LjPmeMgr Class Reference

#include <LjPmeMgr.h>

Public Member Functions
	LjPmeMgr ()
	~LjPmeMgr ()
void	initialize (const SimParameters *simParams, const int nAtoms)
void	computeLongRange (const double *ljPmeCoord, const Lattice &lattice, const double &alphaLJ, double *force, double &energy, double virial[][3], bool doEnergy)
void	optimizeFFT ()
void	setScaledCoordinates (const double *refPos, const Lattice &lattice)
void	gridCalculation (const double &alpha, const Lattice &lattice)
double	selfCompute (const double &alphaLJ)

Detailed Description

Definition at line 48 of file LjPmeMgr.h.

Constructor & Destructor Documentation

LjPmeMgr()

LjPmeMgr::LjPmeMgr ( )

inline

Definition at line 50 of file LjPmeMgr.h.

             : myRealSpace(0), myKSpace(0), dataArr(0), qGrid(0),
          q_arr(0), f_arr(0), fz_arr(0) {
    setSelf = false;
    initialized = false;
    numAtoms = 0;
  }

~LjPmeMgr()

LjPmeMgr::~LjPmeMgr

(

)

Definition at line 69 of file LjPmeMgr.C.

                    {
  setSelf = false;
  initialized = false;
  if (myRealSpace) delete myRealSpace;
  if (myKSpace) delete myKSpace;
  if (dataArr) delete [] dataArr;
  if (qGrid) delete [] qGrid;
  if (f_arr) delete [] f_arr;
  if (fz_arr) delete [] fz_arr;
  if (work) delete [] work;

  for (int i = 0; i < fsize; ++i) {
    if (q_arr[i]) {
      delete [] q_arr[i];
    }
  }
}

Member Function Documentation

computeLongRange()

void LjPmeMgr::computeLongRange	(	const double *	ljPmeCoord,
		const Lattice &	lattice,
		const double &	alphaLJ,
		double *	force,
		double &	energy,
		double	virial[][3],
		bool	doEnergy
	)

Definition at line 157 of file LjPmeMgr.C.

References LjPmeRealSpace::compute_scaledForces(), LjPmeGrid::dim3, LjPmeRealSpace::fill_charges(), gridCalculation(), selfCompute(), and setScaledCoordinates().

Referenced by LjPmeCompute::computeLJpotential().

                       {
  for (int i = 0; i < fsize; ++i) {
    if (q_arr[i]) {
      memset((void *)(q_arr[i]), 0, myGrid.dim3 * sizeof(float));
    }
  }
  //memset((void *)qGrid, 0, qsize * sizeof(float)); // Do I need this?
  memset((void *)f_arr, 0, fsize * sizeof(char));
  memset((void *)fz_arr, 0, myGrid.dim3 * sizeof(char));
  recipEnergy = 0.0;
  for(int i = 0; i < 6; i++) {
    recipVirial[i] = 0.0;
  }

  // Store the charge and scaled coordinates in dataArr buffer
  this->setScaledCoordinates(ljPmeCoord, lattice);
  // Compute and store the self term
  if(!setSelf) {
    selfEnergy = this->selfCompute(alphaLJ);
    setSelf = true;
  }
  // Split charges into the grid
  myRealSpace->fill_charges(q_arr, f_arr, fz_arr, dataArr);
  this->gridCalculation(alphaLJ, lattice);
  myRealSpace->compute_scaledForces(q_arr, dataArr, force, lattice);

  // Add energy and virial
  if(doEnergy) {
    energy += recipEnergy + selfEnergy;
    virial[0][0] += recipVirial[0];
    virial[0][1] += recipVirial[1];
    virial[0][2] += recipVirial[2];
    virial[1][0] += recipVirial[1];
    virial[1][1] += recipVirial[3];
    virial[1][2] += recipVirial[4];
    virial[2][0] += recipVirial[2];
    virial[2][1] += recipVirial[4];
    virial[2][2] += recipVirial[5];
  }
}

gridCalculation()

void LjPmeMgr::gridCalculation	(	const double &	alpha,
		const Lattice &	lattice
	)

Calculates and return the self-energy term for LJ-PME

Definition at line 250 of file LjPmeMgr.C.

References LjPmeKSpace::compute_energy(), LjPmeGrid::dim2, LjPmeGrid::dim3, LjPmeGrid::K1, LjPmeGrid::K2, and NAMD_die().

