ComputeLCPO Class Reference

#include <ComputeLCPO.h>

Inheritance diagram for ComputeLCPO:
Compute ComputeNonbondedUtil

List of all members.

Public Member Functions

 ComputeLCPO (ComputeID c, PatchID pid[], int t[], ComputeNonbondedWorkArrays *_workArrays, int minPartition, int maxPartition, int numPartitions, int numPatches)
virtual ~ComputeLCPO ()
virtual void initialize ()
virtual void atomUpdate ()
virtual void doWork ()
virtual int noWork ()

Protected Member Functions

virtual void doForce ()

Protected Attributes

int numAtoms [8]
int valid [8][8]
int invalidPatch [8]
CompAtomExt * posExt [8]
CompAtom * pos [8]
Results * force [8]
int * lcpoType [8]
int step
Patch * patch [8]
PatchID patchID [8]
int trans [8]
Box< Patch, CompAtom > * positionBox [8]
Box< Patch, Results > * forceBox [8]
Box< Patch, int > * lcpoTypeBox [8]
ComputeNonbondedWorkArrays *const workArrays
int minPart
int maxPart
int numParts
SubmitReduction * reduction

Detailed Description

Definition at line 100 of file ComputeLCPO.h.

Constructor & Destructor Documentation

ComputeLCPO::ComputeLCPO ( ComputeID  c,
PatchID  pid[],
int  t[],
ComputeNonbondedWorkArrays *  _workArrays,
int  minPartition,
int  maxPartition,
int  numPartitions,
int  numPatches 
)

Definition at line 36 of file ComputeLCPO.C.

References forceBox, Compute::getNumPatches(), lcpoTypeBox, Node::Object(), ReductionMgr::Object(), patch, patchID, positionBox, reduction, REDUCTIONS_BASIC, Compute::setNumPatches(), Node::simParameters, simParams, SimParameters::surface_tension, trans, and ReductionMgr::willSubmit().

00039   : Compute(c), workArrays(_workArrays),
00040     minPart(minPartition), maxPart(maxPartition),
00041     strideIg(numPartitions), numParts(numPartitions),
00042     maxAtomRadius(1.9+1.4)
00043   {
00044 
00045   reduction = ReductionMgr::Object()->willSubmit(REDUCTIONS_BASIC);
00046 
00047   setNumPatches(8);
00048   SimParameters *simParams = Node::Object()->simParameters;
00049   surfTen = simParams->surface_tension;
00050 
00051   for (int i=0; i<getNumPatches(); i++) {
00052     patchID[i] = p[i];
00053     trans[i] = t[i];
00054     patch[i] = NULL;
00055     positionBox[i] = NULL;
00056     forceBox[i] = NULL;
00057     lcpoTypeBox[i] = NULL;
00058   } // for all patches
00059 } // constructor

ComputeLCPO::~ComputeLCPO (  )  [virtual]

Definition at line 61 of file ComputeLCPO.C.

References Compute::cid, DebugM, forceBox, Compute::getNumPatches(), lcpoTypeBox, numAtoms, PatchMap::Object(), PatchMap::patch(), patch, patchID, positionBox, reduction, Patch::unregisterForceDeposit(), Patch::unregisterLcpoTypePickup(), and Patch::unregisterPositionPickup().

00061                           {
00062   DebugM(4, "~ComputeLCPO("<<cid<<") numAtoms("<<patchID[0]<<") = " 
00063     << numAtoms[0] 
00064     << " numAtoms("<<patchID[1]<<") = " << numAtoms[1] << "\n" );
00065   DebugM(4, "~ComputeLCPO("<<cid<<") addr("<<patchID[0]<<") = " 
00066     << PatchMap::Object()->patch(patchID[0]) << " addr("<<patchID[1]<<") = "
00067     << PatchMap::Object()->patch(patchID[1]) << "\n");
00068 
00069   for (int i=0; i<getNumPatches(); i++) {
00070     if (positionBox[i] != NULL) {
00071       PatchMap::Object()->patch(patchID[i])->unregisterPositionPickup(this,
00072          &positionBox[i]);
00073     }
00074     if (forceBox[i] != NULL) {
00075       PatchMap::Object()->patch(patchID[i])->unregisterForceDeposit(this,
00076                 &forceBox[i]);
00077     }
00078     if (lcpoTypeBox[i] != NULL) {
00079       PatchMap::Object()->patch(patchID[i])->unregisterLcpoTypePickup(this,
00080                 &lcpoTypeBox[i]);
00081     }
00082   }
00083   delete reduction;
00084 } // destructor

Member Function Documentation

void ComputeLCPO::atomUpdate ( void   )  [virtual]

Reimplemented from Compute.

