ComputeExtMgr Class Reference

Inheritance diagram for ComputeExtMgr:

Public Member Functions
	ComputeExtMgr ()
	~ComputeExtMgr ()
void	setCompute (ComputeExt *c)
void	recvCoord (ExtCoordMsg *)
void	recvForce (ExtForceMsg *)

Detailed Description

Definition at line 54 of file ComputeExt.C.

Constructor & Destructor Documentation

ComputeExtMgr()

ComputeExtMgr::ComputeExtMgr

(

)

Definition at line 77 of file ComputeExt.C.

                             :
  extProxy(thisgroup), extCompute(0), numSources(0), numArrived(0),
  coordMsgs(0), coord(0), force(0), oldmsg(0), numAtoms(0) {
  CkpvAccess(BOCclass_group).computeExtMgr = thisgroup;
}

~ComputeExtMgr()

ComputeExtMgr::~ComputeExtMgr

(

)

Definition at line 83 of file ComputeExt.C.

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

Member Function Documentation

recvCoord()

void ComputeExtMgr::recvCoord

(

ExtCoordMsg *

msg

)

Definition at line 168 of file ComputeExt.C.

References Lattice::a(), Lattice::a_p(), Lattice::b(), Lattice::b_p(), Lattice::c(), Lattice::c_p(), ComputeExtAtom::charge, ExtCoordMsg::coord, ExtForceMsg::energy, ExtForceMsg::force, ExtForce::force, ComputeExtAtom::id, ExtCoordMsg::lattice, Node::molecule, NAMD_die(), ExtCoordMsg::numAtoms, Molecule::numAtoms, PatchMap::Object(), Node::Object(), ComputeExtAtom::position, ExtForce::replace, Node::simParameters, simParams, ExtCoordMsg::sourceNode, ExtForceMsg::virial, Vector::x, Vector::y, and Vector::z.

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

  int i;
  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;
  FILE *file;
  int iret;

  // write coordinates to file
  //iout << "writing to file " << simParams->extCoordFilename << "\n" << endi;
  file = fopen(simParams->extCoordFilename,"w");
  if ( ! file ) { NAMD_die(strerror(errno)); }
  for ( i=0; i<numAtoms; ++i ) {
    int id = coord[i].id + 1;
    double charge = coord[i].charge;
    double x = coord[i].position.x;
    double y = coord[i].position.y;
    double z = coord[i].position.z;
    iret = fprintf(file,"%d %f %f %f %f\n",id,charge,x,y,z);
    if ( iret < 0 ) { NAMD_die(strerror(errno)); }
  }
  // write periodic cell lattice (0 0 0 if non-periodic)
  Vector a = lattice.a();  if ( ! lattice.a_p() ) a = Vector(0,0,0);
  Vector b = lattice.b();  if ( ! lattice.b_p() ) b = Vector(0,0,0);
  Vector c = lattice.c();  if ( ! lattice.c_p() ) c = Vector(0,0,0);
  iret = fprintf(file,"%f %f %f\n%f %f %f\n%f %f %f\n",
                 a.x, a.y, a.z, b.x, b.y, b.z, c.x, c.y, c.z);
  if ( iret < 0 ) { NAMD_die(strerror(errno)); }
  fclose(file);

  // run user-specified command
  //iout << "running command " << simParams->extForcesCommand << "\n" << endi;
  iret = system(simParams->extForcesCommand);
  if ( iret == -1 ) { NAMD_die(strerror(errno)); }
  if ( iret ) { NAMD_die("Error running command for external forces."); }

  // remove coordinate file
  iret = remove(simParams->extCoordFilename);
  if ( iret ) { NAMD_die(strerror(errno)); }

  // read forces from file (overwrite positions)
  //iout << "reading from file " << simParams->extForceFilename << "\n" << endi;
  file = fopen(simParams->extForceFilename,"r");
  if ( ! file ) { NAMD_die(strerror(errno)); }
  for ( i=0; i<numAtoms; ++i ) {
    int id, replace;
    double x, y, z;
    iret = fscanf(file,"%d %d %lf %lf %lf\n", &id, &replace, &x, &y, &z);
    if ( iret != 5 ) { NAMD_die("Error reading external forces file."); }
    if ( id != i + 1 ) { NAMD_die("Atom ID error in external forces file."); }
    force[i].force.x = x; force[i].force.y = y; force[i].force.z = z;
    force[i].replace = replace;
  }
  // read energy and virial if they are present
  // virial used by NAMD is -'ve of normal convention, so reverse it!
  // virial[i][j] in file should be sum of -1 * f_i * r_j
  double energy;
  double virial[3][3];
  iret = fscanf(file,"%lf\n", &energy);
  if ( iret != 1 ) {
    energy = 0;
    for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
  } else {
    iret = fscanf(file,"%lf %lf %lf\n%lf %lf %lf\n%lf %lf %lf\n",
      &virial[0][0], &virial[0][1], &virial[0][2],
      &virial[1][0], &virial[1][1], &virial[1][2],
      &virial[2][0], &virial[2][1], &virial[2][2]);
    if ( iret != 9 ) {
      for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
    } else {
      // virial used by NAMD is -'ve of normal convention, so reverse it!
      for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] *= -1.0;
    }
  }
  fclose(file);

  // remove force file
  iret = remove(simParams->extForceFilename);
  if ( iret ) { NAMD_die(strerror(errno)); }

  // distribute forces

  for ( int j=0; j < numSources; ++j ) {
    ExtCoordMsg *cmsg = coordMsgs[j];
    coordMsgs[j] = 0;
    ExtForceMsg *fmsg = new (cmsg->numAtoms, 0) ExtForceMsg;
    for ( int i=0; i < cmsg->numAtoms; ++i ) {
      fmsg->force[i] = force[cmsg->coord[i].id];
    }
    if ( ! j ) {
      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 {
      fmsg->energy = 0;
      for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
        fmsg->virial[k][l] = 0;
    }
    extProxy[cmsg->sourceNode].recvForce(fmsg);
    delete cmsg;
  }

}

recvForce()

void ComputeExtMgr::recvForce

(

ExtForceMsg *

msg

)

Definition at line 292 of file ComputeExt.C.

References ComputeExt::saveResults().

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

setCompute()

void ComputeExtMgr::setCompute ( ComputeExt *  c )

inline

Definition at line 59 of file ComputeExt.C.

{ extCompute = c; }

---

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

• ComputeExt.C