Referenced by computeLongRange().

{
  // place compatibility guards around function until we get FFTW3 working
#ifdef NAMD_FFTW_3
  NAMD_die("LJPMESerial requires FFTW 2");
#else
  // Part 1:
  int i, j, k = 0;
  for (i = 0; i < myGrid.K1 * myGrid.K2; i++) {
    for (j = 0; j < myGrid.dim3; j++) {
      qGrid[k++] = q_arr[i][j];
    }
  }
  #ifdef NAMD_FFTW
  #ifdef NAMD_FFTW_3
  fftwf_execute(forward_plan_yz);
  #else
  rfftwnd_real_to_complex(forward_plan_yz, myGrid.K1,
                          (fftw_real *)qGrid, 1, myGrid.dim2 * myGrid.dim3,
                          0, 0, 0);
  #endif
  #endif

  // Part2:
  int zdim = myGrid.dim3;
  int ny = myGrid.dim2;

  // finish forward FFT (x dimension)
  #ifdef NAMD_FFTW
  #ifdef NAMD_FFTW_3
  fftwf_execute(forward_plan_x);
  #else
  fftw(forward_plan_x, ny * zdim / 2, (fftw_complex *)qGrid,
       ny * zdim / 2, 1, work, 1, 0);
  #endif
  #endif

  // Calculate energy and virial
  double tempVir[6];
  recipEnergy += myKSpace->compute_energy(qGrid, lattice, alpha, tempVir);
  for(i = 0; i < 6; i++) {
    recipVirial[i] += tempVir[i];
  }

  #ifdef NAMD_FFTW
  #ifdef NAMD_FFTW_3
  fftwf_execute(backward_plan_x);
  #else
  // start backward FFT (x dimension)
  fftw(backward_plan_x, ny * zdim / 2, (fftw_complex *)qGrid,
       ny * zdim / 2, 1, work, 1, 0);
  #endif
  #endif

  // Part 3:
  #ifdef NAMD_FFTW
  #ifdef NAMD_FFTW_3
  fftwf_execute(backward_plan_yz);
  #else
  rfftwnd_complex_to_real(backward_plan_yz, myGrid.K1,
                          (fftw_complex *)qGrid, 1, myGrid.dim2 * myGrid.dim3 / 2,
                          0, 0, 0);
  #endif
  #endif
  k = 0;
  for (i = 0; i < myGrid.K1 * myGrid.K2; i++) {
    for (j = 0; j < myGrid.dim3; j++) {
      q_arr[i][j] = qGrid[k++];
    }
  }
#endif
}

initialize()

void LjPmeMgr::initialize	(	const SimParameters *	simParams,
		const int	nAtoms
	)

Calculate and add force and energy for reciprocal LJ-PME

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 14 of file LjPmeMgr.C.

References LjPmeGrid::block1, LjPmeGrid::block2, LjPmeGrid::dim2, LjPmeGrid::dim3, LjPmeGrid::K1, LjPmeGrid::K2, LjPmeGrid::K3, NAMD_die(), optimizeFFT(), LjPmeGrid::order, and simParams.

Referenced by LjPmeCompute::initialize().

                                                                          {
#if defined(NAMD_FFTW_3) || ! defined(NAMD_FFTW)
  NAMD_die("LJPMESerial requires FFTW 2");
#endif
  if (initialized) {
                NAMD_die("LjPmeMgr has already been initialized!");
  }
  int numRecipPes = 1;
  selfEnergy = recipEnergy = 0.0;
  setSelf = false;
  numAtoms = nAtoms;
  // Store grid informations
  myGrid.K1 = simParams->LJPMEGridSizeX;
  myGrid.K2 = simParams->LJPMEGridSizeY;
  myGrid.K3 = simParams->LJPMEGridSizeZ;
  myGrid.order = simParams->LJPMEInterpOrder;
  myGrid.dim2 = myGrid.K2;
  myGrid.dim3 = 2 * (myGrid.K3 / 2 + 1);
  myGrid.block1 = (myGrid.K1 + numRecipPes - 1) / numRecipPes;
  myGrid.block2 = (myGrid.K2 + numRecipPes - 1) / numRecipPes;

