Main Page | Namespace List | Class Hierarchy | Alphabetical List | Class List | File List | Class Members | File Members

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 ()

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
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   lattice = Node::Object()->simParameters->lattice;
00046 }

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 115 of file Patch.C.

References avgPositionPtrBegin, and boxClosed().

00116 {
00117    avgPositionPtrBegin = 0;
00118    this->boxClosed(3);
00119 }

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 105 of file Patch.C.

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

00106 {
00107    DebugM(4, "patchID("<<patchID<<") forceBoxClosed! call\n");
00108    for (int j = 0; j < Results::maxNumForces; ++j )
00109    {
00110      results.f[j] = 0;
00111    }
00112    this->boxClosed(1);
00113 }

int Patch::getNumAtoms (   )  [inline]
 

Definition at line 55 of file Patch.h.

Referenced by WorkDistrib::assignNodeToPatch(), ComputePatchPair::atomUpdate(), ComputePatch::atomUpdate(), ComputeHomePatch::atomUpdate(), dumpbench(), ComputePatchPair::initialize(), ComputePatch::initialize(), ComputeHomePatch::initialize(), ComputeHomeTuples< BondElem, Bond, BondValue >::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 99 of file Patch.C.

References boxClosed().

00100 {
00101    //positionPtrBegin = 0;
00102    this->boxClosed(0);
00103 }

void Patch::positionsReady (  int  n = 0  ) 
 

Reimplemented in HomePatch.

Definition at line 123 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, PatchMap::node(), numAtoms, PatchMap::Object(), Sync::Object(), AtomMap::Object(), ComputeMap::Object(), OwnerBox< Owner, Data >::open(), p, patchID, Compute::patchReady(), positionBox, positionComputeList, AtomMap::registerIDs(), ResizeArray< Elem >::resize(), results, and Flags::sequence.

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

00124 {
00125    DebugM(4,"Patch::positionsReady() - patchID(" << patchID <<")"<<std::endl );
00126    ComputeMap *computeMap = ComputeMap::Object();
00127 
00128    if ( doneMigration ){
00129 #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
00130        AtomMap::Object()->registerIDs(patchID,positionPtrBegin,positionPtrEnd);       
00131 #else
00132        AtomMap::Object()->registerIDs(patchID,p.begin(),p.end());
00133 #endif
00134    }
00135 
00136    boxesOpen = 2;
00137    if ( flags.doMolly ) boxesOpen++;
00138    _hasNewAtoms = (doneMigration != 0);
00139 
00140 #if CMK_VERSION_BLUEGENE
00141    CmiNetworkProgressAfter (0);
00142 #endif
00143 
00144    // Give all position pickup boxes access to positions
00145    //positionPtrBegin = p.begin();
00146 #ifdef REMOVE_PROXYDATAMSG_EXTRACOPY
00147    positionBox.open(positionPtrBegin);
00148 #else
00149    positionBox.open(p.begin());
00150 #endif
00151    if ( flags.doMolly ) {
00152      //avgPositionPtrBegin = p_avg.begin();
00153      avgPositionBox.open(avgPositionPtrBegin);
00154    }
00155 
00156 #if CMK_VERSION_BLUEGENE
00157    CmiNetworkProgressAfter (0);
00158 #endif
00159    
00160    // Give all force deposit boxes access to forces
00161    Force *forcePtr;
00162    for ( int j = 0; j < Results::maxNumForces; ++j )
00163     {
00164       f[j].resize(numAtoms);
00165       forcePtr = f[j].begin();
00166       memset (forcePtr, 0, sizeof (Force) * numAtoms);
00167       results.f[j] = forcePtr;
00168     }
00169    forceBox.open(&results);
00170 
00171    // Iterate over compute objects that need to be informed we are ready
00172    ComputeIDListIter cid(positionComputeList);
00173    // gzheng
00174    if (useSync) {
00175      if (Sync::Object()->holdComputes(patchID, cid, doneMigration))
00176        return;
00177    }
00178 
00179    int compute_count = 0;
00180    int seq = flags.sequence;
00181    for(cid = cid.begin(); cid != cid.end(); cid++)
00182    {
00183          compute_count++;
00184          computeMap->compute(*cid)->patchReady(patchID,doneMigration,seq);
00185    }
00186    if (compute_count == 0 && PatchMap::Object()->node(patchID) != CkMyPe()) {
00187        iout << iINFO << "PATCH_COUNT: Patch " << patchID 
00188             << " on PE " << CkMyPe() <<" home patch " 
00189             << PatchMap::Object()->node(patchID)
00190             << " does not have any computes\n" 
00191             << endi;
00192    }
00193 }

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

Definition at line 67 of file Patch.C.

