applications/staticProps/pAngle.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 */

/* Calculates Rho(theta) */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/pAngle.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "brains/Thermo.hpp"

namespace OpenMD {
  
  pAngle::pAngle(SimInfo* info, const std::string& filename, 
                 const std::string& sele1, int nthetabins)
    : StaticAnalyser(info, filename), selectionScript1_(sele1),  
      evaluator1_(info),  evaluator2_(info), seleMan1_(info), seleMan2_(info), 
      nThetaBins_(nthetabins),
      doVect_(true), doOffset_(false) {
    
    setOutputName(getPrefix(filename) + ".pAngle");

    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }            
    
    count_.resize(nThetaBins_);
    histogram_.resize(nThetaBins_); 
  }

  pAngle::pAngle(SimInfo* info, const std::string& filename, 
                 const std::string& sele1, const std::string& sele2, 
                 int nthetabins)
    : StaticAnalyser(info, filename), selectionScript1_(sele1), 
      selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), 
      seleMan1_(info), seleMan2_(info), nThetaBins_(nthetabins),
      doVect_(false), doOffset_(false) {
    
    setOutputName(getPrefix(filename) + ".pAngle");

    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }            
    
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }            
    
    count_.resize(nThetaBins_);
    histogram_.resize(nThetaBins_); 
  }

  pAngle::pAngle(SimInfo* info, const std::string& filename, 
                 const std::string& sele1, int seleOffset, int nthetabins)
    : StaticAnalyser(info, filename), selectionScript1_(sele1),  
      evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info),
      nThetaBins_(nthetabins), seleOffset_(seleOffset), 
      doVect_(false), doOffset_(true) {
    
    setOutputName(getPrefix(filename) + ".pAngle");
    
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }            
    
    count_.resize(nThetaBins_);
    histogram_.resize(nThetaBins_);    
  }
  
  void pAngle::process() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    StuntDouble* sd1;
    StuntDouble* sd2;
    int ii; 
    int jj;

    Thermo thermo(info_);
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();

    nProcessed_ = nFrames/step_;

    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::fill(count_.begin(), count_.end(), 0);
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();

      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        //change the positions of atoms which belong to the rigidbodies
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }
      }
      
      Vector3d CenterOfMass = thermo.getCom();      

      if  (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
      
      if (doVect_) {

        
        for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; 
             sd1 = seleMan1_.nextSelected(ii)) {
          
          Vector3d pos = sd1->getPos();
          
          Vector3d r1 = CenterOfMass - pos;
          // only do this if the stunt double actually has a vector associated
          // with it
          if (sd1->isDirectional()) {
            Vector3d vec = sd1->getA().getColumn(2);
            RealType distance = r1.length();
            
            vec.normalize();
            r1.normalize();
            RealType cosangle = dot(r1, vec);
            
            int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
            count_[binNo]++;
          }
        }
      } else {
        if (doOffset_) {
          
          for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
               sd1 = seleMan1_.nextSelected(ii)) {
            
            // This will require careful rewriting if StaticProps is
            // ever parallelized.  For an example, see
            // Thermo::getTaggedAtomPairDistance
            
            int sd2Index = sd1->getGlobalIndex() + seleOffset_;
            sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
            
            Vector3d r1 = CenterOfMass - sd1->getPos();
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(r1);
            
            Vector3d r2 = CenterOfMass - sd2->getPos();
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(r1);
            
            Vector3d rc = 0.5*(r1 + r2);
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(rc);
            
            Vector3d vec = r1-r2;
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(vec);
            
            rc.normalize();
            vec.normalize();
            RealType cosangle = dot(rc, vec);
            int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
            count_[binNo]++;
          }        
        } else {
          
          if  (evaluator2_.isDynamic()) {
            seleMan2_.setSelectionSet(evaluator2_.evaluate());
          }
          
          if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
            sprintf( painCave.errMsg,
                     "In frame %d, the number of selected StuntDoubles are\n"
                     "\tnot the same in --sele1 and sele2\n", istep);
            painCave.severity = OPENMD_INFO;
            painCave.isFatal = 0;
            simError();            
          }
          
          for (sd1 = seleMan1_.beginSelected(ii), 
                 sd2 = seleMan2_.beginSelected(jj);
               sd1 != NULL && sd2 != NULL;
               sd1 = seleMan1_.nextSelected(ii), 
                 sd2 = seleMan2_.nextSelected(jj)) {
            
