Patch Class Reference

#include <Patch.h>

Inheritance diagram for Patch:

Public Member Functions
	Patch (PatchID pd)
int	hasNewAtoms ()
virtual	~Patch ()
Box< Patch, CompAtom > *	registerPositionPickup (Compute *cid)
void	unregisterPositionPickup (Compute *cid, Box< Patch, CompAtom > **const box)
Box< Patch, CompAtom > *	registerAvgPositionPickup (Compute *cid)
void	unregisterAvgPositionPickup (Compute *cid, Box< Patch, CompAtom > **const box)
Box< Patch, CompAtom > *	registerVelocityPickup (Compute *cid)
void	unregisterVelocityPickup (Compute *cid, Box< Patch, CompAtom > **const box)
Box< Patch, Real > *	registerIntRadPickup (Compute *cid)
void	unregisterIntRadPickup (Compute *cid, Box< Patch, Real > **const box)
Box< Patch, GBReal > *	registerPsiSumDeposit (Compute *cid)
void	unregisterPsiSumDeposit (Compute *cid, Box< Patch, GBReal > **const box)
Box< Patch, Real > *	registerBornRadPickup (Compute *cid)
void	unregisterBornRadPickup (Compute *cid, Box< Patch, Real > **const box)
Box< Patch, GBReal > *	registerDEdaSumDeposit (Compute *cid)
void	unregisterDEdaSumDeposit (Compute *cid, Box< Patch, GBReal > **const box)
Box< Patch, Real > *	registerDHdrPrefixPickup (Compute *cid)
void	unregisterDHdrPrefixPickup (Compute *cid, Box< Patch, Real > **const box)
Box< Patch, int > *	registerLcpoTypePickup (Compute *cid)
void	unregisterLcpoTypePickup (Compute *cid, Box< Patch, int > **const box)
Box< Patch, Results > *	registerForceDeposit (Compute *cid)
void	unregisterForceDeposit (Compute *cid, Box< Patch, Results > **const box)
void	positionsReady (int n=0, int startup=1)
void	positionBoxClosed (void)
void	forceBoxClosed (void)
void	avgPositionBoxClosed (void)
void	velocityBoxClosed (void)
void	intRadBoxClosed (void)
void	psiSumBoxClosed (void)
void	bornRadBoxClosed (void)
void	dEdaSumBoxClosed (void)
void	dHdrPrefixBoxClosed (void)
void	gbisP2Ready ()
void	gbisP3Ready ()
void	lcpoTypeBoxClosed (void)
int	getNumAtoms () const
int	getNumFixedAtoms () const
void	setNumFixedAtoms (int numFixed)
PatchID	getPatchID () const
int	getNumComputes () const
CompAtomExt *	getCompAtomExtInfo ()
CompAtom *	getCompAtomInfo ()
CudaAtom *	getCudaAtomList ()

Public Attributes
Lattice &	lattice
Flags	flags

Protected Member Functions
virtual void	boxClosed (int)=0

Protected Attributes
const PatchID	patchID
int	numAtoms
int	numFixedAtoms
CompAtomList	p
CompAtomList	p_avg
CompAtomList	v
AtomMapper *	atomMapper
RealList	intRad
GBRealList	psiSum
GBRealList	psiFin
RealList	bornRad
RealList	dHdrPrefix
GBRealList	dEdaSum
IntList	lcpoType
CompAtomExtList	pExt
CompAtom *	avgPositionPtrBegin
CompAtom *	avgPositionPtrEnd
CompAtom *	velocityPtrBegin
CompAtom *	velocityPtrEnd
CudaAtom *	cudaAtomPtr
ForceList	f [Results::maxNumForces]
Results	results
int	computesSortedByPriority
int	firstHoldableCompute
OwnerBox< Patch, CompAtom >	positionBox
ComputePtrList	positionComputeList
OwnerBox< Patch, CompAtom >	avgPositionBox
ComputePtrList	avgPositionComputeList
OwnerBox< Patch, CompAtom >	velocityBox
ComputePtrList	velocityComputeList
OwnerBox< Patch, Real >	intRadBox
ComputePtrList	intRadComputeList
OwnerBox< Patch, GBReal >	psiSumBox
ComputePtrList	psiSumComputeList
OwnerBox< Patch, Real >	bornRadBox
ComputePtrList	bornRadComputeList
OwnerBox< Patch, GBReal >	dEdaSumBox
ComputePtrList	dEdaSumComputeList
OwnerBox< Patch, Real >	dHdrPrefixBox
ComputePtrList	dHdrPrefixComputeList
OwnerBox< Patch, int >	lcpoTypeBox
ComputePtrList	lcpoTypeComputeList
OwnerBox< Patch, Results >	forceBox
ComputePtrList	forceComputeList
int	boxesOpen
int	_hasNewAtoms
int *	child
int	nChild

Detailed Description

Definition at line 35 of file Patch.h.

Constructor & Destructor Documentation

Patch()

Patch::Patch

(

PatchID

pd

)

Definition at line 44 of file Patch.C.

References atomMapper, child, cudaAtomPtr, lattice, SimParameters::lattice, nChild, Node::Object(), ReductionMgr::Object(), REDUCTIONS_BASIC, Node::simParameters, and ReductionMgr::willSubmit().

                       :
   lattice(flags.lattice),
   patchID(pd), numAtoms(0), numFixedAtoms(0),
   avgPositionPtrBegin(0), avgPositionPtrEnd(0),
   velocityPtrBegin(0), velocityPtrEnd(0),      // BEGIN LA, END LA
   positionBox(this,&Patch::positionBoxClosed,pd,0),
   avgPositionBox(this,&Patch::avgPositionBoxClosed,pd,3),
   velocityBox(this,&Patch::velocityBoxClosed,pd,4), // BEGIN LA, END LA
   psiSumBox(this,&Patch::psiSumBoxClosed,pd,5), // begin gbis
   intRadBox(this,&Patch::intRadBoxClosed,pd,6),
   bornRadBox(this,&Patch::bornRadBoxClosed,pd,7),
   dEdaSumBox(this,&Patch::dEdaSumBoxClosed,pd,8),
   dHdrPrefixBox(this,&Patch::dHdrPrefixBoxClosed,pd,9), //end gbis
   lcpoTypeBox(this,&Patch::lcpoTypeBoxClosed,pd,10),
   forceBox(this,&Patch::forceBoxClosed,pd,1),
   boxesOpen(0), _hasNewAtoms(0),
   computesSortedByPriority(0), firstHoldableCompute(0)

   // DMK - Atom Separation (water vs. non-water)
   #if NAMD_SeparateWaters != 0
     ,numWaterAtoms(-1)
   #endif
{
  //CkPrintf("GBIS: PatchCreated\n");
#ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
    positionPtrBegin = 0;
    positionPtrEnd = 0;
#endif

        nChild = 0;
        child = NULL;
#ifdef NODEAWARE_PROXY_SPANNINGTREE
  #ifdef USE_NODEPATCHMGR
  nodeChildren = NULL;
  numNodeChild = 0;
  #endif
#endif

  lattice = Node::Object()->simParameters->lattice;
  atomMapper = new AtomMapper(pd);
#if !(defined(NAMD_CUDA) || defined(NAMD_HIP))
  reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);
#endif

  // DMK
  #if defined(NAMD_MIC)
    cudaAtomPtr = NULL;
    #if MIC_SUBMIT_ATOMS_ON_ARRIVAL != 0
      pthread_mutex_init(&mic_atomData_mutex, NULL);
      mic_atomData = NULL;
      mic_atomData_seq = -1;
      mic_atomData_allocSize_host = 0;
      for (int i = 0; i < MIC_MAX_DEVICES_PER_NODE; i++) {
        mic_atomData_prev[i] = NULL;
        mic_atomData_deviceSeq[i] = -1;
        mic_atomData_devicePtr[i] = 0;
        mic_atomData_allocSize_device[i] = 0;
      }
    #endif
  #endif
}

~Patch()

Patch::~Patch ( )

virtual

Definition at line 37 of file Patch.C.