Definition at line 193 of file ComputeLCPO.C.

References Patch::getNumAtoms(), numAtoms, and patch.

00193                              {
00194   for (int i=0; i<8; i++) {
00195           numAtoms[i] = patch[i]->getNumAtoms();
00196   }
00197 }

void ComputeLCPO::doForce (  )  [protected, virtual]

Definition at line 290 of file ComputeLCPO.C.

References calcOverlap(), Results::f, LCPOAtom::f, Patch::flags, FLOPS, force, CompAtom::hydrogenGroupSize, CompAtomExt::id, invalidPatch, SubmitReduction::item(), j, lcpoType, minPart, Results::nbond, LCPONeighborList::newlist(), Pairlists::newlist(), Pairlists::newsize(), LCPONeighborList::newsize(), LCPONeighborList::nextlist(), Pairlists::nextlist(), numAtoms, numParts, patch, PI, pos, posExt, CompAtom::position, LCPOAtom::r, reduction, REDUCTION_COMPUTE_CHECKSUM, REDUCTION_ELECT_ENERGY, LCPONeighborList::reset(), Pairlists::reset(), Flags::sequence, step, SubmitReduction::submit(), valid, LCPOAtom::x, Vector::x, LCPOAtom::y, Vector::y, LCPOAtom::z, and Vector::z.

Referenced by doWork().