            Vector3d r1 = CenterOfMass - sd1->getPos();
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(r1);
            
            Vector3d r2 = CenterOfMass - sd2->getPos();
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(r1);
          
            Vector3d rc = 0.5*(r1 + r2);
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(rc);
            
            Vector3d vec = r1-r2;
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(vec);
            
            rc.normalize();
            vec.normalize();
            RealType cosangle = dot(rc, vec);
            int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
            count_[binNo]++;
            
          }
        }
      }
    }
      
    processHistogram();
    writeProbs();
    
  }
  
  void pAngle::processHistogram() {
    
    int atot = 0;
    for(unsigned int i = 0; i < count_.size(); ++i) 
      atot += count_[i];
    
    for(unsigned int i = 0; i < count_.size(); ++i) {
      histogram_[i] = double(count_[i] / double(atot));
    }    
  }
  
  
  void pAngle::writeProbs() {

    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#pAngle\n";
      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")";
      if (!doVect_) {
        rdfStream << "\tselection2: (" << selectionScript2_ << ")";
      }
      rdfStream << "\n";
      rdfStream << "#cos(theta)\tp(cos(theta))\n";
      RealType dct = 2.0 / histogram_.size();
      for (unsigned int i = 0; i < histogram_.size(); ++i) {
        RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
        rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
      }
      
    } else {
      
      sprintf(painCave.errMsg, "pAngle: unable to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    
    rdfStream.close();
  }
  
