msm::PatchData Struct Reference

List of all members.

Public Member Functions

AtomCoordArray & coordArray ()
ForceArray & forceArray ()
 PatchData (ComputeMsmMgr *pmgr, int pid)
void init (int natoms)
void anterpolation ()
void sendCharge ()
void addPotential (const Grid< Float > &epart)
void interpolation ()
void anterpolationC1Hermite ()
void sendChargeC1Hermite ()
void addPotentialC1Hermite (const Grid< C1Vector > &epart)
void interpolationC1Hermite ()

Public Attributes

ComputeMsmMgr * mgr
Map * map
PatchDiagram * pd
AtomCoordArray coord
ForceArray force
Grid< Float > qh
Grid< Float > eh
Grid< Float > subgrid
Grid< C1Vector > qh_c1hermite
Grid< C1Vector > eh_c1hermite
Grid< C1Vector > subgrid_c1hermite
BigReal energy
int cntRecvs
int patchID
int sequence

Detailed Description

Definition at line 1738 of file ComputeMsm.C.

Constructor & Destructor Documentation

msm::PatchData::PatchData ( ComputeMsmMgr *  pmgr,
int  pid 
)

Definition at line 6227 of file ComputeMsm.C.

References ComputeMsmMgr::approx, msm::Map::bsx, msm::Map::bsy, msm::Map::bsz, ComputeMsmMgr::C1HERMITE, eh, eh_c1hermite, msm::Grid< T >::init(), map, ComputeMsmMgr::mapData(), mgr, msm::PatchDiagram::nrange, patchID, msm::Map::patchList, pd, qh, qh_c1hermite, msm::Grid< T >::resize(), subgrid, and subgrid_c1hermite.

06227                                                    {
06228     mgr = pmgr;
06229     map = &(mgr->mapData());
06230     patchID = pid;
06231     //PatchMap *pm = PatchMap::Object();
06232     pd = &(map->patchList[pid]);
06233     if (mgr->approx == ComputeMsmMgr::C1HERMITE) {
06234       qh_c1hermite.init(pd->nrange);
06235       eh_c1hermite.init(pd->nrange);
06236       subgrid_c1hermite.resize(map->bsx[0] * map->bsy[0] * map->bsz[0]);
06237     }
06238     else {
06239       qh.init(pd->nrange);
06240       eh.init(pd->nrange);
06241       subgrid.resize(map->bsx[0] * map->bsy[0] * map->bsz[0]);
06242     }
06243 #ifdef MSM_TIMING
06244     mgr->addTiming();
06245 #endif
06246   }

Member Function Documentation

void msm::PatchData::addPotential ( const Grid< Float > &  epart  ) 

Definition at line 6402 of file ComputeMsm.C.

References cntRecvs, MsmTimer::COMM, eh, interpolation(), mgr, msm::PatchDiagram::numRecvs, and pd.

06402                                                        {
06403 #ifdef MSM_TIMING
06404     double startTime, stopTime;
06405     startTime = CkWallTimer();
06406 #endif
06407     eh += epart;
06408 #ifdef MSM_TIMING
06409     stopTime = CkWallTimer();
06410     mgr->msmTiming[MsmTimer::COMM] += stopTime - startTime;
06411 #endif
06412     if (++cntRecvs == pd->numRecvs) {
06413       interpolation();
06414     }
06415   }

void msm::PatchData::addPotentialC1Hermite ( const Grid< C1Vector > &  epart  ) 

Definition at line 6678 of file ComputeMsm.C.

References cntRecvs, MsmTimer::COMM, eh_c1hermite, interpolationC1Hermite(), mgr, msm::PatchDiagram::numRecvs, and pd.

06678                                                                    {
06679 #ifdef MSM_TIMING
06680     double startTime, stopTime;
06681     startTime = CkWallTimer();
06682 #endif
06683     eh_c1hermite += epart;
06684 #ifdef MSM_TIMING
06685     stopTime = CkWallTimer();
06686     mgr->msmTiming[MsmTimer::COMM] += stopTime - startTime;
06687 #endif
06688     if (++cntRecvs == pd->numRecvs) {
06689       interpolationC1Hermite();
06690     }
06691   }

void msm::PatchData::anterpolation (  ) 

Definition at line 6265 of file ComputeMsm.C.

References MsmTimer::ANTERP, ComputeMsmMgr::approx, msm::Array< T >::buffer(), coord, msm::Grid< T >::data(), msm::IndexRange::ia(), msm::IndexRange::ib(), msm::IndexRange::ja(), msm::IndexRange::jb(), msm::IndexRange::ka(), msm::IndexRange::kb(), ComputeMsmMgr::lattice, msm::Array< T >::len(), ComputeMsmMgr::MAX_POLY_DEGREE, mgr, NAMD_die(), msm::IndexRange::ni(), msm::IndexRange::nj(), patchID, ComputeMsmMgr::PolyDegree, qh, ComputeMsmMgr::s_edge, Lattice::scale(), sendCharge(), ComputeMsmMgr::sglower, ComputeMsmMgr::shx_1, ComputeMsmMgr::shy_1, ComputeMsmMgr::shz_1, ComputeMsmMgr::stencil_1d(), Vector::x, Vector::y, and Vector::z.

