ComputeLjPmeSerial Class Reference

#include <ComputeLjPmeSerial.h>

Inheritance diagram for ComputeLjPmeSerial:

Public Member Functions
	ComputeLjPmeSerial (ComputeID c)
virtual	~ComputeLjPmeSerial ()
void	doWork ()
void	saveResults (LjPmeSerialForceMsg *)
Public Member Functions inherited from ComputeHomePatches
	ComputeHomePatches (ComputeID c)
virtual	~ComputeHomePatches ()
virtual void	initialize ()
virtual void	atomUpdate ()
Flags *	getFlags (void)
Public Member Functions inherited from Compute
	Compute (ComputeID)
int	type ()
virtual	~Compute ()
void	setNumPatches (int n)
int	getNumPatches ()
virtual void	patchReady (PatchID, int doneMigration, int seq)
virtual int	noWork ()
virtual void	finishPatch (int)
int	sequence (void)
int	priority (void)
int	getGBISPhase (void)
virtual void	gbisP2PatchReady (PatchID, int seq)
virtual void	gbisP3PatchReady (PatchID, int seq)

Additional Inherited Members
Public Attributes inherited from Compute
const ComputeID	cid
LDObjHandle	ldObjHandle
LocalWorkMsg *const	localWorkMsg
Protected Member Functions inherited from Compute
void	enqueueWork ()
Protected Attributes inherited from ComputeHomePatches
int	useAvgPositions
int	hasPatchZero
ComputeHomePatchList	patchList
PatchMap *	patchMap
Protected Attributes inherited from Compute
int	computeType
int	basePriority
int	gbisPhase
int	gbisPhasePriority [3]

Detailed Description

Definition at line 17 of file ComputeLjPmeSerial.h.

Constructor & Destructor Documentation

ComputeLjPmeSerial()

ComputeLjPmeSerial::ComputeLjPmeSerial

(

ComputeID

c

)

Definition at line 130 of file ComputeLjPmeSerial.C.

References ReductionMgr::Object(), REDUCTIONS_BASIC, and ReductionMgr::willSubmit().

                                                  :
  ComputeHomePatches(c)
{
  CProxy_ComputeLjPmeSerialMgr::ckLocalBranch(
        CkpvAccess(BOCclass_group).computeLjPmeSerialMgr)->setCompute(this);
  reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);
}

~ComputeLjPmeSerial()

ComputeLjPmeSerial::~ComputeLjPmeSerial ( )

virtual

Definition at line 128 of file ComputeLjPmeSerial.C.

{}

Member Function Documentation

doWork()

void ComputeLjPmeSerial::doWork ( void  )

virtual

Reimplemented from Compute.

Definition at line 288 of file ComputeLjPmeSerial.C.

References ResizeArrayIter< T >::begin(), LjPmeSerialCoordMsg::coord, ResizeArrayIter< T >::end(), LjPmeSerialAtom::id, CompAtomExt::id, LjPmeSerialCoordMsg::lattice, LjPmeSerialCoordMsg::numAtoms, ComputeHomePatches::patchList, LjPmeSerialAtom::position, CompAtom::position, LjPmeSerialCoordMsg::sourceNode, LjPmeSerialAtom::vdwType, and CompAtom::vdwType.

{
  ResizeArrayIter<PatchElem> ap(patchList);

  // For now we do the LJ-PME calculation every steps

  // Skip computations if nothing to do.
  // if ( ! patchList[0].p->flags.doFullElectrostatics )
  // {
  //   for (ap = ap.begin(); ap != ap.end(); ap++) {
  //     CompAtom *x = (*ap).positionBox->open();
  //     Results *r = (*ap).forceBox->open();
  //     (*ap).positionBox->close(&x);
  //     (*ap).forceBox->close(&r);
  //   }
  //   reduction->submit();
  //   return;
  // }

  // allocate message
  int numLocalAtoms = 0;
  for (ap = ap.begin(); ap != ap.end(); ap++) {
    numLocalAtoms += (*ap).p->getNumAtoms();
  }

  LjPmeSerialCoordMsg *msg = new (numLocalAtoms, 0) LjPmeSerialCoordMsg;
  msg->sourceNode = CkMyPe();
  msg->numAtoms = numLocalAtoms;
  msg->lattice = patchList[0].p->flags.lattice;
  LjPmeSerialAtom *data_ptr = msg->coord;

  // get positions
  for (ap = ap.begin();  ap != ap.end();  ap++) {
    CompAtom *x = (*ap).positionBox->open();
    CompAtomExt *xExt = (*ap).p->getCompAtomExtInfo();
    if ( patchList[0].p->flags.doMolly ) {
      (*ap).positionBox->close(&x);
      x = (*ap).avgPositionBox->open();
    }
    int numAtoms = (*ap).p->getNumAtoms();

    for(int i=0;  i < numAtoms;  i++)
    {
      data_ptr->position = x[i].position;
      data_ptr->vdwType = x[i].vdwType;
      data_ptr->id = xExt[i].id;
      ++data_ptr;
    }

    if ( patchList[0].p->flags.doMolly ) { (*ap).avgPositionBox->close(&x); }
    else { (*ap).positionBox->close(&x); }
  }

  CProxy_ComputeLjPmeSerialMgr ljPmeProxy(
      CkpvAccess(BOCclass_group).computeLjPmeSerialMgr);
  ljPmeProxy[0].recvCoord(msg);
}

saveResults()

void ComputeLjPmeSerial::saveResults

(

LjPmeSerialForceMsg *

msg

)

Definition at line 514 of file ComputeLjPmeSerial.C.

