void DiffractionDataSingleCrystal::CalcIcalc() const
{
TAU_PROFILE("DiffractionData::CalcIcalc()","void ()",TAU_DEFAULT);
VFN_DEBUG_MESSAGE("DiffractionData::CalcIcalc():"<<this->GetName(),3)
this->GetFhklCalcSq();
if( (mClockStructFactorSq<mClockIcalc) && (mClockScaleFactor<mClockIcalc)
&& ((0==mGroupOption.GetChoice()) || (mClockPrepareTwinningCorr<mClockIcalc)) ) return;
mCalcIntensity=mFhklCalcSq;
mCalcIntensity*=mScaleFactor;
if(0!=mGroupOption.GetChoice())
{
if(1==mGroupOption.GetChoice()) this->PrepareTwinningCalc();
mGroupIcalc.resize(mNbGroup);
mGroupIcalc=0;
long first=0;
for(long i=0;i<mNbGroup;i++)
{
//cout<<"Group #"<<i<<":"<<first<<"->"<<mGroupIndex(i)<<endl;
for(long j=first;j<mGroupIndex(i);j++)
{
//cout <<" " << mIntH(j)<<" "<< mIntK(j)<<" "<< mIntL(j)<<" " << mCalcIntensity(j)<<endl;
mGroupIcalc(i)+=mCalcIntensity(j);
}
first=mGroupIndex(i);
//cout << " => Icalc="<< mGroupIcalc(i) <<" , Iobs="<< mGroupIobs(i)<<endl<<endl;
}
}
mClockIcalc.Click();
}
REAL DiffractionDataSingleCrystal::GetBestRFactor() const
{
TAU_PROFILE("DiffractionData::GetBestRFactor()","void ()",TAU_DEFAULT);
VFN_DEBUG_MESSAGE("DiffractionData::GetBestRFactor()",3);
this->FitScaleFactorForR();
return this->GetR();
}
void DiffractionDataSingleCrystal::CalcIcalc_FullDeriv(std::set<RefinablePar *> &vPar)
{
TAU_PROFILE("DiffractionDataSingleCrystal::CalcIcalc_FullDeriv()","void ()",TAU_DEFAULT);
this->GetFhklCalcSq_FullDeriv(vPar);
// :TODO: instead of clear(), only add/remove when necessary ?
mCalcIntensity_FullDeriv.clear();
mCalcIntensity_FullDeriv=mFhklCalcSq_FullDeriv;
//:TODO: multiplication only up to mNbReflUsed
for(std::map<RefinablePar*, CrystVector_REAL>::iterator pos=mCalcIntensity_FullDeriv.begin(); pos!=mCalcIntensity_FullDeriv.end();pos++)
{
if(pos->first==0)
{// This is Icalc, not derived
pos->second *=mScaleFactor;
continue;
}
if(pos->first->GetPointer()!=&mScaleFactor)
{
/*if(pos->second.size()>0) */ // not needed
pos->second *=mScaleFactor;
}
else
{
pos->second=mFhklCalcSq;
}
}
if(0!=mGroupOption.GetChoice())
{//:TODO:
if(1==mGroupOption.GetChoice()) this->PrepareTwinningCalc();
// :TODO: instead of clear(), only add/remove when necessary ?
mGroupIcalc_FullDeriv.clear();
for(std::map<RefinablePar*, CrystVector_REAL>::iterator pos=mCalcIntensity_FullDeriv.begin(); pos!=mCalcIntensity_FullDeriv.end();pos++)
{
mGroupIcalc_FullDeriv[pos->first].resize(mNbGroup);
mGroupIcalc_FullDeriv[pos->first]=0;
long first=0;
for(long i=0;i<mNbGroup;i++)
{
for(long j=first;j<mGroupIndex(i);j++)
{
mGroupIcalc_FullDeriv[pos->first](i)+=mCalcIntensity_FullDeriv[pos->first](j);
}
first=mGroupIndex(i);
}
}
}
}
void DiffractionDataSingleCrystal::FitScaleFactorForRw() const
{
TAU_PROFILE("DiffractionData::FitScaleFactorForRw()","void ()",TAU_DEFAULT);
VFN_DEBUG_MESSAGE("DiffractionData::FitScaleFactorForRw()",3);
if(mHasObservedData==false)
{//throw exception here ?