References atomMapper.

              {
  delete atomMapper;
#if !(defined(NAMD_CUDA) || defined(NAMD_HIP))
  delete reduction;
#endif
}

Member Function Documentation

avgPositionBoxClosed()

void Patch::avgPositionBoxClosed

(

void

)

Definition at line 359 of file Patch.C.

References avgPositionPtrBegin, and boxClosed().

{
   avgPositionPtrBegin = 0;
   this->boxClosed(3);
}

bornRadBoxClosed()

void Patch::bornRadBoxClosed

(

void

)

Definition at line 384 of file Patch.C.

References boxClosed().

                                 {
   //bornRadPtr = 0;
   this->boxClosed(7);
}

boxClosed()

virtual void Patch::boxClosed ( int  )

protectedpure virtual

Implemented in HomePatch, and ProxyPatch.

Referenced by avgPositionBoxClosed(), bornRadBoxClosed(), dEdaSumBoxClosed(), dHdrPrefixBoxClosed(), forceBoxClosed(), intRadBoxClosed(), lcpoTypeBoxClosed(), positionBoxClosed(), psiSumBoxClosed(), and velocityBoxClosed().

dEdaSumBoxClosed()

void Patch::dEdaSumBoxClosed

(

void

)

Definition at line 388 of file Patch.C.

References boxClosed().

                                 {
   //dEdaSumPtr = 0;
   this->boxClosed(8);
}

dHdrPrefixBoxClosed()

void Patch::dHdrPrefixBoxClosed

(

void

)

Definition at line 392 of file Patch.C.

References boxClosed().

                                    {
   //dHdrPrefixPtr = 0;
   this->boxClosed(9);
}

forceBoxClosed()

void Patch::forceBoxClosed

(

void

)

Definition at line 252 of file Patch.C.

References ResizeArray< Elem >::begin(), boxClosed(), DebugM, Flags::doFullElectrostatics, Flags::doVirial, Results::f, f, flags, SubmitReduction::item(), lattice, Results::maxNumForces, Results::nbond, numAtoms, PatchMap::Object(), Node::Object(), p, patchID, ResizeArray< Elem >::resize(), results, Results::slow, SubmitReduction::submit(), Lattice::unscale(), virial_xx, virial_xy, virial_xz, virial_yy, virial_yz, virial_zz, Vector::x, Vector::y, and Vector::z.

{
   DebugM(4, "patchID("<<patchID<<") forceBoxClosed! call\n");

#if ! ( defined(NAMD_CUDA) || defined(NAMD_HIP))
   // calculate direct nonbonded virial from segregated forces and aggregate forces
   const Vector center = lattice.unscale( PatchMap::Object()->center(patchID) );
#ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
   const CompAtom * const __restrict pd = positionPtrBegin;
#else
   const CompAtom * const __restrict pd = p.begin();
#endif
   const int n = numAtoms;
   int roff = 0;

#ifdef NAMD_AVXTILES
   // If "Tiles" algorithm is active, perform same reduction and virial calc
   // in BigReal precision, but add in forces stored in tiles data structures
   // if they were touched on this patch.
   if (Node::Object()->simParameters->useAVXTiles) {
     double virialHold[6], virialSlowHold[6];
     tiles.nativeForceVirialUpdate(flags.doFullElectrostatics, flags.doVirial,
                                   pd, center, results.f[Results::nbond], 
                                   results.f[Results::slow],
                                   results.f[Results::nbond_virial],
                                   results.f[Results::slow_virial],
                                   virialHold, virialSlowHold);
     f[Results::nbond_virial].resize(0);
     f[Results::slow_virial].resize(0);
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_XX) += virialHold[0];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_XY) += virialHold[1];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_XZ) += virialHold[2];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_YX) += virialHold[1];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_YY) += virialHold[3];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_YZ) += virialHold[4];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZX) += virialHold[2];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZY) += virialHold[4];
     reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZZ) += virialHold[5];
     if (flags.doFullElectrostatics) {
       roff += REDUCTION_VIRIAL_SLOW_XX - REDUCTION_VIRIAL_NBOND_XX;
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_XX) += virialSlowHold[0];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_XY) += virialSlowHold[1];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_XZ) += virialSlowHold[2];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_YX) += virialSlowHold[1];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_YY) += virialSlowHold[3];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_YZ) += virialSlowHold[4];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZX) += virialSlowHold[2];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZY) += virialSlowHold[4];
       reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZZ) += virialSlowHold[5];
     }
     reduction->submit();
     for (int j = 0; j < Results::maxNumForces; ++j ) results.f[j] = 0;
     this->boxClosed(1);
     return;
   }
#endif

   for ( int j1 = Results::nbond; j1 <= Results::slow; ++j1, roff += REDUCTION_VIRIAL_SLOW_XX - REDUCTION_VIRIAL_NBOND_XX ) {
      int j2 = j1 + ( Results::nbond_virial - Results::nbond );
      Force * __restrict f1 = results.f[j1];
      Force * __restrict f2 = results.f[j2];
      BigReal virial_xx = 0.;
      BigReal virial_xy = 0.;
      BigReal virial_xz = 0.;
      BigReal virial_yy = 0.;
      BigReal virial_yz = 0.;
      BigReal virial_zz = 0.;
#pragma omp simd reduction(+:virial_xx,virial_xy,virial_xz,virial_yy,virial_yz,virial_zz)
#pragma ivdep
      for ( int i=0; i<n; ++i ) {
        BigReal p_x = pd[i].position.x - center.x;
        BigReal p_y = pd[i].position.y - center.y;
        BigReal p_z = pd[i].position.z - center.z;
        BigReal f_x = f2[i].x;
        BigReal f_y = f2[i].y;
        BigReal f_z = f2[i].z;
        virial_xx += f_x * p_x;
        virial_xy += f_x * p_y;
        virial_xz += f_x * p_z;
        virial_yy += f_y * p_y;
        virial_yz += f_y * p_z;
        virial_zz += f_z * p_z;
        f1[i].x += f_x;
        f1[i].y += f_y;
        f1[i].z += f_z;
      }
      f[j2].resize(0);
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_XX) += virial_xx;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_XY) += virial_xy;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_XZ) += virial_xz;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_YX) += virial_xy;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_YY) += virial_yy;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_YZ) += virial_yz;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZX) += virial_xz;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZY) += virial_yz;
      reduction->item(roff + REDUCTION_VIRIAL_NBOND_ZZ) += virial_zz;
   }
   reduction->submit();
#endif

   for (int j = 0; j < Results::maxNumForces; ++j )
   {
     results.f[j] = 0;
   }
   this->boxClosed(1);
}

gbisP2Ready()

void Patch::gbisP2Ready

(

)

Definition at line 598 of file Patch.C.