00290                           {
00291   //CkPrintf("ComputeLCPO::doForce\n");
00292   step = patch[0]->flags.sequence;
00293 
00294   Real probeRadius = 1.4f;
00295   Real cutMargin = 0.f;//regenerating pairlists every step
00296 
00297   Position ngir, ngjr, ngkr;
00298   Real ri, rj, rk;
00299   BigReal dxij, dyij, dzij, r2ij;
00300   BigReal dxik, dyik, dzik, r2ik;
00301   BigReal dxjk, dyjk, dzjk, r2jk;
00302 
00303 #ifdef COUNT_FLOPS
00304  int flops = 0;
00305 #endif
00306 
00308 // Build Pairlists
00310 //generate pairlists every step since contain coordinates
00311 if ( true ) {
00312   double t_start = 1.0*clock()/CLOCKS_PER_SEC;
00313 
00314   inAtomsPl.reset();
00315   lcpoNeighborList.reset();
00316   FLOPS(8);
00317   cut2 = 2*maxAtomRadius+cutMargin; cut2 *= cut2;
00318   maxAtomRadius = 0;
00319   //find in-bounds atoms in each patch
00320   for (int pI = 0; pI < 8; pI++) {
00321     if (invalidPatch[pI]) continue;
00322     if (numAtoms[pI] == 0) continue;
00323 
00324     int minIg = 0;
00325     for (int s = 0; s < minPart; s++) {
00326       minIg += pos[pI][minIg].hydrogenGroupSize;
00327       FLOPS(1)
00328     }
00329     strideIg = numParts;//stride through partitions
00330     plint *inAtoms = inAtomsPl.newlist(numAtoms[pI]);
00331     int numAtomsInBounds = 0;
00332 
00333     //iterate over heavy atoms only
00334     for ( int ngi = minIg; ngi < numAtoms[pI]; /* ngi */) {
00335       ngir = pos[pI][ngi].position;
00336       if ( isInBounds(ngir.x, ngir.y, ngir.z) && lcpoType[pI][ngi] > 0 ) {
00337         inAtoms[numAtomsInBounds++] = ngi;
00338         ri = probeRadius+lcpoParams[ lcpoType[pI][ngi] ][0];
00339         maxAtomRadius = (ri > maxAtomRadius) ? ri : maxAtomRadius;
00340         FLOPS(1);
00341 
00342         int maxAtoms = 0;
00343         for (int pJ = 0; pJ < 8; pJ++) {
00344           if (numAtoms[pJ] > 0) {
00345             maxAtoms += numAtoms[pJ];
00346           }
00347         }
00348         LCPOAtom *lcpoNeighbors = lcpoNeighborList.newlist(maxAtoms);
00349         int numLcpoNeighbors = 0;
00350 
00351         //find pairs of this inAtom from all 8 patches
00352         for (int pJ = 0; pJ < 8; pJ++) {
00353           if (invalidPatch[pJ]) continue;
00354           if (!valid[pI][pJ]) continue;
00355 
00356           // j atom pairs
00357           for ( int ngj = 0; ngj < numAtoms[pJ]; /* ngj */) {
00358             FLOPS(1)
00359             ngjr = pos[pJ][ngj].position;
00360             dxij = ngir.x - ngjr.x;
00361             dyij = ngir.y - ngjr.y;
00362             dzij = ngir.z - ngjr.z;
00363 
00364             // i-j coarse check if too far apart
00365             r2ij = dxij*dxij + dyij*dyij + dzij*dzij;
00366             FLOPS(8)
00367             if (r2ij < cut2 && r2ij > 0.01) {
00368 
00369               // i-j precise check if too far apart
00370               rj = probeRadius+lcpoParams[ lcpoType[pJ][ngj] ][0];
00371               FLOPS(5)
00372               BigReal rirjcutMargin2 = ri+rj+cutMargin;
00373               rirjcutMargin2 *= rirjcutMargin2;
00374               if (r2ij < rirjcutMargin2 && r2ij > 0.0001 &&
00375                   lcpoType[pJ][ngj] > 0) {
00376                 lcpoNeighbors[numLcpoNeighbors].x = ngjr.x;
00377                 lcpoNeighbors[numLcpoNeighbors].y = ngjr.y;
00378                 lcpoNeighbors[numLcpoNeighbors].z = ngjr.z;
00379                 lcpoNeighbors[numLcpoNeighbors].r = rj;
00380                 lcpoNeighbors[numLcpoNeighbors].f =
00381                   &force[pJ]->f[Results::nbond][ngj];
00382                 numLcpoNeighbors++;
00383                 FLOPS(2)
00384                 maxAtomRadius = (rj > maxAtomRadius) ? rj : maxAtomRadius;
00385               } // precise cutoff
00386             } // coarse cutoff
00387             //jump to next nonbonded group
00388             ngj += pos[pJ][ngj].hydrogenGroupSize;
00389             FLOPS(1)
00390           } // for j atoms
00391         } // for patches J
00392         lcpoNeighborList.newsize(numLcpoNeighbors);
00393       } // in bounds
00394       //jump to next nonbonded group for round-robin
00395       for (int s = 0; s < strideIg; s++) {
00396         ngi += pos[pI][ngi].hydrogenGroupSize;
