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Minor changes in libTFitPofB - the bigger problems have to be debugged later

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This commit is contained in:
Bastian M. Wojek 2009-10-26 19:10:38 +00:00
parent 9a693de0ce
commit 8e942948a5
10 changed files with 189 additions and 132 deletions
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4
src/external/TFitPofB-lib/classes/Makefile.libTFitPofB vendored
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@ -37,14 +37,14 @@ endif
# -- Linux
ifeq ($(OS),LINUX)
CXX = g++-4.4.0
CXX = g++-4.4.2
CXXFLAGS = -O3 -fopenmp -Wall -Wno-trigraphs -fPIC
PMUSRPATH = ../../../include
MNPATH = $(ROOTSYS)/include
LOCALPATH = ../include
FFTW3PATH = /usr/include
INCLUDES = -I$(PMUSRPATH) -I$(MNPATH) -I$(LOCALPATH) -I$(FFTW3PATH)
LD = g++-4.4.0
LD = g++-4.4.2
LDFLAGS = -O
SOFLAGS = -shared -fopenmp
SHLIB = libTFitPofB.so

25
src/external/TFitPofB-lib/classes/TBulkVortexFieldCalc.cpp vendored
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@ -10,7 +10,7 @@
***************************************************************************/
/***************************************************************************
* Copyright (C) 2009 by Bastian M. Wojek *
* Copyright (C) 2009 by Bastian M. Wojek, Alexander Maisuradze *
* *
* *
* This program is free software; you can redistribute it and/or modify *
@ -41,7 +41,7 @@ using namespace std;
#define TWOPI 6.28318530717958647692
const double fluxQuantum(2.067833667e7); // 10e14 times CGS units %% in CGS units should be 10^-7
// in this case this is Gauss per square nm
// in this case this is Gauss times square nm
const double sqrt3(sqrt(3.0));
double getXi(const double hc2) { // get xi given Hc2 in Gauss
@ -82,11 +82,13 @@ TBulkVortexFieldCalc::~TBulkVortexFieldCalc() {
TBulkTriVortexLondonFieldCalc::TBulkTriVortexLondonFieldCalc(const string& wisdom, const unsigned int steps) {
fWisdom = wisdom;
fSteps = steps;
if (steps % 2) {
fSteps = steps + 1;
} else {
fSteps = steps;
}
fParam.resize(3);
fGridExists = false;
if (fSteps%2)
fSteps++;
int init_threads(fftw_init_threads());
if (init_threads)
@ -195,22 +197,21 @@ TBulkTriVortexLondonFieldCalc::TBulkTriVortexLondonFieldCalc(const string& wisdo
void TBulkTriVortexLondonFieldCalc::CalculateGrid() const {
// SetParameters - method has to be called from the user before the calculation!!
