ComputeFmmSerialMgr Class Reference

Inheritance diagram for ComputeFmmSerialMgr:

Public Member Functions
	ComputeFmmSerialMgr ()
	~ComputeFmmSerialMgr ()
void	setCompute (ComputeFmmSerial *c)
void	recvCoord (FmmSerialCoordMsg *)
void	recvForce (FmmSerialForceMsg *)

Detailed Description

Definition at line 77 of file ComputeFmmSerial.C.

Constructor & Destructor Documentation

ComputeFmmSerialMgr::ComputeFmmSerialMgr

(

)

Definition at line 109 of file ComputeFmmSerial.C.

                                         :
  fmmProxy(thisgroup), fmmCompute(0), numSources(0), numArrived(0),
  coordMsgs(0), coord(0), force(0), oldmsg(0), numAtoms(0),
  fmmsolver(0), nlevels(0), scaling(0), center(0),
  chargebuffer(0), epotbuffer(0), posbuffer(0), forcebuffer(0)
{
  CkpvAccess(BOCclass_group).computeFmmSerialMgr = thisgroup;
}

ComputeFmmSerialMgr::~ComputeFmmSerialMgr

(

)

Definition at line 118 of file ComputeFmmSerial.C.

{
  for (int i=0;  i < numSources;  i++)  delete coordMsgs[i];
  delete [] coordMsgs;
  delete [] coord;
  delete [] force;
  delete oldmsg;
  if (chargebuffer) delete[] chargebuffer;
  if (epotbuffer)   delete[] epotbuffer;
  if (posbuffer)    delete[] posbuffer;
  if (forcebuffer)  delete[] forcebuffer;
}

Member Function Documentation

void ComputeFmmSerialMgr::recvCoord

(

FmmSerialCoordMsg *

msg

)

Definition at line 200 of file ComputeFmmSerial.C.

References Lattice::a_p(), Lattice::b_p(), Lattice::c_p(), ComputeFmmSerialAtom::charge, FmmSerialCoordMsg::coord, COULOMB, SimParameters::dielectric, endi(), FmmSerialForceMsg::energy, SimParameters::FMMLevels, SimParameters::FMMPadding, FmmSerialForceMsg::force, ComputeFmmSerialAtom::id, iINFO(), iout, FmmSerialCoordMsg::lattice, Node::molecule, NAMD_die(), FmmSerialCoordMsg::numAtoms, Molecule::numAtoms, PatchMap::Object(), Node::Object(), ComputeFmmSerialAtom::position, Node::simParameters, simParams, FmmSerialCoordMsg::sourceNode, FmmSerialForceMsg::virial, Vector::x, Vector::y, and Vector::z.

                                                          {
  int i;
  if ( ! numSources ) {
    numSources = (PatchMap::Object())->numNodesWithPatches();
    coordMsgs = new FmmSerialCoordMsg*[numSources];
    for ( i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
    numArrived = 0;
    numAtoms = Node::Object()->molecule->numAtoms;
    coord = new ComputeFmmSerialAtom[numAtoms];
    force = new FmmSerialForce[numAtoms];
  }

  for ( i=0; i < msg->numAtoms; ++i ) {
    coord[msg->coord[i].id] = msg->coord[i];
  }

  coordMsgs[numArrived] = msg;
  ++numArrived;

  if ( numArrived < numSources ) return;
  numArrived = 0;

  // ALL DATA ARRIVED --- CALCULATE FORCES
  Lattice lattice = msg->lattice;
  SimParameters *simParams = Node::Object()->simParameters;

  double energy = 0;
  double virial[3][3] = { 0 };  // FMM does not calculate virial

  int rc = 0;  // return code

  if ( ! fmmsolver ) {
    //
    // setup FMM solver
    //

    // check boundary conditions
    if (lattice.a_p() || lattice.b_p() || lattice.c_p()) {
      NAMD_die("FMM solver requires non-periodic boundaries");
    }

    // setup number of levels
    if (simParams->FMMLevels > 0) {
      // explicitly set in config file
      nlevels = simParams->FMMLevels;
    }
    else {
      // otherwise estimate number of levels as round(log_8(numAtoms))
      nlevels = (int) floor(log((double)numAtoms) / log(8.) + 0.5);
    }

