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Patch Class Reference

#include <Patch.h>

Inheritance diagram for Patch:

HomePatch ProxyPatch List of all members.

Public Member Functions

 Patch (PatchID pd)
int hasNewAtoms ()
virtual ~Patch (void)
Box< Patch, CompAtom > * registerPositionPickup (ComputeID cid, int trans=13)
void unregisterPositionPickup (ComputeID cid, Box< Patch, CompAtom > **const box)
Box< Patch, CompAtom > * registerAvgPositionPickup (ComputeID cid, int trans=13)
void unregisterAvgPositionPickup (ComputeID cid, Box< Patch, CompAtom > **const box)
Box< Patch, Results > * registerForceDeposit (ComputeID cid)
void unregisterForceDeposit (ComputeID cid, Box< Patch, Results > **const box)
void positionsReady (int n=0)
void positionBoxClosed (void)
void forceBoxClosed (void)
void avgPositionBoxClosed (void)
int getNumAtoms ()
int getNumFixedAtoms ()
void setNumFixedAtoms (int numFixed)
PatchID getPatchID ()
int getNumComputes ()
CompAtomExt * getCompAtomExtInfo ()

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
CompAtomExtList pExt
CompAtom * avgPositionPtrBegin
CompAtom * avgPositionPtrEnd
ForceList f [Results::maxNumForces]
Results results
OwnerBox< Patch, CompAtom > positionBox
ComputeIDList positionComputeList
OwnerBox< Patch, CompAtom > avgPositionBox
ComputeIDList avgPositionComputeList
OwnerBox< Patch, Results > forceBox
ComputeIDList forceComputeList
int boxesOpen
int _hasNewAtoms

Constructor & Destructor Documentation

Patch::Patch (  PatchID  pd  ) 
 

Definition at line 27 of file Patch.C.

References SimParameters::lattice, lattice, NAMD_SeparateWaters, Node::Object(), and Node::simParameters.

00027                        :
00028    lattice(flags.lattice),
00029    patchID(pd), numAtoms(0), numFixedAtoms(0),
00030    avgPositionPtrBegin(0), avgPositionPtrEnd(0),
00031    positionBox(this,&Patch::positionBoxClosed),
00032    avgPositionBox(this,&Patch::avgPositionBoxClosed),
00033    forceBox(this,&Patch::forceBoxClosed),
00034    boxesOpen(0), _hasNewAtoms(0)
00035 
00036    // DMK - Atom Separation (water vs. non-water)
00037    #if NAMD_SeparateWaters != 0
00038      ,numWaterAtoms(-1)
00039    #endif
00040 {
00041 #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
00042     positionPtrBegin = 0;
00043     positionPtrEnd = 0;
00044 #endif
00045 
00046 #ifdef NODEAWARE_PROXY_SPANNINGTREE
00047   numChild = 0;
00048   children = NULL;
00049   #ifdef USE_NODEPATCHMGR
00050   nodeChildren = NULL;
00051   numNodeChild = 0;
00052   #endif
00053 #endif
00054 
00055   lattice = Node::Object()->simParameters->lattice;
00056 }

virtual Patch::~Patch (  void   )  [inline, virtual]
 

Definition at line 34 of file Patch.h.

00034 { };

Member Function Documentation

void Patch::avgPositionBoxClosed (  void   ) 
 

Definition at line 125 of file Patch.C.

References avgPositionPtrBegin, and boxClosed().

00126 {
00127    avgPositionPtrBegin = 0;
00128    this->boxClosed(3);
00129 }

virtual void Patch::boxClosed (  int   )  [protected, pure virtual]
 

Implemented in HomePatch, and ProxyPatch.

Referenced by avgPositionBoxClosed(), forceBoxClosed(), and positionBoxClosed().

void Patch::forceBoxClosed (  void   ) 
 

Definition at line 115 of file Patch.C.

References boxClosed(), DebugM, Results::f, j, patchID, and results.

00116 {
00117    DebugM(4, "patchID("<<patchID<<") forceBoxClosed! call\n");
00118    for (int j = 0; j < Results::maxNumForces; ++j )
00119    {
00120      results.f[j] = 0;
00121    }
00122    this->boxClosed(1);
00123 }

CompAtomExt* Patch::getCompAtomExtInfo (   )  [inline]
 

Definition at line 67 of file Patch.h.

Referenced by ComputePatchPair::doWork(), ComputePatch::doWork(), and ComputeNonbondedCUDA::doWork().

