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
#	Content
1	/*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	*/
42
43	/* Calculates Rho(theta) */
44
45	#include <algorithm>
46	#include <fstream>
47	#include "applications/staticProps/pAngle.hpp"
48	#include "utils/simError.h"
49	#include "io/DumpReader.hpp"
50	#include "primitives/Molecule.hpp"
51	#include "brains/Thermo.hpp"
52
53	namespace OpenMD {
54
55	pAngle::pAngle(SimInfo* info, const std::string& filename,
56	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
62	setOutputName(getPrefix(filename) + ".pAngle");
63
64	evaluator1_.loadScriptString(sele1);
65	if (!evaluator1_.isDynamic()) {
66	seleMan1_.setSelectionSet(evaluator1_.evaluate());
67	}
68
69	count_.resize(nThetaBins_);
70	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
81	setOutputName(getPrefix(filename) + ".pAngle");
82
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	}
96
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
115	void pAngle::process() {
116	Molecule* mol;
117	RigidBody* rb;
118	SimInfo::MoleculeIterator mi;
119	Molecule::RigidBodyIterator rbIter;
120	StuntDouble* sd1;
121	StuntDouble* sd2;
122	int ii;
123	int jj;
124
125	Thermo thermo(info_);
126	DumpReader reader(info_, dumpFilename_);
127	int nFrames = reader.getNFrames();
128
129	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	Vector3d CenterOfMass = thermo.getCom();
148
149	if (evaluator1_.isDynamic()) {
150	seleMan1_.setSelectionSet(evaluator1_.evaluate());
151	}
152
153	if (doVect_) {
154
155	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
156	sd1 = seleMan1_.nextSelected(ii)) {
157
158	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	}
175	} 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	}
256	}
257
258	processHistogram();
259	writeProbs();
260
261	}
262
263	void pAngle::processHistogram() {
264
265	int atot = 0;
266	for(unsigned int i = 0; i < count_.size(); ++i)
267	atot += count_[i];
268
269	for(unsigned int i = 0; i < count_.size(); ++i) {
270	histogram_[i] = double(count_[i] / double(atot));
271	}
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	rdfStream << "#selection1: (" << selectionScript1_ << ")";
282	if (!doVect_) {
283	rdfStream << "\tselection2: (" << selectionScript2_ << ")";
284	}
285	rdfStream << "\n";
286	rdfStream << "#cos(theta)\tp(cos(theta))\n";
287	RealType dct = 2.0 / histogram_.size();
288	for (unsigned int i = 0; i < histogram_.size(); ++i) {
289	RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
290	rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
291	}
292
293	} else {
294
295	sprintf(painCave.errMsg, "pAngle: unable to open %s\n",
296	outputFilename_.c_str());
297	painCave.isFatal = 1;
298	simError();
299	}
300
301	rdfStream.close();
302	}
303
304	}
305