References ResizeArrayPrimIter< T >::begin(), computeNonbondedCUDA2Type, computeNonbondedPairType, computeNonbondedSelfType, ResizeArrayPrimIter< T >::end(), flags, patchID, positionComputeList, and Flags::sequence.

Referenced by HomePatch::gbisP2Ready(), and ProxyPatch::receiveData().

                        {
 ComputePtrListIter cid(positionComputeList);

  int seq = flags.sequence;
  for(cid = cid.begin(); cid != cid.end(); cid++) {
    if ( (*cid)->type() == computeNonbondedSelfType ||
         (*cid)->type() == computeNonbondedPairType
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
         || (*cid)->type() == computeNonbondedCUDA2Type
#endif
         ) {
      (*cid)->gbisP2PatchReady(patchID,seq);
    }
  }
}

gbisP3Ready()

void Patch::gbisP3Ready

(

)

Definition at line 614 of file Patch.C.

References ResizeArrayPrimIter< T >::begin(), computeNonbondedCUDA2Type, computeNonbondedPairType, computeNonbondedSelfType, ResizeArrayPrimIter< T >::end(), flags, patchID, positionComputeList, and Flags::sequence.

Referenced by HomePatch::gbisP3Ready(), and ProxyPatch::receiveData().

                        {

  ComputePtrListIter cid(positionComputeList);

  int seq = flags.sequence;
  for(cid = cid.begin(); cid != cid.end(); cid++) {
    if ( (*cid)->type() == computeNonbondedSelfType ||
         (*cid)->type() == computeNonbondedPairType
#if defined(NAMD_CUDA) || defined(NAMD_HIP)
         || (*cid)->type() == computeNonbondedCUDA2Type
#endif
         ) {
      (*cid)->gbisP3PatchReady(patchID,seq);
    }
  }
}

getCompAtomExtInfo()

CompAtomExt* Patch::getCompAtomExtInfo ( )

inline

Definition at line 117 of file Patch.h.

References ResizeArray< Elem >::begin(), and pExt.

Referenced by ComputePme::doQMWork(), ComputePatch::doWork(), ComputePatchPair::doWork(), ComputeLCPO::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), and positionsReady().

{ return pExt.begin(); }

getCompAtomInfo()

CompAtom* Patch::getCompAtomInfo ( )

inline

Definition at line 118 of file Patch.h.

References ResizeArray< Elem >::begin(), and p.

{return p.begin(); }

getCudaAtomList()

CudaAtom* Patch::getCudaAtomList ( )

inline

Definition at line 125 of file Patch.h.

References cudaAtomPtr.

{ return cudaAtomPtr; }

getNumAtoms()

int Patch::getNumAtoms ( ) const

inline

Definition at line 105 of file Patch.h.

References numAtoms.

Referenced by WorkDistrib::assignNodeToPatch(), ComputePatch::atomUpdate(), ComputeHomePatch::atomUpdate(), ComputePatchPair::atomUpdate(), ComputeLCPO::atomUpdate(), ComputeGridForce::checkGridForceRatio(), ComputeGridForce::createGridForcedIdxList(), ComputeGridForce::doForce(), ComputePme::doQMWork(), ComputePme::doWork(), dumpbench(), ComputePatch::initialize(), ComputeHomePatch::initialize(), ComputePatchPair::initialize(), ComputePme::initialize(), ComputeLCPO::initialize(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), PatchMgr::moveAllBy(), Node::outputPatchComputeMaps(), recursive_bisect_with_curve(), ComputePme::ungridForces(), and ComputeLonepairsCUDA::updateAtoms().

{ return numAtoms; }

getNumComputes()

int Patch::getNumComputes ( ) const

inline

Definition at line 115 of file Patch.h.

References positionComputeList, and ResizeArray< Elem >::size().

{ return positionComputeList.size(); }

getNumFixedAtoms()

int Patch::getNumFixedAtoms ( ) const

inline

Definition at line 112 of file Patch.h.

References numFixedAtoms.

{ return numFixedAtoms; }  // not updated

getPatchID()

PatchID Patch::getPatchID ( ) const

inline

Definition at line 114 of file Patch.h.

References patchID.

Referenced by ProxyMgr::createProxy(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeNonbondedPair::doForce(), ComputeGridForce::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::doPairlistCheck(), ComputePatch::initialize(), ComputeHomePatch::initialize(), Sequencer::integrate(), Sequencer::integrate_SOA(), CudaComputeNonbonded::launchWork(), PatchElem::PatchElem(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Sequencer::rebalanceLoad(), Sequencer::run(), Sequencer::runComputeObjects(), Sequencer::runComputeObjects_SOA(), Sequencer::Sequencer(), and TuplePatchElem::TuplePatchElem().

{ return patchID; }

hasNewAtoms()

int Patch::hasNewAtoms ( )

inline

Definition at line 40 of file Patch.h.

References _hasNewAtoms.

{ return _hasNewAtoms; }

intRadBoxClosed()

void Patch::intRadBoxClosed

(

void

)

Definition at line 380 of file Patch.C.

References boxClosed().

                                {
   //dHdrPrefixPtr = 0;
   this->boxClosed(6);
}

lcpoTypeBoxClosed()

void Patch::lcpoTypeBoxClosed

(

void

)

Definition at line 399 of file Patch.C.

References boxClosed().

                                  {
   this->boxClosed(10);
}

positionBoxClosed()

void Patch::positionBoxClosed

(

void

)

Definition at line 246 of file Patch.C.

References boxClosed().

{
   //positionPtrBegin = 0;
   this->boxClosed(0);
}

positionsReady()

void Patch::positionsReady	(	int	n = 0,
		int	startup = 1
	)

Definition at line 403 of file Patch.C.

References _hasNewAtoms, atomMapper, avgPositionBox, avgPositionPtrBegin, ResizeArray< Elem >::begin(), bornRad, bornRadBox, boxesOpen, computesSortedByPriority, DebugM, dEdaSum, dEdaSumBox, dHdrPrefix, dHdrPrefixBox, Flags::doFullElectrostatics, Flags::doGBIS, Flags::doLCPO, Flags::doLoweAndersen, Flags::doMolly, ResizeArray< Elem >::end(), endi(), Results::f, f, firstHoldableCompute, flags, forceBox, getCompAtomExtInfo(), iINFO(), intRad, intRadBox, iout, lattice, lcpoType, lcpoTypeBox, Results::maxNumForces, PatchMap::node(), numAtoms, PatchMap::Object(), Sync::Object(), Node::Object(), OwnerBox< Owner, Data >::open(), p, patchID, pExt, PME_PRIORITY, CompAtom::position, positionBox, positionComputeList, psiFin, psiSum, psiSumBox, AtomMapper::registerIDsCompAtomExt(), ResizeArray< Elem >::resize(), results, Flags::sequence, ResizeArray< Elem >::setall(), Node::simParameters, simParams, ResizeArray< Elem >::size(), Lattice::unscale(), SimParameters::useAVXTiles, CompAtom::vdwType, velocityBox, velocityPtrBegin, Vector::x, Vector::y, and Vector::z.