return;
//throw ObjCrystException("DiffractionData::FitScaleFactorForRw() Cannot compute Rw
// or scale factor: there is no observed data !");
}
REAL tmp1=0;
REAL tmp2=0;
const REAL *p1;
const REAL *p2;
const REAL *p3;
long nb;
if(mGroupOption.GetChoice()==0)
{
p1=mCalcIntensity.data();
p2=mObsIntensity.data();
p3=mWeight.data();
nb=mNbReflUsed;
}
else
{
p1=mGroupIcalc.data();
p2=mGroupIobs.data();
p3=mGroupWeight.data();
nb=mGroupIobs.numElements();
}
for(long i=nb;i>0;i--)
{
tmp1 += *p3 * (*p1) * (*p2++);
tmp2 += *p3++ * (*p1) * (*p1);
p1++;
}
mScaleFactor *= tmp1/tmp2;
mClockScaleFactor.Click();
mCalcIntensity *= tmp1/tmp2;
if(0!=mGroupOption.GetChoice()) mGroupIcalc*= tmp1/tmp2;
mClockIcalc.Click();
}
REAL DiffractionDataSingleCrystal::GetRw()const
{
TAU_PROFILE("DiffractionData::Rw()"," REAL()",TAU_DEFAULT);
VFN_DEBUG_MESSAGE("DiffractionData::Rw()",3);
if(mHasObservedData==false)
{
return 0;
}
REAL tmp1=0;
REAL tmp2=0;
const REAL *p1;
const REAL *p2;
const REAL *p3;
long nb;
if(mGroupOption.GetChoice()==0)
{
p1=mCalcIntensity.data();
p2=mObsIntensity.data();
p3=mWeight.data();
nb=mNbReflUsed;
}
else
{
p1=mGroupIcalc.data();
p2=mGroupIobs.data();
p3=mGroupWeight.data();
nb=mGroupIobs.numElements();
}
for(long i=nb;i>0;i--)
{
tmp1 += *p3 * ( *p1 - *p2) * ( *p1 - *p2);
tmp2 += *p3 * *p2 * *p2;
p1++;p2++;p3++;
}
tmp1=sqrt(tmp1/tmp2);
VFN_DEBUG_MESSAGE("DiffractionData::Rw()="<<tmp1,3);
return tmp1 ;// /this->GetNbRefl();
}
void AsymmetricUnit::SetSpaceGroup(const SpaceGroup &spg)
{
VFN_DEBUG_MESSAGE("AsymmetricUnit::SetSpaceGroup(SpGroup)",5)
tmp_C_Numeric_locale tmploc;
# if 0
TAU_PROFILE("(AsymmetricUnit::SetSpaceGroup)","void (SpaceGroup)",TAU_DEFAULT);
mXmin=0.;
mYmin=0.;
mZmin=0.;
mXmax=1.;
mYmax=1.;
mZmax=1.;
if(1==spg.GetSpaceGroupNumber()) return;//no need to search an asymmetric unit
// Test points=reular grid of points inside the unit cell
// All points must be or have at least a symmetric in the asymmetric unit
const long nbPoints=13;
CrystMatrix_REAL testPoints(nbPoints*nbPoints*nbPoints,3);
{
long l=0;
for(long i=0;i<nbPoints;i++)
for(long j=0;j<nbPoints;j++)
for(long k=0;k<nbPoints;k++)
{
testPoints(l ,0)=i/(REAL)nbPoints;
testPoints(l ,1)=j/(REAL)nbPoints;
testPoints(l++,2)=k/(REAL)nbPoints;
}
}
testPoints += 0.01;
CrystVector_REAL vert(8);//vertices limits
vert(0)=1/8.; vert(1)=1/6.; vert(2)=1/4.; vert(3)=1/3.;
vert(4)=1/2.; vert(5)=2/3.; vert(6)=3/4.; vert(7)=1.;
const int NbStep=vert.numElements();