References ResizeArrayIter< T >::begin(), ResizeArrayIter< T >::end(), LjPmeSerialForceMsg::energyNonbond, LjPmeSerialForceMsg::energySlow, Results::f, LjPmeSerialForceMsg::forceNonbond, LjPmeSerialForceMsg::forceSlow, SubmitReduction::item(), Results::nbond, ComputeHomePatches::patchList, REDUCTION_LJ_ENERGY, Results::slow, SubmitReduction::submit(), LjPmeSerialForceMsg::virialNonbond, LjPmeSerialForceMsg::virialSlow, Vector::x, Vector::y, and Vector::z.

Referenced by ComputeLjPmeSerialMgr::recvForce().

{
  ResizeArrayIter<PatchElem> ap(patchList);

  LjPmeSerialForce *results_Nonbond_ptr = msg->forceNonbond;
  LjPmeSerialForce *results_Slow_ptr = msg->forceSlow;

  // add in forces
  for (ap = ap.begin(); ap != ap.end(); ap++) {
    Results *r = (*ap).forceBox->open();
    Force *fSlow = r->f[Results::slow];
    Force *fNonbond = r->f[Results::nbond];
    int numAtoms = (*ap).p->getNumAtoms();

    for(int i=0; i<numAtoms; ++i) {
      fSlow[i].x += results_Slow_ptr->x;
      fSlow[i].y += results_Slow_ptr->y;
      fSlow[i].z += results_Slow_ptr->z;
      fNonbond[i].x += results_Nonbond_ptr->x;
      fNonbond[i].y += results_Nonbond_ptr->y;
      fNonbond[i].z += results_Nonbond_ptr->z;
      ++results_Slow_ptr;
      ++results_Nonbond_ptr;
    }
  
    (*ap).forceBox->close(&r);
  }

  // reduction->item(REDUCTION_LJ_ENERGY) += msg->energyNonbond;
  // reduction->item(REDUCTION_ELECT_ENERGY_SLOW) +=  msg->energySlow;

  // reduction->item(REDUCTION_VIRIAL_SLOW_XX) += msg->virialSlow[0][0];
  // reduction->item(REDUCTION_VIRIAL_SLOW_XY) += msg->virialSlow[0][1];
  // reduction->item(REDUCTION_VIRIAL_SLOW_XZ) += msg->virialSlow[0][2];
  // reduction->item(REDUCTION_VIRIAL_SLOW_YX) += msg->virialSlow[1][0];
  // reduction->item(REDUCTION_VIRIAL_SLOW_YY) += msg->virialSlow[1][1];
  // reduction->item(REDUCTION_VIRIAL_SLOW_YZ) += msg->virialSlow[1][2];
  // reduction->item(REDUCTION_VIRIAL_SLOW_ZX) += msg->virialSlow[2][0];
  // reduction->item(REDUCTION_VIRIAL_SLOW_ZY) += msg->virialSlow[2][1];
  // reduction->item(REDUCTION_VIRIAL_SLOW_ZZ) += msg->virialSlow[2][2];

  // reduction->item(REDUCTION_VIRIAL_NBOND_XX) += msg->virialNonbond[0][0];
  // reduction->item(REDUCTION_VIRIAL_NBOND_XY) += msg->virialNonbond[0][1];
  // reduction->item(REDUCTION_VIRIAL_NBOND_XZ) += msg->virialNonbond[0][2];
  // reduction->item(REDUCTION_VIRIAL_NBOND_YX) += msg->virialNonbond[1][0];
  // reduction->item(REDUCTION_VIRIAL_NBOND_YY) += msg->virialNonbond[1][1];
  // reduction->item(REDUCTION_VIRIAL_NBOND_YZ) += msg->virialNonbond[1][2];
  // reduction->item(REDUCTION_VIRIAL_NBOND_ZX) += msg->virialNonbond[2][0];
  // reduction->item(REDUCTION_VIRIAL_NBOND_ZY) += msg->virialNonbond[2][1];
  // reduction->item(REDUCTION_VIRIAL_NBOND_ZZ) += msg->virialNonbond[2][2];

  reduction->item(REDUCTION_LJ_ENERGY) += msg->energyNonbond + msg->energySlow;

  reduction->item(REDUCTION_VIRIAL_NBOND_XX) += msg->virialNonbond[0][0] + msg->virialSlow[0][0];
  reduction->item(REDUCTION_VIRIAL_NBOND_XY) += msg->virialNonbond[0][1] + msg->virialSlow[0][1];
  reduction->item(REDUCTION_VIRIAL_NBOND_XZ) += msg->virialNonbond[0][2] + msg->virialSlow[0][2];
  reduction->item(REDUCTION_VIRIAL_NBOND_YX) += msg->virialNonbond[1][0] + msg->virialSlow[1][0];
  reduction->item(REDUCTION_VIRIAL_NBOND_YY) += msg->virialNonbond[1][1] + msg->virialSlow[1][1];
  reduction->item(REDUCTION_VIRIAL_NBOND_YZ) += msg->virialNonbond[1][2] + msg->virialSlow[1][2];
  reduction->item(REDUCTION_VIRIAL_NBOND_ZX) += msg->virialNonbond[2][0] + msg->virialSlow[2][0];
  reduction->item(REDUCTION_VIRIAL_NBOND_ZY) += msg->virialNonbond[2][1] + msg->virialSlow[2][1];
  reduction->item(REDUCTION_VIRIAL_NBOND_ZZ) += msg->virialNonbond[2][2] + msg->virialSlow[2][2];
  reduction->submit();
}

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

• ComputeLjPmeSerial.h
• ComputeLjPmeSerial.C