double field(abs(fParam[0])), lambda(abs(fParam[1])), xi(abs(fParam[2]));
double field(fabs(fParam[0])), lambda(fabs(fParam[1])), xi(fabs(fParam[2]));
double Hc2(getHc2(xi));
double latConstTr(sqrt(fluxQuantum/field*sqrt(4.0/3.0)));
double latConstTr(2.0*sqrt(fluxQuantum/(field*sqrt3)));
double xisq_2_scaled(2.0/3.0*pow(xi*PI/latConstTr,2.0)), lambdasq_scaled(4.0/3.0*pow(lambda*PI/latConstTr,2.0));
int NFFT(fSteps);
int NFFT_2(fSteps/2);
int NFFTsq(fSteps*fSteps);
const int NFFT(fSteps);
const int NFFT_2(fSteps/2);
const int NFFTsq(fSteps*fSteps);
// fill the field Fourier components in the matrix
int m;
// ... but first check that the field is not larger than Hc2 and that we are dealing with a type II SC
if ((field >= Hc2) || (lambda < xi/sqrt(2.0))) {
int m;
#pragma omp parallel for default(shared) private(m) schedule(dynamic)
for (m = 0; m < NFFTsq; m++) {
fFFTout[m] = field;

135
src/external/TFitPofB-lib/classes/TFitPofBStartupHandler.cpp vendored
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@ -97,7 +97,11 @@ void TFitPofBStartupHandler::OnEndDocument()
*/
void TFitPofBStartupHandler::OnStartElement(const char *str, const TList *attributes)
{
if (!strcmp(str, "data_path")) {
if (!strcmp(str, "LEM")) {
fKey = eLEM;
} else if (!strcmp(str, "VortexLattice")) {
fKey = eVortex;
} else if (!strcmp(str, "data_path")) {
fKey = eDataPath;
} else if (!strcmp(str, "energy")) {
fKey = eEnergy;
@ -111,8 +115,8 @@ void TFitPofBStartupHandler::OnStartElement(const char *str, const TList *attrib
fKey = eNSteps;
} else if (!strcmp(str, "N_VortexGrid")) {
fKey = eGridSteps;
} else if (!strcmp(str, "N_VortexFourier")) {
fKey = eVortexFourierComp;
} else if (!strcmp(str, "VortexSymmetry")) {
fKey = eVortexSymmetry;
}
}
@ -140,6 +144,12 @@ void TFitPofBStartupHandler::OnEndElement(const char *str)
void TFitPofBStartupHandler::OnCharacters(const char *str)
{
switch (fKey) {
case eLEM:
fLEM = true;
break;
case eVortex:
fVortex = true;
break;
case eDataPath:
// set the data path to the given path
fDataPath = str;
@ -168,9 +178,12 @@ void TFitPofBStartupHandler::OnCharacters(const char *str)
// convert str to int and assign it to the GridSteps-member
fGridSteps = atoi(str);
break;
case eVortexFourierComp:
// convert str to int and assign it to the VortexFourierComp-member
fVortexFourierComp = atoi(str);
case eVortexSymmetry:
// convert str to int and assign it to the VortexSymmetry-member (square = 0, triangular = 1)
if (!strcmp(str, "square"))
fVortexSymmetry = 2;
else
fVortexSymmetry = 1;
break;
default:
break;
@ -256,68 +269,92 @@ void TFitPofBStartupHandler::CheckLists()
{
// check if anything was set, and if not set some default stuff
// check if any data path is given
cout << endl << "TFitPofBStartupHandler::CheckLists: check data path ...";
if (!fDataPath.size()) {
cout << endl << "TFitPofBStartupHandler::CheckLists: This is not going to work, you have to set a valid data path where to find the rge-files in the xml-file!" << endl;
exit(-1);
}
// check if any energies are given
cout << endl << "TFitPofBStartupHandler::CheckLists: check energy list ..." << endl;
if (!fEnergyList.size()) {
cout << endl << "TFitPofBStartupHandler::CheckLists: Energy list empty! Setting the default list." << endl;
char eChar[5];
for(unsigned int i(0); i<33; i++) {
for(unsigned int j(0); j<10; j++) {
sprintf(eChar, "%02u_%u", i, j);
fEnergyList.push_back(string(eChar));
}
}
}
// check if delta_t is given, if not set default
cout << endl << "TFitPofBStartupHandler::CheckLists: check specified time resolution ..." << endl;