06265                                 {
06266 #ifdef DEBUG_MSM_GRID
06267     printf("patchID %d:  anterpolation\n", patchID);
06268 #endif
06269 
06270 #ifdef MSM_TIMING
06271     double startTime, stopTime;
06272     startTime = CkWallTimer();
06273 #endif
06274 #ifndef MSM_COMM_ONLY
06275     Float xphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06276     Float yphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06277     Float zphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06278 
06279     const Double rs_edge = Double( mgr->s_edge );
06280     const int s_size = ComputeMsmMgr::PolyDegree[mgr->approx] + 1;
06281 
06282     const int ia = qh.ia();
06283     const int ib = qh.ib();
06284     const int ja = qh.ja();
06285     const int jb = qh.jb();
06286     const int ka = qh.ka();
06287     const int kb = qh.kb();
06288     const int ni = qh.ni();
06289     const int nj = qh.nj();
06290     Float *qhbuffer = qh.data().buffer();
06291 
06292     // loop over atoms
06293     for (int n = 0;  n < coord.len();  n++) {
06294       Float q = coord[n].charge;
06295       if (0==q) continue;
06296 
06297       ScaledPosition s = mgr->lattice.scale(coord[n].position);
06298 
06299       BigReal sx_hx = (s.x - mgr->sglower.x) * mgr->shx_1;
06300       BigReal sy_hy = (s.y - mgr->sglower.y) * mgr->shy_1;
06301       BigReal sz_hz = (s.z - mgr->sglower.z) * mgr->shz_1;
06302 
06303       BigReal xlo = floor(sx_hx) - rs_edge;
06304       BigReal ylo = floor(sy_hy) - rs_edge;
06305       BigReal zlo = floor(sz_hz) - rs_edge;
06306 
06307       // calculate Phi stencils along each dimension
06308       Float xdelta = Float(sx_hx - xlo);
06309       mgr->stencil_1d(xphi, xdelta);
06310       Float ydelta = Float(sy_hy - ylo);
06311       mgr->stencil_1d(yphi, ydelta);
06312       Float zdelta = Float(sz_hz - zlo);
06313       mgr->stencil_1d(zphi, zdelta);
06314 
06315       int ilo = int(xlo);
06316       int jlo = int(ylo);
06317       int klo = int(zlo);
06318 
06319       // test to see if stencil is within edges of grid
06320       int iswithin = ( ia <= ilo && (ilo+(s_size-1)) <= ib &&
06321                        ja <= jlo && (jlo+(s_size-1)) <= jb &&
06322                        ka <= klo && (klo+(s_size-1)) <= kb );
06323 
06324       if ( ! iswithin ) {
06325 #if 0
06326         printf("PE %d:  atom %d:  pos= %g %g %g  patchID=%d\n",
06327             CkMyPe(), coord[n].id,
06328             coord[n].position.x, coord[n].position.y, coord[n].position.z,
06329             patchID);
06330         printf("PE %d:  atom subgrid [%d..%d] x [%d..%d] x [%d..%d]\n",
06331             CkMyPe(),
06332             ilo, ilo+s_size-1, jlo, jlo+s_size-1, klo, klo+s_size-1);
06333         printf("PE %d:  patch grid [%d..%d] x [%d..%d] x [%d..%d]\n",
06334             CkMyPe(),
06335             ia, ib, ja, jb, ka, kb);
06336 #endif
06337         char msg[100];
06338         snprintf(msg, sizeof(msg), "Atom %d is outside of the MSM grid.",
06339             coord[n].id);
06340         NAMD_die(msg);
06341       }
06342 
06343       // determine charge on cube of grid points around atom
06344       for (int k = 0;  k < s_size;  k++) {
06345         int koff = ((k+klo) - ka) * nj;
06346         Float ck = zphi[k] * q;
06347         for (int j = 0;  j < s_size;  j++) {
06348           int jkoff = (koff + (j+jlo) - ja) * ni;
06349           Float cjk = yphi[j] * ck;
06350           for (int i = 0;  i < s_size;  i++) {
06351             int ijkoff = jkoff + (i+ilo) - ia;
06352             qhbuffer[ijkoff] += xphi[i] * cjk;
06353           }
06354         }
06355       }
06356 
06357     } // end loop over atoms
06358 #endif // !MSM_COMM_ONLY
06359 #ifdef MSM_TIMING
06360     stopTime = CkWallTimer();
06361     mgr->msmTiming[MsmTimer::ANTERP] += stopTime - startTime;
06362 #endif
06363 
06364     sendCharge();
06365   }

void msm::PatchData::anterpolationC1Hermite (  ) 

Definition at line 6543 of file ComputeMsm.C.

References MsmTimer::ANTERP, msm::Array< T >::buffer(), coord, D000, D001, D010, D011, D100, D101, D110, D111, msm::Grid< T >::data(), ComputeMsmMgr::hxlen, ComputeMsmMgr::hylen, ComputeMsmMgr::hzlen, msm::IndexRange::ia(), msm::IndexRange::ib(), msm::IndexRange::ja(), msm::IndexRange::jb(), msm::IndexRange::ka(), msm::IndexRange::kb(), ComputeMsmMgr::lattice, msm::Array< T >::len(), mgr, NAMD_die(), msm::IndexRange::ni(), msm::IndexRange::nj(), patchID, qh_c1hermite, Lattice::scale(), sendChargeC1Hermite(), ComputeMsmMgr::sglower, ComputeMsmMgr::shx_1, ComputeMsmMgr::shy_1, ComputeMsmMgr::shz_1, ComputeMsmMgr::stencil_1d_c1hermite(), C1Vector::velem, Vector::x, Vector::y, and Vector::z.