00067 { return pExt.begin(); }

int Patch::getNumAtoms (   )  [inline]
 

Definition at line 55 of file Patch.h.

Referenced by WorkDistrib::assignNodeToPatch(), ComputePatchPair::atomUpdate(), ComputePatch::atomUpdate(), ComputeHomePatch::atomUpdate(), ComputeGridForce::doForce(), ComputeNonbondedCUDA::doWork(), dumpbench(), ComputeGridForce::finishForce(), ComputePatchPair::initialize(), ComputePatch::initialize(), ComputeHomePatch::initialize(), ComputeHomeTuples< ExclElem, Exclusion, int >::loadTuples(), and PatchMgr::moveAllBy().

00055 { return numAtoms; }

int Patch::getNumComputes (   )  [inline]
 

Definition at line 65 of file Patch.h.

00065 { return positionComputeList.size(); }

int Patch::getNumFixedAtoms (   )  [inline]
 

Definition at line 62 of file Patch.h.

00062 { return numFixedAtoms; }  // not updated

PatchID Patch::getPatchID (   )  [inline]
 

Definition at line 64 of file Patch.h.

References PatchID.

Referenced by ProxyMgr::createProxy(), ComputePatch::initialize(), ComputeHomePatch::initialize(), PatchElem::PatchElem(), Sequencer::rebalanceLoad(), Sequencer::Sequencer(), and TuplePatchElem::TuplePatchElem().

00064 { return patchID; }

int Patch::hasNewAtoms (   )  [inline]
 

Definition at line 33 of file Patch.h.

00033 { return _hasNewAtoms; }

void Patch::positionBoxClosed (  void   ) 
 

Definition at line 109 of file Patch.C.

References boxClosed().

00110 {
00111    //positionPtrBegin = 0;
00112    this->boxClosed(0);
00113 }

void Patch::positionsReady (  int  n = 0  ) 
 

Reimplemented in HomePatch.

Definition at line 133 of file Patch.C.

References _hasNewAtoms, avgPositionBox, avgPositionPtrBegin, ResizeArrayPrimIter< T >::begin(), ResizeArray< Elem >::begin(), boxesOpen, ComputeMap::compute(), ComputeIDListIter, DebugM, Flags::doMolly, ResizeArrayPrimIter< T >::end(), ResizeArray< Elem >::end(), Results::f, f, flags, Force, forceBox, Sync::holdComputes(), iINFO(), iout, j, PatchMap::node(), numAtoms, PatchMap::Object(), Sync::Object(), AtomMap::Object(), ComputeMap::Object(), OwnerBox< Owner, Data >::open(), p, patchID, Compute::patchReady(), pExt, positionBox, positionComputeList, AtomMap::registerIDs(), ResizeArray< Elem >::resize(), results, and Flags::sequence.

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

00134 {
00135    DebugM(4,"Patch::positionsReady() - patchID(" << patchID <<")"<<std::endl );
00136    ComputeMap *computeMap = ComputeMap::Object();
00137 
00138    if ( doneMigration ){
00139 // #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
00140 //       AtomMap::Object()->registerIDs(patchID,positionPtrBegin,positionPtrEnd);       
00141 // #else
00142        AtomMap::Object()->registerIDs(patchID,pExt.begin(),pExt.end());
00143 // #endif
00144    }
00145 
00146    boxesOpen = 2;
00147    if ( flags.doMolly ) boxesOpen++;
00148    _hasNewAtoms = (doneMigration != 0);
00149 
00150 #if CMK_BLUEGENEL
00151    CmiNetworkProgressAfter (0);
00152 #endif
00153 
00154    // Give all position pickup boxes access to positions
00155    //positionPtrBegin = p.begin();
00156 #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
00157    positionBox.open(positionPtrBegin);
00158 #else
00159    positionBox.open(p.begin());
00160 #endif
00161    if ( flags.doMolly ) {
00162      //avgPositionPtrBegin = p_avg.begin();
00163      avgPositionBox.open(avgPositionPtrBegin);
00164    }
00165 
00166 #if CMK_BLUEGENEL
00167    CmiNetworkProgressAfter (0);
00168 #endif
00169    
00170    // Give all force deposit boxes access to forces
00171    Force *forcePtr;
00172    for ( int j = 0; j < Results::maxNumForces; ++j )
00173     {
00174       f[j].resize(numAtoms);
00175       forcePtr = f[j].begin();
00176       memset (forcePtr, 0, sizeof (Force) * numAtoms);
00177       results.f[j] = forcePtr;
00178     }
00179    forceBox.open(&results);
00180 
00181    // Iterate over compute objects that need to be informed we are ready
00182    ComputeIDListIter cid(positionComputeList);
00183    // gzheng
00184    if (useSync) {
00185      if (Sync::Object()->holdComputes(patchID, cid, doneMigration))
00186        return;
00187    }
00188 
00189    int compute_count = 0;
00190    int seq = flags.sequence;
00191    for(cid = cid.begin(); cid != cid.end(); cid++)
00192    {
00193          compute_count++;
00194          computeMap->compute(*cid)->patchReady(patchID,doneMigration,seq);
00195    }
00196    if (compute_count == 0 && PatchMap::Object()->node(patchID) != CkMyPe()) {
00197        iout << iINFO << "PATCH_COUNT: Patch " << patchID 
00198             << " on PE " << CkMyPe() <<" home patch " 
00199             << PatchMap::Object()->node(patchID)
00200             << " does not have any computes\n" 
00201             << endi;
00202    }
00203 }

