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),       
      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:	1979
Committed:	Sat Apr 5 20:56:01 2014 UTC (11 years, 6 months ago) by gezelter
File size:	10723 byte(s)
Log Message:	* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
#	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			nThetaBins_(nthetabins),
102			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	1782
155	gezelter	1979	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
156			sd1 = seleMan1_.nextSelected(ii)) {
157	gezelter	1413
158	gezelter	1979	Vector3d pos = sd1->getPos();
159
160			Vector3d r1 = CenterOfMass - pos;
161			// only do this if the stunt double actually has a vector associated
162			// with it
163			if (sd1->isDirectional()) {
164			Vector3d vec = sd1->getA().getColumn(2);
165			RealType distance = r1.length();
166
167			vec.normalize();
168			r1.normalize();
169			RealType cosangle = dot(r1, vec);
170
171			int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
172			count_[binNo]++;
173			}
174	gezelter	1413	}
175	gezelter	1979	} else {
176			if (doOffset_) {
177
178			for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
179			sd1 = seleMan1_.nextSelected(ii)) {
180
181			// This will require careful rewriting if StaticProps is
182			// ever parallelized. For an example, see
183			// Thermo::getTaggedAtomPairDistance
184
185			int sd2Index = sd1->getGlobalIndex() + seleOffset_;
186			sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
187
188			Vector3d r1 = CenterOfMass - sd1->getPos();
189			if (usePeriodicBoundaryConditions_)
190			currentSnapshot_->wrapVector(r1);
191
192			Vector3d r2 = CenterOfMass - sd2->getPos();
193			if (usePeriodicBoundaryConditions_)
194			currentSnapshot_->wrapVector(r1);
195
196			Vector3d rc = 0.5*(r1 + r2);
197			if (usePeriodicBoundaryConditions_)
198			currentSnapshot_->wrapVector(rc);
199
200			Vector3d vec = r1-r2;
201			if (usePeriodicBoundaryConditions_)
202			currentSnapshot_->wrapVector(vec);
203
204			rc.normalize();
205			vec.normalize();
206			RealType cosangle = dot(rc, vec);
207			int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
208			count_[binNo]++;
209			}
210			} else {
211
212			if (evaluator2_.isDynamic()) {
213			seleMan2_.setSelectionSet(evaluator2_.evaluate());
214			}
215
216			if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
217			sprintf( painCave.errMsg,
218			"In frame %d, the number of selected StuntDoubles are\n"
219			"\tnot the same in --sele1 and sele2\n", istep);
220			painCave.severity = OPENMD_INFO;
221			painCave.isFatal = 0;
222			simError();
223			}
224
225			for (sd1 = seleMan1_.beginSelected(ii),
226			sd2 = seleMan2_.beginSelected(jj);
227			sd1 != NULL && sd2 != NULL;
228			sd1 = seleMan1_.nextSelected(ii),
229			sd2 = seleMan2_.nextSelected(jj)) {
230
231			Vector3d r1 = CenterOfMass - sd1->getPos();
232			if (usePeriodicBoundaryConditions_)
233			currentSnapshot_->wrapVector(r1);
234
235			Vector3d r2 = CenterOfMass - sd2->getPos();
236			if (usePeriodicBoundaryConditions_)
237			currentSnapshot_->wrapVector(r1);
238
239			Vector3d rc = 0.5*(r1 + r2);
240			if (usePeriodicBoundaryConditions_)
241			currentSnapshot_->wrapVector(rc);
242
243			Vector3d vec = r1-r2;
244			if (usePeriodicBoundaryConditions_)
245			currentSnapshot_->wrapVector(vec);
246
247			rc.normalize();
248			vec.normalize();
249			RealType cosangle = dot(rc, vec);
250			int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
251			count_[binNo]++;
252
253			}
254			}
255	gezelter	1413	}
256			}
257	gezelter	1979
258	gezelter	1413	processHistogram();
259			writeProbs();
260
261			}
262
263			void pAngle::processHistogram() {
264
265			int atot = 0;
266	gezelter	1782	for(unsigned int i = 0; i < count_.size(); ++i)
267	gezelter	1413	atot += count_[i];
268
269	gezelter	1782	for(unsigned int i = 0; i < count_.size(); ++i) {
270			histogram_[i] = double(count_[i] / double(atot));
271	gezelter	1413	}
272			}
273
274
275			void pAngle::writeProbs() {
276
277			std::ofstream rdfStream(outputFilename_.c_str());
278			if (rdfStream.is_open()) {
279			rdfStream << "#pAngle\n";
280			rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
281	gezelter	1979	rdfStream << "#selection1: (" << selectionScript1_ << ")";
282			if (!doVect_) {
283			rdfStream << "\tselection2: (" << selectionScript2_ << ")";
284			}
285			rdfStream << "\n";
286	gezelter	1413	rdfStream << "#cos(theta)\tp(cos(theta))\n";
287	kstocke1	1522	RealType dct = 2.0 / histogram_.size();
288	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i) {
289	kstocke1	1522	RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
290			rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
291	gezelter	1413	}
292
293			} else {
294
295	gezelter	1979	sprintf(painCave.errMsg, "pAngle: unable to open %s\n",
296			outputFilename_.c_str());
297	gezelter	1413	painCave.isFatal = 1;
298			simError();
299			}
300
301			rdfStream.close();
302			}
303
304			}
305