06543                                          {
06544 #ifdef DEBUG_MSM_GRID
06545     printf("patchID %d:  anterpolationC1Hermite\n", patchID);
06546 #endif
06547 
06548 #ifdef MSM_TIMING
06549     double startTime, stopTime;
06550     startTime = CkWallTimer();
06551 #endif
06552 #ifndef MSM_COMM_ONLY
06553     Float xphi[2], xpsi[2];
06554     Float yphi[2], ypsi[2];
06555     Float zphi[2], zpsi[2];
06556 
06557     const Float hx = Float(mgr->hxlen);  // real space grid spacing
06558     const Float hy = Float(mgr->hylen);
06559     const Float hz = Float(mgr->hzlen);
06560 
06561     const int ia = qh_c1hermite.ia();
06562     const int ib = qh_c1hermite.ib();
06563     const int ja = qh_c1hermite.ja();
06564     const int jb = qh_c1hermite.jb();
06565     const int ka = qh_c1hermite.ka();
06566     const int kb = qh_c1hermite.kb();
06567     const int ni = qh_c1hermite.ni();
06568     const int nj = qh_c1hermite.nj();
06569     C1Vector *qhbuffer = qh_c1hermite.data().buffer();
06570 
06571     // loop over atoms
06572     for (int n = 0;  n < coord.len();  n++) {
06573       Float q = coord[n].charge;
06574       if (0==q) continue;
06575 
06576       ScaledPosition s = mgr->lattice.scale(coord[n].position);
06577 
06578       BigReal sx_hx = (s.x - mgr->sglower.x) * mgr->shx_1;
06579       BigReal sy_hy = (s.y - mgr->sglower.y) * mgr->shy_1;
06580       BigReal sz_hz = (s.z - mgr->sglower.z) * mgr->shz_1;
06581 
06582       BigReal xlo = floor(sx_hx);
06583       BigReal ylo = floor(sy_hy);
06584       BigReal zlo = floor(sz_hz);
06585 
06586       // calculate Phi stencils along each dimension
06587       Float xdelta = Float(sx_hx - xlo);
06588       mgr->stencil_1d_c1hermite(xphi, xpsi, xdelta, hx);
06589       Float ydelta = Float(sy_hy - ylo);
06590       mgr->stencil_1d_c1hermite(yphi, ypsi, ydelta, hy);
06591       Float zdelta = Float(sz_hz - zlo);
06592       mgr->stencil_1d_c1hermite(zphi, zpsi, zdelta, hz);
06593 
06594       int ilo = int(xlo);
06595       int jlo = int(ylo);
06596       int klo = int(zlo);
06597 
06598       // test to see if stencil is within edges of grid
06599       int iswithin = ( ia <= ilo && ilo < ib &&
06600                        ja <= jlo && jlo < jb &&
06601                        ka <= klo && klo < kb );
06602 
06603       if ( ! iswithin ) {
06604         char msg[100];
06605         snprintf(msg, sizeof(msg), "Atom %d is outside of the MSM grid.",
06606             coord[n].id);
06607         NAMD_die(msg);
06608       }
06609 
06610       // determine charge on cube of grid points around atom
06611       for (int k = 0;  k < 2;  k++) {
06612         int koff = ((k+klo) - ka) * nj;
06613         Float c_zphi = zphi[k] * q;
06614         Float c_zpsi = zpsi[k] * q;
06615         for (int j = 0;  j < 2;  j++) {
06616           int jkoff = (koff + (j+jlo) - ja) * ni;
06617           Float c_yphi_zphi = yphi[j] * c_zphi;
06618           Float c_ypsi_zphi = ypsi[j] * c_zphi;
06619           Float c_yphi_zpsi = yphi[j] * c_zpsi;
06620           Float c_ypsi_zpsi = ypsi[j] * c_zpsi;
06621           for (int i = 0;  i < 2;  i++) {
06622             int ijkoff = jkoff + (i+ilo) - ia;
06623             qhbuffer[ijkoff].velem[D000] += xphi[i] * c_yphi_zphi;
06624             qhbuffer[ijkoff].velem[D100] += xpsi[i] * c_yphi_zphi;
06625             qhbuffer[ijkoff].velem[D010] += xphi[i] * c_ypsi_zphi;
06626             qhbuffer[ijkoff].velem[D001] += xphi[i] * c_yphi_zpsi;
06627             qhbuffer[ijkoff].velem[D110] += xpsi[i] * c_ypsi_zphi;
06628             qhbuffer[ijkoff].velem[D101] += xpsi[i] * c_yphi_zpsi;
06629             qhbuffer[ijkoff].velem[D011] += xphi[i] * c_ypsi_zpsi;
06630             qhbuffer[ijkoff].velem[D111] += xpsi[i] * c_ypsi_zpsi;
06631           }
06632         }
06633       }
06634 
06635     } // end loop over atoms
06636 
06637 #endif // !MSM_COMM_ONLY
06638 #ifdef MSM_TIMING
06639     stopTime = CkWallTimer();
06640     mgr->msmTiming[MsmTimer::ANTERP] += stopTime - startTime;
06641 #endif
06642 
06643     sendChargeC1Hermite();
06644   }

AtomCoordArray& msm::PatchData::coordArray (  )  [inline]

Definition at line 1756 of file ComputeMsm.C.

Referenced by ComputeMsm::doWork().

01756 { return coord; }

ForceArray& msm::PatchData::forceArray (  )  [inline]

Definition at line 1757 of file ComputeMsm.C.