Referenced by HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), and ProxyPatch::receiveData().

{
   DebugM(4,"Patch::positionsReady() - patchID(" << patchID <<")"<<std::endl );
   SimParameters *simParams = Node::Object()->simParameters;

   // The atom map needs to be updated for host migration, device migration startup and 
   // device migration + some advanced features
   const bool updateAtomMap = (startup || 
                               !simParams->useDeviceMigration || 
                               simParams->updateAtomMap);
   if (doneMigration && updateAtomMap) {
// #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
//       AtomMap::Object()->registerIDs(patchID,positionPtrBegin,positionPtrEnd);       
// #else
       atomMapper->registerIDsCompAtomExt(pExt.begin(),pExt.end());
// #endif
     
     #ifdef NAMD_AVXTILES
     if (Node::Object()->simParameters->useAVXTiles) {
       #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
       const CompAtom * const pd = positionPtrBegin;
       #else
       const CompAtom * const pd = p.begin();
       #endif
       tiles.atomUpdate(pd, getCompAtomExtInfo());
     }
     #endif
   }

#ifdef NAMD_KNL
  #if defined(NAMD_AVXTILES)
  if (!Node::Object()->simParameters->useAVXTiles)
  #endif
   {
     const Vector center = lattice.unscale( PatchMap::Object()->center(patchID) );
     const int n = numAtoms;
     pFlt.resize(n);
     CompAtomFlt * const pf = pFlt.begin();
#ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
     const CompAtom * const pd = positionPtrBegin;
#else
     const CompAtom * const pd = p.begin();
#endif
     for ( int i=0; i<n; ++i ) {
       // need to subtract center in double precision, then assign to float
       pf[i].position.x = pd[i].position.x - center.x;
       pf[i].position.y = pd[i].position.y - center.y;
       pf[i].position.z = pd[i].position.z - center.z;
       pf[i].vdwType = pd[i].vdwType;
     }
   }
#endif
   boxesOpen = 2;
   if ( flags.doMolly ) boxesOpen++;
   // BEGIN LA
   if (flags.doLoweAndersen) {
       DebugM(4, "Patch::positionsReady, flags.doMolly = " << flags.doMolly << "\n");
       boxesOpen++;
   }
   // END LA
   _hasNewAtoms = (doneMigration != 0);

#if CMK_BLUEGENEL
   CmiNetworkProgressAfter (0);
#endif

   // Give all position pickup boxes access to positions
   //positionPtrBegin = p.begin();
#ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
   positionBox.open(positionPtrBegin);
#else
   positionBox.open(p.begin());
#endif
   if ( flags.doMolly ) {
     //avgPositionPtrBegin = p_avg.begin();
     avgPositionBox.open(avgPositionPtrBegin);
   }
   
   // BEGIN LA
   if (flags.doLoweAndersen) {
       velocityBox.open(velocityPtrBegin);
   }
   // END LA
   // begin gbis
    if (flags.doGBIS) {
      boxesOpen += 5;
      //intRad should already be taken care of
      intRadBox.open(intRad.begin());
      psiSum.resize(numAtoms);//resize array
      psiSum.setall(0);
      psiSumBox.open(psiSum.begin());
      psiFin.resize(numAtoms);//has no box
      psiFin.setall(0);
      bornRad.resize(numAtoms);
      bornRad.setall(0);
      bornRadBox.open(bornRad.begin());
      dEdaSum.resize(numAtoms);//resize array
      dEdaSum.setall(0);
      dEdaSumBox.open(dEdaSum.begin());
      dHdrPrefix.resize(numAtoms);
      dHdrPrefix.setall(0);
      dHdrPrefixBox.open(dHdrPrefix.begin());
    }
   // end gbis

  //LCPO
  if (flags.doLCPO) {
    boxesOpen++;
    lcpoTypeBox.open(lcpoType.begin());
  }

#if CMK_BLUEGENEL
   CmiNetworkProgressAfter (0);
#endif
   
   // Give all force deposit boxes access to forces
   Force *forcePtr;
#ifdef NODEGROUP_FORCE_REGISTER
//#if 0
   // Clear forces if GPU-offload or GPU-resident without device migration
   const bool clearForces = (!simParams->CUDASOAintegrate || 
                             (doneMigration && !simParams->useDeviceMigration) );
   for ( int j = 0; j < Results::maxNumForces; ++j )
   {
     f[j].resize(numAtoms);
     forcePtr = f[j].begin();
     if(clearForces) memset (forcePtr, 0, sizeof (Force) * numAtoms);
     results.f[j] = forcePtr;
   }
#else
    for ( int j = 0; j < Results::maxNumForces; ++j )
     {
       f[j].resize(numAtoms);
       forcePtr = f[j].begin();
       memset (forcePtr, 0, sizeof (Force) * numAtoms);
       results.f[j] = forcePtr;
     }
#ifdef DEBUG_MINIMIZE
    Force *pf = results.f[1];
    int k=0;
    printf("%s, line %d\n", __FILE__, __LINE__);
    printf("  initial:  pf[%d] = %f %f %f\n", k, pf[k].x, pf[k].y, pf[k].z);
#endif
#endif
   // fprintf(stderr, "(Pe[%d] tstep %d) opening box on patch %d\n", 
   //   CkMyPe(), this->flags.step, this->patchID);
   forceBox.open(&results);

   #ifdef NAMD_AVXTILES
   // Zero data in arrays in "Tiles" data structures if they have been touched
   if (Node::Object()->simParameters->useAVXTiles)
     tiles.zeroForces(flags.doFullElectrostatics);
   #endif

   if ( ! computesSortedByPriority ) {
     if (positionComputeList.size() == 0 && PatchMap::Object()->node(patchID) != CkMyPe()) {
       iout << iINFO << "PATCH_COUNT: Patch " << patchID 
            << " on PE " << CkMyPe() <<" home patch " 
            << PatchMap::Object()->node(patchID)
            << " does not have any computes\n" 
            << endi;
     }

     // XXX TODO: Maybe get rid of this sorting and see what happens
     cptr_sortop_priority so;
     std::sort(positionComputeList.begin(), positionComputeList.end(), so);
     computesSortedByPriority = 1;
     int i;
     for ( i=0; i<positionComputeList.size(); ++i ) {
       if ( positionComputeList[i]->priority() > PME_PRIORITY ) break;
     }
     firstHoldableCompute = i;
   }

   int seq = flags.sequence;

   // Iterate over compute objects that need to be informed we are ready
   Compute **cid = positionComputeList.begin();
   for ( int i=0; i < firstHoldableCompute; ++i, ++cid ) {
     (*cid)->patchReady(patchID,doneMigration,seq);
   }
   Compute **cend = positionComputeList.end();
   // gzheng
   if (Sync::Object()->holdComputes(patchID, cid, cend, doneMigration, seq)) {
     return;
   }

   for( ; cid != cend; cid++ ) {
     (*cid)->patchReady(patchID,doneMigration,seq);
   }
   
}

psiSumBoxClosed()

void Patch::psiSumBoxClosed

(

void

)

Definition at line 377 of file Patch.C.

References boxClosed().

                                {
  this->boxClosed(5);
}

registerAvgPositionPickup()

Box< Patch, CompAtom > * Patch::registerAvgPositionPickup

(

Compute *

cid

)

Definition at line 133 of file Patch.C.