cout << endl << "TFitPofBStartupHandler::CheckLists: check specified time resolution ... " << endl;
if(!fDeltat) {
cout << endl << "TFitPofBStartupHandler::CheckLists: You did not specify the time resolution. Setting the default." << endl;
cout << "TFitPofBStartupHandler::CheckLists: You did not specify the time resolution. Setting the default (10 ns)." << endl;
fDeltat = 0.01;
} else {
cout << fDeltat << " us" << endl;
}
// check if delta_B is given, if not set default
cout << endl << "TFitPofBStartupHandler::CheckLists: check specified field resolution ..." << endl;
if(!fDeltaB) {
cout << endl << "TFitPofBStartupHandler::CheckLists: You did not specify the field resolution. Setting the default." << endl;
fDeltaB = 0.05;
cout << "TFitPofBStartupHandler::CheckLists: You did not specify the field resolution. Setting the default (0.1 G)." << endl;
fDeltaB = 0.1;
} else {
cout << fDeltaB << " G" << endl;
}
// check if any wisdom-file is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check wisdom-file ..." << endl;
if (!fWisdomFile.size()) {
cout << endl << "TFitPofBStartupHandler::CheckLists: You did not specify a wisdom file. Setting the default." << endl;
fWisdomFile = "WordsOfWisdom.dat";
cout << "TFitPofBStartupHandler::CheckLists: You did not specify a wisdom file. No FFTW plans will be loaded or saved." << endl;
fWisdomFile = "";
} else {
cout << fWisdomFile << endl;
}
// check if any number of steps for the theory function is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check number of steps for theory ..." << endl;
if (!fNSteps) {
cout << endl << "TFitPofBStartupHandler::CheckLists: You did not specify the number of steps for the theory. Setting the default." << endl;
fNSteps = 3000;
if (fLEM) {
// check if any data path is given
cout << endl << "TFitPofBStartupHandler::CheckLists: check data path ..." << endl;
if (!fDataPath.size()) {
cout << "TFitPofBStartupHandler::CheckLists: This is not going to work, you have to set a valid data path where to find the rge-files in the xml-file!" << endl;
exit(-1);
} else {
cout << fDataPath << endl;
}
// check if any energies are given
cout << endl << "TFitPofBStartupHandler::CheckLists: check energy list ..." << endl;
if (!fEnergyList.size()) {
cout << "TFitPofBStartupHandler::CheckLists: Energy list empty! Setting the default list ( 0.0:0.1:32.9 keV)." << endl;
char eChar[5];
for(unsigned int i(0); i<33; i++) {
for(unsigned int j(0); j<10; j++) {
sprintf(eChar, "%02u_%u", i, j);
fEnergyList.push_back(string(eChar));
}
}
} else {
for (unsigned int i (0); i < fEnergyList.size(); i++)
cout << fEnergyList[i] << " ";
cout << endl;
}
// check if any number of steps for the theory function is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check number of steps for theory ..." << endl;
if (!fNSteps) {
cout << "TFitPofBStartupHandler::CheckLists: You did not specify the number of steps for the theory. Setting the default (3000)." << endl;
fNSteps = 3000;
} else {
cout << fNSteps << endl;
}
}
// check if any number of steps for the theory function is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check number of steps for Vortex grid ..." << endl;
if (!fGridSteps) {
cout << endl << "TFitPofBStartupHandler::CheckLists: You did not specify the number of steps for the grid. Setting the default." << endl;
fGridSteps = 200;
}
if (fVortex) {
// check if any number of steps for the theory function is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check number of steps for Vortex lattice Fourier components ..." << endl;
if (!fVortexFourierComp) {
