applications/dynamicProps/CorrelationFunction.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include "applications/dynamicProps/CorrelationFunction.hpp"
#include "utils/simError.h"
#include "primitives/Molecule.hpp"
namespace oopse {

CorrelationFunction::CorrelationFunction(SimInfo* info, const std::string& filename, 
    const std::string& sele1, const std::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();
    int nStuntDoubles =   nAtoms + nRigidBodies;

    std::set<AtomType*> atomTypes = info->getUniqueAtomTypes();
    std::set<AtomType*>::iterator i;
    bool hasDirectionalAtom = false;
    bool hasMultipole = false;    
    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
        if ((*i)->isDirectional()){
            hasDirectionalAtom = true;
        }
        if ((*i)->isMultipole()){
            hasMultipole = true;
        }
    }
    
    if (nRigidBodies > 0 || hasDirectionalAtom) {
        storageLayout_ |= DataStorage::dslAmat;
    }
    if (hasMultipole) {
        storageLayout_ |= DataStorage::dslElectroFrame;
        if (nRigidBodies > 0) { 
            storageLayout_ |= DataStorage::dslAngularMomentum;        
        }
    }
        
    bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
    info_->setSnapshotManager(bsMan_);

    //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 Fixed Me */
    Globals* simParams = info_->getSimParams();
    if (simParams->haveSampleTime()){
        deltaTime_ = simParams->getSampleTime();
    } else {
            sprintf(painCave.errMsg,
                "CorrelationFunction::writeCorrelate Error: can not figure out deltaTime\n");
            painCave.isFatal = 1;
            simError();  
    }

    int nframes =  bsMan_->getNFrames();
    nTimeBins_ = nframes;
    histogram_.resize(nTimeBins_);
    count_.resize(nTimeBins_);
    time_.resize(nTimeBins_);

    for (int i = 0; i < nTimeBins_; ++i) {
        time_[i] = i * deltaTime_;
    }
    
}


void CorrelationFunction::doCorrelate() {
    preCorrelate();

    int nblocks = bsMan_->getNBlocks();

    for (int i = 0; i < nblocks; ++i) {
        bsMan_->loadBlock(i);
        for (int j = i; j < nblocks; ++j) {
            bsMan_->loadBlock(j);
            correlateBlocks(i, j);

            if (i != j) {
                //if i equals to j, the block is still used, should not unload it
                bsMan_->unloadBlock(j);
            }
        }
        bsMan_->unloadBlock(i);
    }
    
    postCorrelate();

    writeCorrelate();
}

void CorrelationFunction::correlateBlocks(int block1, int block2) {

  int jstart, jend;
  
  assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));

  SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
  SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);

  jend = snapshotBlock2.second;
  
  for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
    
    //evaluate selection if it is dynamic
    if (evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
      validateSelection(seleMan1_);
    }
    
    //update the position or velocity of the atoms belong to rigid bodies
    updateFrame(i);
    
    // if the two blocks are the same, we don't want to correlate
    // backwards in time, so start j at the same frame as i

    if (block1 == block2) 
      jstart = i;
    else
      jstart = snapshotBlock2.first;
    
    for(int j  = jstart; j < jend; ++j) {
      //evaluate selection
      if (!evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
        validateSelection(seleMan2_);
      }   
      //update the position or velocity of the atoms belong to rigid bodies
      updateFrame(j);
      
      correlateFrames(i, j);
    }
  }
}


void CorrelationFunction::correlateFrames(int frame1, int frame2) {
    int count = seleMan1_.getSelectionCount();
    assert(  count == seleMan2_.getSelectionCount());

    Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot1 && snapshot2);

    double time1 = snapshot1->getTime();
    double time2 = snapshot2->getTime();

    if (time2 < time1) { printf("BARF ON NON POSITIVE DT!\n"); stop;}

    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
    count_[timeBin] += count;    
    
    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;

    switch (correlationFunctionType()) {

    case frame:
      double corrVal = calcCorrVal(frame1, frame2);
      histogram_[timeBin] += corrVal;
      count_[timeBin] += 1;
      break;
      
    case particle:
      for (sd1 = seleMan1_.beginSelected(i), sd1 != NULL;
           sd1 = seleMan1_.nextSelected(i)) {
        double corrVal = calcCorrVal(frame1, frame2, sd);
        histogram_[timeBin] += corrVal;    
        count_[timeBin] += 1;
      }
      break;

    case cross:
      for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; sd1 = seleMan1_.nextSelected(i)) {
        
        for (sd2 = seleMan2_.beginSelected(j); sd2 != NULL; sd2 = seleMan2_.nextSelected(j)) {
          double corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
          histogram_[timeBin] += corrVal;    
          count_[timeBin] += 1;
        }            
      }
      break;

    default:
      return NULL;