CrystMatrix_REAL coords;
double junk;
REAL minVolume=1.;
bool allPtsInAsym,tmp;
for(long nx=0;nx<NbStep;nx++)
for(long ny=0;ny<NbStep;ny++)
for(long nz=0;nz<NbStep;nz++)
{
if(minVolume<(vert(nx)*vert(ny)*vert(nz)-.0001)) break;
allPtsInAsym=true;
for(int i=0;i<testPoints.rows();i++)
{
coords=spg.GetAllSymmetrics(testPoints(i,0),testPoints(i,1),testPoints(i,2));
for(long j=0;j<coords.numElements();j++) coords(j)=modf(coords(j)+10.,&junk) ;
tmp=false;
for(long j=0;j<coords.rows();j++)
{//Test if at least one of the symmetrics is in the parallelepiped
if( (coords(j,0) < vert(nx))
&&(coords(j,1) < vert(ny))
&&(coords(j,2) < vert(nz)))
{
//cout << modf(coords(j,0)+10.,junk) << " "
// << modf(coords(j,1)+10.,junk) << " "
// << modf(coords(j,2)+10.,junk) << endl;
tmp=true;
break;
}
}
if(false==tmp)
{
//cout << " Rejected:"<<vert(nx)<<" "<<vert(ny)<<" "<<vert(nz)<<" "<<i<<endl;
//cout << coords <<endl;
allPtsInAsym=false;
break;
}
}
if( (true==allPtsInAsym))
{
mXmax=vert(nx);
mYmax=vert(ny);
mZmax=vert(nz);
VFN_DEBUG_MESSAGE("->ACCEPTED:" << mXmax <<" "<< mYmax <<" "<< mZmax <<endl,2)
//cout << "->ACCEPTED:" << mXmax <<" "<< mYmax <<" "<< mZmax <<endl;
minVolume=vert(nx)*vert(ny)*vert(nz);
break;//no need to grow any more along z
}
}
cout<<"->Finished Generating (pseudo) Asymmetric Unit, with:"<<endl
<<" 0 <= x <= "<< mXmax<<endl
<<" 0 <= y <= "<< mYmax<<endl
<<" 0 <= z <= "<< mZmax<<endl<<endl;
#else
const cctbx::sgtbx::brick b(spg.GetCCTbxSpg().type());
#ifdef __DEBUG__
cout<<"->>Parallelepipedic Asymmetric Unit, from cctbx::sgtbx::brick:"<<endl
<<b.as_string()<<endl;
#endif
mXmin=boost::rational_cast<REAL,int>(b(0,0).value());
mYmin=boost::rational_cast<REAL,int>(b(1,0).value());
mZmin=boost::rational_cast<REAL,int>(b(2,0).value());
mXmax=boost::rational_cast<REAL,int>(b(0,1).value());
mYmax=boost::rational_cast<REAL,int>(b(1,1).value());
mZmax=boost::rational_cast<REAL,int>(b(2,1).value());
#endif
}
int
main(int argc, char** argv)
{
ios::sync_with_stdio();
#ifdef USE_TAU
TAU_PROFILE_INIT(argc,argv);
TAU_PROFILE("main","int (int argc, char** argv)",TAU_DEFAULT);
TAU_PROFILE_TIMER(loop_timer,"Computation Loop","", TAU_USER);
TAU_PROFILE_TIMER(bc_timer,"Boundary Condition","", TAU_USER);
TAU_PROFILE_TIMER(update_timer,"Ghost Boundary Update","", TAU_USER);
TAU_PROFILE_TIMER(copy_timer,"Array Copy","", TAU_USER);
#endif
int Number_of_Processors=0;
Optimization_Manager::setForceVSG_Update(Off);