References avgPositionBox, OwnerBox< Owner, Data >::checkOut(), and Compute::cid.

Referenced by ComputeNonbondedPair::initialize(), ComputeNonbondedSelf::initialize(), ComputePme::initialize(), PatchElem::PatchElem(), and TuplePatchElem::TuplePatchElem().

{
   //DebugM(4, "registerAvgPositionPickup("<<patchID<<") from " << cid->cid << "\n");
   return avgPositionBox.checkOut(cid->cid);
}

registerBornRadPickup()

Box< Patch, Real > * Patch::registerBornRadPickup

(

Compute *

cid

)

Definition at line 195 of file Patch.C.

References bornRadBox, OwnerBox< Owner, Data >::checkOut(), and Compute::cid.

Referenced by ComputeNonbondedPair::initialize(), and ComputeNonbondedSelf::initialize().

                                                          {
  return bornRadBox.checkOut(cid->cid);
}

registerDEdaSumDeposit()

Box< Patch, GBReal > * Patch::registerDEdaSumDeposit

(

Compute *

cid

)

Definition at line 203 of file Patch.C.

References SortedArray< Elem >::add(), OwnerBox< Owner, Data >::checkOut(), Compute::cid, DebugM, dEdaSumBox, dEdaSumComputeList, and ResizeArray< Elem >::size().

Referenced by ComputeNonbondedPair::initialize(), and ComputeNonbondedSelf::initialize().

                                                             {
  if (dEdaSumComputeList.add(cid) < 0) {
    DebugM(7, "registerDEdaSumDeposit() failed for cid " << cid->cid << std::endl);
    DebugM(7, "  size of dEdaSumCompueList " << dEdaSumComputeList.size() << std::endl);
     return NULL;
  }
  return dEdaSumBox.checkOut(cid->cid);
}

registerDHdrPrefixPickup()

Box< Patch, Real > * Patch::registerDHdrPrefixPickup

(

Compute *

cid

)

Definition at line 217 of file Patch.C.

References OwnerBox< Owner, Data >::checkOut(), Compute::cid, and dHdrPrefixBox.

Referenced by ComputeNonbondedPair::initialize(), and ComputeNonbondedSelf::initialize().

{
  return dHdrPrefixBox.checkOut(cid->cid);
}

registerForceDeposit()

Box< Patch, Results > * Patch::registerForceDeposit

(

Compute *

cid

)

Definition at line 227 of file Patch.C.

References SortedArray< Elem >::add(), OwnerBox< Owner, Data >::checkOut(), Compute::cid, DebugM, forceBox, forceComputeList, and ResizeArray< Elem >::size().

Referenced by ComputePatch::initialize(), ComputeHomePatch::initialize(), ComputePatchPair::initialize(), ComputePme::initialize(), ComputeLCPO::initialize(), PatchElem::PatchElem(), and TuplePatchElem::TuplePatchElem().

{
   if (forceComputeList.add(cid) < 0)
   {
     DebugM(7, "registerForceDeposit() failed for cid " << cid->cid << std::endl);
     DebugM(7, "  size of forceCompueList " << forceComputeList.size() << std::endl);
     return NULL;
   }
   return forceBox.checkOut(cid->cid);
}

registerIntRadPickup()

Box< Patch, Real > * Patch::registerIntRadPickup

(

Compute *

cid

)

Definition at line 178 of file Patch.C.

References OwnerBox< Owner, Data >::checkOut(), Compute::cid, and intRadBox.

Referenced by ComputeNonbondedPair::initialize(), and ComputeNonbondedSelf::initialize().

                                                         {
  return intRadBox.checkOut(cid->cid);
}

registerLcpoTypePickup()

Box< Patch, int > * Patch::registerLcpoTypePickup

(

Compute *

cid

)

Definition at line 187 of file Patch.C.

References OwnerBox< Owner, Data >::checkOut(), Compute::cid, and lcpoTypeBox.

Referenced by ComputeLCPO::initialize().

                                                          {
  return lcpoTypeBox.checkOut(cid->cid);
}

registerPositionPickup()

Box< Patch, CompAtom > * Patch::registerPositionPickup

(

Compute *

cid

)

Definition at line 106 of file Patch.C.

References SortedArray< Elem >::add(), OwnerBox< Owner, Data >::checkOut(), Compute::cid, computesSortedByPriority, DebugM, positionBox, positionComputeList, and SortedArray< Elem >::sort().

Referenced by ComputePatch::initialize(), ComputeHomePatch::initialize(), ComputePatchPair::initialize(), ComputePme::initialize(), ComputeLCPO::initialize(), PatchElem::PatchElem(), and TuplePatchElem::TuplePatchElem().

{
   if ( computesSortedByPriority ) {
     positionComputeList.sort();
     computesSortedByPriority = 0;
   }
   //DebugM(4, "registerPositionPickupa("<<patchID<<") from " << cid->cid << "\n");
   if (positionComputeList.add(cid) < 0)
   {
     DebugM(7, "registerPositionPickup() failed for cid " << cid->cid << std::endl);
     return NULL;
   }
   return positionBox.checkOut(cid->cid);
}

registerPsiSumDeposit()

Box< Patch, GBReal > * Patch::registerPsiSumDeposit

(

Compute *

cid

)

Definition at line 163 of file Patch.C.

References SortedArray< Elem >::add(), OwnerBox< Owner, Data >::checkOut(), Compute::cid, DebugM, psiSumBox, psiSumComputeList, and ResizeArray< Elem >::size().

Referenced by ComputeNonbondedPair::initialize(), and ComputeNonbondedSelf::initialize().

                                                            {

  if (psiSumComputeList.add(cid) < 0) {
    DebugM(7, "registerPsiSumDeposit() failed for cid " << cid->cid << std::endl);
    DebugM(7, "  size of psiSumCompueList " << psiSumComputeList.size() << std::endl);
     return NULL;
  }
  return psiSumBox.checkOut(cid->cid);
}

registerVelocityPickup()

Box< Patch, CompAtom > * Patch::registerVelocityPickup

(

Compute *

cid

)

Definition at line 147 of file Patch.C.

References OwnerBox< Owner, Data >::checkOut(), Compute::cid, and velocityBox.

Referenced by ComputeNonbondedPair::initialize(), and ComputeNonbondedSelf::initialize().

{
   //DebugM(4, "registerVelocityPickup("<<patchID<<") from " << cid->cid << "\n");
   return velocityBox.checkOut(cid->cid);
}

setNumFixedAtoms()

void Patch::setNumFixedAtoms ( int  numFixed )

inline

Definition at line 113 of file Patch.h.

References numFixedAtoms.

Referenced by PatchMgr::setHomePatchFixedAtomNum().

{ numFixedAtoms=numFixed; }  // not updated

unregisterAvgPositionPickup()

void Patch::unregisterAvgPositionPickup	(	Compute *	cid,
		Box< Patch, CompAtom > **const	box
	)

Definition at line 139 of file Patch.C.

References avgPositionBox, OwnerBox< Owner, Data >::checkIn(), Compute::cid, and DebugM.

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), ComputeNonbondedSelf::~ComputeNonbondedSelf(), ComputePmeCUDA::~ComputePmeCUDA(), and ComputeSelfTuples< TholeElem, Thole, TholeValue >::~ComputeSelfTuples().

