ComputeGBISserMgr Class Reference

Inheritance diagram for ComputeGBISserMgr:

Public Member Functions
	ComputeGBISserMgr ()
	~ComputeGBISserMgr ()
void	setCompute (ComputeGBISser *c)
void	recvCoord (GBISCoordMsg *)
void	recvForce (GBISForceMsg *)

Detailed Description

Definition at line 158 of file ComputeGBISser.C.

Constructor & Destructor Documentation

ComputeGBISserMgr()

ComputeGBISserMgr::ComputeGBISserMgr

(

)

Definition at line 207 of file ComputeGBISser.C.

                                     :
  gbisProxy(thisgroup), gbisCompute(0), numSources(0), numArrived(0),
  inittime(0), 
  psitime(0), 
  alphatime(0), 
  dEdrtime(0), 
  dEdasumtime(0), 
  dEdaprefixtime(0), 
  dEdalooptime(0), slowForce(0),
  coordMsgs(0), coord(0), force(0), oldmsg(0), numAtoms(0), timestep(0) {
  CkpvAccess(BOCclass_group).computeGBISserMgr = thisgroup;
  t_start = clock();
  t_stop = clock();
  all2all = false;
}

~ComputeGBISserMgr()

ComputeGBISserMgr::~ComputeGBISserMgr

(

)

Definition at line 223 of file ComputeGBISser.C.

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

Member Function Documentation

recvCoord()

void ComputeGBISserMgr::recvCoord

(

GBISCoordMsg *

msg

)

Definition at line 742 of file ComputeGBISser.C.

References BENCH_PERIOD, GBISCoordMsg::coord, GBISForceMsg::coulEnergy, GBISCoordMsg::doSlow, GBISForceMsg::force, GBISForceMsg::gbInterEnergy, GBISForceMsg::gbSelfEnergy, ComputeGBISAtom::id, Node::molecule, GBISCoordMsg::numAtoms, Molecule::numAtoms, PatchMap::Object(), Node::Object(), GBISCoordMsg::sequence, GBISForceMsg::slowForce, and GBISCoordMsg::sourceNode.

                                                   {
  //printf("GBIS recvCoord()\n");
  if ( ! numSources ) {//init receiving coord
    numSources = (PatchMap::Object())->numNodesWithPatches();
    coordMsgs = new GBISCoordMsg*[numSources];
    for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
    numArrived = 0;
    numAtoms = Node::Object()->molecule->numAtoms;
    coord = new ComputeGBISAtom[numAtoms];
    force = new ExtForce[numAtoms];
    slowForce = new ExtForce[numAtoms];
    timestep = msg[0].sequence;
  }
  

  //receive coord
  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 sources arrived; calculate energy, forces
   *
   **********************************************************/
  t_start = clock();
  //how long did namd take to cycle back here
  double namdtime = (double)((double)t_start-(double)t_stop)/CLOCKS_PER_SEC;
  totalnamdtime += namdtime;
  //choice choose
  calcGBISReg(msg->doSlow);
  
  t_stop = clock();
  double gbistime = (double)((double)t_stop-(double)t_start)/CLOCKS_PER_SEC;
  //printf("GBIS: elapsednamd(%i)=%f\n", timestep, namdtime);
  //printf("GBIS: elapsedgbis(%i)=%f\n", timestep, gbistime);
  totalgbistime += gbistime;
  //printf("GBIS: total(%i)=%f\n", timestep, totaltime);
  if (timestep % BENCH_PERIOD == 0) {
    printf("\n");
    printf("GBIS:       t_GB=%f sec for %i steps\n",totalgbistime,BENCH_PERIOD);
    printf("GBIS:       t_MD=%f sec for %i steps\n",totalnamdtime,BENCH_PERIOD);
    printf("GBIS:       init=%f sec for %i steps\n", inittime, BENCH_PERIOD);
    printf("GBIS:        psi=%f sec for %i steps\n", psitime, BENCH_PERIOD);
    printf("GBIS:      alpha=%f sec for %i steps\n", alphatime, BENCH_PERIOD);
    printf("GBIS:    dEdasum=%f sec for %i steps\n", dEdasumtime, BENCH_PERIOD);
    printf("GBIS: dEdaprefix=%f sec for %i steps\n",dEdaprefixtime,BENCH_PERIOD);
    printf("GBIS:   dEdaloop=%f sec for %i steps\n", dEdalooptime,BENCH_PERIOD);
    printf("GBIS:      loop1=%i iters\n", loop1Iter);
    printf("GBIS:      loop2=%i iters\n", loop2Iter);
    printf("GBIS:      loop3=%i iters\n", loop3Iter);
    printf("\n");
    totalgbistime = 0;
    totalnamdtime = 0;
    inittime = 0;
    psitime = 0;
    alphatime = 0;
    dEdrtime = 0;
    dEdasumtime = 0;
    dEdaprefixtime = 0;
    dEdalooptime = 0;
  }

  // distribute forces
  //printf("GBIS distributing forces\n");
  for ( int j=0; j < numSources; ++j ) {
    GBISCoordMsg *cmsg = coordMsgs[j];
    coordMsgs[j] = 0;
    GBISForceMsg *fmsg = new (cmsg->numAtoms, cmsg->numAtoms, 0) GBISForceMsg;
    //does this init slowForce, force?
    for ( int i=0; i < cmsg->numAtoms; ++i ) {
      fmsg->force[i] = force[cmsg->coord[i].id];
      fmsg->slowForce[i] = slowForce[cmsg->coord[i].id];
      /*
      if (i == 1000 ) {
        printf("%i force: <", i);
        printf("%f, ", fmsg->force[i].force.x);
        printf("%f, ", fmsg->force[i].force.y);
        printf("%f>\n", fmsg->force[i].force.z);
        printf("%i slwfr: <", i);
        printf("%f, ", fmsg->slowForce[i].force.x);
        printf("%f, ", fmsg->slowForce[i].force.y);
        printf("%f>\n", fmsg->slowForce[i].force.z);
      }
      */
    }

    //CkPrintf("GBISENERGY[%i] c = % e, b = % e\n",timestep,coulEnergy, gbEnergy);
   if ( ! j ) {
#if GBIS_DEDR_FORCE
      fmsg->gbSelfEnergy = gbSelfEnergy;
      fmsg->gbInterEnergy = gbInterEnergy;
#else
      fmsg->gbSelfEnergy = 0;
      fmsg->gbInterEnergy = 0;
#endif
#if GBIS_COUL_FORCE
      fmsg->coulEnergy = coulEnergy;
#else
      fmsg->coulEnergy = 0;
#endif
    } else {
      fmsg->gbSelfEnergy = 0;
      fmsg->gbInterEnergy = 0;
      fmsg->coulEnergy = 0;
    }
    gbisProxy[cmsg->sourceNode].recvForce(fmsg);
    delete cmsg;
  }
  //printf("GBIS distributing forces COMPLETE!\n");
}

recvForce()

void ComputeGBISserMgr::recvForce

(

GBISForceMsg *

msg

)

Definition at line 862 of file ComputeGBISser.C.

References ComputeGBISser::saveResults().

                                                   {
  //printf("GBIS recvForce()\n");
  gbisCompute->saveResults(msg);
  delete oldmsg;
  oldmsg = msg;
}

setCompute()

void ComputeGBISserMgr::setCompute ( ComputeGBISser *  c )

inline

Definition at line 163 of file ComputeGBISser.C.

{ gbisCompute = c; }

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

• ComputeGBISser.C