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)
    : info_(info), storageLayout_(storageLayout),
      dumpFilename_(filename), selectionScript1_(sele1), 
      selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), 
      seleMan1_(info), seleMan2_(info) {
    
    int nAtoms = info->getNGlobalAtoms();
    int nRigidBodies = info->getNGlobalRigidBodies();

    // 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:	2056
Committed:	Fri Feb 20 15:12:07 2015 UTC (10 years, 6 months ago) by gezelter
File size:	9754 byte(s)
Log Message:	Fixes to HullFinder (and by extension to RNEMD) for getSurfaceArea() call. Adding Multipass Correlation Function (unused right now).
#	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			: info_(info), storageLayout_(storageLayout),
53			dumpFilename_(filename), selectionScript1_(sele1),
54			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
55			seleMan1_(info), seleMan2_(info) {
56
57			int nAtoms = info->getNGlobalAtoms();
58			int nRigidBodies = info->getNGlobalRigidBodies();
59
60			// Request maximum needed storage for the simulation (including of
61			// whatever was passed down by the individual correlation
62			// function).
63
64			storageLayout_ = info->getStorageLayout() \| storageLayout;
65
66			DumpReader reader(info_, dumpFilename_);
67
68			evaluator1_.loadScriptString(selectionScript1_);
69			evaluator2_.loadScriptString(selectionScript2_);
70
71			//if selection is static, we only need to evaluate it once
72			if (!evaluator1_.isDynamic()) {
73			seleMan1_.setSelectionSet(evaluator1_.evaluate());
74			validateSelection(seleMan1_);
75			}
76
77			if (!evaluator2_.isDynamic()) {
78			seleMan2_.setSelectionSet(evaluator2_.evaluate());
79			validateSelection(seleMan2_);
80			}
81
82			/*@todo Fix Me /
83			Globals* simParams = info_->getSimParams();
84			if (simParams->haveSampleTime()){
85			deltaTime_ = simParams->getSampleTime();
86			} else {
87			sprintf(painCave.errMsg,
88			"MultipassCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
89			painCave.isFatal = 1;
90			simError();
91			}
92
93			}
94
95			void MultipassCorrFunc::preCorrelate() {
96			Molecule* mol;
97			RigidBody* rb;
98			SimInfo::MoleculeIterator mi;
99			Molecule::RigidBodyIterator rbIter;
100			StuntDouble* sd;
101
102			int index, isd1, isd2;
103
104			fill(histogram_.begin(), histogram_.end(), 0.0);
105			fill(count_.begin(), count_.end(), 0);
106
107			DumpReader reader(info_, dumpFilename_);
108
109			nFrames_ = reader.getNFrames();
110			times_.resize(nFrames_);
111
112			for (int istep = 0; istep < nFrames_; istep++) {
113			reader.readFrame(istep);
114			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
115			times_[istep] = currentSnapshot_->getTime();
116
117			// update the positions of atoms which belong to the rigidbodies
118			for (mol = info_->beginMolecule(mi); mol != NULL;
119			mol = info_->nextMolecule(mi)) {
120			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
121			rb = mol->nextRigidBody(rbIter)) {
122			rb->updateAtoms();
123			}
124			}
125
126			if (evaluator1_.isDynamic()) {
127			seleMan1_.setSelectionSet(evaluator1_.evaluate());
128			}
129
130			if (evaluator2_.isDynamic()) {
131			seleMan2_.setSelectionSet(evaluator2_.evaluate());
132			}
133
134			for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
135			sd = seleMan1_.nextSelected(isd1)) {
136
137			sele1ToIndex_[istep].push_back(sd->getGlobalIndex());
138			index = sele1ToIndex_[istep].size();
139			computeProperty1(istep, sd, index);
140			}
141
142			for (sd = seleMan2_.beginSelected(isd2); sd != NULL;
143			sd = seleMan2_.nextSelected(isd2)) {
144
145			sele2ToIndex_[istep].push_back(sd->getGlobalIndex());
146			index = sele2ToIndex_[istep].size();
147
148			computeProperty2(istep, sd, index);
149			}
150			}
151			}
152
153