Optimization_Manager::Initialize_Virtual_Machine("",Number_of_Processors,argc,argv);
Partitioning_Type::SpecifyDefaultInternalGhostBoundaryWidths(1);
Optimization_Manager::setForceVSG_Update(Off);
Index::setBoundsCheck(off);
int myid = Communication_Manager::My_Process_Number;
int numProcs = Communication_Manager::Number_Of_Processors;
const int Xsize=1003*numProcs, Ysize=1003;
const Range ix(-1,Xsize-2), iy(-1,Ysize-2), all;
const Range ix1(0,Xsize-3), iy1(0,Ysize-3);
Partitioning_Type thePartition;
thePartition.SpecifyDecompositionAxes(1);
doubleArray A(ix,iy), old_A(ix,iy), x(ix,iy), y(ix,iy), temp(ix,iy);
const double dx=1./(Xsize-3), dy=1./(Ysize-3), dt=0.1/(Xsize+Ysize);
double theTime=0.0,maxError;
A.partition(thePartition);
old_A.partition(thePartition);
temp.partition(thePartition);
x.partition(thePartition);
y.partition(thePartition);
intSerialArray theProcessorSet = (A.getPartition()).getProcessorSet();
doubleSerialArray xlocal = x.getLocalArray();
doubleSerialArray ylocal = y.getLocalArray();
cout<<"size of xlocal: "<<xlocal.getSize()<<endl;
Optimization_Manager::setOptimizedScalarIndexing(On);
for( int i=xlocal.getBase(0);i<=xlocal.getBound(0);i++)
xlocal(i,all) = dx*i;
for( int j=ylocal.getBase(1);j<=ylocal.getBound(1);j++)
ylocal(all,j) = dy*j;
Optimization_Manager::setOptimizedScalarIndexing(Off);
x.updateGhostBoundaries();
y.updateGhostBoundaries();
A = (1.0 + theTime)*(2.0 + x + y);
doubleSerialArray oldALocal = old_A.getLocalArray();
doubleSerialArray ALocal = A.getLocalArray();
doubleSerialArray tempLocal = temp.getLocalArray();
int iLower = (myid>0)?ALocal.getBase(0)+1:ALocal.getBase(0)+1;
int iUpper = (myid<numProcs-1)?ALocal.getBound(0)-1:ALocal.getBound(0)-1;
int jLower = ALocal.getBase(1)+1;
int jUpper = ALocal.getBound(1)-1;
Range ILocInterior(iLower,iUpper);
Range JLocInterior(jLower,jUpper);
iLower = (myid>0)?ALocal.getBase(0)+1:ALocal.getBase(0);
iUpper = (myid<numProcs-1)?ALocal.getBound(0)-1:ALocal.getBound(0);
jLower = ALocal.getBase(1);
jUpper = ALocal.getBound(1);
Range ILoc(iLower,iUpper);
Range JLoc(jLower,jUpper);
if (myid == 0)
cout << "-----Starting computation" << endl;
double t = MPI_Wtime();
#ifdef USE_TAU
TAU_PROFILE_START(copy_timer);
#endif
oldALocal = ALocal;
#ifdef USE_TAU
TAU_PROFILE_STOP(copy_timer);
TAU_PROFILE_START(update_timer);
#endif
old_A.updateGhostBoundaries();
#ifdef USE_TAU
TAU_PROFILE_STOP(update_timer);
TAU_PROFILE_START(loop_timer);
#endif
tempLocal(ILocInterior,JLocInterior) = ALocal(ILocInterior,JLocInterior) -