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

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

00068 {
00069    //DebugM(4, "registerAvgPositionPickup("<<patchID<<") from " << cid << "\n");
00070    return avgPositionBox.checkOut();
00071 }

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

Definition at line 80 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(), and TuplePatchElem::TuplePatchElem().

00081 {
00082    if (forceComputeList.add(cid) < 0)
00083    {
00084      DebugM(7, "registerForceDeposit() failed for cid " << cid << std::endl);
00085      DebugM(7, "  size of forceCompueList " << forceComputeList.size() << std::endl);
00086      return NULL;
00087    }
00088    return forceBox.checkOut();
00089 }

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

Definition at line 48 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(), and TuplePatchElem::TuplePatchElem().

00049 {
00050    //DebugM(4, "registerPositionPickupa("<<patchID<<") from " << cid << "\n");
00051    if (positionComputeList.add(cid) < 0)
00052    {
00053      DebugM(7, "registerPositionPickup() failed for cid " << cid << std::endl);
00054      return NULL;
00055    }
00056    return positionBox.checkOut();
00057 }

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 73 of file Patch.C.

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

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

00074 {
00075    DebugM(4, "UnregisterAvgPositionPickup from " << cid << "\n");
00076    avgPositionBox.checkIn(*box);
00077    *box = 0;
00078 }

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

Definition at line 91 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().

00092 {
00093    DebugM(4, "unregisterForceDeposit() computeID("<<cid<<")"<<std::endl);
00094    forceComputeList.del(cid);
00095    forceBox.checkIn(*box);
00096    *box = 0;
00097 }

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

Definition at line 59 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().

00060 {
00061    DebugM(4, "UnregisterPositionPickup from " << cid << "\n");
00062    positionComputeList.del(cid);
00063    positionBox.checkIn(*box);
00064    *box = 0;
00065 }

Member Data Documentation

int Patch::_hasNewAtoms [protected]
 

Definition at line 125 of file Patch.h.

Referenced by positionsReady().

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

Definition at line 117 of file Patch.h.

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

ComputeIDList Patch::avgPositionComputeList [protected]
 

Definition at line 118 of file Patch.h.

CompAtom* Patch::avgPositionPtrBegin [protected]
 

Definition at line 109 of file Patch.h.

Referenced by avgPositionBoxClosed(), and positionsReady().

CompAtom* Patch::avgPositionPtrEnd [protected]
 

Definition at line 110 of file Patch.h.

int Patch::boxesOpen [protected]
 

Definition at line 123 of file Patch.h.

Referenced by positionsReady().

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

Definition at line 112 of file Patch.h.

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

Flags Patch::flags
 

Definition at line 72 of file Patch.h.

Referenced by ComputeStir::doForce(), ComputeEField::doForce(), Sync::holdComputes(), Sequencer::integrate(), Sequencer::minimize(), ComputeNonbondedPair::noWork(), positionsReady(), and Sequencer::runComputeObjects().

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

Definition at line 119 of file Patch.h.

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

ComputeIDList Patch::forceComputeList [protected]
 

Definition at line 120 of file Patch.h.

Referenced by registerForceDeposit(), and unregisterForceDeposit().

Lattice& Patch::lattice
 

Definition at line 71 of file Patch.h.

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

int Patch::numAtoms [protected]
 

Definition at line 77 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::newMinimizeDirection(), Sequencer::newMinimizePosition(), positionsReady(), Sequencer::quenchVelocities(), Sequencer::reassignVelocities(), Sequencer::reinitVelocities(), Sequencer::reloadCharges(), Sequencer::rescaleVelocities(), Sequencer::rescaleVelocitiesByFactor(), ComputeGlobal::saveTotalForces(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitMomentum(), Sequencer::submitReductions(), and Sequencer::tcoupleVelocities().

int Patch::numFixedAtoms [protected]
 

Definition at line 78 of file Patch.h.

CompAtomList Patch::p [protected]
 

Definition at line 79 of file Patch.h.

Referenced by positionsReady().

CompAtomList Patch::p_avg [protected]
 

Definition at line 80 of file Patch.h.

const PatchID Patch::patchID [protected]
 

Definition at line 76 of file Patch.h.

Referenced by forceBoxClosed(), and positionsReady().

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

Definition at line 115 of file Patch.h.

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

ComputeIDList Patch::positionComputeList [protected]
 

Definition at line 116 of file Patch.h.

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

Results Patch::results [protected]
 

Definition at line 113 of file Patch.h.

Referenced by forceBoxClosed(), and positionsReady().

The documentation for this class was generated from the following files:
Generated on Sun Jul 6 04:07:47 2008 for NAMD by  doxygen 1.3.9.1