01757 { return force; }

void msm::PatchData::init ( int  natoms  ) 

Definition at line 6248 of file ComputeMsm.C.

References ComputeMsmMgr::approx, ComputeMsmMgr::C1HERMITE, cntRecvs, coord, eh, eh_c1hermite, energy, force, mgr, qh, qh_c1hermite, msm::Grid< T >::reset(), and msm::Array< T >::resize().

Referenced by ComputeMsm::doWork().

06248                                  {
06249     coord.resize(natoms);
06250     force.resize(natoms);
06251     cntRecvs = 0;
06252     energy = 0;
06253     //memset(virial, 0, 3*3*sizeof(BigReal));
06254     for (int i = 0;  i < natoms;  i++)  force[i] = 0;
06255     if (mgr->approx == ComputeMsmMgr::C1HERMITE) {
06256       qh_c1hermite.reset(0);
06257       eh_c1hermite.reset(0);
06258     }
06259     else {
06260       qh.reset(0);
06261       eh.reset(0);
06262     }
06263   }

void msm::PatchData::interpolation (  ) 

Definition at line 6417 of file ComputeMsm.C.

References ComputeMsmMgr::approx, msm::Array< T >::buffer(), coord, ComputeMsmMgr::d_stencil_1d(), msm::Grid< T >::data(), ComputeMsmMgr::doneCompute(), eh, energy, force, ComputeMsmMgr::gzero, ComputeMsmMgr::hxlen_1, ComputeMsmMgr::hylen_1, ComputeMsmMgr::hzlen_1, msm::IndexRange::ia(), msm::IndexRange::ib(), MsmTimer::INTERP, msm::IndexRange::ja(), msm::IndexRange::jb(), msm::IndexRange::ka(), msm::IndexRange::kb(), ComputeMsmMgr::lattice, msm::Array< T >::len(), ComputeMsmMgr::MAX_POLY_DEGREE, mgr, NAMD_die(), msm::IndexRange::ni(), msm::IndexRange::nj(), patchID, ComputeMsmMgr::PolyDegree, ComputeMsmMgr::s_edge, Lattice::scale(), ComputeMsmMgr::sglower, ComputeMsmMgr::shx_1, ComputeMsmMgr::shy_1, ComputeMsmMgr::shz_1, ComputeMsmMgr::srx_x, ComputeMsmMgr::srx_y, ComputeMsmMgr::srx_z, ComputeMsmMgr::sry_x, ComputeMsmMgr::sry_y, ComputeMsmMgr::sry_z, ComputeMsmMgr::srz_x, ComputeMsmMgr::srz_y, ComputeMsmMgr::srz_z, Vector::x, Vector::y, and Vector::z.

Referenced by addPotential().