dt*( ( ALocal(ILocInterior+1,JLocInterior) - ALocal(ILocInterior-1,JLocInterior) ) / (2.0*dx) +
( ALocal(ILocInterior,JLocInterior+1) - ALocal(ILocInterior,JLocInterior-1) ) / (2.0*dy) -
(4.0 + 2.0*theTime + xlocal(ILocInterior,JLocInterior) + ylocal(ILocInterior,JLocInterior)) );
#ifdef USE_TAU
TAU_PROFILE_STOP(loop_timer);
TAU_PROFILE_START(copy_timer);
#endif
//
// copy temp into A
//
ALocal(ILocInterior,JLocInterior) = tempLocal(ILocInterior,JLocInterior);
#ifdef USE_TAU
TAU_PROFILE_STOP(copy_timer);
TAU_PROFILE_START(bc_timer);
#endif
A(all,Ysize-2) = (1.0+(theTime+dt))*(2.0+x(all,Ysize-2)+y(all,Ysize-2));
A(all,-1) = (1.0+(theTime+dt))*(2.0+x(all,-1)+y(all,-1));
A(-1,iy1) = (1.0+(theTime+dt))*(2.0+x(-1,iy1)+y(-1,iy1));
A(Xsize-2,iy1) = (1.0+(theTime+dt))*(2.0+x(Xsize-2,iy1)+y(Xsize-2,iy1));
#ifdef USE_TAU
TAU_PROFILE_STOP(bc_timer);
TAU_PROFILE_START(update_timer);
#endif
A.updateGhostBoundaries();
#ifdef USE_TAU
TAU_PROFILE_STOP(update_timer);
#endif
theTime += dt;
for (int k = 0; k<100; k++)
{
#ifdef USE_TAU
TAU_PROFILE_START(loop_timer);
#endif
tempLocal(ILocInterior,JLocInterior) = oldALocal(ILocInterior,JLocInterior) -
2.*dt*( ( ALocal(ILocInterior+1,JLocInterior) - ALocal(ILocInterior-1,JLocInterior) ) / (2.0*dx) +
( ALocal(ILocInterior,JLocInterior+1) - ALocal(ILocInterior,JLocInterior-1) ) / (2.0*dy) -
(4.0 + 2.0*theTime + xlocal(ILocInterior,JLocInterior) + ylocal(ILocInterior,JLocInterior)) );
#ifdef USE_TAU
TAU_PROFILE_STOP(loop_timer);
TAU_PROFILE_START(copy_timer);
#endif
oldALocal(ILoc,JLoc) = ALocal(ILoc,JLoc);
ALocal(ILoc,JLoc) = tempLocal(ILoc,JLoc);
#ifdef USE_TAU
TAU_PROFILE_STOP(copy_timer);
TAU_PROFILE_START(bc_timer);
#endif
A(all,Ysize-2) = (1.0+(theTime+dt))*(2.0+x(all,Ysize-2)+y(all,Ysize-2));
A(all,-1) = (1.0+(theTime+dt))*(2.0+x(all,-1)+y(all,-1));
A(-1,iy1) = (1.0+(theTime+dt))*(2.0+x(-1,iy1)+y(-1,iy1));
A(Xsize-2,iy1) = (1.0+(theTime+dt))*(2.0+x(Xsize-2,iy1)+y(Xsize-2,iy1));
#ifdef USE_TAU
TAU_PROFILE_STOP(bc_timer);
TAU_PROFILE_START(update_timer);
#endif
A.updateGhostBoundaries();
#ifdef USE_TAU
TAU_PROFILE_STOP(update_timer);
#endif
theTime += dt;
}
t = MPI_Wtime() - t;
double maxTime;
MPI_Reduce(&t, &maxTime, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
if (myid == 0)
{
cout << " Total Time= " << maxTime<< " s" << endl;
}
maxError = max(fabs(A(ix,iy)-(1.0+theTime)*(2.0+x(ix,iy)+y(ix,iy))));
if (myid == 0)
{
cout << "max error at t="<<theTime<<" is: "<<maxError<<endl;