154			void MultipassCorrFunc::doCorrelate() {
155			preCorrelate();
156			correlation();
157			postCorrelate();
158			writeCorrelate();
159			}
160
161			void MultipassCorrFunc::correlation() {
162			std::vector<int> s1;
163			std::vector<int> s2;
164
165			std::vector<int>::iterator i1;
166			std::vector<int>::iterator i2;
167
168
169			for (int i = 0; i < nFrames_; ++i) {
170
171			RealType time1 = times_[i];
172			s1 = sele1ToIndex_[i];
173
174			for(int j = i; j < nFrames_; ++j) {
175
176			// Perform a sanity check on the actual configuration times to
177			// make sure the configurations are spaced the same amount the
178			// sample time said they were spaced:
179
180			RealType time2 = times_[j];
181
182			if ( fabs( (time2 - time1) - (j-i)*deltaTime_ ) > 1.0e-4 ) {
183			sprintf(painCave.errMsg,
184			"MultipassCorrFunc::correlateBlocks Error: sampleTime (%f)\n"
185			"\tin %s does not match actual time-spacing between\n"
186			"\tconfigurations %d (t = %f) and %d (t = %f).\n",
187			deltaTime_, dumpFilename_.c_str(), i, time1, j, time2);
188			painCave.isFatal = 1;
189			simError();
190			}
191
192			int timeBin = int ((time2 - time1) / deltaTime_ + 0.5);
193			s2 = sele2ToIndex_[j];
194
195			for (i1 = s1.begin(), i2 = s2.begin();
196			i1 != s1.end() && i2 != s2.end(); ++i1, ++i2){
197
198			// If the selections are dynamic, they might not have the
199			// same objects in both frames, so we need to roll either of
200			// the selections until we have the same object to
201			// correlate.
202
203			while ( i1 < i2 && i1 != s1.end()) {
204			++i1;
205			}
206
207			while ( i2 < i1 && i2 != s2.end() ) {
208			++i2;
209			}
210
211			if ( i1 == s1.end() \|\| i2 == s2.end() ) break;
212
213			RealType corrVal = calcCorrVal(i, j, i1, i2);
214			histogram_[timeBin] += corrVal;
215			count_[timeBin]++;
216
217			}
218			}
219			}
220			}
221
222
223
224			void MultipassCorrFunc::postCorrelate() {
225			for (int i =0 ; i < nTimeBins_; ++i) {
226			if (count_[i] > 0) {
227			histogram_[i] /= count_[i];
228			} else {
229			histogram_[i] = 0;
230			}
231			}
232			}
233
234
235			void MultipassCorrFunc::updateFrame(int frame){
236			Molecule* mol;
237			RigidBody* rb;
238			SimInfo::MoleculeIterator mi;
239			Molecule::RigidBodyIterator rbIter;
240			/** @todo need improvement */
241			if (storageLayout_ & DataStorage::dslPosition) {
242			for (mol = info_->beginMolecule(mi); mol != NULL;
243			mol = info_->nextMolecule(mi)) {
244
245			//change the positions of atoms which belong to the rigidbodies
246			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
247			rb = mol->nextRigidBody(rbIter)) {
248			rb->updateAtoms(frame);
249			}
250			}
251			}
252
253			if (storageLayout_ & DataStorage::dslVelocity) {
254			for (mol = info_->beginMolecule(mi); mol != NULL;
255			mol = info_->nextMolecule(mi)) {
256
257			//change the positions of atoms which belong to the rigidbodies
258			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
259			rb = mol->nextRigidBody(rbIter)) {
260			rb->updateAtomVel(frame);
261			}
262			}
263			}
264			}
265
266
267
268			void MultipassCorrFunc::writeCorrelate() {
269			ofstream ofs(outputFilename_.c_str());
270
271			if (ofs.is_open()) {
272
273			ofs << "#" << getCorrFuncType() << "\n";
274			ofs << "#selection script1: \"" << selectionScript1_ ;
275			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
276			ofs << "#extra information: " << extra_ << "\n";
277			ofs << "#time\tcorrVal\n";
278
279			for (int i = 0; i < nTimeBins_; ++i) {
280			ofs << times_[i]-times_[0] << "\t" << histogram_[i] << "\n";
281			}
282
283			} else {
284			sprintf(painCave.errMsg,
285			"MultipassCorrFunc::writeCorrelate Error: fail to open %s\n",
286			outputFilename_.c_str());
287			painCave.isFatal = 1;
288			simError();
289			}
290
291			ofs.close();
292			}
293
294			}