06417                                 {
06418 #ifdef DEBUG_MSM_GRID
06419     printf("patchID %d:  interpolation\n", patchID);
06420 #endif
06421 
06422 #ifdef MSM_TIMING
06423     double startTime, stopTime;
06424     startTime = CkWallTimer();
06425 #endif
06426 #ifndef MSM_COMM_ONLY
06427     BigReal energy_self = 0;
06428 
06429     Float xphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06430     Float yphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06431     Float zphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06432     Float dxphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06433     Float dyphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06434     Float dzphi[ComputeMsmMgr::MAX_POLY_DEGREE+1];
06435 
06436     const Double rs_edge = Double( mgr->s_edge );
06437     const int s_size = ComputeMsmMgr::PolyDegree[mgr->approx] + 1;
06438 
06439     const Float hx_1 = Float(mgr->hxlen_1);  // real space inverse grid spacing
06440     const Float hy_1 = Float(mgr->hylen_1);
06441     const Float hz_1 = Float(mgr->hzlen_1);
06442 
06443     const int ia = eh.ia();
06444     const int ib = eh.ib();
06445     const int ja = eh.ja();
06446     const int jb = eh.jb();
06447     const int ka = eh.ka();
06448     const int kb = eh.kb();
06449     const int ni = eh.ni();
06450     const int nj = eh.nj();
06451     Float *ehbuffer = eh.data().buffer();
06452 
06453     // loop over atoms
06454     for (int n = 0;  n < coord.len();  n++) {
06455       Float q = coord[n].charge;
06456       if (0==q) continue;
06457 
06458       ScaledPosition s = mgr->lattice.scale(coord[n].position);
06459 
06460       BigReal sx_hx = (s.x - mgr->sglower.x) * mgr->shx_1;
06461       BigReal sy_hy = (s.y - mgr->sglower.y) * mgr->shy_1;
06462       BigReal sz_hz = (s.z - mgr->sglower.z) * mgr->shz_1;
06463 
06464       BigReal xlo = floor(sx_hx) - rs_edge;
06465       BigReal ylo = floor(sy_hy) - rs_edge;
06466       BigReal zlo = floor(sz_hz) - rs_edge;
06467 
06468       // calculate Phi stencils along each dimension
06469       Float xdelta = Float(sx_hx - xlo);
06470       mgr->d_stencil_1d(dxphi, xphi, xdelta, hx_1);
06471       Float ydelta = Float(sy_hy - ylo);
06472       mgr->d_stencil_1d(dyphi, yphi, ydelta, hy_1);
06473       Float zdelta = Float(sz_hz - zlo);
06474       mgr->d_stencil_1d(dzphi, zphi, zdelta, hz_1);
06475 
06476       int ilo = int(xlo);
06477       int jlo = int(ylo);
06478       int klo = int(zlo);
06479 
06480 #if 0
06481       // XXX don't need to test twice!
06482 
06483       // test to see if stencil is within edges of grid
06484       int iswithin = ( ia <= ilo && (ilo+(s_size-1)) <= ib &&
06485                        ja <= jlo && (jlo+(s_size-1)) <= jb &&
06486                        ka <= klo && (klo+(s_size-1)) <= kb );
06487 
06488       if ( ! iswithin ) {
06489         char msg[100];
06490         snprintf(msg, sizeof(msg), "Atom %d is outside of the MSM grid.",
06491             coord[n].id);
06492         NAMD_die(msg);
06493       }
06494 #endif
06495 
06496       // determine force on atom from surrounding potential grid points
06497       //Force f = 0;
06498       //BigReal e = 0;
06499       Float fx=0, fy=0, fz=0, e=0;
06500       for (int k = 0;  k < s_size;  k++) {
06501         int koff = ((k+klo) - ka) * nj;
06502         for (int j = 0;  j < s_size;  j++) {
06503           int jkoff = (koff + (j+jlo) - ja) * ni;
06504           Float cx = yphi[j] * zphi[k];
06505           Float cy = dyphi[j] * zphi[k];
06506           Float cz = yphi[j] * dzphi[k];
06507           for (int i = 0;  i < s_size;  i++) {
06508             int ijkoff = jkoff + (i+ilo) - ia;
06509             Float ec = ehbuffer[ijkoff];
06510             fx += ec * dxphi[i] * cx;
06511             fy += ec * xphi[i] * cy;
06512             fz += ec * xphi[i] * cz;
06513             e += ec * xphi[i] * cx;
06514           }
06515         }
06516       }
06517 
06518 #if 0
06519       force[n].x -= q * (mgr->srx_x * fx + mgr->srx_y * fy + mgr->srx_z * fz);
06520       force[n].y -= q * (mgr->sry_x * fx + mgr->sry_y * fy + mgr->sry_z * fz);
06521       force[n].z -= q * (mgr->srz_x * fx + mgr->srz_y * fy + mgr->srz_z * fz);
06522 #endif
06523       force[n].x -= q * fx;
06524       force[n].y -= q * fy;
06525       force[n].z -= q * fz;
06526       energy += q * e;
06527       energy_self += q * q;
06528 
06529     } // end loop over atoms
06530 
06531     energy_self *= mgr->gzero;
06532     energy -= energy_self;
06533     energy *= 0.5;
06534 #endif // !MSM_COMM_ONLY
06535 #ifdef MSM_TIMING
06536     stopTime = CkWallTimer();
06537     mgr->msmTiming[MsmTimer::INTERP] += stopTime - startTime;
06538     mgr->doneTiming();
06539 #endif
06540     mgr->doneCompute();
06541   }

void msm::PatchData::interpolationC1Hermite (  ) 

Definition at line 6693 of file ComputeMsm.C.

References msm::Array< T >::buffer(), coord, D000, D001, D010, D011, D100, D101, D110, D111, ComputeMsmMgr::d_stencil_1d_c1hermite(), msm::Grid< T >::data(), ComputeMsmMgr::doneCompute(), eh_c1hermite, energy, force, ComputeMsmMgr::gzero, ComputeMsmMgr::hxlen, ComputeMsmMgr::hxlen_1, ComputeMsmMgr::hylen, ComputeMsmMgr::hylen_1, ComputeMsmMgr::hzlen, ComputeMsmMgr::hzlen_1, msm::IndexRange::ia(), msm::IndexRange::ib(), MsmTimer::INTERP, msm::IndexRange::ja(), msm::IndexRange::jb(), msm::IndexRange::ka(), msm::IndexRange::kb(), ComputeMsmMgr::lattice, msm::Array< T >::len(), mgr, NAMD_die(), msm::IndexRange::ni(), msm::IndexRange::nj(), patchID, Lattice::scale(), ComputeMsmMgr::sglower, ComputeMsmMgr::shx_1, ComputeMsmMgr::shy_1, ComputeMsmMgr::shz_1, ComputeMsmMgr::srx_x, ComputeMsmMgr::srx_y, ComputeMsmMgr::srx_z, ComputeMsmMgr::sry_x, ComputeMsmMgr::sry_y, ComputeMsmMgr::sry_z, ComputeMsmMgr::srz_x, ComputeMsmMgr::srz_y, ComputeMsmMgr::srz_z, C1Vector::velem, Vector::x, Vector::y, and Vector::z.

Referenced by addPotentialC1Hermite().