cout << "number of messages sent= "<<Diagnostic_Manager::getNumberOfMessagesSent()<<endl;
cout << "number of messages received= "<<Diagnostic_Manager::getNumberOfMessagesReceived()<<endl;
ofstream OutFile;
OutFile.open("/p/gb1/bmiller/ConvectPpp/ConvectPppNew.ConstSizePerProc.out",ios::app);
OutFile << numProcs << " " << maxTime << " " << maxError << endl;
OutFile.close();
}
#ifdef USE_TAU
TAU_PROFILE_EXIT("Finishing Profiling.");
#endif
Optimization_Manager::Exit_Virtual_Machine();
return 0;
}
REAL DiffractionDataSingleCrystal::GetChi2()const
{
if(mHasObservedData==false)
{
mChi2=0;
return mChi2;
}
this->GetNbReflBelowMaxSinThetaOvLambda();
if(mClockChi2>mClockMaster) return mChi2;
this->CalcIcalc();
if(mClockChi2>mClockIcalc) return mChi2;
TAU_PROFILE("DiffractionData::Chi2()"," REAL()",TAU_DEFAULT);
VFN_DEBUG_ENTRY("DiffractionData::Chi2()",3);
this->FitScaleFactorForRw();
mChi2=0;
const REAL *p1;
const REAL *p2;
const REAL *p3;
long nb;
if(mGroupOption.GetChoice()==0)
{
p1=mCalcIntensity.data();
p2=mObsIntensity.data();
p3=mWeight.data();
nb=mNbReflUsed;
}
else
{
p1=mGroupIcalc.data();
p2=mGroupIobs.data();
p3=mGroupWeight.data();
nb=mGroupIobs.numElements();
}
for(long i=nb;i>0;i--)
{
mChi2 += *p3++ * ( *p1 - *p2) * ( *p1 - *p2);
p1++;p2++;
}
/*
// SSE code gives about 30% faster code on P3 (tested with 10000 reflections),
// but scarcely any improvement on athlon-xp
union sse4f
{
__m128 m128;
struct
{
float x, y, z, w;
};
} ;
const long nb=mNbReflUsed/4;
const float* p1=mCalcIntensity.data();
const float* p2=mObsIntensity.data();
const float* p3=mWeight.data();
for(long i=0;i<nb;i++)
{
//segfaults with _mm_load_ps() instead of _mm_loadu_ps? Alignment problem ?
__m128 a = _mm_sub_ps(_mm_loadu_ps(p1),_mm_loadu_ps(p2));
union sse4f b;
b.m128= _mm_mul_ps(_mm_loadu_ps(p3),_mm_mul_ps(a,a));
mChi2 += b.x+b.y+b.z+b.w;
p1+=4;p2+=4;p3+=4;
}
p1-=4;p2-=4;p3-=4;
for(long i=nb*4;i<mNbReflUsed;i++)
{
mChi2 += *p3++ * ( *p1 - *p2) * ( *p1 - *p2);
p1++;p2++;
}
*/
mClockChi2.Click();
VFN_DEBUG_EXIT("DiffractionData::Chi2()="<<mChi2,3);
return mChi2;
}
CrystVector_long DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda(const REAL maxSTOL)
{
TAU_PROFILE("DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda()","void ()",TAU_DEFAULT);
VFN_DEBUG_ENTRY("DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda()",5)
// ScatteringData::SortReflectionBySinThetaOverLambda only sorts H,K,L and multiplicity.
