PmeAtomFiler Class Reference

#include <ComputePmeCUDAMgr.h>

Inheritance diagram for PmeAtomFiler:

Public Member Functions
	PmeAtomFiler ()
	PmeAtomFiler (CkMigrateMessage *)
	~PmeAtomFiler ()
void	fileAtoms (const int numAtoms, const CudaAtom *atoms, Lattice &lattice, const PmeGrid &pmeGrid, const int pencilIndexY, const int pencilIndexZ, const int ylo, const int yhi, const int zlo, const int zhi)
int	getNumAtoms (int p)
int *	getAtomIndex (int p)

Detailed Description

Definition at line 400 of file ComputePmeCUDAMgr.h.

Constructor & Destructor Documentation

PmeAtomFiler() [1/2]

PmeAtomFiler::PmeAtomFiler

(

)

Definition at line 108 of file ComputePmeCUDAMgr.C.

                           {
  for (int p=0;p < 10;p++) {
    pencil[p] = NULL;
    pencilCapacity[p] = 0;
  }  
}

PmeAtomFiler() [2/2]

PmeAtomFiler::PmeAtomFiler

(

CkMigrateMessage *

m

)

Definition at line 114 of file ComputePmeCUDAMgr.C.

                                              {
  for (int p=0;p < 10;p++) {
    pencil[p] = NULL;
    pencilCapacity[p] = 0;
  }
}

~PmeAtomFiler()

PmeAtomFiler::~PmeAtomFiler

(

)

Definition at line 120 of file ComputePmeCUDAMgr.C.

                            {
  for (int p=0;p < 10;p++) {
    if (pencil[p] != NULL) delete [] pencil[p];
  }
}

Member Function Documentation

fileAtoms()

void PmeAtomFiler::fileAtoms	(	const int	numAtoms,
		const CudaAtom *	atoms,
		Lattice &	lattice,
		const PmeGrid &	pmeGrid,
		const int	pencilIndexY,
		const int	pencilIndexZ,
		const int	ylo,
		const int	yhi,
		const int	zlo,
		const int	zhi
	)

Definition at line 132 of file ComputePmeCUDAMgr.C.

References Lattice::a_r(), Lattice::b_r(), Lattice::c_r(), PmeRealSpaceCompute::calcGridCoord(), DebugM, endi(), getPencilIndexY(), getPencilIndexZ(), PmeGrid::K1, PmeGrid::K2, PmeGrid::K3, PmeGrid::order, Vector::x, Vector::y, PmeGrid::yBlocks, Vector::z, and PmeGrid::zBlocks.

Referenced by ComputePmeCUDADevice::recvAtoms().

                                                                                                              {
  DebugM(2, "PmeAtomFiler::fileAtoms\n" << endi);
  // Make sure there's enough room in the pencil arrays
  for (int p=0;p < 10;p++) {
    if (pencil[p] != NULL && pencilCapacity[p] < numAtoms) {
      delete [] pencil[p];
      pencil[p] = NULL;
      pencilCapacity[p] = 0;
    }
    if (pencil[p] == NULL) {
      int newSize = (int)(numAtoms*1.5);
      pencil[p] = new int[newSize];
      pencilCapacity[p] = newSize;
    }
    pencilSize[p] = 0;
  }

  const float recip11 = lattice.a_r().x;
  const float recip22 = lattice.b_r().y;
  const float recip33 = lattice.c_r().z;
  const int order1 = pmeGrid.order - 1;
  const int K1 = pmeGrid.K1;
  const int K2 = pmeGrid.K2;
  const int K3 = pmeGrid.K3;
  const int yBlocks = pmeGrid.yBlocks;
  const int zBlocks = pmeGrid.zBlocks;

  for (int i=0;i < numAtoms;i++) {
    float frx, fry, frz;
    // PmeRealSpaceCompute::calcGridCoord(atoms[i].uix, atoms[i].uiy, atoms[i].uiz,
    //   K1, K2, K3, frx, fry, frz);
    PmeRealSpaceCompute::calcGridCoord(atoms[i].x, atoms[i].y, atoms[i].z, K1, K2, K3, frx, fry, frz);
    // Charge is spread in the region [y0 ... y0+order-1] x [z0 ... z0+order-1]
    int y0 = (int)fry;
    int z0 = (int)frz;
    if (y0 < 0 || y0 >= K2 || z0 < 0 || z0 >= K3) {
      // Add to "Stray pencil" and skip to next atom
      pencil[9][pencilSize[9]++] = i;
      continue;
      // fprintf(stderr, "%lf %lf %lf\n", atoms[i].x, atoms[i].y, atoms[i].z);
      // NAMD_bug("PmeAtomFiler::fileAtoms, charge out of bounds");
    }
    // Calculate pencil index for the four corners of the order X order area
    // The corners determine the pencil indices for this atom.
    int occupied = 0;
    int plist[4];
#pragma unroll
    for (int j=0;j < 4;j++) {

      int py = getPencilIndexY(pmeGrid, (y0 + (j%2)*order1) % K2) - pencilIndexY;
      if (py < ylo) py += yBlocks;
      if (py > yhi) py -= yBlocks;

      int pz = getPencilIndexZ(pmeGrid, (z0 + (j/2)*order1) % K3) - pencilIndexZ;
      if (pz < zlo) pz += zBlocks;
      if (pz > zhi) pz -= zBlocks;

      if (py < ylo || py > yhi || pz < zlo || pz > zhi) {
        // Add to "Stray pencil" and skip to next atom
        pencil[9][pencilSize[9]++] = i;
        goto breakjloop;
        // fprintf(stderr, "py %d [%d ... %d] pz %d [%d ... %d]\n", pz, zlo, zhi);
        // NAMD_bug("PmeAtomFiler::fileAtoms, py,pz outside bounds");
      }
      // p = 0,1,2,3,4,5,6,7,8 (maximum range)
      plist[j] = (py-ylo) + (pz-zlo)*3;
    }

#pragma unroll
    for (int j=0;j < 4;j++) {
      int p = plist[j];
      // pbit = 0, 2, 4, 8, 16, 32, 64, 128, 256
      int pbit = (1 << p);
      if (!(occupied & pbit)) {
        pencil[p][pencilSize[p]++] = i;
        occupied |= pbit;
      }
    }

breakjloop:
    continue;
  }

}

getAtomIndex()

int* PmeAtomFiler::getAtomIndex ( int  p )

inline

Definition at line 410 of file ComputePmeCUDAMgr.h.

Referenced by ComputePmeCUDADevice::recvAtoms().

{return pencil[p];}

getNumAtoms()

int PmeAtomFiler::getNumAtoms ( int  p )

inline

Definition at line 409 of file ComputePmeCUDAMgr.h.

Referenced by ComputePmeCUDADevice::recvAtoms().

{return pencilSize[p];}

---

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

• ComputePmeCUDAMgr.h
• ComputePmeCUDAMgr.C