    }
}


void CorrelationFunction::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 CorrelationFunction::preCorrelate() {
    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::fill(count_.begin(), count_.end(), 0);
}

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


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

    if (ofs.is_open()) {

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

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

    ofs.close();    
}

}
Revision:	2016
Committed:	Mon Feb 14 15:18:09 2005 UTC (19 years, 7 months ago) by gezelter
File size:	10031 byte(s)
Log Message:	bug fix and start of switch for type of correlation function
#	User	Rev	Content
1	tim	2002	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "applications/dynamicProps/CorrelationFunction.hpp"
43			#include "utils/simError.h"
44	tim	2008	#include "primitives/Molecule.hpp"
45	tim	2002	namespace oopse {
46
47			CorrelationFunction::CorrelationFunction(SimInfo* info, const std::string& filename,
48			const std::string& sele1, const std::string& sele2, int storageLayout)
49			: info_(info), storageLayout_(storageLayout), dumpFilename_(filename), selectionScript1_(sele1),
50			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
51
52			int nAtoms = info->getNGlobalAtoms();
53			int nRigidBodies = info->getNGlobalRigidBodies();
54			int nStuntDoubles = nAtoms + nRigidBodies;
55
56			std::set<AtomType*> atomTypes = info->getUniqueAtomTypes();
57			std::set<AtomType*>::iterator i;
58			bool hasDirectionalAtom = false;
59			bool hasMultipole = false;
60			for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
61			if ((*i)->isDirectional()){
62			hasDirectionalAtom = true;
63			}
64			if ((*i)->isMultipole()){
65	tim	2013	hasMultipole = true;
66	tim	2002	}
67			}
68
69			if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
70			storageLayout_ \|= DataStorage::dslAmat;
71			}
72			if (hasMultipole) {
73			storageLayout_ \|= DataStorage::dslElectroFrame;
74	tim	2014	if (nRigidBodies > 0) {
75			storageLayout_ \|= DataStorage::dslAngularMomentum;
76			}
77	tim	2002	}
78
79	tim	2008	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
80			info_->setSnapshotManager(bsMan_);
81	tim	2002
82			//if selection is static, we only need to evaluate it once
83			if (!evaluator1_.isDynamic()) {
84			seleMan1_.setSelectionSet(evaluator1_.evaluate());
85			validateSelection(seleMan1_);
86			}
87			if (!evaluator2_.isDynamic()) {
88			seleMan2_.setSelectionSet(evaluator2_.evaluate());
89			validateSelection(seleMan2_);
90			}
91
92	tim	2010	/*@todo Fixed Me /
93			Globals* simParams = info_->getSimParams();
94			if (simParams->haveSampleTime()){
95			deltaTime_ = simParams->getSampleTime();
96			} else {
97			sprintf(painCave.errMsg,
98			"CorrelationFunction::writeCorrelate Error: can not figure out deltaTime\n");
99			painCave.isFatal = 1;
100			simError();
101			}
102
103	tim	2002	int nframes = bsMan_->getNFrames();
104	tim	2010	nTimeBins_ = nframes;
105	tim	2002	histogram_.resize(nTimeBins_);
106			count_.resize(nTimeBins_);
107	tim	2008	time_.resize(nTimeBins_);
108	tim	2010
109			for (int i = 0; i < nTimeBins_; ++i) {
110			time_[i] = i * deltaTime_;
111			}
112
113	tim	2002	}
114
115
116	tim	2007	void CorrelationFunction::doCorrelate() {
117	tim	2002	preCorrelate();
118
119			int nblocks = bsMan_->getNBlocks();
120
121			for (int i = 0; i < nblocks; ++i) {
122			bsMan_->loadBlock(i);
123			for (int j = i; j < nblocks; ++j) {
124			bsMan_->loadBlock(j);
125			correlateBlocks(i, j);
126
127			if (i != j) {
128			//if i equals to j, the block is still used, should not unload it
129			bsMan_->unloadBlock(j);
130			}
131			}
132			bsMan_->unloadBlock(i);
133			}
134
135			postCorrelate();
136
137			writeCorrelate();
138			}
139
140			void CorrelationFunction::correlateBlocks(int block1, int block2) {
141
142	gezelter	2016	int jstart, jend;
143
144			assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
145	tim	2002
146	gezelter	2016	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
147			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
148
149			jend = snapshotBlock2.second;
150
151			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
152	tim	2002
153	gezelter	2016	//evaluate selection if it is dynamic
154			if (evaluator1_.isDynamic()) {
155			seleMan1_.setSelectionSet(evaluator1_.evaluate());