cout << endl << "TFitPofBStartupHandler::CheckLists: You did not specify the number of Vortex lattice Fourier components. Setting the default." << endl;
fVortexFourierComp = 17;
}
// check if any number of steps for the theory function is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check number of steps for Vortex grid ..." << endl;
if (!fGridSteps) {
cout << "TFitPofBStartupHandler::CheckLists: You did not specify the number of steps for the grid. Setting the default (256)." << endl;
fGridSteps = 256;
} else {
cout << fGridSteps << endl;
}
// check if any number of steps for the theory function is specified
cout << endl << "TFitPofBStartupHandler::CheckLists: check symmetry of the Vortex lattice ..." << endl;
if (!fVortexSymmetry) {
cout << "TFitPofBStartupHandler::CheckLists: You did not specify the symmetry of the vortex lattice. Setting the default (triangular)." << endl;
fVortexSymmetry = 1;
} else {
cout << (fVortexSymmetry == 2 ? "square" : "triangular") << endl;
}
}
}
// end ---------------------------------------------------------------------

4
src/external/TFitPofB-lib/classes/TPofBCalc.cpp vendored
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@ -391,7 +391,7 @@ void TPofBCalc::Calculate(const TBulkVortexFieldCalc *vortexLattice, const vecto
if (lastZerosStart >= fPBSize)
lastZerosStart = fPBSize - 1;
// cout << endl << fBmin << " " << fBmax << " " << firstZerosEnd << " " << lastZerosStart << " " << numberOfPoints << endl;
// cout << endl << fBmin << " " << fBmax << " " << firstZerosEnd << " " << lastZerosStart << " " << numberOfSteps << endl;
if (!vortexLattice->GridExists()) {
vortexLattice->CalculateGrid();
@ -401,7 +401,7 @@ void TPofBCalc::Calculate(const TBulkVortexFieldCalc *vortexLattice, const vecto
unsigned int fill_index, counter(0);
for (unsigned int j(0); j < numberOfStepsSq_2; j++) {
fill_index = static_cast<unsigned int>(ceil(abs((vortexFields[j]/fDB))));
fill_index = static_cast<unsigned int>(ceil(fabs((vortexFields[j]/fDB))));
if (fill_index >= fPBSize)
fPB[fPBSize - 1] += 1.0;
else

2
src/external/TFitPofB-lib/classes/TPofTCalc.cpp vendored
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@ -80,7 +80,7 @@ TPofTCalc::TPofTCalc (const TPofBCalc *PofB, const string &wisdom, const vector<
fTBin = 1.0/(gBar*double(fNFFT-1)*par[2]);
int NFFT_2p1(fNFFT/2 + 1);
const int NFFT_2p1(fNFFT/2 + 1);
// allocating memory for the time- and polarisation vectors

2
src/external/TFitPofB-lib/classes/TVortex.cpp vendored
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@ -133,7 +133,7 @@ double TBulkTriVortexLondon::operator()(double t, const vector<double> &par) con
if(fFirstCall){
fPar = par;
for (unsigned int i(0); i < 3; i++){
for (unsigned int i(0); i < 3; i++) {
fParForVortex[i] = fPar[i+1];
}
fFirstCall = false;

10
src/external/TFitPofB-lib/include/TFitPofBStartupHandler.h vendored
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@ -14,7 +14,7 @@
***************************************************************************/
/***************************************************************************
* Copyright (C) 2007 by Andreas Suter, Bastian M. Wojek *
* Copyright (C) 2007-2008 by Andreas Suter, Bastian M. Wojek *
* *
* *
* This program is free software; you can redistribute it and/or modify *
@ -66,13 +66,15 @@ class TFitPofBStartupHandler : public TQObject {
virtual const string GetWisdomFile() const { return fWisdomFile; }
virtual const unsigned int GetNSteps() const { return fNSteps; }
virtual const unsigned int GetGridSteps() const { return fGridSteps; }