06693                                          {
06694 #ifdef DEBUG_MSM_GRID
06695     printf("patchID %d:  interpolation\n", patchID);
06696 #endif
06697 
06698 #ifdef MSM_TIMING
06699     double startTime, stopTime;
06700     startTime = CkWallTimer();
06701 #endif
06702 #ifndef MSM_COMM_ONLY
06703     BigReal energy_self = 0;
06704 
06705     Float xphi[2], dxphi[2], xpsi[2], dxpsi[2];
06706     Float yphi[2], dyphi[2], ypsi[2], dypsi[2];
06707     Float zphi[2], dzphi[2], zpsi[2], dzpsi[2];
06708 
06709     const Float hx = Float(mgr->hxlen);      // real space grid spacing
06710     const Float hy = Float(mgr->hylen);
06711     const Float hz = Float(mgr->hzlen);
06712 
06713     const Float hx_1 = Float(mgr->hxlen_1);  // real space inverse grid spacing
06714     const Float hy_1 = Float(mgr->hylen_1);
06715     const Float hz_1 = Float(mgr->hzlen_1);
06716 
06717     const int ia = eh_c1hermite.ia();
06718     const int ib = eh_c1hermite.ib();
06719     const int ja = eh_c1hermite.ja();
06720     const int jb = eh_c1hermite.jb();
06721     const int ka = eh_c1hermite.ka();
06722     const int kb = eh_c1hermite.kb();
06723     const int ni = eh_c1hermite.ni();
06724     const int nj = eh_c1hermite.nj();
06725     C1Vector *ehbuffer = eh_c1hermite.data().buffer();
06726 
06727     // loop over atoms
06728     for (int n = 0;  n < coord.len();  n++) {
06729       Float q = coord[n].charge;
06730       if (0==q) continue;
06731 
06732       ScaledPosition s = mgr->lattice.scale(coord[n].position);
06733 
06734       BigReal sx_hx = (s.x - mgr->sglower.x) * mgr->shx_1;
06735       BigReal sy_hy = (s.y - mgr->sglower.y) * mgr->shy_1;
06736       BigReal sz_hz = (s.z - mgr->sglower.z) * mgr->shz_1;
06737 
06738       BigReal xlo = floor(sx_hx);
06739       BigReal ylo = floor(sy_hy);
06740       BigReal zlo = floor(sz_hz);
06741 
06742       // calculate Phi stencils along each dimension
06743       Float xdelta = Float(sx_hx - xlo);
06744       mgr->d_stencil_1d_c1hermite(dxphi, xphi, dxpsi, xpsi,
06745           xdelta, hx, hx_1);
06746       Float ydelta = Float(sy_hy - ylo);
06747       mgr->d_stencil_1d_c1hermite(dyphi, yphi, dypsi, ypsi,
06748           ydelta, hy, hy_1);
06749       Float zdelta = Float(sz_hz - zlo);
06750       mgr->d_stencil_1d_c1hermite(dzphi, zphi, dzpsi, zpsi,
06751           zdelta, hz, hz_1);
06752 
06753       int ilo = int(xlo);
06754       int jlo = int(ylo);
06755       int klo = int(zlo);
06756 
06757 #if 0
06758       // XXX don't need to test twice!
06759 
06760       // test to see if stencil is within edges of grid
06761       int iswithin = ( ia <= ilo && ilo < ib &&
06762                        ja <= jlo && jlo < jb &&
06763                        ka <= klo && klo < kb );
06764 
06765       if ( ! iswithin ) {
06766         char msg[100];
06767         snprintf(msg, sizeof(msg), "Atom %d is outside of the MSM grid.",
06768             coord[n].id);
06769         NAMD_die(msg);
06770       }
06771 #endif
06772 
06773       // determine force on atom from surrounding potential grid points
06774       Float fx=0, fy=0, fz=0, e=0;
06775       for (int k = 0;  k < 2;  k++) {
06776         int koff = ((k+klo) - ka) * nj;
06777         for (int j = 0;  j < 2;  j++) {
06778           int jkoff = (koff + (j+jlo) - ja) * ni;
06779           Float c_yphi_zphi = yphi[j] * zphi[k];
06780           Float c_ypsi_zphi = ypsi[j] * zphi[k];
06781           Float c_yphi_zpsi = yphi[j] * zpsi[k];
06782           Float c_ypsi_zpsi = ypsi[j] * zpsi[k];
06783           Float c_yphi_dzphi = yphi[j] * dzphi[k];
06784           Float c_ypsi_dzphi = ypsi[j] * dzphi[k];
06785           Float c_yphi_dzpsi = yphi[j] * dzpsi[k];
06786           Float c_ypsi_dzpsi = ypsi[j] * dzpsi[k];
06787           Float c_dyphi_zphi = dyphi[j] * zphi[k];
06788           Float c_dypsi_zphi = dypsi[j] * zphi[k];
06789           Float c_dyphi_zpsi = dyphi[j] * zpsi[k];
06790           Float c_dypsi_zpsi = dypsi[j] * zpsi[k];
06791           for (int i = 0;  i < 2;  i++) {
06792             int ijkoff = jkoff + (i+ilo) - ia;
06793             fx += dxphi[i] * (c_yphi_zphi * ehbuffer[ijkoff].velem[D000]
06794                 + c_ypsi_zphi * ehbuffer[ijkoff].velem[D010]
06795                 + c_yphi_zpsi * ehbuffer[ijkoff].velem[D001]
06796                 + c_ypsi_zpsi * ehbuffer[ijkoff].velem[D011])
06797               + dxpsi[i] * (c_yphi_zphi * ehbuffer[ijkoff].velem[D100]
06798                   + c_ypsi_zphi * ehbuffer[ijkoff].velem[D110]
06799                   + c_yphi_zpsi * ehbuffer[ijkoff].velem[D101]
06800                   + c_ypsi_zpsi * ehbuffer[ijkoff].velem[D111]);
06801             fy += xphi[i] * (c_dyphi_zphi * ehbuffer[ijkoff].velem[D000]
06802                 + c_dypsi_zphi * ehbuffer[ijkoff].velem[D010]
06803                 + c_dyphi_zpsi * ehbuffer[ijkoff].velem[D001]
06804                 + c_dypsi_zpsi * ehbuffer[ijkoff].velem[D011])
06805               + xpsi[i] * (c_dyphi_zphi * ehbuffer[ijkoff].velem[D100]
06806                   + c_dypsi_zphi * ehbuffer[ijkoff].velem[D110]
06807                   + c_dyphi_zpsi * ehbuffer[ijkoff].velem[D101]
06808                   + c_dypsi_zpsi * ehbuffer[ijkoff].velem[D111]);
06809             fz += xphi[i] * (c_yphi_dzphi * ehbuffer[ijkoff].velem[D000]
06810                 + c_ypsi_dzphi * ehbuffer[ijkoff].velem[D010]
06811                 + c_yphi_dzpsi * ehbuffer[ijkoff].velem[D001]
06812                 + c_ypsi_dzpsi * ehbuffer[ijkoff].velem[D011])
06813               + xpsi[i] * (c_yphi_dzphi * ehbuffer[ijkoff].velem[D100]
06814                   + c_ypsi_dzphi * ehbuffer[ijkoff].velem[D110]
06815                   + c_yphi_dzpsi * ehbuffer[ijkoff].velem[D101]
06816                   + c_ypsi_dzpsi * ehbuffer[ijkoff].velem[D111]);
06817             e += xphi[i] * (c_yphi_zphi * ehbuffer[ijkoff].velem[D000]
06818                 + c_ypsi_zphi * ehbuffer[ijkoff].velem[D010]
06819                 + c_yphi_zpsi * ehbuffer[ijkoff].velem[D001]
06820                 + c_ypsi_zpsi * ehbuffer[ijkoff].velem[D011])
06821               + xpsi[i] * (c_yphi_zphi * ehbuffer[ijkoff].velem[D100]
06822                   + c_ypsi_zphi * ehbuffer[ijkoff].velem[D110]
06823                   + c_yphi_zpsi * ehbuffer[ijkoff].velem[D101]
06824                   + c_ypsi_zpsi * ehbuffer[ijkoff].velem[D111]);
06825           }
06826         }
06827       }
06828 
06829 #if 0
06830       force[n].x -= q * (mgr->srx_x * fx + mgr->srx_y * fy + mgr->srx_z * fz);
06831       force[n].y -= q * (mgr->sry_x * fx + mgr->sry_y * fy + mgr->sry_z * fz);
06832       force[n].z -= q * (mgr->srz_x * fx + mgr->srz_y * fy + mgr->srz_z * fz);
06833 #endif
06834       force[n].x -= q * fx;
06835       force[n].y -= q * fy;
06836       force[n].z -= q * fz;
06837       energy += q * e;
06838       energy_self += q * q;
06839 
06840     } // end loop over atoms
06841 
06842     energy_self *= mgr->gzero;
06843     energy -= energy_self;
06844     energy *= 0.5;
06845 #endif // !MSM_COMM_ONLY
06846 #ifdef MSM_TIMING
06847     stopTime = CkWallTimer();
06848     mgr->msmTiming[MsmTimer::INTERP] += stopTime - startTime;
06849     mgr->doneTiming();
06850 #endif
06851     mgr->doneCompute();
06852   }