  // Allocate memory
  myKSpace = new LjPmeKSpace(myGrid);
  myRealSpace = new LjPmeRealSpace(myGrid, numAtoms);
  dataArr = new double[4*numAtoms];
  if (dataArr == 0) NAMD_die("can't allocate LJ-PME Manager dataArr buffer");

  qsize = myGrid.K1 * myGrid.dim2 * myGrid.dim3;
  fsize = myGrid.K1 * myGrid.dim2;
  q_arr = new float *[fsize];
  if (q_arr == 0) NAMD_die("can't allocate LJ-PME Manager q_arr buffer");
  memset((void *)q_arr, 0, fsize * sizeof(float *));

  // kludge so we won't segfault
  for (int i = 0; i < fsize; i++)
  {
    q_arr[i] = new float[myGrid.dim3];
    if (q_arr[i] == 0) NAMD_die("can't allocate LJ-PME Manager q_arr[i] buffer");
    memset((void *)q_arr[i], 0, myGrid.dim3 * sizeof(float));
  }
  // end kludge

  f_arr = new char[fsize];
  if (f_arr == 0) NAMD_die("can't allocate LJ-PME Manager f_arr buffer");
  fz_arr = new char[myGrid.dim3];
  if (fz_arr == 0) NAMD_die("can't allocate LJ-PME Manager fz_arr buffer");

  qGrid = new float[qsize];
  if (qGrid == 0) NAMD_die("can't allocate LJ-PME Manager qGrid buffer");

  this->optimizeFFT();
  memset((void *)qGrid, 0, qsize * sizeof(float));
  initialized = true;
}

optimizeFFT()

void LjPmeMgr::optimizeFFT

(

)

Store the charge and scaled coordinates into dataArr buffer

Definition at line 87 of file LjPmeMgr.C.

References LjPmeGrid::dim2, LjPmeGrid::dim3, endi(), iINFO(), iout, LjPmeGrid::K1, LjPmeGrid::K2, LjPmeGrid::K3, and NAMD_die().

Referenced by initialize().

                           {
  int n[3];
  n[0] = myGrid.K1;
  n[1] = myGrid.K2;
  n[2] = myGrid.K3;
  /*
  *  see if using FFTW_ESTIMATE makes start up faster
  */
  #ifdef NAMD_FFTW
  #ifdef NAMD_FFTW_3
  // place compatibility guards until we get FFTW3 working
#if 0
  work = new fftwf_complex[n[0]];

  iout << iINFO << "Optimizing 4 LJ-PME FFT steps.  1..." << endi;
  forward_plan_yz = fftwf_plan_many_dft_r2c(2, n+1, 
                myGrid.K1, qGrid, NULL, 1, myGrid.dim2 * myGrid.dim3,
                (fftwf_complex *)qGrid, NULL, 1, 
                myGrid.dim2 * (myGrid.dim3 / 2), FFTW_ESTIMATE);

  iout << " 2..." << endi;
  int zdim = myGrid.dim3;
  int xStride=myGrid.dim2 *( myGrid.dim3 / 2);
  forward_plan_x = fftwf_plan_many_dft(1, n, xStride,
                                                (fftwf_complex *)qGrid, NULL, xStride, 1,
                                                (fftwf_complex *)qGrid, NULL, xStride, 1,
                                                FFTW_FORWARD, FFTW_ESTIMATE);

  iout << " 3..." << endi;          
  backward_plan_x = fftwf_plan_many_dft(1, n, xStride,
                                                (fftwf_complex *)qGrid, NULL, xStride, 1,
                                                (fftwf_complex *)qGrid, NULL, xStride, 1,
                                                FFTW_BACKWARD, FFTW_ESTIMATE);

  iout << " 4..." << endi;
        backward_plan_yz = fftwf_plan_many_dft_c2r(2, n+1, 
                                                      myGrid.K1,(fftwf_complex *)qGrid,
                                                      NULL, 1, myGrid.dim2 * (myGrid.dim3 / 2),
                                                      qGrid, NULL, 1, myGrid.dim2 * myGrid.dim3,
                                                      FFTW_ESTIMATE);
  iout << "   Done.\n" << endi;
#else
  NAMD_die("LJPMESerial requires FFTW 2");
#endif
  #else
  work = new fftw_complex[n[0]];