00397         FLOPS(1)
00398       }
00399     } // for i atoms
00400     inAtomsPl.newsize(numAtomsInBounds);
00401   } // for patches I
00402 #ifdef COUNT_FLOPS
00403   double t_stop = 1.0*clock()/CLOCKS_PER_SEC;
00404   CkPrintf("LCPO_TIME_P %7.3f Gflops %9d @ %f\n", flops*1e-9/(t_stop-t_start),flops,(t_stop-t_start));
00405 #endif
00406 }
00407 #ifdef COUNT_FLOPS
00408   double t_start = 1.0*clock()/CLOCKS_PER_SEC;
00409   flops = 0;
00410 #endif
00411 
00412   //reset pairlists
00413   inAtomsPl.reset();
00414   lcpoNeighborList.reset();
00415   cut2 = maxAtomRadius*2; cut2 *= cut2;
00416 
00417   //init values
00418   BigReal totalSurfaceArea = 0;
00419 
00427   //for each patch in octet
00428   for (int pI = 0; pI < 8; pI++) {
00429     if (invalidPatch[pI]) continue;
00430     if (numAtoms[pI] == 0) continue;
00431     plint *inAtoms;
00432     int numInAtoms;
00433     inAtomsPl.nextlist( &inAtoms, &numInAtoms );
00434     //for each inAtom in each patch
00435     for (int i = 0; i < numInAtoms; i++) {
00436       int iIndex = inAtoms[i];
00437       int idi = posExt[pI][iIndex].id;
00438       Real xi = pos[pI][iIndex].position.x;
00439       Real yi = pos[pI][iIndex].position.y;
00440       Real zi = pos[pI][iIndex].position.z;
00441       const Real *lcpoParamI = lcpoParams[ lcpoType[pI][iIndex] ];
00442       ri = probeRadius+lcpoParamI[0];
00443       FLOPS(1)
00444 
00445       Real P1 = lcpoParamI[1];
00446       Real P2 = lcpoParamI[2];
00447       Real P3 = lcpoParamI[3];
00448       Real P4 = lcpoParamI[4];
00449 
00451 // S1
00453       BigReal S1 = 4.0*PI*ri*ri; // a
00454       FLOPS(3)
00455 
00456       //for surface area calculation
00457       BigReal AijSum = 0; // b
00458       BigReal AjkSum = 0; // c
00459       BigReal AjkjSum = 0; // d'
00460       BigReal AijAjkSum = 0; // d
00461 
00462       //for force calculation
00463       BigReal dAijdrijdxiSum    = 0.0;
00464       BigReal dAijdrijdyiSum    = 0.0;
00465       BigReal dAijdrijdziSum    = 0.0;
00466       BigReal dAijdrijdxiAjkSum = 0.0;
00467       BigReal dAijdrijdyiAjkSum = 0.0;
00468       BigReal dAijdrijdziAjkSum = 0.0;
00469 
00471 // for J Atoms
00473       LCPOAtom *lcpoNeighbors;
00474       int numLcpoNeighbors;
00475       lcpoNeighborList.nextlist( &lcpoNeighbors, &numLcpoNeighbors );
00476 
00477       for (int j = 0; j < numLcpoNeighbors; j++) {
00478         Real xj = lcpoNeighbors[j].x;
00479         Real yj = lcpoNeighbors[j].y;
00480         Real zj = lcpoNeighbors[j].z;
00481         Real rj = lcpoNeighbors[j].r;
00482 
00483         // i-j coarse check if too far away
00484         dxij = xj-xi;
00485         dyij = yj-yi;
00486         dzij = zj-zi;
00487         r2ij = dxij*dxij + dyij*dyij + dzij*dzij;
00488         FLOPS(7);
00489         if (r2ij >= cut2 || r2ij < 0.01) { continue; }
00490 
00491         // i-j precise check if too far away
00492         FLOPS(5)
00493         BigReal rirj2 = ri+rj;
00494         rirj2 *= rirj2;
00495         if ( r2ij >= rirj2 ) { continue; }
00496 
00497         BigReal rij = sqrt(r2ij);
00498         BigReal rij_1 = 1.f / rij;
00499           
00501 // S2
00503         BigReal Aij = calcOverlap(rij, ri, rj);
00504         AijSum += Aij;
00505         FLOPS(12)
00506 
00507         //for dAi_drj force calculation
00508         BigReal dAijdrij = PI*ri*(rij_1*rij_1*(ri*ri-rj*rj)-1);
00509         BigReal dAijdrijdxj = dAijdrij*dxij*rij_1; // g k' i' l'
00510         BigReal dAijdrijdyj = dAijdrij*dyij*rij_1;
00511         BigReal dAijdrijdzj = dAijdrij*dzij*rij_1;
00512         FLOPS(14)
00513 
00514         BigReal AjkjSum = 0; // i' l'
00515         BigReal dAjkdrjkdxjSum = 0.0;
00516         BigReal dAjkdrjkdyjSum = 0.0;
00517         BigReal dAjkdrjkdzjSum = 0.0;
00518 
00520 // for K Atoms
00522         for (int k = 0; k < numLcpoNeighbors; k++) {
00523           Real xk = lcpoNeighbors[k].x;
00524           Real yk = lcpoNeighbors[k].y;
00525           Real zk = lcpoNeighbors[k].z;
00526           Real rk = lcpoNeighbors[k].r;
00527 
00528           // i-k coarse check if too far away
00529           dxik = xk-xi;
00530           dyik = yk-yi;
00531           dzik = zk-zi;