void msm::PatchData::sendCharge (  ) 

Definition at line 6367 of file ComputeMsm.C.

References MsmTimer::COMM, msm::Grid< T >::data(), msm::Grid< T >::extract(), msm::Ivec::i, msm::Grid< T >::init(), msm::Ivec::j, msm::Ivec::k, msm::Array< T >::len(), msm::BlockIndex::level, mgr, MSM_PRIORITY, ComputeMsmMgr::msmBlock, msm::BlockIndex::n, pd, GridMsg::put(), qh, msm::PatchDiagram::send, sequence, SET_PRIORITY, subgrid, and msm::Grid< T >::updateLower().

Referenced by anterpolation().

06367                              {
06368 #ifdef MSM_TIMING
06369     double startTime, stopTime;
06370 #endif
06371     int priority = 1;
06372     // buffer portions of grid to send to Blocks on level 0
06373     // allocate the largest buffer space we'll need
06374     //Grid<BigReal> subgrid;
06375     //subgrid.resize(map->bsx[0] * map->bsy[0] * map->bsz[0]);
06376     for (int n = 0;  n < pd->send.len();  n++) {
06377 #ifdef MSM_TIMING
06378       startTime = CkWallTimer();
06379 #endif
06380       // initialize the proper subgrid indexing range
06381       subgrid.init( pd->send[n].nrange );
06382       // extract the values from the larger grid into the subgrid
06383       qh.extract(subgrid);
06384       // translate the subgrid indexing range to match the MSM block
06385       subgrid.updateLower( pd->send[n].nrange_wrap.lower() );
06386       // add the subgrid charges into the block
06387       BlockIndex& bindex = pd->send[n].nblock_wrap;
06388       // place subgrid into message
06389       int msgsz = subgrid.data().len() * sizeof(Float);
06390       GridMsg *gm = new(msgsz, sizeof(int)) GridMsg;
06391       SET_PRIORITY(gm, sequence, MSM_PRIORITY + priority);
06392       gm->put(subgrid, bindex.level, sequence);
06393 #ifdef MSM_TIMING
06394       stopTime = CkWallTimer();
06395       mgr->msmTiming[MsmTimer::COMM] += stopTime - startTime;
06396 #endif
06397       mgr->msmBlock[bindex.level](
06398           bindex.n.i, bindex.n.j, bindex.n.k).addCharge(gm);
06399     }
06400   }

void msm::PatchData::sendChargeC1Hermite (  ) 

Definition at line 6646 of file ComputeMsm.C.

