PmeAtomStorage Class Reference

#include <ComputePmeCUDAMgr.h>

Inheritance diagram for PmeAtomStorage:

Public Member Functions
	PmeAtomStorage (const bool useIndex)
virtual	~PmeAtomStorage ()
int	addAtoms (const int natom, const CudaAtom *src, const std::vector< float *> &lambdaArrays)
int	addAtomsWithIndex (const int natom, const CudaAtom *src, const int *index, const std::vector< float *> &lambdaArrays)
void	finish ()
void	clear ()
CudaAtom *	getAtoms ()
float *	getAtomElecFactors (unsigned int iGrid)
void	setupAlch (const SimParameters &simParams)
int *	getPatchPos ()
int	getNumPatches ()
int	getNumAtoms ()
int *	getAtomIndex ()

Protected Attributes
CudaAtom *	atom
int *	atomIndex
CudaAtom *	overflowAtom
int *	overflowAtomIndex
std::vector< float * >	atomElecFactorArrays
std::vector< float * >	overflowAtomElecFactorArrays
std::vector< int >	overflowAtomElecFactorCapacities
std::vector< bool >	enabledGrid
unsigned int	totalFactorArrays
bool	alchOn
bool	alchFepOn
bool	alchDecouple

Detailed Description

Definition at line 25 of file ComputePmeCUDAMgr.h.

Constructor & Destructor Documentation

PmeAtomStorage()

PmeAtomStorage::PmeAtomStorage ( const bool  useIndex )

inline

Definition at line 27 of file ComputePmeCUDAMgr.h.

References alchDecouple, alchFepOn, alchOn, atom, atomElecFactorArrays, atomIndex, overflowAtom, overflowAtomElecFactorArrays, overflowAtomElecFactorCapacities, overflowAtomIndex, and totalFactorArrays.

                                      : useIndex(useIndex) {
    numAtoms = 0;
    atomCapacity = 0;
    atom = NULL;
    atomIndexCapacity = 0;
    atomIndex = NULL;
    overflowStart = 0;
    overflowEnd = 0;
    overflowAtomCapacity = 0;
    overflowAtom = NULL;
    overflowAtomIndexCapacity = 0;
    overflowAtomIndex = NULL;
    totalFactorArrays = 0;
    atomElecFactorArrays = std::vector<float*>(0);
    overflowAtomElecFactorArrays = std::vector<float*>(0);
    overflowAtomElecFactorCapacities = std::vector<int>(0);
    alchOn = false;
    alchFepOn = false;
    alchDecouple = false;
    lock_ = CmiCreateLock();
  }

~PmeAtomStorage()

virtual PmeAtomStorage::~PmeAtomStorage ( )

inlinevirtual

Definition at line 48 of file ComputePmeCUDAMgr.h.

                            {
    CmiDestroyLock(lock_);
  }

Member Function Documentation

addAtoms()

int PmeAtomStorage::addAtoms ( const int  natom, const CudaAtom *  src, const std::vector< float *> &  lambdaArrays  )

inline

Definition at line 52 of file ComputePmeCUDAMgr.h.

                                                                                            {
    return addAtoms_(natom, src, NULL, lambdaArrays);
  }

addAtomsWithIndex()

int PmeAtomStorage::addAtomsWithIndex ( const int  natom, const CudaAtom *  src, const int *  index, const std::vector< float *> &  lambdaArrays  )

inline

Definition at line 56 of file ComputePmeCUDAMgr.h.

                                                                                                                       {
    return addAtoms_(natom, src, index, lambdaArrays);
  }

clear()

void PmeAtomStorage::clear ( )

inline

Definition at line 87 of file ComputePmeCUDAMgr.h.

               {
    patchPos.clear();
    numAtoms = 0;    
  }

finish()

void PmeAtomStorage::finish ( )

inline

Definition at line 62 of file ComputePmeCUDAMgr.h.

References alchOn, atom, atomElecFactorArrays, atomIndex, enabledGrid, overflowAtom, overflowAtomElecFactorArrays, overflowAtomIndex, and totalFactorArrays.

                {
    if (overflowEnd-overflowStart > 0) {
      resize_((void **)&atom, numAtoms, atomCapacity, sizeof(CudaAtom));
      if (useIndex) resize_((void **)&atomIndex, numAtoms, atomIndexCapacity, sizeof(int));
      if (alchOn) {
        for (unsigned int i = 0; i < totalFactorArrays; ++i) {
          if (enabledGrid[i] == true)
            resize_((void **)&(atomElecFactorArrays[i]), numAtoms, overflowAtomCapacity, sizeof(float));
        }
      }
      memcpy_(atom+overflowStart, overflowAtom, (overflowEnd - overflowStart)*sizeof(CudaAtom));
      if (useIndex) memcpy_(atomIndex+overflowStart, overflowAtomIndex, (overflowEnd - overflowStart)*sizeof(int));
      if (alchOn) {
        for (unsigned int i = 0; i < totalFactorArrays; ++i) {
          if (enabledGrid[i] == true)
            memcpy_(atomElecFactorArrays[i]+overflowStart, overflowAtomElecFactorArrays[i], (overflowEnd - overflowStart)*sizeof(float));
        }
      }
      overflowStart = 0;
      overflowEnd = 0;
    }
  }

getAtomElecFactors()

float* PmeAtomStorage::getAtomElecFactors ( unsigned int  iGrid )

inline

Definition at line 98 of file ComputePmeCUDAMgr.h.

References atomElecFactorArrays.

