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/* ObjCryst++ Object-Oriented Crystallographic Library
(c) 2000-2002 Vincent Favre-Nicolin vincefn@users.sourceforge.net
2000-2001 University of Geneva (Switzerland)
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
/*
* Global refinement example on PbSO4.
*
*/
#include <stdlib.h>
#include <fstream>
#include "ObjCryst/ZScatterer.h"
#include "ObjCryst/Atom.h"
#include "ObjCryst/PowderPattern.h"
#include "Quirks/VFNStreamFormat.h"
#include "Quirks/Chronometer.h"
#include "Quirks/VFNDebug.h"
#include "RefinableObj/GlobalOptimObj.h"
//#ifdef __MWERKS__
//#include <Profiler.h>
//#else
//#include "Profile/Profiler.h" //TAU profiling package
//#endif
using namespace ObjCryst;
void testPbSO4()
{
//Create 'real' PBSO4 structure (for reference only-no cheating !)
Crystal cryst_orig(8.482,5.398,6.959,"Pnma");
cryst_orig.SetName("PbSO4 (reference structure)");
cryst_orig.Print();
{//Create 'real' PBSO4 structure (for reference only)
ScatteringPowerAtom *ScattPowPb=new ScatteringPowerAtom("Pb","Pb",1.48);
ScatteringPowerAtom *ScattPowS =new ScatteringPowerAtom("S" ,"S",0.74);
ScatteringPowerAtom *ScattPowO1=new ScatteringPowerAtom("O1","O",1.87);
ScatteringPowerAtom *ScattPowO2=new ScatteringPowerAtom("O2","O",1.76);
ScatteringPowerAtom *ScattPowO3=new ScatteringPowerAtom("O3","O",1.34);
cryst_orig.AddScatteringPower(ScattPowPb);
cryst_orig.AddScatteringPower(ScattPowS);
cryst_orig.AddScatteringPower(ScattPowO1);
cryst_orig.AddScatteringPower(ScattPowO2);
cryst_orig.AddScatteringPower(ScattPowO3);
Atom *Pb=new Atom(.188,.250,.167,"Pb",ScattPowPb ,1.);
Atom *S=new Atom (.437,.750,.186,"S" ,ScattPowS ,1.);
Atom *O1=new Atom(.595,.750,.100,"O1",ScattPowO1 ,1.);
Atom *O2=new Atom(.319,.750,.043,"O2",ScattPowO2 ,1.);
Atom *O3=new Atom(.415,.974,.306,"O3",ScattPowO3 ,1.);
cryst_orig.AddScatterer(Pb);
cryst_orig.AddScatterer(S);
cryst_orig.AddScatterer(O1);
cryst_orig.AddScatterer(O2);
cryst_orig.AddScatterer(O3);
}
cryst_orig.PrintMinDistanceTable(.05);
//cryst_orig.GLDisplayCrystal();
//Creating PbSo4 refined crystal, either with independent atoms or a SO4 tetrahedron
cout << "Creating PBSO4 crystal..."<<endl;
// PbSo4 crystal, version with SO4 tetrahedron
Crystal cryst(8.482,5.398,6.959,"Pnma");
cryst.SetName("PbSO4");
{//create the refined crystal
ScatteringPowerAtom *ScattPowPb=new ScatteringPowerAtom("Pb","Pb",1.5);
ScatteringPowerAtom *ScattPowS =new ScatteringPowerAtom("S" ,"S" ,1);
ScatteringPowerAtom *ScattPowO =new ScatteringPowerAtom("O" ,"O" ,1.5);
cryst.AddScatteringPower(ScattPowPb);
cryst.AddScatteringPower(ScattPowS);
cryst.AddScatteringPower(ScattPowO);
Atom *Pb=new Atom(.0,.0,.0,"Pb",ScattPowPb ,1.);
ZPolyhedron *SO4=new ZPolyhedron(TETRAHEDRON,cryst,.1,.2,.3,"SO4",
ScattPowS,ScattPowO,1.5,1);
cryst.AddScatterer(Pb);
//SO4.SetUseGlobalScatteringPower(true);
cryst.AddScatterer(SO4);
}
cryst.RefinableObj::Print();
//Create Diffraction data object
PowderPattern data;
data.SetRadiationType(RAD_XRAY);
data.SetWavelength("CuA1");
data.SetName("PbSO4-RR");