{
   DebugM(4, "UnregisterAvgPositionPickup from " << cid->cid << "\n");
   avgPositionBox.checkIn(*box);
   *box = 0;
}

unregisterBornRadPickup()

void Patch::unregisterBornRadPickup	(	Compute *	cid,
		Box< Patch, Real > **const	box
	)

Definition at line 198 of file Patch.C.

References bornRadBox, and OwnerBox< Owner, Data >::checkIn().

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), and ComputeNonbondedSelf::~ComputeNonbondedSelf().

                                                                            {
  bornRadBox.checkIn(*box);
  *box = 0;
}

unregisterDEdaSumDeposit()

void Patch::unregisterDEdaSumDeposit	(	Compute *	cid,
		Box< Patch, GBReal > **const	box
	)

Definition at line 211 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), dEdaSumBox, dEdaSumComputeList, and SortedArray< Elem >::del().

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), and ComputeNonbondedSelf::~ComputeNonbondedSelf().

                                                                              {
  dEdaSumComputeList.del(cid);
  dEdaSumBox.checkIn(*box);
  *box = 0;
}

unregisterDHdrPrefixPickup()

void Patch::unregisterDHdrPrefixPickup	(	Compute *	cid,
		Box< Patch, Real > **const	box
	)

Definition at line 221 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), and dHdrPrefixBox.

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), and ComputeNonbondedSelf::~ComputeNonbondedSelf().

                                                                               {
  dHdrPrefixBox.checkIn(*box);
  *box = 0;
}

unregisterForceDeposit()

void Patch::unregisterForceDeposit	(	Compute *	cid,
		Box< Patch, Results > **const	box
	)

Definition at line 238 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), DebugM, SortedArray< Elem >::del(), forceBox, and forceComputeList.

Referenced by ComputeHomePatch::~ComputeHomePatch(), ComputeLCPO::~ComputeLCPO(), ComputePatch::~ComputePatch(), ComputePatchPair::~ComputePatchPair(), ComputePmeCUDA::~ComputePmeCUDA(), and ComputeSelfTuples< TholeElem, Thole, TholeValue >::~ComputeSelfTuples().

{
   DebugM(4, "unregisterForceDeposit() computeID("<<cid<<")"<<std::endl);
   forceComputeList.del(cid);
   forceBox.checkIn(*box);
   *box = 0;
}

unregisterIntRadPickup()

void Patch::unregisterIntRadPickup	(	Compute *	cid,
		Box< Patch, Real > **const	box
	)

Definition at line 181 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), and intRadBox.

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), and ComputeNonbondedSelf::~ComputeNonbondedSelf().

                                                                           {
  intRadBox.checkIn(*box);
  *box = 0;
}

unregisterLcpoTypePickup()

void Patch::unregisterLcpoTypePickup	(	Compute *	cid,
		Box< Patch, int > **const	box
	)

Definition at line 190 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), and lcpoTypeBox.

Referenced by ComputeLCPO::~ComputeLCPO().

                                                                            {
  lcpoTypeBox.checkIn(*box);
  *box = 0;
}

unregisterPositionPickup()

void Patch::unregisterPositionPickup	(	Compute *	cid,
		Box< Patch, CompAtom > **const	box
	)

Definition at line 121 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), Compute::cid, computesSortedByPriority, DebugM, SortedArray< Elem >::del(), positionBox, positionComputeList, and SortedArray< Elem >::sort().

Referenced by ComputeHomePatch::~ComputeHomePatch(), ComputeLCPO::~ComputeLCPO(), ComputePatch::~ComputePatch(), ComputePatchPair::~ComputePatchPair(), ComputePmeCUDA::~ComputePmeCUDA(), and ComputeSelfTuples< TholeElem, Thole, TholeValue >::~ComputeSelfTuples().

{
   if ( computesSortedByPriority ) {
     positionComputeList.sort();
     computesSortedByPriority = 0;
   }
   DebugM(4, "UnregisterPositionPickup from " << cid->cid << "\n");
   positionComputeList.del(cid);
   positionBox.checkIn(*box);
   *box = 0;
}

unregisterPsiSumDeposit()

void Patch::unregisterPsiSumDeposit	(	Compute *	cid,
		Box< Patch, GBReal > **const	box
	)

Definition at line 173 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), SortedArray< Elem >::del(), psiSumBox, and psiSumComputeList.

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), and ComputeNonbondedSelf::~ComputeNonbondedSelf().

                                                                              {
  psiSumComputeList.del(cid);
  psiSumBox.checkIn(*box);
  *box = 0;
}

unregisterVelocityPickup()

void Patch::unregisterVelocityPickup	(	Compute *	cid,
		Box< Patch, CompAtom > **const	box
	)

Definition at line 153 of file Patch.C.

References OwnerBox< Owner, Data >::checkIn(), Compute::cid, DebugM, and velocityBox.

Referenced by ComputeNonbondedPair::~ComputeNonbondedPair(), and ComputeNonbondedSelf::~ComputeNonbondedSelf().

{
   DebugM(4, "UnregisterVelocityPickup from " << cid->cid << "\n");
   velocityBox.checkIn(*box);
   *box = 0;
}

velocityBoxClosed()

void Patch::velocityBoxClosed

(

void

)

Definition at line 366 of file Patch.C.

References boxClosed(), DebugM, patchID, and velocityPtrBegin.

{
   DebugM(4, "patchID("<<patchID<<") velocityBoxClosed! call\n");
   velocityPtrBegin = 0;
   this->boxClosed(4);  // ?? Don't know about number
}

Member Data Documentation

_hasNewAtoms

int Patch::_hasNewAtoms

protected

Definition at line 252 of file Patch.h.

Referenced by hasNewAtoms(), and positionsReady().

atomMapper

AtomMapper* Patch::atomMapper

protected

Definition at line 159 of file Patch.h.

Referenced by HomePatch::doAtomMigration(), Sequencer::integrate(), Sequencer::minimize(), Patch(), positionsReady(), ProxyPatch::receiveAll(), HomePatch::recvCheckpointLoad(), HomePatch::recvExchangeMsg(), HomePatch::revert(), HomePatch::~HomePatch(), ~Patch(), and ProxyPatch::~ProxyPatch().

avgPositionBox

OwnerBox<Patch,CompAtom> Patch::avgPositionBox

protected

Definition at line 222 of file Patch.h.

Referenced by positionsReady(), registerAvgPositionPickup(), and unregisterAvgPositionPickup().

avgPositionComputeList

ComputePtrList Patch::avgPositionComputeList

protected

Definition at line 223 of file Patch.h.

avgPositionPtrBegin

CompAtom* Patch::avgPositionPtrBegin

protected

Definition at line 204 of file Patch.h.

Referenced by avgPositionBoxClosed(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), and ProxyPatch::receiveData().

avgPositionPtrEnd

CompAtom* Patch::avgPositionPtrEnd

protected

Definition at line 205 of file Patch.h.

Referenced by HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), and ProxyPatch::receiveData().

bornRad

RealList Patch::bornRad

protected

Definition at line 165 of file Patch.h.

Referenced by HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), HomePatch::gbisP2Ready(), positionsReady(), and ProxyPatch::receiveData().

bornRadBox

OwnerBox<Patch,Real> Patch::bornRadBox

protected

Definition at line 234 of file Patch.h.