    // find bounding cube length
    if (numAtoms <= 0) {
      NAMD_die("setting up FMM with no atoms");
    }
    Vector min, max;
    min = max = coord[0].position;
    for (i = 1;  i < numAtoms;  i++) {
      Vector r = coord[i].position;
      if      (r.x < min.x)  min.x = r.x;
      else if (r.x > max.x)  max.x = r.x;
      if      (r.y < min.y)  min.y = r.y;
      else if (r.y > max.y)  max.y = r.y;
      if      (r.z < min.z)  min.z = r.z;
      else if (r.z > max.z)  max.z = r.z;
    }
    double padding = simParams->FMMPadding;
    if (padding <= 0) padding = 0.01;  // pad by at least a delta margin
    min -= padding;
    max += padding;
    double len = max.x - min.x;
    if (len < max.y - min.y)  len = max.y - min.y;
    if (len < max.z - min.z)  len = max.z - min.z;
    scaling = 1.0 / len;  // scale coordinates by length of the cube
    center = 0.5*(min + max);  // center of cube
    iout << iINFO << "FMM scaling length set to " << len << " A\n" << endi;
    iout << iINFO << "FMM center set to " << center << "\n" << endi;

    // allocate buffer space
    chargebuffer = new double[numAtoms];     // double *
    epotbuffer   = new double[numAtoms];     // double *
    posbuffer    = new double[numAtoms][3];  // double(*)[3]
    forcebuffer  = new double[numAtoms][3];  // double(*)[3]
    if (chargebuffer == 0 || epotbuffer == 0 ||
        posbuffer == 0 || forcebuffer == 0) {
      NAMD_die("can't allocate buffer space for FMM data");
    }

    // scale the charges - these won't change
    double celec = sqrt(COULOMB / simParams->dielectric);
    for (i = 0;  i < numAtoms;  i++) {
      chargebuffer[i] = celec * coord[i].charge;
    }
    fmmsolver = 1;  // is setup
  }

  // translate and scale positions into [-1/2,1/2]^3
  for (i = 0;  i < numAtoms;  i++) {
    posbuffer[i][0] = scaling*(coord[i].position.x - center.x);
    posbuffer[i][1] = scaling*(coord[i].position.y - center.y);
    posbuffer[i][2] = scaling*(coord[i].position.z - center.z);
  }

  // call the FMM solver
  int errcode = 0;
#ifdef FMM_SOLVER
  fmmlap_uni_(&numAtoms, posbuffer, chargebuffer, epotbuffer, forcebuffer,
      &nlevels, &errcode);
#else
  NAMD_die("Must link to FMM library to use FMM\n");
#endif

  // scale force and potentials
  for (i = 0;  i < numAtoms;  i++) {
    double qs = chargebuffer[i] * scaling;
    force[i].x = qs * scaling * forcebuffer[i][0];
    force[i].y = qs * scaling * forcebuffer[i][1];
    force[i].z = qs * scaling * forcebuffer[i][2];
    energy += qs * epotbuffer[i];
  }
  energy *= 0.5;

  // distribute forces
  for (int j=0;  j < numSources;  j++) {
    FmmSerialCoordMsg *cmsg = coordMsgs[j];
    coordMsgs[j] = 0;
    FmmSerialForceMsg *fmsg = new (cmsg->numAtoms, 0) FmmSerialForceMsg;

    for (int i=0;  i < cmsg->numAtoms;  i++) {
      fmsg->force[i] = force[cmsg->coord[i].id];
    }

    if ( ! j ) {  // set virial and energy only for first message
      fmsg->energy = energy;
      for (int k=0;  k < 3;  k++) {
        for (int l=0;  l < 3;  l++) {
          fmsg->virial[k][l] = virial[k][l];
        }
      }
    }
    else {  // set other messages to zero, add into reduction only once
      fmsg->energy = 0;
      for (int k=0;  k < 3;  k++) {
        for (int l=0;  l < 3;  l++) {
          fmsg->virial[k][l] = 0;
        }
      }
    }

    fmmProxy[cmsg->sourceNode].recvForce(fmsg);
    delete cmsg;
  }
}

void ComputeFmmSerialMgr::recvForce

(

FmmSerialForceMsg *

msg

)

Definition at line 354 of file ComputeFmmSerial.C.

References ComputeFmmSerial::saveResults().

                                                          {
  fmmCompute->saveResults(msg);
  delete oldmsg;
  oldmsg = msg;
}

void ComputeFmmSerialMgr::setCompute ( ComputeFmmSerial *  c )

inline

Definition at line 82 of file ComputeFmmSerial.C.

{ fmmCompute = c; }

---

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

• ComputeFmmSerial.C