void updatePMLHFieldUtilHz(int xStart, int xEnd, int yStart, int yEnd, int zStart, int zEnd, int xBound, int yBound, int zBound, pmlConstStruct cx[], pmlConstStruct cy[], pmlConstStruct cz[], int n){
int i, j, k; // These are the indexes
int x,y,z;// There are indexes for the pmlConstStruct indexs
long p;
int m;
double bzStore;
double mu;
// Either this, or make cOnes a bigger array with number of elements which are the max of xLen, yLen, zLen
for (i=xStart;i<xEnd+1;i++){
x = abs(xBound - i)%PML_LAYERS;
for (j=yStart;j<yEnd+1;j++){
y = abs(yBound - j)%PML_LAYERS;
for (k=zStart;k<zEnd+1;k++){
z = abs(zBound - k)%PML_LAYERS;
p = PMLINDEX(i,j,k);
bzStore = BZ(p);
mu = MUR(m)*MUNOT;
BZ(p) = cx[x].c1*BZ(p) + cx[x].c2*(EX(i,j+1,k) - EX(i,j,k) + EY(i,j,k) - EY(i+1,j,k) - MSZ(m));
HZ(i,j,k) = cy[y].c3*HZ(i,j,k) + cy[y].c4*(cz[z].c5*BZ(p)-cz[z].c6*bzStore)/mu;
}}} // end for
}// end updatePMLHFieldUtilHz
static inline void calcH(void)
{
//todo mu = mu0?
for(int i=1; i<N_PX-1; i++)
for(int j=1; j<N_PY-1; j++)
Hz[ind(i,j)] = BZ(i,j)/MU_0_S;
}
static inline void calcH(void)
{
int i,j;
for(i=1; i<N_PX-1; i++)
for(j=1; j<N_PY-1; j++)
Hz[ind(i,j)] = BZ(i,j)/MU_0_S;
}
static inline void calcMB(void)
{
for(int i=1; i<N_PX-1; i++){
for(int j=1; j<N_PY-1; j++){
double complex nowMz = MZ(i,j);
Mz[ind(i,j)] = CMZ(i,j)*MZ(i,j) - CMZEXEY(i,j)*(EY(i+1,j) - EY(i,j) - EX(i,j+1) + EX(i,j));
Bz[ind(i,j)] = CBZ(i,j)*BZ(i,j) + CBZMZ1(i,j)*MZ(i,j) - CBZMZ0(i,j)*nowMz;
}
}
}
void SMACOF::run( const Matrix<double>& Weights, const Matrix<double>& Distances, const double& tol, const unsigned& maxloops, Matrix<double>& InitialZ ) {
unsigned M = Distances.nrows();
// Calculate V
Matrix<double> V(M,M); double totalWeight=0.;
for(unsigned i=0; i<M; ++i) {
for(unsigned j=0; j<M; ++j) {
if(i==j) continue;
V(i,j)=-Weights(i,j);
if( j<i ) totalWeight+=Weights(i,j);
}
for(unsigned j=0; j<M; ++j) {
if(i==j)continue;
V(i,i)-=V(i,j);
}
}
// And pseudo invert V
Matrix<double> mypseudo(M, M); pseudoInvert(V, mypseudo);
Matrix<double> dists( M, M ); double myfirstsig = calculateSigma( Weights, Distances, InitialZ, dists ) / totalWeight;
// initial sigma is made up of the original distances minus the distances between the projections all squared.
Matrix<double> temp( M, M ), BZ( M, M ), newZ( M, InitialZ.ncols() );
for(unsigned n=0; n<maxloops; ++n) {
if(n==maxloops-1) plumed_merror("ran out of steps in SMACOF algorithm");
// Recompute BZ matrix
for(unsigned i=0; i<M; ++i) {
for(unsigned j=0; j<M; ++j) {
if(i==j) continue; //skips over the diagonal elements
if( dists(i,j)>0 ) BZ(i,j) = -Weights(i,j)*Distances(i,j) / dists(i,j);
else BZ(i,j)=0.;
}
//the diagonal elements are -off diagonal elements BZ(i,i)-=BZ(i,j) (Equation 8.25)
BZ(i,i)=0; //create the space memory for the diagonal elements which are scalars
for(unsigned j=0; j<M; ++j) {
if(i==j) continue;
BZ(i,i)-=BZ(i,j);
}
}
mult( mypseudo, BZ, temp); mult(temp, InitialZ, newZ);
//Compute new sigma
double newsig = calculateSigma( Weights, Distances, newZ, dists ) / totalWeight;
//Computing whether the algorithm has converged (has the mass of the potato changed
//when we put it back in the oven!)
