applications/dynamicProps/MultipassCorrFunc.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).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "applications/dynamicProps/MultipassCorrFunc.hpp"
#include "utils/simError.h"
#include "primitives/Molecule.hpp"
using namespace std;
namespace OpenMD {

  MultipassCorrFunc::MultipassCorrFunc(SimInfo* info, const string& filename, 
                                       const string& sele1, const string& sele2,
                                       int storageLayout)
    : storageLayout_(storageLayout), info_(info), dumpFilename_(filename),
      seleMan1_(info_), seleMan2_(info_), 
      selectionScript1_(sele1), selectionScript2_(sele2), 
      evaluator1_(info_), evaluator2_(info_) { 
    
    // Request maximum needed storage for the simulation (including of
    // whatever was passed down by the individual correlation
    // function).

    storageLayout_ = info->getStorageLayout() | storageLayout;

    DumpReader reader(info_, dumpFilename_);    
    
    evaluator1_.loadScriptString(selectionScript1_);
    evaluator2_.loadScriptString(selectionScript2_);
    
    //if selection is static, we only need to evaluate it once
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
      validateSelection(seleMan1_);
    }
    
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
      validateSelection(seleMan2_);
    }
    
    /**@todo Fix Me */
    Globals* simParams = info_->getSimParams();
    if (simParams->haveSampleTime()){
      deltaTime_ = simParams->getSampleTime();
    } else {
      sprintf(painCave.errMsg,
              "MultipassCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
      painCave.isFatal = 1;
      simError();  
    }
  }

  void MultipassCorrFunc::preCorrelate() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    StuntDouble* sd;

    int index, isd1, isd2;
    
    fill(histogram_.begin(), histogram_.end(), 0.0);
    fill(count_.begin(), count_.end(), 0);

    DumpReader reader(info_, dumpFilename_);    

    nFrames_ = reader.getNFrames();
    times_.resize(nFrames_);
    
    for (int istep = 0; istep < nFrames_; istep++) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      times_[istep] = currentSnapshot_->getTime();

      // update the positions of atoms which belong to the rigidbodies
      for (mol = info_->beginMolecule(mi); mol != NULL;
           mol = info_->nextMolecule(mi)) {
        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }
      }
      
      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
      
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
      }      

      for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
           sd = seleMan1_.nextSelected(isd1)) {

        sele1ToIndex_[istep].push_back(sd->getGlobalIndex());
        index = sele1ToIndex_[istep].size();
        computeProperty1(istep, sd, index);
      }
      
      for (sd = seleMan2_.beginSelected(isd2); sd != NULL;
           sd = seleMan2_.nextSelected(isd2)) {

        sele2ToIndex_[istep].push_back(sd->getGlobalIndex());
        index = sele2ToIndex_[istep].size();
                
        computeProperty2(istep, sd, index);
      }
    }     
  }

  
  void MultipassCorrFunc::doCorrelate() {
    preCorrelate();
    correlation();   
    postCorrelate();
    writeCorrelate();
  }

  void MultipassCorrFunc::correlation() {
    std::vector<int> s1;
    std::vector<int> s2;

    std::vector<int>::iterator i1;
    std::vector<int>::iterator i2;

    
    for (int i = 0; i < nFrames_; ++i) {

      RealType time1 = times_[i];
      s1 = sele1ToIndex_[i];
      
      for(int j  = i; j < nFrames_; ++j) {

        // Perform a sanity check on the actual configuration times to
        // make sure the configurations are spaced the same amount the
        // sample time said they were spaced:
               
        RealType time2 = times_[j];

        if ( fabs( (time2 - time1) - (j-i)*deltaTime_ ) > 1.0e-4 ) {
          sprintf(painCave.errMsg,
                  "MultipassCorrFunc::correlateBlocks Error: sampleTime (%f)\n"
                  "\tin %s does not match actual time-spacing between\n"
                  "\tconfigurations %d (t = %f) and %d (t = %f).\n",
                  deltaTime_, dumpFilename_.c_str(), i, time1, j, time2);
          painCave.isFatal = 1;
          simError();  
        }
        
        int timeBin = int ((time2 - time1) / deltaTime_ + 0.5);        
        s2 = sele2ToIndex_[j];

        for (i1 = s1.begin(), i2 = s2.begin();
             i1 != s1.end() && i2 != s2.end(); ++i1, ++i2){
          
          // If the selections are dynamic, they might not have the
          // same objects in both frames, so we need to roll either of
          // the selections until we have the same object to
          // correlate.
          
          while ( *i1 < *i2 && i1 != s1.end()) {
            ++i1;
          }
          
          while ( *i2 < *i1 && i2 != s2.end() ) {
            ++i2;
          }
          
          if ( i1 == s1.end() || i2 == s2.end() ) break;

          RealType corrVal = calcCorrVal(i, j, *i1, *i2);
          histogram_[timeBin] += corrVal;
          count_[timeBin]++;
          