}

Revision:	1988
Committed:	Fri Apr 18 19:49:54 2014 UTC (11 years ago) by gezelter
File size:	10743 byte(s)
Log Message:	Fixed an initialization bug in pAngle selection offset branch
#	User	Rev	Content
1	gezelter	1413	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	gezelter	1413	*/
42
43			/* Calculates Rho(theta) */
44
45			#include <algorithm>
46	gezelter	1782	#include <fstream>
47	gezelter	1413	#include "applications/staticProps/pAngle.hpp"
48			#include "utils/simError.h"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51	gezelter	1782	#include "brains/Thermo.hpp"
52
53	gezelter	1413	namespace OpenMD {
54
55			pAngle::pAngle(SimInfo* info, const std::string& filename,
56	gezelter	1979	const std::string& sele1, int nthetabins)
57			: StaticAnalyser(info, filename), selectionScript1_(sele1),
58			evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info),
59			nThetaBins_(nthetabins),
60			doVect_(true), doOffset_(false) {
61	gezelter	1413
62	gezelter	1979	setOutputName(getPrefix(filename) + ".pAngle");
63
64			evaluator1_.loadScriptString(sele1);
65			if (!evaluator1_.isDynamic()) {
66			seleMan1_.setSelectionSet(evaluator1_.evaluate());
67	gezelter	1413	}
68
69			count_.resize(nThetaBins_);
70	gezelter	1979	histogram_.resize(nThetaBins_);
71			}
72
73			pAngle::pAngle(SimInfo* info, const std::string& filename,
74			const std::string& sele1, const std::string& sele2,
75			int nthetabins)
76			: StaticAnalyser(info, filename), selectionScript1_(sele1),
77			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
78			seleMan1_(info), seleMan2_(info), nThetaBins_(nthetabins),
79			doVect_(false), doOffset_(false) {
80	gezelter	1413
81			setOutputName(getPrefix(filename) + ".pAngle");
82	gezelter	1979
83			evaluator1_.loadScriptString(sele1);
84			if (!evaluator1_.isDynamic()) {
85			seleMan1_.setSelectionSet(evaluator1_.evaluate());
86			}
87
88			evaluator2_.loadScriptString(sele2);
89			if (!evaluator2_.isDynamic()) {
90			seleMan2_.setSelectionSet(evaluator2_.evaluate());
91			}
92
93			count_.resize(nThetaBins_);
94			histogram_.resize(nThetaBins_);
95	gezelter	1413	}
96	gezelter	1979
97			pAngle::pAngle(SimInfo* info, const std::string& filename,
98			const std::string& sele1, int seleOffset, int nthetabins)
99			: StaticAnalyser(info, filename), selectionScript1_(sele1),
100			evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info),
101	gezelter	1988	nThetaBins_(nthetabins), seleOffset_(seleOffset),
102	gezelter	1979	doVect_(false), doOffset_(true) {
103
104			setOutputName(getPrefix(filename) + ".pAngle");
105
106			evaluator1_.loadScriptString(sele1);
107			if (!evaluator1_.isDynamic()) {
108			seleMan1_.setSelectionSet(evaluator1_.evaluate());
109			}
110
111			count_.resize(nThetaBins_);
112			histogram_.resize(nThetaBins_);
113			}
114	gezelter	1413
115			void pAngle::process() {
116			Molecule* mol;
117			RigidBody* rb;
118			SimInfo::MoleculeIterator mi;
119			Molecule::RigidBodyIterator rbIter;
120	gezelter	1979	StuntDouble* sd1;
121			StuntDouble* sd2;
122			int ii;
123			int jj;
124	gezelter	1413
125	gezelter	1782	Thermo thermo(info_);
126	gezelter	1413	DumpReader reader(info_, dumpFilename_);
127			int nFrames = reader.getNFrames();
128	gezelter	1979
129	gezelter	1413	nProcessed_ = nFrames/step_;
130
131			std::fill(histogram_.begin(), histogram_.end(), 0.0);
132			std::fill(count_.begin(), count_.end(), 0);
133
134			for (int istep = 0; istep < nFrames; istep += step_) {
135			reader.readFrame(istep);
136			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
137
138			for (mol = info_->beginMolecule(mi); mol != NULL;
139			mol = info_->nextMolecule(mi)) {
140			//change the positions of atoms which belong to the rigidbodies
141			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
142			rb = mol->nextRigidBody(rbIter)) {
143			rb->updateAtoms();
144			}
145			}
146
147	gezelter	1782	Vector3d CenterOfMass = thermo.getCom();
148	gezelter	1413
149	gezelter	1979	if (evaluator1_.isDynamic()) {
150			seleMan1_.setSelectionSet(evaluator1_.evaluate());
151	gezelter	1413	}
152
153	gezelter	1979	if (doVect_) {
154	gezelter	1988
155	gezelter	1782
156	gezelter	1979	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
157			sd1 = seleMan1_.nextSelected(ii)) {
158	gezelter	1413
159	gezelter	1979	Vector3d pos = sd1->getPos();
160
161			Vector3d r1 = CenterOfMass - pos;