virtual const unsigned int GetVortexFourierComp() const { return fVortexFourierComp; }
virtual const unsigned int GetVortexSymmetry() const { return fVortexSymmetry; }
private:
enum EKeyWords {eEmpty, eComment, eDataPath, eEnergy, eEnergyList, eDeltat, eDeltaB, eWisdomFile, eNSteps, eGridSteps, eVortexFourierComp};
enum EKeyWords {eEmpty, eComment, eLEM, eVortex, eDataPath, eEnergy, eEnergyList, eDeltat, eDeltaB, eWisdomFile, eNSteps, eGridSteps, eVortexSymmetry};
EKeyWords fKey;
bool fLEM;
bool fVortex;
string fDataPath;
vector<string> fEnergyList;
double fDeltat;
@ -80,7 +82,7 @@ class TFitPofBStartupHandler : public TQObject {
string fWisdomFile;
unsigned int fNSteps;
unsigned int fGridSteps;
unsigned int fVortexFourierComp;
unsigned int fVortexSymmetry;
ClassDef(TFitPofBStartupHandler, 1)
};

4
src/external/TFitPofB-lib/test/Makefile.testVortex-v2 vendored
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@ -6,12 +6,12 @@ ROOTLIBS = $(shell $(ROOTSYS)/bin/root-config --libs)
#---------------------------------------------------
CXX = g++-4.4.0
CXX = g++-4.4.2
CXXFLAGS = -O3 -Wall
LOCALINCLUDE = ../include
ROOTINCLUDE = $(ROOTSYS)/include
INCLUDES = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
LD = g++-4.4.0
LD = g++-4.4.2
LDFLAGS = -O3 -L../classes -lTFitPofB -lfftw3_threads -lfftw3 -lm -lpthread -fopenmp -lPMusr
# the output from the root-config script:

79
src/external/TFitPofB-lib/test/TFitPofB_startup.xml vendored
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@ -2,39 +2,56 @@
<TFitPofB>
<comment>
TFitPofB_startup.xml
Defines path/prefix and energies (keV, format: %02u_%1u) of TrimSP-rge-files,
path/name to the FFTW-wisdom-file and time/field binning (us/G)
N_theory determines the number of points in "real space" where the theory function will be calculated
N_VortexGrid determines the number of points in which each axis of the "real space" will be divided when calculating the vortex B(x,y)
N_VortexFourier defines the number of Fourier components which should be summed up in order to get B(x,y)
</comment>
<data_path>/home/l_wojek/TrimSP/YBCOxtal/YBCOxtal-500000-</data_path>
Here some external parameters used in conjunction with the TFitPofB-library are set.
There are different sections:
* Common parameters which are used for any kind of function
* Parameters for low energy uSR data analysis with given B(z)
* Parameters for bulk uSR data analysis (currently only one model to calculate field distributions for a triangular vortex lattice)
Common parameters:
- wisdom : sets the path to an FFTW-wisdom file - if there is no valid wisdom at the given path, wisdom handling will be disabled
- delta_t : time resolution of P(t) in microseconds
- delta_B : field resolution of P(B) in Gauss
LEM parameters (if the LEM tag is present it is expected that the data_path tag contains a valid path):
- data_path, energy_list : Defines path/prefix and energies (keV, format: %02u_%1u) of TrimSP-rge-files,
- N_theory : determines the number of points in "real space" where the theory function B(z) will be calculated (if necessary)
bulk parameters:
- N_VortexGrid : determines the number of points used for the calculation of the vortex lattice field distribution (the grid will be N*N)
- VortexSymmetry : specify the vortex lattice symmetry - either "square" or "triangular"
</comment>
<wisdom>/home/l_wojek/analysis/WordsOfWisdom.dat</wisdom>
<delta_t>0.01</delta_t>
<delta_B>0.1</delta_B>
<N_theory>5000</N_theory>
<N_VortexGrid>200</N_VortexGrid>
<N_VortexFourier>17</N_VortexFourier>
<energy_list>
<energy>03_0</energy>