00532           r2ik = dxik*dxik + dyik*dyik + dzik*dzik;
00533           FLOPS(8)
00534           if (r2ik >= cut2 || r2ik < 0.01) { continue; }
00535 
00536           // j-k coarse check if too far away
00537           dxjk = xk-xj;
00538           dyjk = yk-yj;
00539           dzjk = zk-zj;
00540           r2jk = dxjk*dxjk + dyjk*dyjk + dzjk*dzjk;
00541           FLOPS(8)
00542           if (r2jk >= cut2 || r2jk < 0.01) { continue; }
00543 
00544           // i-k precise check if too far away
00545           FLOPS(3)
00546           BigReal rirk2 = ri+rk;
00547           rirk2 *= rirk2;
00548           if ( r2ik >= rirk2 ) { continue; }
00549 
00550           // j-k precise check if too far away
00551           FLOPS(2)
00552           BigReal rjrk2 = rj+rk;
00553           rjrk2 *= rjrk2;
00554           if ( r2jk >= rjrk2 ) { continue; }
00555           BigReal rjk  = sqrt(r2jk);
00556 
00558 // S3
00560           BigReal rjk_1 = 1.0/rjk;
00561           BigReal Ajk = calcOverlap(rjk, rj, rk);
00562           FLOPS(12)
00563           AjkSum  += Ajk;
00564           AjkjSum += Ajk; // i' l'
00565           FLOPS(5)
00566 
00568 // Force dAi_drk
00570           BigReal dAjkdrjk = PI*rj*rjk_1*(rjk_1*rjk_1*(rj*rj-rk*rk) - 1.f);//ef'
00571           BigReal dAjkdrjkdxj = -dAjkdrjk*dxjk; // e f h'
00572           BigReal dAjkdrjkdyj = -dAjkdrjk*dyjk;
00573           BigReal dAjkdrjkdzj = -dAjkdrjk*dzjk;
00574           lcpoNeighbors[k].f->x -= -dAjkdrjkdxj*(P3+P4*Aij)*surfTen; // e f
00575           lcpoNeighbors[k].f->y -= -dAjkdrjkdyj*(P3+P4*Aij)*surfTen;
00576           lcpoNeighbors[k].f->z -= -dAjkdrjkdzj*(P3+P4*Aij)*surfTen;
00577 
00578           dAjkdrjkdxjSum += dAjkdrjkdxj; // h j'
00579           dAjkdrjkdyjSum += dAjkdrjkdyj;
00580           dAjkdrjkdzjSum += dAjkdrjkdzj;
00581           FLOPS(34)
00582 
00583         } // k atoms
00585 // S4
00587         AijAjkSum += Aij*AjkjSum;
00588 
00590 // Force dAi_drj
00592         BigReal lastxj = dAijdrijdxj*AjkjSum + Aij*dAjkdrjkdxjSum; // i j
00593         BigReal lastyj = dAijdrijdyj*AjkjSum + Aij*dAjkdrjkdyjSum;
00594         BigReal lastzj = dAijdrijdzj*AjkjSum + Aij*dAjkdrjkdzjSum;
00595         BigReal dAidxj = (P2*dAijdrijdxj + P3*dAjkdrjkdxjSum + P4*lastxj);//ghij
00596         BigReal dAidyj = (P2*dAijdrijdyj + P3*dAjkdrjkdyjSum + P4*lastyj);
00597         BigReal dAidzj = (P2*dAijdrijdzj + P3*dAjkdrjkdzjSum + P4*lastzj);
00598         lcpoNeighbors[j].f->x -= dAidxj*surfTen;
00599         lcpoNeighbors[j].f->y -= dAidyj*surfTen;
00600         lcpoNeighbors[j].f->z -= dAidzj*surfTen;
00601 
00602         //for dAi_dri force calculation
00603         dAijdrijdxiSum -= dAijdrijdxj; // k
00604         dAijdrijdyiSum -= dAijdrijdyj;
00605         dAijdrijdziSum -= dAijdrijdzj;
00606         dAijdrijdxiAjkSum -= dAijdrijdxj*AjkjSum; // l
00607         dAijdrijdyiAjkSum -= dAijdrijdyj*AjkjSum;
00608         dAijdrijdziAjkSum -= dAijdrijdzj*AjkjSum;
00609         FLOPS(41)
00610       } // j atoms
00611 
00613 // Force dAi_dri
00615       BigReal dAidxi = (P2*dAijdrijdxiSum + P4*dAijdrijdxiAjkSum); // k l
00616       BigReal dAidyi = (P2*dAijdrijdyiSum + P4*dAijdrijdyiAjkSum);
00617       BigReal dAidzi = (P2*dAijdrijdziSum + P4*dAijdrijdziAjkSum);
00618       force[pI]->f[Results::nbond][iIndex].x -= dAidxi*surfTen;
00619       force[pI]->f[Results::nbond][iIndex].y -= dAidyi*surfTen;
00620       force[pI]->f[Results::nbond][iIndex].z -= dAidzi*surfTen;
00621 
00623 // Atom I Surface Area
00625       BigReal SAi = P1*S1 + P2*AijSum + P3*AjkSum + P4*AijAjkSum;
00626       //CkPrintf("SurfArea[%05d] = % 7.3f\n",idi,SAi);
00627       //SAi = (SAi > 0) ? SAi : 0;
00628       totalSurfaceArea += SAi;
00629       FLOPS(22)
00630     } // for inAtoms
00631   } // for patches I
00632 #ifdef COUNT_FLOPS
00633   double t_stop = 1.0*clock()/CLOCKS_PER_SEC;
00634   CkPrintf("LCPO_TIME_F %7.3f Gflops %9d @ %f\n", 1e-9*flops/(t_stop-t_start),flops, (t_stop-t_start));
00635 #endif
00636 
00638 //  end calculation by submitting reduction
00640 
00641   reduction->item(REDUCTION_COMPUTE_CHECKSUM) += 1.;
00642   reduction->item(REDUCTION_ELECT_ENERGY) += totalSurfaceArea * surfTen;
00643   reduction->submit();
00644 
00645 }//end do Force