162			// only do this if the stunt double actually has a vector associated
163			// with it
164			if (sd1->isDirectional()) {
165			Vector3d vec = sd1->getA().getColumn(2);
166			RealType distance = r1.length();
167
168			vec.normalize();
169			r1.normalize();
170			RealType cosangle = dot(r1, vec);
171
172			int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
173			count_[binNo]++;
174			}
175	gezelter	1413	}
176	gezelter	1979	} else {
177			if (doOffset_) {
178
179			for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
180			sd1 = seleMan1_.nextSelected(ii)) {
181
182			// This will require careful rewriting if StaticProps is
183			// ever parallelized. For an example, see
184			// Thermo::getTaggedAtomPairDistance
185
186			int sd2Index = sd1->getGlobalIndex() + seleOffset_;
187			sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
188
189			Vector3d r1 = CenterOfMass - sd1->getPos();
190			if (usePeriodicBoundaryConditions_)
191			currentSnapshot_->wrapVector(r1);
192
193			Vector3d r2 = CenterOfMass - sd2->getPos();
194			if (usePeriodicBoundaryConditions_)
195			currentSnapshot_->wrapVector(r1);
196
197			Vector3d rc = 0.5*(r1 + r2);
198			if (usePeriodicBoundaryConditions_)
199			currentSnapshot_->wrapVector(rc);
200
201			Vector3d vec = r1-r2;
202			if (usePeriodicBoundaryConditions_)
203			currentSnapshot_->wrapVector(vec);
204
205			rc.normalize();
206			vec.normalize();
207			RealType cosangle = dot(rc, vec);
208			int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
209			count_[binNo]++;
210			}
211			} else {
212
213			if (evaluator2_.isDynamic()) {
214			seleMan2_.setSelectionSet(evaluator2_.evaluate());
215			}
216
217			if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
218			sprintf( painCave.errMsg,
219			"In frame %d, the number of selected StuntDoubles are\n"
220			"\tnot the same in --sele1 and sele2\n", istep);
221			painCave.severity = OPENMD_INFO;
222			painCave.isFatal = 0;
223			simError();
224			}
225
226			for (sd1 = seleMan1_.beginSelected(ii),
227			sd2 = seleMan2_.beginSelected(jj);
228			sd1 != NULL && sd2 != NULL;
229			sd1 = seleMan1_.nextSelected(ii),
230			sd2 = seleMan2_.nextSelected(jj)) {
231
232			Vector3d r1 = CenterOfMass - sd1->getPos();
233			if (usePeriodicBoundaryConditions_)
234			currentSnapshot_->wrapVector(r1);
235
236			Vector3d r2 = CenterOfMass - sd2->getPos();
237			if (usePeriodicBoundaryConditions_)
238			currentSnapshot_->wrapVector(r1);
239
240			Vector3d rc = 0.5*(r1 + r2);
241			if (usePeriodicBoundaryConditions_)
242			currentSnapshot_->wrapVector(rc);
243
244			Vector3d vec = r1-r2;
245			if (usePeriodicBoundaryConditions_)
246			currentSnapshot_->wrapVector(vec);
247
248			rc.normalize();
249			vec.normalize();
250			RealType cosangle = dot(rc, vec);
251			int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
252			count_[binNo]++;
253
254			}
255			}
256	gezelter	1413	}
257			}
258	gezelter	1979
259	gezelter	1413	processHistogram();
260			writeProbs();
261
262			}
263
264			void pAngle::processHistogram() {
265
266			int atot = 0;
267	gezelter	1782	for(unsigned int i = 0; i < count_.size(); ++i)
268	gezelter	1413	atot += count_[i];
269
270	gezelter	1782	for(unsigned int i = 0; i < count_.size(); ++i) {
271			histogram_[i] = double(count_[i] / double(atot));
272	gezelter	1413	}
273			}
274
275
276			void pAngle::writeProbs() {
277
278			std::ofstream rdfStream(outputFilename_.c_str());
279			if (rdfStream.is_open()) {
280			rdfStream << "#pAngle\n";
281			rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
282	gezelter	1979	rdfStream << "#selection1: (" << selectionScript1_ << ")";
283			if (!doVect_) {
284			rdfStream << "\tselection2: (" << selectionScript2_ << ")";
285			}
286			rdfStream << "\n";
287	gezelter	1413	rdfStream << "#cos(theta)\tp(cos(theta))\n";
288	kstocke1	1522	RealType dct = 2.0 / histogram_.size();
289	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i) {
290	kstocke1	1522	RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
291			rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
292	gezelter	1413	}
293
294			} else {
295
296	gezelter	1979	sprintf(painCave.errMsg, "pAngle: unable to open %s\n",
297			outputFilename_.c_str());
298	gezelter	1413	painCave.isFatal = 1;
299			simError();
300			}
301
302			rdfStream.close();
303			}
304
305			}
306