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, 5 months ago) by tim
File size:	9372 byte(s)
Log Message:	maximum length defaults to the cutoff radius
#	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. 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	#include "primitives/Molecule.hpp"
45	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	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
77	info_->setSnapshotManager(bsMan_);
78
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	/*@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	int nframes = bsMan_->getNFrames();
101	nTimeBins_ = nframes;
102	histogram_.resize(nTimeBins_);
103	count_.resize(nTimeBins_);
104	time_.resize(nTimeBins_);
105
106	for (int i = 0; i < nTimeBins_; ++i) {
107	time_[i] = i * deltaTime_;
108	}
109
110	}
111
112
113	void CorrelationFunction::doCorrelate() {
114	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	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); sd1 != NULL && sd2 != NULL;
187	sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
188
189	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	histogram_[i] /= count_[i];
243	}
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	ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
255	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	}