Referenced by positionsReady(), registerBornRadPickup(), and unregisterBornRadPickup().

bornRadComputeList

ComputePtrList Patch::bornRadComputeList

protected

Definition at line 235 of file Patch.h.

boxesOpen

int Patch::boxesOpen

protected

Definition at line 250 of file Patch.h.

Referenced by ProxyPatch::boxClosed(), HomePatch::boxClosed(), positionsReady(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), and HomePatch::receiveResult().

child

int* Patch::child

protected

Definition at line 269 of file Patch.h.

Referenced by ProxyPatch::getSpanningTreeChild(), ProxyPatch::getSpanningTreeChildPtr(), Patch(), ProxyPatch::ProxyPatch(), ProxyPatch::setSpanningTree(), and ProxyPatch::~ProxyPatch().

computesSortedByPriority

int Patch::computesSortedByPriority

protected

Definition at line 217 of file Patch.h.

Referenced by positionsReady(), registerPositionPickup(), and unregisterPositionPickup().

cudaAtomPtr

CudaAtom* Patch::cudaAtomPtr

protected

Definition at line 212 of file Patch.h.

Referenced by getCudaAtomList(), Patch(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), and ProxyPatch::receiveData().

dEdaSum

GBRealList Patch::dEdaSum

protected

Definition at line 167 of file Patch.h.

Referenced by ProxyPatch::boxClosed(), HomePatch::gbisComputeAfterP2(), and positionsReady().

dEdaSumBox

OwnerBox<Patch,GBReal> Patch::dEdaSumBox

protected

Definition at line 236 of file Patch.h.

Referenced by HomePatch::boxClosed(), positionsReady(), registerDEdaSumDeposit(), and unregisterDEdaSumDeposit().

dEdaSumComputeList

ComputePtrList Patch::dEdaSumComputeList

protected

Definition at line 237 of file Patch.h.

Referenced by registerDEdaSumDeposit(), and unregisterDEdaSumDeposit().

dHdrPrefix

RealList Patch::dHdrPrefix

protected

Definition at line 166 of file Patch.h.

Referenced by HomePatch::gbisComputeAfterP2(), HomePatch::gbisP3Ready(), positionsReady(), ProxyPatch::receiveData(), and HomePatch::receiveResult().

dHdrPrefixBox

OwnerBox<Patch,Real> Patch::dHdrPrefixBox

protected

Definition at line 238 of file Patch.h.

Referenced by positionsReady(), registerDHdrPrefixPickup(), and unregisterDHdrPrefixPickup().

dHdrPrefixComputeList

ComputePtrList Patch::dHdrPrefixComputeList

protected

Definition at line 239 of file Patch.h.

f

ForceList Patch::f[Results::maxNumForces]

protected

Definition at line 214 of file Patch.h.

Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), HomePatch::addRattleForce(), HomePatch::boxClosed(), Sequencer::calcFixVirial(), forceBoxClosed(), HomePatch::minimize_rattle2(), Sequencer::minimizeMoveDownhill(), HomePatch::mollyMollify(), Sequencer::multigratorPressure(), Sequencer::newMinimizeDirection(), positionsReady(), Sequencer::rattle1(), HomePatch::rattle1old(), HomePatch::receiveResults(), HomePatch::replaceForces(), Sequencer::rescaleaccelMD(), Sequencer::runComputeObjects(), HomePatch::saveForce(), ComputeGlobal::saveTotalForces(), Sequencer::submitCollections(), Sequencer::submitCollections_SOA(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().

firstHoldableCompute

int Patch::firstHoldableCompute

protected

Definition at line 218 of file Patch.h.

Referenced by positionsReady().

flags

Flags Patch::flags

Definition at line 128 of file Patch.h.

Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition(), Sequencer::addVelocityToPosition_SOA(), ProxyPatch::boxClosed(), HomePatch::boxClosed(), HomePatch::buildRattleList(), HomePatch::buildRattleList_SOA(), AngleElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), ComputeGridForce::do_calc(), ComputeEField::doForce(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeGridForce::doForce(), ComputeNonbondedSelf::doForce(), ComputeRestraints::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doPairlistCheck(), ComputePatch::doWork(), ComputePme::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), forceBoxClosed(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), gbisP2Ready(), HomePatch::gbisP2Ready(), gbisP3Ready(), HomePatch::gbisP3Ready(), Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2(), Sequencer::langevinVelocitiesBBK2_SOA(), CudaComputeNonbonded::launchWork(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), Sequencer::minimize(), Sequencer::multigratorPressure(), Sequencer::newtonianVelocities(), ComputeNonbondedSelf::noWork(), ComputePme::noWork(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Sequencer::rattle1(), Sequencer::rattle1_SOA(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), HomePatch::receiveResult(), Sequencer::runComputeObjects(), Sequencer::runComputeObjects_SOA(), Sequencer::submitCollections(), Sequencer::submitCollections_SOA(), Sequencer::submitHalfstep(), Sequencer::submitHalfstep_SOA(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), and ComputePme::ungridForces().

forceBox

OwnerBox<Patch,Results> Patch::forceBox

protected

Definition at line 246 of file Patch.h.

Referenced by positionsReady(), HomePatch::receiveResults(), registerForceDeposit(), HomePatch::registerProxy(), unregisterForceDeposit(), and HomePatch::unregisterProxy().

forceComputeList

ComputePtrList Patch::forceComputeList

protected

Definition at line 247 of file Patch.h.

Referenced by registerForceDeposit(), and unregisterForceDeposit().

intRad

RealList Patch::intRad

protected

Definition at line 162 of file Patch.h.

Referenced by HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), and HomePatch::setGBISIntrinsicRadii().

intRadBox

OwnerBox<Patch,Real> Patch::intRadBox

protected

Definition at line 230 of file Patch.h.

Referenced by positionsReady(), registerIntRadPickup(), and unregisterIntRadPickup().

intRadComputeList

ComputePtrList Patch::intRadComputeList

protected

Definition at line 231 of file Patch.h.

lattice

Lattice& Patch::lattice

Definition at line 127 of file Patch.h.

Referenced by Sequencer::berendsenPressure(), Sequencer::berendsenPressure_SOA(), HomePatch::checkpoint(), AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), HomePatch::depositMigration(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeConsForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeGridForce::doForce(), ComputeRestraints::doForce(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), HomePatch::exchangeAtoms(), forceBoxClosed(), HomePatch::hardWallDrude(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), PatchMgr::moveAllBy(), PatchMgr::moveAtom(), Sequencer::multigratorPressure(), Patch(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), HomePatch::rattle1old(), HomePatch::recvCheckpointLoad(), HomePatch::recvExchangeMsg(), HomePatch::revert(), Sequencer::scalePositionsVelocities(), PatchMgr::setLattice(), Sequencer::submitCollections(), Sequencer::submitCollections_SOA(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), and Sequencer::submitReductions_SOA().

lcpoType

IntList Patch::lcpoType

protected

Definition at line 171 of file Patch.h.

Referenced by positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), HomePatch::setLcpoType(), and ProxyPatch::~ProxyPatch().

lcpoTypeBox

OwnerBox<Patch,int> Patch::lcpoTypeBox

protected

Definition at line 243 of file Patch.h.