void ComputeLCPO::doWork ( void   )  [virtual]

Reimplemented from Compute.

Definition at line 202 of file ComputeLCPO.C.

References Box< Owner, Data >::close(), doForce(), LdbCoordinator::endWork(), force, forceBox, Patch::getCompAtomExtInfo(), Compute::getNumPatches(), lcpoType, lcpoTypeBox, Compute::ldObjHandle, LdbCoordinator::Object(), Box< Owner, Data >::open(), patch, pos, posExt, positionBox, and LdbCoordinator::startWork().

00202                          {
00203   LdbCoordinator::Object()->startWork(ldObjHandle);
00204   for (int i=0; i<8; i++) {
00205     pos[i] = positionBox[i]->open();
00206     force[i] = forceBox[i]->open();
00207     posExt[i] = patch[i]->getCompAtomExtInfo();
00208     lcpoType[i] = lcpoTypeBox[i]->open();
00209   }
00210 
00211   doForce();
00212 
00213  // Inform load balancer
00214   LdbCoordinator::Object()->endWork(ldObjHandle);
00215 
00216   // Close up boxes
00217   for (int i=0; i<getNumPatches(); i++) {
00218     positionBox[i]->close(&pos[i]);
00219     forceBox[i]->close(&force[i]);
00220     lcpoTypeBox[i]->close(&lcpoType[i]);
00221   }
00222 } // doWork

void ComputeLCPO::initialize ( void   )  [virtual]

Reimplemented from Compute.

Definition at line 86 of file ComputeLCPO.C.

References Compute::basePriority, DebugM, forceBox, Patch::getNumAtoms(), PatchMap::gridsize_a(), PatchMap::gridsize_b(), PatchMap::gridsize_c(), PatchMap::index_a(), PatchMap::index_b(), PatchMap::index_c(), invalidPatch, lcpoTypeBox, PatchMap::max_a(), PatchMap::max_b(), PatchMap::max_c(), PatchMap::min_a(), PatchMap::min_b(), PatchMap::min_c(), numAtoms, PatchMap::Object(), PatchMap::patch(), patch, PATCH_PRIORITY, patchID, positionBox, PROXY_RESULTS_PRIORITY, Patch::registerForceDeposit(), Patch::registerLcpoTypePickup(), Patch::registerPositionPickup(), and valid.