References MsmTimer::COMM, msm::Grid< T >::data(), msm::Grid< T >::extract(), msm::Ivec::i, msm::Grid< T >::init(), msm::Ivec::j, msm::Ivec::k, msm::Array< T >::len(), msm::BlockIndex::level, mgr, MSM_PRIORITY, ComputeMsmMgr::msmC1HermiteBlock, msm::BlockIndex::n, pd, GridMsg::put(), qh_c1hermite, msm::PatchDiagram::send, sequence, SET_PRIORITY, subgrid_c1hermite, and msm::Grid< T >::updateLower().

Referenced by anterpolationC1Hermite().

06646                                       {
06647 #ifdef MSM_TIMING
06648     double startTime, stopTime;
06649 #endif
06650     int priority = 1;
06651     // buffer portions of grid to send to Blocks on level 0
06652     for (int n = 0;  n < pd->send.len();  n++) {
06653 #ifdef MSM_TIMING
06654       startTime = CkWallTimer();
06655 #endif
06656       // initialize the proper subgrid indexing range
06657       subgrid_c1hermite.init( pd->send[n].nrange );
06658       // extract the values from the larger grid into the subgrid
06659       qh_c1hermite.extract(subgrid_c1hermite);
06660       // translate the subgrid indexing range to match the MSM block
06661       subgrid_c1hermite.updateLower( pd->send[n].nrange_wrap.lower() );
06662       // add the subgrid charges into the block
06663       BlockIndex& bindex = pd->send[n].nblock_wrap;
06664       // place subgrid into message
06665       int msgsz = subgrid_c1hermite.data().len() * sizeof(C1Vector);
06666       GridMsg *gm = new(msgsz, sizeof(int)) GridMsg;
06667       SET_PRIORITY(gm, sequence, MSM_PRIORITY + priority);
06668       gm->put(subgrid_c1hermite, bindex.level, sequence);
06669 #ifdef MSM_TIMING
06670       stopTime = CkWallTimer();
06671       mgr->msmTiming[MsmTimer::COMM] += stopTime - startTime;
06672 #endif
06673       mgr->msmC1HermiteBlock[bindex.level](
06674           bindex.n.i, bindex.n.j, bindex.n.k).addCharge(gm);
06675     }
06676   }

Member Data Documentation

int msm::PatchData::cntRecvs

Definition at line 1752 of file ComputeMsm.C.

Referenced by addPotential(), addPotentialC1Hermite(), and init().

AtomCoordArray msm::PatchData::coord

Definition at line 1742 of file ComputeMsm.C.

Referenced by anterpolation(), anterpolationC1Hermite(), init(), interpolation(), and interpolationC1Hermite().

Grid<Float> msm::PatchData::eh

Definition at line 1745 of file ComputeMsm.C.

Referenced by addPotential(), init(), interpolation(), and PatchData().

Grid<C1Vector> msm::PatchData::eh_c1hermite

Definition at line 1748 of file ComputeMsm.C.

Referenced by addPotentialC1Hermite(), init(), interpolationC1Hermite(), and PatchData().

BigReal msm::PatchData::energy

Definition at line 1750 of file ComputeMsm.C.

Referenced by init(), interpolation(), interpolationC1Hermite(), and ComputeMsm::saveResults().

ForceArray msm::PatchData::force

Definition at line 1743 of file ComputeMsm.C.

Referenced by init(), interpolation(), interpolationC1Hermite(), and ComputeMsm::saveResults().

Map* msm::PatchData::map

Definition at line 1740 of file ComputeMsm.C.

Referenced by PatchData().

ComputeMsmMgr* msm::PatchData::mgr

Definition at line 1739 of file ComputeMsm.C.

Referenced by addPotential(), addPotentialC1Hermite(), anterpolation(), anterpolationC1Hermite(), init(), interpolation(), interpolationC1Hermite(), PatchData(), sendCharge(), and sendChargeC1Hermite().

int msm::PatchData::patchID

Definition at line 1753 of file ComputeMsm.C.

Referenced by anterpolation(), anterpolationC1Hermite(), interpolation(), interpolationC1Hermite(), and PatchData().

PatchDiagram* msm::PatchData::pd

Definition at line 1741 of file ComputeMsm.C.

Referenced by addPotential(), addPotentialC1Hermite(), PatchData(), sendCharge(), and sendChargeC1Hermite().

Grid<Float> msm::PatchData::qh

Definition at line 1744 of file ComputeMsm.C.

Referenced by anterpolation(), init(), PatchData(), and sendCharge().

Grid<C1Vector> msm::PatchData::qh_c1hermite

Definition at line 1747 of file ComputeMsm.C.

Referenced by anterpolationC1Hermite(), init(), PatchData(), and sendChargeC1Hermite().

int msm::PatchData::sequence

Definition at line 1754 of file ComputeMsm.C.

Referenced by ComputeMsm::doWork(), sendCharge(), and sendChargeC1Hermite().

Grid<Float> msm::PatchData::subgrid

Definition at line 1746 of file ComputeMsm.C.

Referenced by PatchData(), and sendCharge().

Grid<C1Vector> msm::PatchData::subgrid_c1hermite

Definition at line 1749 of file ComputeMsm.C.

Referenced by PatchData(), and sendChargeC1Hermite().

The documentation for this struct was generated from the following file:
Generated on 8 Dec 2019 for NAMD by  doxygen 1.6.1