Referenced by positionsReady(), registerLcpoTypePickup(), and unregisterLcpoTypePickup().

lcpoTypeComputeList

ComputePtrList Patch::lcpoTypeComputeList

protected

Definition at line 244 of file Patch.h.

nChild

int Patch::nChild

protected

Definition at line 270 of file Patch.h.

Referenced by ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), ProxyPatch::getSpanningTreeChild(), ProxyPatch::getSpanningTreeNChild(), Patch(), ProxyPatch::ProxyPatch(), and ProxyPatch::setSpanningTree().

numAtoms

int Patch::numAtoms

protected

Definition at line 151 of file Patch.h.

Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), Sequencer::addMovDragToPosition(), HomePatch::addRattleForce(), Sequencer::addRotDragToPosition(), Sequencer::addVelocityToPosition(), Sequencer::berendsenPressure(), ProxyPatch::boxClosed(), HomePatch::boxClosed(), HomePatch::buildRattleList(), HomePatch::buildRattleList_SOA(), Sequencer::calcFixVirial(), Sequencer::calcKineticEnergy(), Sequencer::correctMomentum(), HomePatch::depositMigration(), HomePatch::doAtomMigration(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), HomePatch::exchangeAtoms(), forceBoxClosed(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), HomePatch::gbisP2Ready(), HomePatch::gbisP3Ready(), getNumAtoms(), HomePatch::hardWallDrude(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), HomePatch::loweAndersenVelocities(), Sequencer::maximumMove(), Sequencer::minimizationQuenchVelocity(), HomePatch::minimize_rattle2(), Sequencer::minimizeMoveDownhill(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::ProxyPatch(), HomePatch::qmSwapAtoms(), Sequencer::quenchVelocities(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), Sequencer::reassignVelocities(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), HomePatch::recvCheckpointLoad(), HomePatch::recvExchangeMsg(), Sequencer::reinitVelocities(), Sequencer::reloadCharges(), Sequencer::rescaleaccelMD(), Sequencer::rescaleSoluteCharges(), Sequencer::rescaleVelocities(), Sequencer::rescaleVelocitiesByFactor(), HomePatch::revert(), Sequencer::runComputeObjects(), Sequencer::runComputeObjects_SOA(), HomePatch::saveForce(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), Sequencer::scaleVelocities(), HomePatch::setGBISIntrinsicRadii(), HomePatch::setLcpoType(), Sequencer::stochRescaleVelocities(), Sequencer::submitHalfstep(), HomePatch::submitLoadStats(), Sequencer::submitMinimizeReductions(), Sequencer::submitMomentum(), Sequencer::submitReductions(), and Sequencer::tcoupleVelocities().

numFixedAtoms

int Patch::numFixedAtoms

protected

Definition at line 152 of file Patch.h.

Referenced by getNumFixedAtoms(), and setNumFixedAtoms().

p

CompAtomList Patch::p

protected

Definition at line 153 of file Patch.h.

Referenced by HomePatch::doPairlistCheck(), forceBoxClosed(), getCompAtomInfo(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::mollyAverage(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), Sequencer::runComputeObjects(), ProxyPatch::setSpanningTree(), and ProxyPatch::~ProxyPatch().

p_avg

CompAtomList Patch::p_avg

protected

Definition at line 154 of file Patch.h.

Referenced by HomePatch::mollyAverage(), HomePatch::mollyMollify(), HomePatch::positionsReady(), and HomePatch::positionsReady_SOA().

patchID

const PatchID Patch::patchID

protected

Definition at line 150 of file Patch.h.

Referenced by ProxyPatch::boxClosed(), HomePatch::boxClosed(), HomePatch::buildRattleList(), HomePatch::buildRattleList_SOA(), HomePatch::buildSpanningTree(), HomePatch::depositMigration(), HomePatch::doAtomMigration(), HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), forceBoxClosed(), gbisP2Ready(), HomePatch::gbisP2Ready(), gbisP3Ready(), HomePatch::gbisP3Ready(), getPatchID(), Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::ProxyPatch(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), HomePatch::receiveResults(), HomePatch::recvCheckpointLoad(), HomePatch::recvCheckpointReq(), HomePatch::recvCheckpointStore(), HomePatch::registerProxy(), Sequencer::runComputeObjects_SOA(), ComputeGlobal::saveTotalForces(), HomePatch::sendProxies(), HomePatch::sendSpanningTree(), HomePatch::submitLoadStats(), velocityBoxClosed(), and ProxyPatch::~ProxyPatch().

pExt

CompAtomExtList Patch::pExt

protected

Definition at line 181 of file Patch.h.

Referenced by HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), getCompAtomExtInfo(), positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), Sequencer::runComputeObjects(), HomePatch::setLcpoType(), Sequencer::submitMinimizeReductions(), and ProxyPatch::~ProxyPatch().

positionBox

OwnerBox<Patch,CompAtom> Patch::positionBox

protected

Definition at line 220 of file Patch.h.

Referenced by positionsReady(), registerPositionPickup(), and unregisterPositionPickup().

positionComputeList

ComputePtrList Patch::positionComputeList

protected

Definition at line 221 of file Patch.h.

Referenced by gbisP2Ready(), gbisP3Ready(), getNumComputes(), positionsReady(), registerPositionPickup(), and unregisterPositionPickup().

psiFin

GBRealList Patch::psiFin

protected

Definition at line 164 of file Patch.h.

Referenced by HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), positionsReady(), and HomePatch::receiveResult().

psiSum

GBRealList Patch::psiSum

protected

Definition at line 163 of file Patch.h.

Referenced by ProxyPatch::boxClosed(), HomePatch::gbisComputeAfterP1(), and positionsReady().

psiSumBox

OwnerBox<Patch,GBReal> Patch::psiSumBox

protected

Definition at line 232 of file Patch.h.

Referenced by HomePatch::boxClosed(), positionsReady(), registerPsiSumDeposit(), and unregisterPsiSumDeposit().

psiSumComputeList

ComputePtrList Patch::psiSumComputeList

protected

Definition at line 233 of file Patch.h.

Referenced by registerPsiSumDeposit(), and unregisterPsiSumDeposit().

results

Results Patch::results

protected

Definition at line 215 of file Patch.h.

Referenced by forceBoxClosed(), and positionsReady().

v

CompAtomList Patch::v

protected

Definition at line 156 of file Patch.h.

Referenced by HomePatch::loweAndersenFinish(), HomePatch::loweAndersenVelocities(), HomePatch::positionsReady(), and HomePatch::positionsReady_SOA().

velocityBox

OwnerBox<Patch,CompAtom> Patch::velocityBox

protected

Definition at line 225 of file Patch.h.

Referenced by positionsReady(), registerVelocityPickup(), and unregisterVelocityPickup().

velocityComputeList

ComputePtrList Patch::velocityComputeList

protected

Definition at line 226 of file Patch.h.

velocityPtrBegin

CompAtom* Patch::velocityPtrBegin

protected

Definition at line 208 of file Patch.h.

Referenced by positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), and velocityBoxClosed().

velocityPtrEnd

CompAtom* Patch::velocityPtrEnd

protected

Definition at line 209 of file Patch.h.

Referenced by HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), and ProxyPatch::receiveData().

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

• Patch.h
• Patch.C