data.ImportPowderPatternFullprof("xray-pattern.dat");
//Components
//diffraction
PowderPatternDiffraction * diffData=new PowderPatternDiffraction;
diffData->SetCrystal(cryst);
data.AddPowderPatternComponent(*diffData);
diffData->SetName("PbSo4-diffraction");
//approximate (hand-determined) background
PowderPatternBackground *backgdData= new PowderPatternBackground;
data.AddPowderPatternComponent(*backgdData);
backgdData->ImportUserBackground("xray-background.dat");
backgdData->SetName("PbSo4-background");
//Profile (approximate parameters,again)
diffData->SetReflectionProfilePar(PROFILE_PSEUDO_VOIGT,
.03*DEG2RAD*DEG2RAD,
0*DEG2RAD*DEG2RAD,
0*DEG2RAD*DEG2RAD,
0.3,0);
//Options for faster calculations
//Use Dynamical population correction for special positions / shared atoms
diffData->GetCrystal().SetUseDynPopCorr(true);
// To go faster -sufficient for structure solution
data.SetMaxSinThetaOvLambda(0.25);
//Create the global optimization object
MonteCarloObj globalOptObj;
globalOptObj.AddRefinableObj(data);
//Refine only positionnal parameters
globalOptObj.FixAllPar();
globalOptObj.SetParIsFixed(gpRefParTypeScattTransl,false);
globalOptObj.SetParIsFixed(gpRefParTypeScattOrient,false);
globalOptObj.SetParIsFixed(gpRefParTypeScattConformBondLength,false);
globalOptObj.SetParIsFixed(gpRefParTypeScattConformBondAngle,false);
globalOptObj.SetParIsFixed(gpRefParTypeScattConformDihedAngle,false);
globalOptObj.SetLimitsRelative(gpRefParTypeScattConformBondLength,-.1,.1);
globalOptObj.SetLimitsRelative(gpRefParTypeScattConformBondAngle,-10.*DEG2RAD,10.*DEG2RAD);
globalOptObj.SetLimitsRelative(gpRefParTypeScattConformDihedAngle,-10.*DEG2RAD,10.*DEG2RAD);
//Don't cheat ;-)
globalOptObj.RandomizeStartingConfig();
//Print Crystal structure
cout << "Random starting configuration"<<endl;
cryst.Print();
//Annealing parameters (schedule, Tmax, Tmin, displacement schedule,
globalOptObj.SetAlgorithmParallTempering(ANNEALING_SMART,1,.00001,
ANNEALING_EXPONENTIAL,8,.125);
//Global Optimization
//The real job-first test
long nbTrial=50000;
globalOptObj.Optimize(nbTrial);
//Save obtained spectrum
//data.SavePowderPattern("calc.out");
//Print calculated reflections
diffData->PrintFhklCalc();
//Print Crystal structure
cryst.Print();
//Print minimum distance between different atoms
// (<.05 are considered identical, if same element)
cryst.PrintMinDistanceTable(.05);
//Also print real structure
cryst_orig.Print();
//Save crystal POVRay file
//ofstream out1("crystal.pov");
//cryst.POVRayDescription(out1);
//out1.close();
//ofstream out2("pbso4/crystal-real.pov");
//cryst_orig.POVRayDescription(out2);
//out2.close();
}
int main (int argc, char *argv[])
{
TAU_PROFILE_SET_NODE(0); // sequential code
TAU_PROFILE("main()","int()",TAU_DEFAULT);
cout << " Beginning PbSO4 example...." << endl ;
int level =10;
if(argc==2)//debug level hase been supplied
{
level=atoi(argv[1]);
}
VFN_DEBUG_GLOBAL_LEVEL(level);
testPbSO4();
cout << " End of PbSO4 example." << endl ;
TAU_REPORT_STATISTICS();
return 0;
}
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