Box< Patch, CompAtom > * Patch::registerAvgPositionPickup (  ComputeID  cid,
int  trans = 13
) 
 

Definition at line 77 of file Patch.C.

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

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

00078 {
00079    //DebugM(4, "registerAvgPositionPickup("<<patchID<<") from " << cid << "\n");
00080    return avgPositionBox.checkOut();
00081 }

Box< Patch, Results > * Patch::registerForceDeposit (  ComputeID  cid  ) 
 

Definition at line 90 of file Patch.C.

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

Referenced by ComputePatchPair::initialize(), ComputePatch::initialize(), ComputeHomePatch::initialize(), PatchElem::PatchElem(), ComputeNonbondedCUDA::requirePatch(), and TuplePatchElem::TuplePatchElem().

00091 {
00092    if (forceComputeList.add(cid) < 0)
00093    {
00094      DebugM(7, "registerForceDeposit() failed for cid " << cid << std::endl);
00095      DebugM(7, "  size of forceCompueList " << forceComputeList.size() << std::endl);
00096      return NULL;
00097    }
00098    return forceBox.checkOut();
00099 }

Box< Patch, CompAtom > * Patch::registerPositionPickup (  ComputeID  cid,
int  trans = 13
) 
 

Definition at line 58 of file Patch.C.

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

Referenced by ComputePatchPair::initialize(), ComputePatch::initialize(), ComputeHomePatch::initialize(), PatchElem::PatchElem(), ComputeNonbondedCUDA::requirePatch(), and TuplePatchElem::TuplePatchElem().

00059 {
00060    //DebugM(4, "registerPositionPickupa("<<patchID<<") from " << cid << "\n");
00061    if (positionComputeList.add(cid) < 0)
00062    {
00063      DebugM(7, "registerPositionPickup() failed for cid " << cid << std::endl);
00064      return NULL;
00065    }
00066    return positionBox.checkOut();
00067 }

void Patch::setNumFixedAtoms (  int  numFixed  )  [inline]
 

Definition at line 63 of file Patch.h.

Referenced by PatchMgr::setHomePatchFixedAtomNum().

00063 { numFixedAtoms=numFixed; }  // not updated

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

Definition at line 83 of file Patch.C.

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

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

00084 {
00085    DebugM(4, "UnregisterAvgPositionPickup from " << cid << "\n");
00086    avgPositionBox.checkIn(*box);
00087    *box = 0;
00088 }

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

Definition at line 101 of file Patch.C.

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

Referenced by ComputeHomePatch::~ComputeHomePatch(), ComputePatch::~ComputePatch(), and ComputePatchPair::~ComputePatchPair().

00102 {
00103    DebugM(4, "unregisterForceDeposit() computeID("<<cid<<")"<<std::endl);
00104    forceComputeList.del(cid);
00105    forceBox.checkIn(*box);
00106    *box = 0;
00107 }

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

Definition at line 69 of file Patch.C.

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

Referenced by ComputeHomePatch::~ComputeHomePatch(), ComputePatch::~ComputePatch(), and ComputePatchPair::~ComputePatchPair().

00070 {
00071    DebugM(4, "UnregisterPositionPickup from " << cid << "\n");
00072    positionComputeList.del(cid);
00073    positionBox.checkIn(*box);
00074    *box = 0;
00075 }

Member Data Documentation

int Patch::_hasNewAtoms [protected]
 

Definition at line 121 of file Patch.h.

