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)
int	addAtomsWithIndex (const int natom, const CudaAtom *src, const int *index)
void	finish ()
void	clear ()
CudaAtom *	getAtoms ()
int *	getPatchPos ()
int	getNumPatches ()
int	getNumAtoms ()
int *	getAtomIndex ()

Protected Attributes
CudaAtom *	atom
int *	atomIndex
CudaAtom *	overflowAtom
int *	overflowAtomIndex

Detailed Description

Definition at line 24 of file ComputePmeCUDAMgr.h.

Constructor & Destructor Documentation

PmeAtomStorage::PmeAtomStorage ( const bool  useIndex )

inline

Definition at line 26 of file ComputePmeCUDAMgr.h.

References atom, atomIndex, overflowAtom, and overflowAtomIndex.

                                      : useIndex(useIndex) {
    numAtoms = 0;
    atomCapacity = 0;
    atom = NULL;
    atomIndexCapacity = 0;
    atomIndex = NULL;
    overflowStart = 0;
    overflowEnd = 0;
    overflowAtomCapacity = 0;
    overflowAtom = NULL;
    overflowAtomIndexCapacity = 0;
    overflowAtomIndex = NULL;
    lock_ = CmiCreateLock();
  }

virtual PmeAtomStorage::~PmeAtomStorage ( )

inlinevirtual

Definition at line 40 of file ComputePmeCUDAMgr.h.

                            {
    CmiDestroyLock(lock_);
  }

Member Function Documentation

int PmeAtomStorage::addAtoms ( const int  natom, const CudaAtom *  src  )

inline

Definition at line 44 of file ComputePmeCUDAMgr.h.

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

int PmeAtomStorage::addAtomsWithIndex ( const int  natom, const CudaAtom *  src, const int *  index  )

inline

Definition at line 48 of file ComputePmeCUDAMgr.h.

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

void PmeAtomStorage::clear ( )

inline

Definition at line 67 of file ComputePmeCUDAMgr.h.

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

void PmeAtomStorage::finish ( )

inline

Definition at line 54 of file ComputePmeCUDAMgr.h.

References atom, atomIndex, overflowAtom, and overflowAtomIndex.

                {
    if (overflowEnd-overflowStart > 0) {
      resize_((void **)&atom, numAtoms, atomCapacity, sizeof(CudaAtom));
      if (useIndex) resize_((void **)&atomIndex, numAtoms, atomIndexCapacity, sizeof(int));
      memcpy_(atom+overflowStart, overflowAtom, (overflowEnd - overflowStart)*sizeof(CudaAtom));
      if (useIndex) memcpy_(atomIndex+overflowStart, overflowAtomIndex, (overflowEnd - overflowStart)*sizeof(int));
      overflowStart = 0;
      overflowEnd = 0;
    }
  }

int* PmeAtomStorage::getAtomIndex ( )

inline

Definition at line 90 of file ComputePmeCUDAMgr.h.

References atomIndex, and NAMD_bug().

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

CudaAtom* PmeAtomStorage::getAtoms ( )

inline

Definition at line 73 of file ComputePmeCUDAMgr.h.

References atom.

                       {
    return atom;
  }

int PmeAtomStorage::getNumAtoms ( )

inline

Definition at line 86 of file ComputePmeCUDAMgr.h.

                    {
    return numAtoms;
  }

int PmeAtomStorage::getNumPatches ( )

inline

Definition at line 82 of file ComputePmeCUDAMgr.h.

                      {
    return patchPos.size();
  }

int* PmeAtomStorage::getPatchPos ( )

inline

Definition at line 78 of file ComputePmeCUDAMgr.h.

                     {
    return patchPos.data();
  }

Member Data Documentation

CudaAtom* PmeAtomStorage::atom

protected

Definition at line 98 of file ComputePmeCUDAMgr.h.

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

int* PmeAtomStorage::atomIndex

protected

Definition at line 100 of file ComputePmeCUDAMgr.h.

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

CudaAtom* PmeAtomStorage::overflowAtom

protected

Definition at line 102 of file ComputePmeCUDAMgr.h.

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

int* PmeAtomStorage::overflowAtomIndex

protected

Definition at line 104 of file ComputePmeCUDAMgr.h.

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

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

• ComputePmeCUDAMgr.h