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()){
            hasDirectionalAtom = true;
        }
    }
    
    if (nRigidBodies > 0 || hasDirectionalAtom) {
        storageLayout_ |= DataStorage::dslAmat;
    }
    if (hasMultipole) {
        storageLayout_ |= DataStorage::dslElectroFrame;
    }
        
    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) {

    assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));

    SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
    SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
    
    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);
        for(int j  = snapshotBlock1.first; j < snapshotBlock1.second; ++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();
    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
    count_[timeBin] += count;    
    
    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;
    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); sd1 != NULL && sd2 != NULL;
        sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {

        double corrVal = calcCorrVal(sd1, frame1, sd2, frame2);
        histogram_[timeBin] += corrVal;    
    }

    //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(sd1, frame1, sd2, frame2);
    //    }            
    //}

}


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:	2010
Committed:	Sun Feb 13 20:05:42 2005 UTC (19 years, 6 months ago) by tim
File size:	9372 byte(s)
Log Message:	maximum length defaults to the cutoff radius
#	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			hasDirectionalAtom = true;
66			}
67			}
68
69			if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
70			storageLayout_ \|= DataStorage::dslAmat;
71			}
72			if (hasMultipole) {
73			storageLayout_ \|= DataStorage::dslElectroFrame;
74			}
75
76	tim	2008	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
77			info_->setSnapshotManager(bsMan_);
78	tim	2002
79			//if selection is static, we only need to evaluate it once
80			if (!evaluator1_.isDynamic()) {
81			seleMan1_.setSelectionSet(evaluator1_.evaluate());
82			validateSelection(seleMan1_);
83			}
84			if (!evaluator2_.isDynamic()) {
85			seleMan2_.setSelectionSet(evaluator2_.evaluate());
86			validateSelection(seleMan2_);
87			}
88
89	tim	2010	/*@todo Fixed Me /
90			Globals* simParams = info_->getSimParams();
91			if (simParams->haveSampleTime()){
92			deltaTime_ = simParams->getSampleTime();
93			} else {
94			sprintf(painCave.errMsg,
95			"CorrelationFunction::writeCorrelate Error: can not figure out deltaTime\n");
96			painCave.isFatal = 1;
97			simError();
98			}
99
100	tim	2002	int nframes = bsMan_->getNFrames();
101	tim	2010	nTimeBins_ = nframes;
102	tim	2002	histogram_.resize(nTimeBins_);
103			count_.resize(nTimeBins_);
104	tim	2008	time_.resize(nTimeBins_);
105	tim	2010
106			for (int i = 0; i < nTimeBins_; ++i) {
107			time_[i] = i * deltaTime_;
108			}
109
110	tim	2002	}
111
112
113	tim	2007	void CorrelationFunction::doCorrelate() {
114	tim	2002	preCorrelate();
115
116			int nblocks = bsMan_->getNBlocks();
117
118			for (int i = 0; i < nblocks; ++i) {
119			bsMan_->loadBlock(i);
120			for (int j = i; j < nblocks; ++j) {
121			bsMan_->loadBlock(j);
122			correlateBlocks(i, j);
123
124			if (i != j) {
125			//if i equals to j, the block is still used, should not unload it
126			bsMan_->unloadBlock(j);
127			}
128			}
129			bsMan_->unloadBlock(i);
130			}
131
132			postCorrelate();
133
134			writeCorrelate();
135			}
136
137			void CorrelationFunction::correlateBlocks(int block1, int block2) {
138
139			assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
140
141			SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
142			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
143
144			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
145
146			//evaluate selection if it is dynamic
147			if (evaluator1_.isDynamic()) {
148			seleMan1_.setSelectionSet(evaluator1_.evaluate());
149			validateSelection(seleMan1_);
150			}
151
152			//update the position or velocity of the atoms belong to rigid bodies
153			updateFrame(i);
154			for(int j = snapshotBlock1.first; j < snapshotBlock1.second; ++j) {
155			//evaluate selection
156			if (!evaluator2_.isDynamic()) {
157			seleMan2_.setSelectionSet(evaluator2_.evaluate());
158			validateSelection(seleMan2_);
159			}
160			//update the position or velocity of the atoms belong to rigid bodies
161			updateFrame(j);
162
163			correlateFrames(i, j);
164			}
165			}
166			}
167
168
169			void CorrelationFunction::correlateFrames(int frame1, int frame2) {
170			int count = seleMan1_.getSelectionCount();
171			assert( count == seleMan2_.getSelectionCount());
172
173			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
174			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
175			assert(snapshot1 && snapshot2);
176
177			double time1 = snapshot1->getTime();
178			double time2 = snapshot2->getTime();
179			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
180			count_[timeBin] += count;
181
182			int i;
183			int j;
184			StuntDouble* sd1;
185			StuntDouble* sd2;
186	tim	2008	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); sd1 != NULL && sd2 != NULL;
187			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
188
189	tim	2002	double corrVal = calcCorrVal(sd1, frame1, sd2, frame2);
190			histogram_[timeBin] += corrVal;
191			}
192
193			//for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL; sd1 = seleMan1_.nextSelected(i)) {
194			//
195			// for (sd2 = seleMan2_.beginSelected(j); sd2 != NULL; sd2 = seleMan2_.nextSelected(j)) {
196			// double corrVal = calcCorrVal(sd1, frame1, sd2, frame2);
197			// }
198			//}
199
200			}
201
202
203			void CorrelationFunction::updateFrame(int frame){
204			Molecule* mol;
205			RigidBody* rb;
206			SimInfo::MoleculeIterator mi;
207			Molecule::RigidBodyIterator rbIter;
208
209			/** @todo need improvement */
210			if (storageLayout_ & DataStorage::dslPosition) {
211			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
212
213			//change the positions of atoms which belong to the rigidbodies
214			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
215			rb->updateAtoms(frame);
216			}
217			}
218			}
219
220			if (storageLayout_ & DataStorage::dslVelocity) {
221			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
222
223			//change the positions of atoms which belong to the rigidbodies
224			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
225			rb->updateAtomVel(frame);
226			}
227			}
228
229			}
230
231			}
232
233
234			void CorrelationFunction::preCorrelate() {
235			std::fill(histogram_.begin(), histogram_.end(), 0.0);
236			std::fill(count_.begin(), count_.end(), 0);
237			}
238
239			void CorrelationFunction::postCorrelate() {
240			for (int i =0 ; i < nTimeBins_; ++i) {
241			if (count_[i] > 0) {
242	tim	2008	histogram_[i] /= count_[i];
243	tim	2002	}
244			}
245			}
246
247
248			void CorrelationFunction::writeCorrelate() {
249			std::ofstream ofs(outputFilename_.c_str());
250
251			if (ofs.is_open()) {
252
253			ofs << "#" << getCorrFuncType() << "\n";
254	tim	2008	ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
255	tim	2002	ofs << "#extra information: " << extra_ << "\n";
256			ofs << "#time\tcorrVal\n";
257
258			for (int i = 0; i < nTimeBins_; ++i) {
259			ofs << time_[i] << "\t" << histogram_[i] << "\n";
260			}
261
262			} else {
263			sprintf(painCave.errMsg,
264			"CorrelationFunction::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
265			painCave.isFatal = 1;
266			simError();
267			}
268
269			ofs.close();
270			}
271
272			}