CrystVector_long index=this->ScatteringData::SortReflectionBySinThetaOverLambda(maxSTOL);
if(mObsIntensity.numElements()==mNbRefl)
{
CrystVector_REAL tmpObs,tmpSigma,tmpWeight;
tmpObs=mObsIntensity;
tmpSigma=mObsSigma;
tmpWeight=mWeight;
for(long i=0;i<mNbRefl;i++)
{
mObsIntensity(i)=tmpObs(index(i));
mObsSigma(i)=tmpSigma(index(i));
mWeight(i)=tmpWeight(index(i));
}
// Keep a copy as squared F(hkl), to enable fourier maps
// :TODO: stop using mObsIntensity and just keep mFhklObsSq ?
mFhklObsSq=mObsIntensity;
mClockFhklObsSq.Click();
if(mGroupOption.GetChoice()==2)
{
CrystVector_long tmp;//,oldgroup(mNbGroup);;
tmp=mGroupIndex;
for(long i=0;i<mNbRefl;i++) mGroupIndex(i)=tmp(index(i));
/*
for(long i=0;i<mNbRefl;i++)
cout<<mIntH(i)<<" "<<mIntK(i)<<" "<<mIntL(i)<<" "
<<mObsIntensity(i)<<" "<<mObsSigma(i)<<" "<<mWeight(i)<< ":"<<mGroupIndex(i)<<endl;
*/
// Now re-index the groups of reflections in
// ascending order
{
index.resize(mNbGroup);
index=-1;
long group=0;
CrystVector_REAL oldGroupIobs, oldGroupWeight,oldGroupSigma;
oldGroupIobs =mGroupIobs;
oldGroupWeight=mGroupWeight;
oldGroupSigma=mGroupSigma;
for(long i=0;i<mNbRefl;i++)
{
if(index(mGroupIndex(i))==-1)// first reflection of a group ?
{
mGroupIobs(group)=oldGroupIobs(mGroupIndex(i));
mGroupSigma(group)=oldGroupSigma(mGroupIndex(i));
mGroupWeight(group)=oldGroupWeight(mGroupIndex(i));
//oldgroup(group)=mGroupIndex(i);
index(mGroupIndex(i))=group++;
}
mGroupIndex(i)=index(mGroupIndex(i));
}
}
/*
cout<<mIntH.numElements()<<","
<<mIntK.numElements()<<","
<<mIntL.numElements()<<","
<<oldgroup.numElements()<<","<<mGroupIndex.numElements()<<endl;
for(long i=0;i<mNbRefl;i++)
cout<<mIntH(i)<<" "<<mIntK(i)<<" "<<mIntL(i)<<endl
<<" :"<<oldgroup(mGroupIndex(i))<<"->"<<mGroupIndex(i)<<endl;
*/
// Now re-group the reflections
index=SortSubs(mGroupIndex);
{
CrystVector_long oldH,oldK,oldL,oldMult;
oldH=mH;
oldK=mK;
oldL=mL;
oldMult=mMultiplicity;
tmpObs=mObsIntensity;
tmpSigma=mObsSigma;
tmpWeight=mWeight;
for(long i=0;i<mNbRefl;i++)
{
const long subs=index(i);
mH(i)=oldH(subs);
mK(i)=oldK(subs);
mL(i)=oldL(subs);
mMultiplicity(i)=oldMult(subs);
mObsIntensity(i)=tmpObs(subs);
mObsSigma(i)=tmpSigma(subs);
mWeight(i)=tmpWeight(subs);
}
mClockHKL.Click();
this->PrepareHKLarrays();
this->CalcSinThetaLambda();
}
// re-write mGroupIndex so that it marks the
// last reflection of each group.
index=mGroupIndex;
mGroupIndex.resize(mNbGroup);
long group=0;
for(long i=0;i<mNbRefl;i++)
if(index(i)!=group)
mGroupIndex(group++)=i;
mGroupIndex(mNbGroup-1)=mNbRefl;
}
}
else
{// if there are no observed values, enter dummy ones
mObsIntensity.resize(mNbRefl);
mObsSigma.resize(mNbRefl);
mWeight.resize(mNbRefl);
mObsIntensity=100.;
mObsSigma=1.;
mWeight=1.;
mFhklObsSq.resize(0);
mClockFhklObsSq.Click();
}
VFN_DEBUG_EXIT("DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda()",5)
return index;
}