        }
      }
    }
  }


  void MultipassCorrFunc::postCorrelate() {
    for (int i =0 ; i < nTimeBins_; ++i) {
      if (count_[i] > 0) {
        histogram_[i] /= count_[i];
      } else {
        histogram_[i] = 0;
      }
    }
  }


  void MultipassCorrFunc::updateFrame(int frame){
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    /** @todo need improvement */    
    if (storageLayout_ & DataStorage::dslPosition) {
      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(frame);
        }
      }        
    }

    if (storageLayout_ & DataStorage::dslVelocity) {
      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->updateAtomVel(frame);
        }
      }      
    }    
  }


  void MultipassCorrFunc::writeCorrelate() {
    ofstream ofs(outputFilename_.c_str());

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#selection script1: \"" << selectionScript1_ ;
      ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
      ofs << "#extra information: " << extra_ << "\n";
      ofs << "#time\tcorrVal\n";

      for (int i = 0; i < nTimeBins_; ++i) {
        ofs << times_[i]-times_[0] << "\t" << histogram_[i] << "\n";
      }
            
    } else {
      sprintf(painCave.errMsg,
              "MultipassCorrFunc::writeCorrelate Error: fail to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();        
    }

    ofs.close();    
  }

}
Revision:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 5 months ago) by gezelter
File size:	9661 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	User	Rev	Content
1	gezelter	2056	/*
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			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include "applications/dynamicProps/MultipassCorrFunc.hpp"
44			#include "utils/simError.h"
45			#include "primitives/Molecule.hpp"
46			using namespace std;
47			namespace OpenMD {
48
49			MultipassCorrFunc::MultipassCorrFunc(SimInfo* info, const string& filename,
50			const string& sele1, const string& sele2,
51			int storageLayout)
52	gezelter	2071	: storageLayout_(storageLayout), info_(info), dumpFilename_(filename),
53			seleMan1_(info_), seleMan2_(info_),
54			selectionScript1_(sele1), selectionScript2_(sele2),
55			evaluator1_(info_), evaluator2_(info_) {
56	gezelter	2056
57			// Request maximum needed storage for the simulation (including of
58			// whatever was passed down by the individual correlation
59			// function).
60
61			storageLayout_ = info->getStorageLayout() \| storageLayout;
62
63			DumpReader reader(info_, dumpFilename_);
64
65			evaluator1_.loadScriptString(selectionScript1_);
66			evaluator2_.loadScriptString(selectionScript2_);
67
68			//if selection is static, we only need to evaluate it once
69			if (!evaluator1_.isDynamic()) {
70			seleMan1_.setSelectionSet(evaluator1_.evaluate());
71			validateSelection(seleMan1_);
72			}
73
74			if (!evaluator2_.isDynamic()) {
75			seleMan2_.setSelectionSet(evaluator2_.evaluate());
76			validateSelection(seleMan2_);
77			}
78
79			/*@todo Fix Me /
80			Globals* simParams = info_->getSimParams();
81			if (simParams->haveSampleTime()){
82			deltaTime_ = simParams->getSampleTime();
83			} else {
84			sprintf(painCave.errMsg,
85			"MultipassCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
86			painCave.isFatal = 1;
87			simError();
88			}
89			}
90
91			void MultipassCorrFunc::preCorrelate() {
92			Molecule* mol;
93			RigidBody* rb;
94			SimInfo::MoleculeIterator mi;
95			Molecule::RigidBodyIterator rbIter;
96			StuntDouble* sd;
97
98			int index, isd1, isd2;
99
100			fill(histogram_.begin(), histogram_.end(), 0.0);
101			fill(count_.begin(), count_.end(), 0);
102
103			DumpReader reader(info_, dumpFilename_);
104
105			nFrames_ = reader.getNFrames();
106			times_.resize(nFrames_);
107
108			for (int istep = 0; istep < nFrames_; istep++) {
109			reader.readFrame(istep);
110			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
111			times_[istep] = currentSnapshot_->getTime();
112
113			// update the positions of atoms which belong to the rigidbodies
114			for (mol = info_->beginMolecule(mi); mol != NULL;
115			mol = info_->nextMolecule(mi)) {
116			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
117			rb = mol->nextRigidBody(rbIter)) {
118			rb->updateAtoms();
119			}
120			}
121
122			if (evaluator1_.isDynamic()) {
123			seleMan1_.setSelectionSet(evaluator1_.evaluate());
124			}
125
126			if (evaluator2_.isDynamic()) {