00086                              {
00087   Compute::initialize();
00088     // How can we tell if BoxOwner has packed up and left?  Need a mechanism
00089     // to handle this or do we assume the Boxes have been dumped?
00090     PatchMap *patchMap = PatchMap::Object();
00091     //Check out Boxes
00092     for (int i=0; i<8; i++) {
00093       //invalid patch so don't even checkout boxes
00094             if (positionBox[i] == NULL) { // We have yet to get boxes
00095         patch[i] = PatchMap::Object()->patch(patchID[i]);
00096               if (!(patch[i] = PatchMap::Object()->patch(patchID[i]))) {
00097                 DebugM(5,"invalid patch(" << patchID[i] 
00098                       << ")  pointer!\n");
00099               }
00100         positionBox[i] = patch[i]->registerPositionPickup(this);
00101         forceBox[i] = patch[i]->registerForceDeposit(this);
00102         lcpoTypeBox[i] = patch[i]->registerLcpoTypePickup(this);
00103         // will need to open a box full of lcpo parameters
00104             }
00105       numAtoms[i] = patch[i]->getNumAtoms();
00106     } // for all patches
00107 
00108   // set priority
00109   basePriority = PATCH_PRIORITY(patchID[0]) + PROXY_RESULTS_PRIORITY;
00110 
00111   //get bounds of inner rectangular prism in octet
00112   bounds[0][0] = 0.5*(patchMap->min_a(patchID[0])+patchMap->max_a(patchID[0]));
00113   bounds[1][0] = 0.5*(patchMap->min_b(patchID[0])+patchMap->max_b(patchID[0]));
00114   bounds[2][0] = 0.5*(patchMap->min_c(patchID[0])+patchMap->max_c(patchID[0]));
00115   bounds[0][1] = 0.5*(patchMap->min_a(patchID[7])+patchMap->max_a(patchID[7]));
00116   bounds[1][1] = 0.5*(patchMap->min_b(patchID[7])+patchMap->max_b(patchID[7]));
00117   bounds[2][1] = 0.5*(patchMap->min_c(patchID[7])+patchMap->max_c(patchID[7]));
00118 
00119   //if only 1 patch in a dimenion, invalidate those patches
00120   int gsa = patchMap->gridsize_a();
00121   int gsb = patchMap->gridsize_b();
00122   int gsc = patchMap->gridsize_c();
00123   invalidPatch[0] = 0;
00124   invalidPatch[1] = 0;
00125   invalidPatch[2] = 0;
00126   invalidPatch[3] = 0;
00127   invalidPatch[4] = 0;
00128   invalidPatch[5] = 0;
00129   invalidPatch[6] = 0;
00130   invalidPatch[7] = 0;
00131 
00132   if (gsa==1) {
00133     //CkPrintf("ONLY 1 PATCH in A DIMENSION!\n");
00134     invalidPatch[1] = 1;
00135     invalidPatch[3] = 1;
00136     invalidPatch[5] = 1;
00137     invalidPatch[7] = 1;
00138   }
00139   if (gsb==1) {
00140     //CkPrintf("ONLY 1 PATCH in B DIMENSION!\n");
00141     invalidPatch[2] = 1;
00142     invalidPatch[3] = 1;
00143     invalidPatch[6] = 1;
00144     invalidPatch[7] = 1;
00145   }
00146   if (gsc==1) {
00147     //CkPrintf("ONLY 1 PATCH in C DIMENSION!\n");
00148     invalidPatch[4] = 1;
00149     invalidPatch[5] = 1;
00150     invalidPatch[6] = 1;
00151     invalidPatch[7] = 1;
00152   }
00153   //relative a,b,c index for 8 patches in ComputeLCPO
00154   int idx[8][3] = {
00155     { 0, 0, 0},
00156     { 1, 0, 0},
00157     { 0, 1, 0},
00158     { 1, 1, 0},
00159     { 0, 0, 1},
00160     { 1, 0, 1},
00161     { 0, 1, 1},
00162     { 1, 1, 1}    };
00163 /*
00164   int i_a = patchMap->index_a(patchID[0]);
00165   int i_b = patchMap->index_b(patchID[0]);
00166   int i_c = patchMap->index_c(patchID[0]);
00167   CkPrintf("VALID[%d,%d,%d]=\n",i_a,i_b,i_c);
00168 */
00169   for (int pI = 0; pI < 8; pI++) {
00170     int iia = patchMap->index_a(patchID[pI]);
00171     int iib = patchMap->index_b(patchID[pI]);
00172     int iic = patchMap->index_c(patchID[pI]);
00173     for (int pJ = 0; pJ < 8; pJ++) {
00174       int jia = patchMap->index_a(patchID[pJ]);
00175       int jib = patchMap->index_b(patchID[pJ]);
00176       int jic = patchMap->index_c(patchID[pJ]);
00177       if (  ( gsa==1 && (jia>iia) != (idx[pJ][0]>idx[pI][0]) ) ||
00178             ( gsb==1 && (jib>iib) != (idx[pJ][1]>idx[pI][1]) ) ||
00179             ( gsc==1 && (jic>iic) != (idx[pJ][2]>idx[pI][2]) ) ||
00180             ( invalidPatch[pI] ) ||
00181             ( invalidPatch[pJ] )   )
00182         valid[pI][pJ] = 0;
00183       else
00184         valid[pI][pJ] = 1;
00185       //CkPrintf("%d ",valid[pI][pJ]);
00186     }
00187     //CkPrintf("\n");
00188   }
00189   //CkPrintf("\n");
00190 
00191 } // initialize

int ComputeLCPO::noWork (  )  [virtual]

Reimplemented from Compute.

Definition at line 225 of file ComputeLCPO.C.