if( fabs( newsig - myfirstsig )<tol ) break;
myfirstsig=newsig;
InitialZ = newZ;
}
}
double mapping(TString SimData, TString ExpData, TString background = "nobackground"){
/////////////////////// OPEN INPUT AND OUTPUT FILES ///////////////////////
// open the data file
ifstream input_exp;
TString fullpathtofile = Form("%s",ExpData.Data() ) ;
if(gVerbose>0) cout<<"opening file : |"<<ExpData<< "| ... ";
input_exp.open( ExpData.Data() );
if (!input_exp) { cout<<"problem opening experimental data file " << fullpathtofile << endl; exit(-1);}
else if(gVerbose>0) cout<<"Experimental file is opened "<<endl;
//open the field files from comsol
ifstream input_sim;
fullpathtofile = Form("%s",SimData.Data() ) ;
if(gVerbose>0) cout<<"opening file : |"<<SimData<< "| ... ";
input_sim.open(SimData.Data() ) ;
if(!input_sim.is_open()) {
if(gVerbose>0) cout<<"problem opening simulation data file |"<< fullpathtofile <<"|"<< endl;
SimData.ReplaceAll("./input/","");
fullpathtofile = Form("/data1/moukaddam/MagnetSimulation/%s",SimData.Data()) ;
if(gVerbose>0) cout<<"trying main directory, opening file : |"<<fullpathtofile<< "| ... ";
input_sim.open(fullpathtofile.Data() ) ; // from local input if not go seek in data 1
if (!input_sim.is_open()) { cout<<"problem opening simulation data file |"<< fullpathtofile <<"|"<< endl<<endl; exit(-1);}
}
else if(gVerbose>0) cout<<" Simulation file " << fullpathtofile << " is opened " <<endl;
// create root output file
ExpData.ReplaceAll("./input/",""); ExpData.ReplaceAll(".dat",""); ExpData.ReplaceAll(".txt","");
SimData.ReplaceAll("./input/",""); SimData.ReplaceAll(".dat",""); SimData.ReplaceAll(".txt","");
TString filename = "./output/compare_" + ExpData + "_" + SimData + ".root";
TFile outputFile(filename,"RECREATE");
TDirectory *dirquad[4] ;
dirquad[0] = outputFile.mkdir("Quad_1");
dirquad[1] = outputFile.mkdir("Quad_2");
dirquad[2] = outputFile.mkdir("Quad_3");
dirquad[3] = outputFile.mkdir("Quad_4");
//Read the simulation file from comsol
// dump the first lines from the top
string s_buffer="buffer";
Int_t d_buffer=-1;
Int_t counter1=0; // counter on the first lines
Int_t counter2=0; // counter on the first lines
// read the first lines
Int_t dimX, dimY, dimZ;
input_sim>>dimX>>dimY>>dimZ;
if(gVerbose>0) cout<<"\nSimulated Field Table dimensions X : "<<dimX<<" Y : "<<dimY<<" Z : "<<dimZ<<endl;
dimX=dimX+10;
dimY=dimY+10;
dimZ=dimZ+10;
TH3D *f3DHistBx = new TH3D("f3DHistBX", "Bx" , dimX,-dimX, dimX, dimY,-dimY, dimY, dimZ, -dimZ, dimZ);
TH3D *f3DHistBy = new TH3D("f3DHistBY", "By" , dimX,-dimX, dimX, dimY,-dimY, dimY, dimZ, -dimZ, dimZ);
TH3D *f3DHistBz = new TH3D("f3DHistBZ", "Bz" , dimX,-dimX, dimX, dimY,-dimY, dimY, dimZ, -dimZ, dimZ);
TH3D *f3DHistBmag = new TH3D("f3DHistBMAG", "Bmag" , dimX,-dimX, dimX, dimY,-dimY, dimY, dimZ, -dimZ, dimZ);
TH3D *f3DHistBtan = new TH3D("f3DHistBTAN", "Btan" , dimX,-dimX, dimX, dimY,-dimY, dimY, dimZ, -dimZ, dimZ);
TH3D *f3DHistBdiff = new TH3D("f3DHistBDIFF", "Bdiff", dimX,-dimX, dimX, dimY,-dimY, dimY, dimZ, -dimZ, dimZ);
d_buffer=-1;
while (d_buffer != 0 && counter1< 15){ // find a solution for this with do while
input_sim>>d_buffer>>s_buffer;
counter2++;
}
getline(input_sim,s_buffer);
if(gVerbose>0) cout<< " Number of skipped lines in comsol file : " <<counter2 << " last line content : "<<s_buffer<<endl;
// read and fill
SimulationPoint* SimPoint = new SimulationPoint();
Double_t X(0), Y(0), Z(0), EX(-100), EY(-100), EZ(-100), Perm(0);
Double_t BX(0), BY(0), BZ(0);
Int_t line=0;
while ( !input_sim.eof() ) {
//Clear parameters
SimPoint->ClearParameters();
// Choose format
if(counter2<9) input_sim >> X >> Y >> Z >> BX >> BY >> BZ >> Perm ;
else input_sim >> X >> Y >> Z >> BX >> BY >> BZ >> EX >> EY >> EZ >> Perm ;
SimPoint->ReadLineAndTreat(X,Y,Z,BX,BY,BZ,EX,EY,EZ,Perm );
//SimPoint->Show();
// fill in TH3D all the simulation data
Int_t binNumber = f3DHistBx->FindBin(X,Y,Z);
f3DHistBx->SetBinContent(binNumber,BX);
f3DHistBy->SetBinContent(binNumber,BY);
f3DHistBz->SetBinContent(binNumber,BZ);
f3DHistBmag->SetBinContent(binNumber,SimPoint->fBFieldMag);
f3DHistBtan->SetBinContent(binNumber,SimPoint->fBFieldTan);
f3DHistBdiff->SetBinContent(binNumber,SimPoint->fBFieldDiff); //fBFieldMag-fBFieldTan
//count the lines for inspection
line++;
if (line%5000 == 0) {
if(gVerbose>0) printf("\r @line : %d ... Still reading ...",line);
if(gVerbose>1) cout<< X<<" "<<Y <<" "<<Z <<" "<<BX <<" "<<BY<<" "<<BZ <<" "<< EX<<" "<< EY<<" "<< EZ<<" "<< Perm<<endl ;
}
}