                                                {
    return atomElecFactorArrays[iGrid];
  }

getAtomIndex()

int* PmeAtomStorage::getAtomIndex ( )

inline

Definition at line 142 of file ComputePmeCUDAMgr.h.

References atomIndex, and NAMD_bug().

                      {
    if (!useIndex)
      NAMD_bug("PmeAtomStorage::getAtomIndex, no indexing enabled");
    return atomIndex;
  }

getAtoms()

CudaAtom* PmeAtomStorage::getAtoms ( )

inline

Definition at line 93 of file ComputePmeCUDAMgr.h.

References atom.

                       {
    return atom;
  }

getNumAtoms()

int PmeAtomStorage::getNumAtoms ( )

inline

Definition at line 138 of file ComputePmeCUDAMgr.h.

                    {
    return numAtoms;
  }

getNumPatches()

int PmeAtomStorage::getNumPatches ( )

inline

Definition at line 134 of file ComputePmeCUDAMgr.h.

                      {
    return patchPos.size();
  }

getPatchPos()

int* PmeAtomStorage::getPatchPos ( )

inline

Definition at line 130 of file ComputePmeCUDAMgr.h.

                     {
    return patchPos.data();
  }

setupAlch()

void PmeAtomStorage::setupAlch ( const SimParameters &  simParams )

inline

Definition at line 101 of file ComputePmeCUDAMgr.h.

References alchDecouple, alchFepOn, alchOn, atomElecFactorArrays, enabledGrid, NUM_GRID_MAX, overflowAtomElecFactorArrays, overflowAtomElecFactorCapacities, simParams, and totalFactorArrays.

                                                 {
    alchOn = simParams.alchOn;
    alchFepOn = simParams.alchFepOn;
    alchDecouple = simParams.alchDecouple;
    if (alchOn) {
      enabledGrid.resize(NUM_GRID_MAX, false);
      totalFactorArrays = 2;
      enabledGrid[0] = true;
      enabledGrid[1] = true;
      if (alchDecouple) {
        totalFactorArrays = 4;
        enabledGrid[2] = true;
        enabledGrid[3] = true;
      }
      if (bool(simParams.alchElecLambdaStart)) {
        totalFactorArrays = 5;
        enabledGrid[4] = true;
      }
      if (simParams.alchThermIntOn) {
        totalFactorArrays = 5;
        enabledGrid[4] = true;
      }
      atomElecFactorArrays.assign(totalFactorArrays, NULL);
      overflowAtomElecFactorArrays.assign(totalFactorArrays, NULL);
      overflowAtomElecFactorCapacities.assign(totalFactorArrays, 0);
    }
  }

Member Data Documentation

alchDecouple

bool PmeAtomStorage::alchDecouple

protected

Definition at line 165 of file ComputePmeCUDAMgr.h.

Referenced by PmeAtomStorage(), and setupAlch().

alchFepOn

bool PmeAtomStorage::alchFepOn

protected

Definition at line 164 of file ComputePmeCUDAMgr.h.

Referenced by PmeAtomStorage(), and setupAlch().

alchOn

bool PmeAtomStorage::alchOn

protected

Definition at line 163 of file ComputePmeCUDAMgr.h.

Referenced by finish(), PmeAtomStorage(), setupAlch(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

atom

CudaAtom* PmeAtomStorage::atom

protected

Definition at line 150 of file ComputePmeCUDAMgr.h.

Referenced by finish(), getAtoms(), PmeAtomStorage(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

atomElecFactorArrays

std::vector<float*> PmeAtomStorage::atomElecFactorArrays

protected

Definition at line 158 of file ComputePmeCUDAMgr.h.

Referenced by finish(), getAtomElecFactors(), PmeAtomStorage(), setupAlch(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

atomIndex

int* PmeAtomStorage::atomIndex

protected

Definition at line 152 of file ComputePmeCUDAMgr.h.

Referenced by finish(), getAtomIndex(), PmeAtomStorage(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

enabledGrid

std::vector<bool> PmeAtomStorage::enabledGrid

protected

Definition at line 161 of file ComputePmeCUDAMgr.h.

Referenced by finish(), and setupAlch().

overflowAtom

CudaAtom* PmeAtomStorage::overflowAtom

protected

Definition at line 154 of file ComputePmeCUDAMgr.h.

Referenced by finish(), PmeAtomStorage(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

overflowAtomElecFactorArrays

std::vector<float*> PmeAtomStorage::overflowAtomElecFactorArrays

protected

Definition at line 159 of file ComputePmeCUDAMgr.h.

Referenced by finish(), PmeAtomStorage(), setupAlch(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

overflowAtomElecFactorCapacities

std::vector<int> PmeAtomStorage::overflowAtomElecFactorCapacities

protected

Definition at line 160 of file ComputePmeCUDAMgr.h.

Referenced by PmeAtomStorage(), and setupAlch().

overflowAtomIndex

int* PmeAtomStorage::overflowAtomIndex

protected

Definition at line 156 of file ComputePmeCUDAMgr.h.

Referenced by finish(), PmeAtomStorage(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

totalFactorArrays

unsigned int PmeAtomStorage::totalFactorArrays

protected

Definition at line 162 of file ComputePmeCUDAMgr.h.

Referenced by finish(), PmeAtomStorage(), setupAlch(), CpuPmeAtomStorage::~CpuPmeAtomStorage(), and CudaPmeAtomStorage::~CudaPmeAtomStorage().

---

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

• ComputePmeCUDAMgr.h