156			validateSelection(seleMan1_);
157			}
158
159			//update the position or velocity of the atoms belong to rigid bodies
160			updateFrame(i);
161
162			// if the two blocks are the same, we don't want to correlate
163			// backwards in time, so start j at the same frame as i
164	tim	2002
165	gezelter	2016	if (block1 == block2)
166			jstart = i;
167			else
168			jstart = snapshotBlock2.first;
169
170			for(int j = jstart; j < jend; ++j) {
171			//evaluate selection
172			if (!evaluator2_.isDynamic()) {
173			seleMan2_.setSelectionSet(evaluator2_.evaluate());
174			validateSelection(seleMan2_);
175			}
176			//update the position or velocity of the atoms belong to rigid bodies
177			updateFrame(j);
178
179			correlateFrames(i, j);
180	tim	2002	}
181	gezelter	2016	}
182	tim	2002	}
183
184
185			void CorrelationFunction::correlateFrames(int frame1, int frame2) {
186			int count = seleMan1_.getSelectionCount();
187			assert( count == seleMan2_.getSelectionCount());
188
189			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
190			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
191			assert(snapshot1 && snapshot2);
192
193			double time1 = snapshot1->getTime();
194			double time2 = snapshot2->getTime();
195	gezelter	2016
196			if (time2 < time1) { printf("BARF ON NON POSITIVE DT!\n"); stop;}
197
198	tim	2002	int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
199			count_[timeBin] += count;
200
201			int i;
202			int j;
203			StuntDouble* sd1;
204			StuntDouble* sd2;
205	tim	2008
206	gezelter	2016	switch (correlationFunctionType()) {
207
208			case frame:
209			double corrVal = calcCorrVal(frame1, frame2);
210			histogram_[timeBin] += corrVal;
211			count_[timeBin] += 1;
212			break;
213
214			case particle:
215			for (sd1 = seleMan1_.beginSelected(i), sd1 != NULL;
216			sd1 = seleMan1_.nextSelected(i)) {
217			double corrVal = calcCorrVal(frame1, frame2, sd);
218	tim	2002	histogram_[timeBin] += corrVal;
219	gezelter	2016	count_[timeBin] += 1;
220			}
221			break;
222	tim	2002
223	gezelter	2016	case cross:
224			for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; sd1 = seleMan1_.nextSelected(i)) {
225
226			for (sd2 = seleMan2_.beginSelected(j); sd2 != NULL; sd2 = seleMan2_.nextSelected(j)) {
227			double corrVal = calcCorrVal(frame1, frame2, sd1, sd2);
228			histogram_[timeBin] += corrVal;
229			count_[timeBin] += 1;
230			}
231			}
232			break;
233	tim	2002
234	gezelter	2016	default:
235			return NULL;
236
237			}
238	tim	2002	}
239
240
241			void CorrelationFunction::updateFrame(int frame){
242			Molecule* mol;
243			RigidBody* rb;
244			SimInfo::MoleculeIterator mi;
245			Molecule::RigidBodyIterator rbIter;
246
247			/** @todo need improvement */
248			if (storageLayout_ & DataStorage::dslPosition) {
249			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
250
251			//change the positions of atoms which belong to the rigidbodies
252			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
253			rb->updateAtoms(frame);
254			}
255			}
256			}
257
258			if (storageLayout_ & DataStorage::dslVelocity) {
259			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
260
261			//change the positions of atoms which belong to the rigidbodies
262			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
263			rb->updateAtomVel(frame);
264			}
265			}
266
267			}
268
269			}
270
271
272			void CorrelationFunction::preCorrelate() {
273			std::fill(histogram_.begin(), histogram_.end(), 0.0);
274			std::fill(count_.begin(), count_.end(), 0);
275			}
276
277			void CorrelationFunction::postCorrelate() {
278			for (int i =0 ; i < nTimeBins_; ++i) {
279			if (count_[i] > 0) {
280	tim	2008	histogram_[i] /= count_[i];
281	tim	2002	}
282			}
283			}
284
285
286			void CorrelationFunction::writeCorrelate() {
287			std::ofstream ofs(outputFilename_.c_str());
288
289			if (ofs.is_open()) {
290
291			ofs << "#" << getCorrFuncType() << "\n";
292	tim	2008	ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
293	tim	2002	ofs << "#extra information: " << extra_ << "\n";
294			ofs << "#time\tcorrVal\n";
295
296			for (int i = 0; i < nTimeBins_; ++i) {
297			ofs << time_[i] << "\t" << histogram_[i] << "\n";
298			}
299
300			} else {
301			sprintf(painCave.errMsg,
302			"CorrelationFunction::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
303			painCave.isFatal = 1;
304			simError();
305			}
306
307			ofs.close();
308			}
309
310			}