  iout << iINFO << "Optimizing 4 LJ-PME FFT steps.  1..." << endi;
  forward_plan_yz = rfftwnd_create_plan_specific(2, n+1, FFTW_REAL_TO_COMPLEX,
                  FFTW_ESTIMATE | FFTW_IN_PLACE | FFTW_USE_WISDOM,
                  qGrid, 1, 0, 0);
  iout << " 2..." << endi;
  forward_plan_x = fftw_create_plan_specific(n[0], FFTW_FORWARD,
                 FFTW_ESTIMATE | FFTW_IN_PLACE | FFTW_USE_WISDOM, (fftw_complex *)qGrid,
                 myGrid.dim2 * myGrid.dim3 / 2, work, 1);
  iout << " 3..." << endi;
  backward_plan_x = fftw_create_plan_specific(n[0], FFTW_BACKWARD,
                  FFTW_ESTIMATE | FFTW_IN_PLACE | FFTW_USE_WISDOM, (fftw_complex *)qGrid,
                  myGrid.dim2 * myGrid.dim3 / 2, work, 1);
  iout << " 4..." << endi;
  backward_plan_yz = rfftwnd_create_plan_specific(2, n + 1, FFTW_COMPLEX_TO_REAL,
                   FFTW_ESTIMATE | FFTW_IN_PLACE | FFTW_USE_WISDOM,
                   qGrid, 1, 0, 0);
  iout << "   Done.\n" << endi;
  #endif
  #else
  NAMD_die("Sorry, FFTW must be compiled in to use LJPMESerial.");
  #endif
}

selfCompute()

double LjPmeMgr::selfCompute

(

const double &

alphaLJ

)

Definition at line 323 of file LjPmeMgr.C.

Referenced by computeLongRange().

                                                 {
        double energy = 0.0;
        double c3Term;
  double alpha6 = pow(alphaLJ, 6.0);
        for(int i=0; i < numAtoms; i++) {
                c3Term = dataArr[4*i+3];
                energy += c3Term*c3Term;
        }
  return (energy * alpha6 / 12.0);
}

setScaledCoordinates()

void LjPmeMgr::setScaledCoordinates	(	const double *	refPos,
		const Lattice &	lattice
	)

Definition at line 201 of file LjPmeMgr.C.

References Lattice::a_r(), Lattice::b_r(), Lattice::c_r(), LjPmeGrid::K1, LjPmeGrid::K2, LjPmeGrid::K3, LjPmeGrid::order, Lattice::origin(), Vector::x, Vector::y, and Vector::z.

Referenced by computeLongRange().

                                                                                {
  Vector origin = lattice.origin();
  Vector recip1 = lattice.a_r();
  Vector recip2 = lattice.b_r();
  Vector recip3 = lattice.c_r();
  double ox = origin.x;
  double oy = origin.y;
  double oz = origin.z;
  double r1x = recip1.x;
  double r1y = recip1.y;
  double r1z = recip1.z;
  double r2x = recip2.x;
  double r2y = recip2.y;
  double r2z = recip2.z;
  double r3x = recip3.x;
  double r3y = recip3.y;
  double r3z = recip3.z;
  int K1 = myGrid.K1;
  int K2 = myGrid.K2;
  int K3 = myGrid.K3;
  double shift1 = ((K1 + myGrid.order - 1)/2)/(double)K1;
  double shift2 = ((K2 + myGrid.order - 1)/2)/(double)K2;
  double shift3 = ((K3 + myGrid.order - 1)/2)/(double)K3;

  for (int i=0; i<numAtoms; i++) {
    int index = 4*i;
    double px = refPos[index]   - ox;
    double py = refPos[index+1] - oy;
    double pz = refPos[index+2] - oz;
    double c3Term = refPos[index+3];
    double sx = shift1 + px*r1x + py*r1y + pz*r1z;
    double sy = shift2 + px*r2x + py*r2y + pz*r2z;
    double sz = shift3 + px*r3x + py*r3y + pz*r3z;
    px = K1 * ( sx - floor(sx) );
    py = K2 * ( sy - floor(sy) );
    pz = K3 * ( sz - floor(sz) );
    //  Check for rare rounding condition where K * ( 1 - epsilon ) == K
    //  which was observed with g++ on Intel x86 architecture.
    if ( px == K1 ) px = 0;
    if ( py == K2 ) py = 0;
    if ( pz == K3 ) pz = 0;

    dataArr[index] = px;
    dataArr[index+1] = py;
    dataArr[index+2] = pz;
    dataArr[index+3] = c3Term;
  }   
}

---

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

• LjPmeMgr.h
• LjPmeMgr.C