127			seleMan2_.setSelectionSet(evaluator2_.evaluate());
128			}
129
130			for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
131			sd = seleMan1_.nextSelected(isd1)) {
132
133			sele1ToIndex_[istep].push_back(sd->getGlobalIndex());
134			index = sele1ToIndex_[istep].size();
135			computeProperty1(istep, sd, index);
136			}
137
138			for (sd = seleMan2_.beginSelected(isd2); sd != NULL;
139			sd = seleMan2_.nextSelected(isd2)) {
140
141			sele2ToIndex_[istep].push_back(sd->getGlobalIndex());
142			index = sele2ToIndex_[istep].size();
143
144			computeProperty2(istep, sd, index);
145			}
146			}
147			}
148
149
150			void MultipassCorrFunc::doCorrelate() {
151			preCorrelate();
152			correlation();
153			postCorrelate();
154			writeCorrelate();
155			}
156
157			void MultipassCorrFunc::correlation() {
158			std::vector<int> s1;
159			std::vector<int> s2;
160
161			std::vector<int>::iterator i1;
162			std::vector<int>::iterator i2;
163
164
165			for (int i = 0; i < nFrames_; ++i) {
166
167			RealType time1 = times_[i];
168			s1 = sele1ToIndex_[i];
169
170			for(int j = i; j < nFrames_; ++j) {
171
172			// Perform a sanity check on the actual configuration times to
173			// make sure the configurations are spaced the same amount the
174			// sample time said they were spaced:
175
176			RealType time2 = times_[j];
177
178			if ( fabs( (time2 - time1) - (j-i)*deltaTime_ ) > 1.0e-4 ) {
179			sprintf(painCave.errMsg,
180			"MultipassCorrFunc::correlateBlocks Error: sampleTime (%f)\n"
181			"\tin %s does not match actual time-spacing between\n"
182			"\tconfigurations %d (t = %f) and %d (t = %f).\n",
183			deltaTime_, dumpFilename_.c_str(), i, time1, j, time2);
184			painCave.isFatal = 1;
185			simError();
186			}
187
188			int timeBin = int ((time2 - time1) / deltaTime_ + 0.5);
189			s2 = sele2ToIndex_[j];
190
191			for (i1 = s1.begin(), i2 = s2.begin();
192			i1 != s1.end() && i2 != s2.end(); ++i1, ++i2){
193
194			// If the selections are dynamic, they might not have the
195			// same objects in both frames, so we need to roll either of
196			// the selections until we have the same object to
197			// correlate.
198
199			while ( i1 < i2 && i1 != s1.end()) {
200			++i1;
201			}
202
203			while ( i2 < i1 && i2 != s2.end() ) {
204			++i2;
205			}
206
207			if ( i1 == s1.end() \|\| i2 == s2.end() ) break;
208
209			RealType corrVal = calcCorrVal(i, j, i1, i2);
210			histogram_[timeBin] += corrVal;
211			count_[timeBin]++;
212
213			}
214			}
215			}
216			}
217
218
219
220			void MultipassCorrFunc::postCorrelate() {
221			for (int i =0 ; i < nTimeBins_; ++i) {
222			if (count_[i] > 0) {
223			histogram_[i] /= count_[i];
224			} else {
225			histogram_[i] = 0;
226			}
227			}
228			}
229
230
231			void MultipassCorrFunc::updateFrame(int frame){
232			Molecule* mol;
233			RigidBody* rb;
234			SimInfo::MoleculeIterator mi;
235			Molecule::RigidBodyIterator rbIter;
236			/** @todo need improvement */
237			if (storageLayout_ & DataStorage::dslPosition) {
238			for (mol = info_->beginMolecule(mi); mol != NULL;
239			mol = info_->nextMolecule(mi)) {
240
241			//change the positions of atoms which belong to the rigidbodies
242			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
243			rb = mol->nextRigidBody(rbIter)) {
244			rb->updateAtoms(frame);
245			}
246			}
247			}
248
249			if (storageLayout_ & DataStorage::dslVelocity) {
250			for (mol = info_->beginMolecule(mi); mol != NULL;
251			mol = info_->nextMolecule(mi)) {
252
253			//change the positions of atoms which belong to the rigidbodies
254			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
255			rb = mol->nextRigidBody(rbIter)) {
256			rb->updateAtomVel(frame);
257			}
258			}
259			}
260			}
261
262
263
264			void MultipassCorrFunc::writeCorrelate() {
265			ofstream ofs(outputFilename_.c_str());
266
267			if (ofs.is_open()) {
268
269			ofs << "#" << getCorrFuncType() << "\n";
270			ofs << "#selection script1: \"" << selectionScript1_ ;
271			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
272			ofs << "#extra information: " << extra_ << "\n";
273			ofs << "#time\tcorrVal\n";
274
275			for (int i = 0; i < nTimeBins_; ++i) {
276			ofs << times_[i]-times_[0] << "\t" << histogram_[i] << "\n";
277			}
278
279			} else {
280			sprintf(painCave.errMsg,
281			"MultipassCorrFunc::writeCorrelate Error: fail to open %s\n",
282			outputFilename_.c_str());
283			painCave.isFatal = 1;
284			simError();
285			}
286
287			ofs.close();
288			}
289
290			}