References forceBox, SubmitReduction::item(), lcpoTypeBox, Compute::ldObjHandle, LdbCoordinator::Object(), patch, positionBox, reduction, REDUCTION_COMPUTE_CHECKSUM, Box< Owner, Data >::skip(), LdbCoordinator::skipWork(), and SubmitReduction::submit().

00225                         {
00226 
00227   if ( patch[0]->flags.doNonbonded) {
00228     return 0;  // work to do, enqueue as usual
00229   } else {
00230 
00231     // skip all boxes
00232     for (int i=0; i<8; i++) {
00233       positionBox[i]->skip();
00234       forceBox[i]->skip();
00235       lcpoTypeBox[i]->skip();
00236     }
00237 
00238     reduction->item(REDUCTION_COMPUTE_CHECKSUM) += 1.;
00239     reduction->submit();
00240     LdbCoordinator::Object()->skipWork(ldObjHandle);
00241 
00242     return 1;  // no work to do, do not enqueue
00243   }
00244   return 0;
00245 } // noWork

Member Data Documentation

Results* ComputeLCPO::force[8] [protected]

Definition at line 121 of file ComputeLCPO.h.

Referenced by doForce(), and doWork().

Box<Patch,Results>* ComputeLCPO::forceBox[8] [protected]

Definition at line 131 of file ComputeLCPO.h.

Referenced by ComputeLCPO(), doWork(), initialize(), noWork(), and ~ComputeLCPO().

int ComputeLCPO::invalidPatch[8] [protected]

Definition at line 118 of file ComputeLCPO.h.

Referenced by doForce(), and initialize().

int* ComputeLCPO::lcpoType[8] [protected]

Definition at line 122 of file ComputeLCPO.h.

Referenced by doForce(), and doWork().

Box<Patch,int>* ComputeLCPO::lcpoTypeBox[8] [protected]

Definition at line 132 of file ComputeLCPO.h.

Referenced by ComputeLCPO(), doWork(), initialize(), noWork(), and ~ComputeLCPO().

int ComputeLCPO::maxPart [protected]

Definition at line 135 of file ComputeLCPO.h.

int ComputeLCPO::minPart [protected]

Definition at line 135 of file ComputeLCPO.h.

Referenced by doForce().

int ComputeLCPO::numAtoms[8] [protected]

Definition at line 115 of file ComputeLCPO.h.

Referenced by atomUpdate(), doForce(), initialize(), and ~ComputeLCPO().

int ComputeLCPO::numParts [protected]

Definition at line 135 of file ComputeLCPO.h.

Referenced by doForce().

Patch* ComputeLCPO::patch[8] [protected]

Definition at line 126 of file ComputeLCPO.h.

Referenced by atomUpdate(), ComputeLCPO(), doForce(), doWork(), initialize(), noWork(), and ~ComputeLCPO().

PatchID ComputeLCPO::patchID[8] [protected]

Definition at line 128 of file ComputeLCPO.h.

Referenced by ComputeLCPO(), initialize(), and ~ComputeLCPO().

CompAtom* ComputeLCPO::pos[8] [protected]

Definition at line 120 of file ComputeLCPO.h.

Referenced by doForce(), and doWork().

CompAtomExt* ComputeLCPO::posExt[8] [protected]

Definition at line 119 of file ComputeLCPO.h.

Referenced by doForce(), and doWork().

Box<Patch,CompAtom>* ComputeLCPO::positionBox[8] [protected]

Definition at line 130 of file ComputeLCPO.h.

Referenced by ComputeLCPO(), doWork(), initialize(), noWork(), and ~ComputeLCPO().

SubmitReduction* ComputeLCPO::reduction [protected]

Definition at line 137 of file ComputeLCPO.h.

Referenced by ComputeLCPO(), doForce(), noWork(), and ~ComputeLCPO().

int ComputeLCPO::step [protected]

Definition at line 123 of file ComputeLCPO.h.

Referenced by doForce().

int ComputeLCPO::trans[8] [protected]

Definition at line 129 of file ComputeLCPO.h.

Referenced by ComputeLCPO().

int ComputeLCPO::valid[8][8] [protected]

Definition at line 116 of file ComputeLCPO.h.

Referenced by doForce(), and initialize().

ComputeNonbondedWorkArrays* const ComputeLCPO::workArrays [protected]

Definition at line 134 of file ComputeLCPO.h.

The documentation for this class was generated from the following files:
Generated on 16 Jun 2022 for NAMD by  doxygen 1.6.1