<energy>03_6</energy>
<energy>05_0</energy>
<energy>05_3</energy>
<energy>07_0</energy>
<energy>07_7</energy>
<energy>08_0</energy>
<energy>09_0</energy>
<energy>10_0</energy>
<energy>10_2</energy>
<energy>12_0</energy>
<energy>14_1</energy>
<energy>16_0</energy>
<energy>16_4</energy>
<energy>18_0</energy>
<energy>19_7</energy>
<energy>20_0</energy>
<energy>22_0</energy>
<energy>24_0</energy>
<energy>24_6</energy>
<VortexLattice>
<N_VortexGrid>256</N_VortexGrid>
<VortexSymmetry>triangular</VortexSymmetry>
</VortexLattice>
<LEM>
<data_path>/home/l_wojek/TrimSP/YBCOxtal/YBCOxtal-500000-</data_path>
<N_theory>5000</N_theory>
<energy_list>
<energy>03_0</energy>
<energy>03_6</energy>
<energy>05_0</energy>
<energy>05_3</energy>
<energy>07_0</energy>
<energy>07_7</energy>
<energy>08_0</energy>
<energy>09_0</energy>
<energy>10_0</energy>
<energy>10_2</energy>
<energy>12_0</energy>
<energy>14_1</energy>
<energy>16_0</energy>
<energy>16_4</energy>
<energy>18_0</energy>
<energy>19_7</energy>
<energy>20_0</energy>
<energy>22_0</energy>
<energy>24_0</energy>
<energy>24_6</energy>
</energy_list>
</LEM>
</TFitPofB>

58
src/external/TFitPofB-lib/test/testVortex-v2.cpp vendored
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@ -9,7 +9,7 @@ using namespace std;
int main(){
unsigned int NFFT(256);
unsigned int NFFT(512);
vector<double> parForVortex;
parForVortex.resize(3);
@ -20,47 +20,47 @@ int main(){
vector<double> parForPofB;
parForPofB.push_back(0.01); //dt
parForPofB.push_back(0.5); //dB
parForPofB.push_back(2.0); //dB
vector<double> parForPofT;
parForPofT.push_back(0.0); //phase
parForPofT.push_back(0.01); //dt
parForPofT.push_back(0.5); //dB
parForPofT.push_back(2.0); //dB
TBulkTriVortexLondonFieldCalc *vortexLattice = new TBulkTriVortexLondonFieldCalc("/home/l_wojek/analysis/WordsOfWisdom.dat", NFFT);
parForVortex[0] = 500.0; //app.field
parForVortex[1] = 300.0; //lambda
parForVortex[2] = 3.0; //xi
parForVortex[0] = 1000.0; //app.field
parForVortex[1] = 1000.0; //lambda
parForVortex[2] = 4.0; //xi
vortexLattice->SetParameters(parForVortex);
vortexLattice->CalculateGrid();
// ofstream ofy("testVortex-B.dat");
// for (unsigned int j(0); j < NFFT * NFFT; j++) {
// ofy << vortexLattice->DataB()[j] << " ";
// if (!((j+1)%(NFFT)))
// ofy << endl;
// }
// ofy.close();
ofstream ofy("testVortex-B.dat");
for (unsigned int j(0); j < NFFT * NFFT; j++) {
ofy << vortexLattice->DataB()[j] << " ";
if (!((j+1)%(NFFT)))
ofy << endl;
}
ofy.close();
TPofBCalc *PofB = new TPofBCalc(parForPofB);
PofB->Calculate(vortexLattice, parForPofB);
// const double *b(PofB->DataB());
// const double *pb(PofB->DataPB());
// unsigned int s(PofB->GetPBSize());
//
double test(0.0);
//
// ofstream ofx("testVortex.dat");
// for (unsigned int i(0); i < s; i++) {
// ofx << b[i] << " " << pb[i] << endl;
// test+=pb[i];
// }
// ofx.close();
const double *b(PofB->DataB());
double *pb(PofB->DataPB());
unsigned int s(PofB->GetPBSize());
// cout << test << endl;
double test(0.0);
ofstream ofx("testVortex.dat");
for (unsigned int i(0); i < s; i++) {
ofx << b[i] << " " << pb[i] << endl;
test+=pb[i];
}
ofx.close();
cout << test << endl;
TPofTCalc poft(PofB, "/home/l_wojek/analysis/WordsOfWisdom.dat", parForPofT);
@ -69,12 +69,12 @@ int main(){
// ofstream of8("testVortex-Pt.dat");
ofstream of8("testVortex-Pt.dat");
for (double i(0.); i<12.0; i+=0.003) {
test = poft.Eval(i);
// of8 << i << " " << poft.Eval(i) << endl;
of8 << i << " " << poft.Eval(i) << endl;
}
// of8.close();
of8.close();
// parForVortex[0] = 500.0; //app.field
// parForVortex[1] = 100.0; //lambda