordination.GetCoordination(_X),
             coordination.GetCoordination(_Y),
             coordination.GetCoordination(_Z));
     }
 
     CKNGeometricUnitCell::SetLength(lpParam->fUnitcellLength, m_pUnitCellInfo->GetUnitcCellSize());
     
     return true;
 }

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void CKNGeometricShape::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 KNGeometricShape.h.

References m_bBackendFace.

Referenced by CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

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

inline

Get bondary condition of shape.

Definition at line 43 of file KNGeometricShape.h.

References m_bConsiderBoundaryCondition.

Referenced by CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

43 { m_bConsiderBoundaryCondition[direction] = bConsider; };

CKNGeometricShape::m_bConsiderBoundaryCondition

bool m_bConsiderBoundaryCondition[3]

Bondary condition for each driection.

Definition: KNGeometricShape.h:72

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void CKNGeometricShape::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 58 of file KNGeometricShape.cpp.

References m_shapDirection, and CKNGeometricDirection::SetDirection().

Referenced by CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

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

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void CKNGeometricShape::SetFrontFace ( bool bFrontFace )

inline

Check is this front face side in MPI running enviroment.

Definition at line 47 of file KNGeometricShape.h.

References m_bFrontFace.

Referenced by CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

47 { m_bFrontFace = bFrontFace; };

CKNGeometricShape::m_bFrontFace

bool m_bFrontFace

Flag of front face or not.

Definition: KNGeometricShape.h:73

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void CKNGeometricShape::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 68 of file KNGeometricShape.cpp.

References _X, _Y, _Z, and m_fLength.

Referenced by CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

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

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bool CKNGeometricShape::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

Definition at line 1016 of file KNGeometricShape.cpp.

References ALLOC_WITH_NULL_INIT, MAX_NEIGHBOR, 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, 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, CKNGeometricAtom::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->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);
     }
 
     bRtn = true;
     return bRtn;
 }

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void CKNGeometricShape::SetMaterialType ( MATERIAL_INDEX type )

inline

Get maetrial typpe of shap.

Definition at line 37 of file KNGeometricShape.h.

References m_MaterialType.

Referenced by SetMaterialType(), CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

37 { m_MaterialType = type; };

CKNGeometricShape::m_MaterialType

MATERIAL_INDEX m_MaterialType

Material type of shape.

Definition: KNGeometricShape.h:77

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void CKNGeometricShape::SetMaterialType ( char * pszType )

Set maetrial type of shape.

Set maetrial type of shape

Parameters

pszType Material type information

Definition at line 78 of file KNGeometricShape.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);
 }

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void CKNGeometricShape::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 48 of file KNGeometricShape.cpp.

References m_originCoordination, and CKNGeometricCoordination::SetCoordination().

Referenced by CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

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

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void CKNGeometricShape::SetShapeForm ( unsigned int form )

inline

Get form type of shape.

Definition at line 40 of file KNGeometricShape.h.

References m_ShapeForm.

Referenced by SetShapeForm(), CKNGeometricConstructionLaunch::SetShapeInformation(), and SetShapeInformation().

40 { m_ShapeForm = form; };

CKNGeometricShape::m_ShapeForm

unsigned int m_ShapeForm

Shape form.

Definition: KNGeometricShape.h:71

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void CKNGeometricShape::SetShapeForm ( char * pszForm )

Get form type of shape.

Get form type of shape

Parameters

pszForm Shape form

Definition at line 91 of file KNGeometricShape.cpp.

References BOX_SHAPE, CYLINDER_SHAPE, and SetShapeForm().

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

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void CKNGeometricShape::SetShapeInformation	(	CKNGeometricShape &	shape,
		CKNCommandFileParser::LPINPUT_CMD_PARAM	lpParam
	)

static

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

Parameters

shape	Geometric Shape
lpParam	Input parameters parsing from command file

Definition at line 901 of file KNGeometricShape.cpp.

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

Referenced by CKNTBMS_Solver::Launching_TBMS_Solver().

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

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void CKNGeometricShape::SetTotalAtomCount ( double fTotalAtomCountinMPI )

inline

Get total valid atom count in shape.

Definition at line 56 of file KNGeometricShape.h.

References m_fTotalAtomCountinMPI.

56 { m_fTotalAtomCountinMPI = fTotalAtomCountinMPI;};

CKNGeometricShape::m_fTotalAtomCountinMPI

double m_fTotalAtomCountinMPI

Total valid atom count in shape.