Referenced by positionsReady().

OwnerBox<Patch,CompAtom> Patch::avgPositionBox [protected]
 

Definition at line 113 of file Patch.h.

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

ComputeIDList Patch::avgPositionComputeList [protected]
 

Definition at line 114 of file Patch.h.

CompAtom* Patch::avgPositionPtrBegin [protected]
 

Definition at line 105 of file Patch.h.

Referenced by avgPositionBoxClosed(), and positionsReady().

CompAtom* Patch::avgPositionPtrEnd [protected]
 

Definition at line 106 of file Patch.h.

int Patch::boxesOpen [protected]
 

Definition at line 119 of file Patch.h.

Referenced by positionsReady().

ForceList Patch::f[Results::maxNumForces] [protected]
 

Definition at line 108 of file Patch.h.

Referenced by Sequencer::minimizeMoveDownhill(), Sequencer::newMinimizeDirection(), positionsReady(), Sequencer::runComputeObjects(), ComputeGlobal::saveTotalForces(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().

Flags Patch::flags
 

Definition at line 70 of file Patch.h.

Referenced by ExclElem::computeForce(), ComputeStir::doForce(), ComputeRestraints::doForce(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeEField::doForce(), ComputeNonbondedCUDA::doWork(), Sync::holdComputes(), Sequencer::integrate(), Sequencer::minimize(), ComputeNonbondedPair::noWork(), positionsReady(), and Sequencer::runComputeObjects().

OwnerBox<Patch,Results> Patch::forceBox [protected]
 

Definition at line 115 of file Patch.h.

Referenced by positionsReady(), registerForceDeposit(), and unregisterForceDeposit().

ComputeIDList Patch::forceComputeList [protected]
 

Definition at line 116 of file Patch.h.

Referenced by registerForceDeposit(), and unregisterForceDeposit().

Lattice& Patch::lattice
 

Definition at line 69 of file Patch.h.

Referenced by Sequencer::berendsenPressure(), ExclElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), BondElem::computeForce(), AngleElem::computeForce(), ComputeStir::doForce(), ComputeRestraints::doForce(), ComputeNonbondedSelf::doForce(), ComputeNonbondedPair::doForce(), ComputeGridForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeConsForce::doForce(), ComputeGridForce::finishForce(), Sequencer::langevinPiston(), PatchMgr::moveAllBy(), PatchMgr::moveAtom(), Patch(), PatchMgr::setLattice(), Sequencer::submitCollections(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

int Patch::numAtoms [protected]
 

Definition at line 75 of file Patch.h.

Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), Sequencer::berendsenPressure(), Sequencer::correctMomentum(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), Sequencer::maximumMove(), Sequencer::minimizationQuenchVelocity(), Sequencer::minimizeMoveDownhill(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), positionsReady(), Sequencer::quenchVelocities(), Sequencer::reassignVelocities(), Sequencer::reinitVelocities(), Sequencer::reloadCharges(), Sequencer::rescaleVelocities(), Sequencer::rescaleVelocitiesByFactor(), Sequencer::runComputeObjects(), ComputeGlobal::saveTotalForces(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitMomentum(), Sequencer::submitReductions(), and Sequencer::tcoupleVelocities().

int Patch::numFixedAtoms [protected]
 

Definition at line 76 of file Patch.h.

CompAtomList Patch::p [protected]
 

Definition at line 77 of file Patch.h.

Referenced by ComputeGridForce::doWork(), and positionsReady().

CompAtomList Patch::p_avg [protected]
 

Definition at line 78 of file Patch.h.

const PatchID Patch::patchID [protected]
 

Definition at line 74 of file Patch.h.

Referenced by forceBoxClosed(), and positionsReady().

CompAtomExtList Patch::pExt [protected]
 

Definition at line 88 of file Patch.h.

Referenced by positionsReady().

OwnerBox<Patch,CompAtom> Patch::positionBox [protected]
 

Definition at line 111 of file Patch.h.

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

ComputeIDList Patch::positionComputeList [protected]
 

Definition at line 112 of file Patch.h.

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

Results Patch::results [protected]
 

Definition at line 109 of file Patch.h.

Referenced by forceBoxClosed(), and positionsReady().

The documentation for this class was generated from the following files:
Generated on Mon Nov 23 05:00:04 2009 for NAMD by  doxygen 1.3.9.1