Definition: KNGeometricShape.h:75

void CKNGeometricShape::ShiftAtomID ( double fShift )

Shift atom id in MPI running enviroment.

Parameters

fShift Increasing count of ID

Definition at line 1088 of file KNGeometricShape.cpp.

References m_vectUnitCell.

Referenced by ExchangeAtomInfoBetweenNode().

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

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Member Data Documentation

bool CKNGeometricShape::m_bBackendFace

private

Flag of back end face or not.

Definition at line 74 of file KNGeometricShape.h.

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

bool CKNGeometricShape::m_bConsiderBoundaryCondition[3]

private

Bondary condition for each driection.

Definition at line 72 of file KNGeometricShape.h.

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

bool CKNGeometricShape::m_bFrontFace

private

Flag of front face or not.

Definition at line 73 of file KNGeometricShape.h.

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

double CKNGeometricShape::m_fAssignedCount[3]

private

Unitcell assigend count in shape for each direction.

Definition at line 70 of file KNGeometricShape.h.

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

double CKNGeometricShape::m_fAtomIDStartIndex

private

Start atom index in current Shape.

Definition at line 76 of file KNGeometricShape.h.

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

double CKNGeometricShape::m_fLength[3]

private

Building Geometric part.

Length of shape

Definition at line 69 of file KNGeometricShape.h.

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

double CKNGeometricShape::m_fTotalAtomCountinMPI

private

Total valid atom count in shape.

Definition at line 75 of file KNGeometricShape.h.

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

MATERIAL_INDEX CKNGeometricShape::m_MaterialType

private

Material type of shape.

Definition at line 77 of file KNGeometricShape.h.

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

unsigned int CKNGeometricShape::m_nAtomFirstLayer

Get Surface atom list.

Building Hamiltonian part First layer information for sending to previous node

Definition at line 60 of file KNGeometricShape.h.

Referenced by ArrangeUnitCell(), InitShape(), and CKNTBMS_Solver::Launching_TBMS_Solver().

unsigned int CKNGeometricShape::m_nAtomLastLayer

Last layer information for sending to next node.

Definition at line 64 of file KNGeometricShape.h.

Referenced by ArrangeUnitCell(), InitShape(), and CKNTBMS_Solver::Launching_TBMS_Solver().

CKNGeometricCoordination CKNGeometricShape::m_originCoordination

private

Orign coordination of shape.

Definition at line 82 of file KNGeometricShape.h.

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

IKNGeometricUnitCellInfo * CKNGeometricShape::m_pUnitCellInfo

static

Unitcell information pointer for using in class internal.

Definition at line 108 of file KNGeometricShape.h.

Referenced by InitShape(), and SetAtomAndNeighborInformation().

CKNMatrixOperation::CKNDMatrix CKNGeometricShape::m_rotationMatrix

static

Rotation matrix for given direction.

Definition at line 109 of file KNGeometricShape.h.

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

CKNGeometricDirection CKNGeometricShape::m_shapDirection

private

Direction of shape.

Definition at line 83 of file KNGeometricShape.h.

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

unsigned int CKNGeometricShape::m_ShapeForm

private

Shape form.

Definition at line 71 of file KNGeometricShape.h.

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

CKNGeometricUnitCellInfo_cubic CKNGeometricShape::m_UnitCellInfo_cubic

static

Definition at line 107 of file KNGeometricShape.h.

Referenced by SetAtomAndNeighborInformation().

CKNGeometricUnitCellInfo_zincblende CKNGeometricShape::m_UnitCellInfo_zincblende

static

Definition at line 106 of file KNGeometricShape.h.

Referenced by SetAtomAndNeighborInformation().

std::vector<CKNGeometricUnitCell> CKNGeometricShape::m_vectNextUnitCell

private

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

Definition at line 80 of file KNGeometricShape.h.

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

std::vector<CKNGeometricUnitCell> CKNGeometricShape::m_vectPrevUnitCell

private

Front edge unit cell that copy from previous side node.

Definition at line 79 of file KNGeometricShape.h.

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

std::vector<CKNGeometricAtom*> CKNGeometricShape::m_vectSurfaceAtom

private

Definition at line 81 of file KNGeometricShape.h.

Referenced by FreeUnitCellList().

std::vector<CKNGeometricUnitCell> CKNGeometricShape::m_vectUnitCell

private

Array of unitcell in shape.

Definition at line 78 of file KNGeometricShape.h.

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

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

D:/For Doxygen/KNGeometricShape.h
D:/For Doxygen/KNGeometricShape.cpp

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