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

TimeCorrFunc::TimeCorrFunc(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_);

    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_);
    } else {
            sprintf(painCave.errMsg,
                "TimeCorrFunc Error: dynamic selection is not supported\n");
            painCave.isFatal = 1;
            simError();  
    }
    
    if (!evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
        validateSelection(seleMan2_);
    } else {
            sprintf(painCave.errMsg,
                "TimeCorrFunc Error: dynamic selection is not supported\n");
            painCave.isFatal = 1;
            simError();  
    }
    

    /**@todo Fix Me */
    Globals* simParams = info_->getSimParams();
    if (simParams->haveSampleTime()){
        deltaTime_ = simParams->getSampleTime();
    } else {
            sprintf(painCave.errMsg,
                "TimeCorrFunc::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 TimeCorrFunc::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 TimeCorrFunc::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) {

        //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) {
            //update the position or velocity of the atoms belong to rigid bodies
            updateFrame(j);

            correlateFrames(i, j);
        }
    }
}

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

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


void TimeCorrFunc::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,
                "TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
            painCave.isFatal = 1;
            simError();        
    }

    ofs.close();    
}

}
Revision:	2018
Committed:	Mon Feb 14 17:57:01 2005 UTC (19 years, 5 months ago) by tim
File size:	8612 byte(s)
Log Message:	begin bug fix
#	User	Rev	Content
1	tim	2017	/*
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/TimeCorrFunc.hpp"
43			#include "utils/simError.h"
44			#include "primitives/Molecule.hpp"
45			namespace oopse {
46
47			TimeCorrFunc::TimeCorrFunc(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			hasMultipole = true;
66			}
67			}
68
69			if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
70			storageLayout_ \|= DataStorage::dslAmat;
71			}
72			if (hasMultipole) {
73			storageLayout_ \|= DataStorage::dslElectroFrame;
74			if (nRigidBodies > 0) {
75			storageLayout_ \|= DataStorage::dslAngularMomentum;
76			}
77			}
78
79			bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
80			info_->setSnapshotManager(bsMan_);
81
82	tim	2018	evaluator1_.loadScriptString(selectionScript1_);
83			evaluator2_.loadScriptString(selectionScript2_);
84
85	tim	2017	//if selection is static, we only need to evaluate it once
86			if (!evaluator1_.isDynamic()) {
87			seleMan1_.setSelectionSet(evaluator1_.evaluate());
88			validateSelection(seleMan1_);
89			} else {
90			sprintf(painCave.errMsg,
91			"TimeCorrFunc Error: dynamic selection is not supported\n");
92			painCave.isFatal = 1;
93			simError();
94			}
95
96			if (!evaluator2_.isDynamic()) {
97			seleMan2_.setSelectionSet(evaluator2_.evaluate());
98			validateSelection(seleMan2_);
99			} else {
100			sprintf(painCave.errMsg,
101			"TimeCorrFunc Error: dynamic selection is not supported\n");
102			painCave.isFatal = 1;
103			simError();
104			}
105
106
107
108	tim	2018	/*@todo Fix Me /
109	tim	2017	Globals* simParams = info_->getSimParams();
110			if (simParams->haveSampleTime()){
111			deltaTime_ = simParams->getSampleTime();
112			} else {
113			sprintf(painCave.errMsg,
114			"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
115			painCave.isFatal = 1;
116			simError();
117			}
118
119			int nframes = bsMan_->getNFrames();
120			nTimeBins_ = nframes;
121			histogram_.resize(nTimeBins_);
122			count_.resize(nTimeBins_);
123			time_.resize(nTimeBins_);
124
125			for (int i = 0; i < nTimeBins_; ++i) {
126			time_[i] = i * deltaTime_;
127			}
128
129			}
130
131
132			void TimeCorrFunc::doCorrelate() {
133			preCorrelate();
134
135			int nblocks = bsMan_->getNBlocks();
136
137			for (int i = 0; i < nblocks; ++i) {
138			bsMan_->loadBlock(i);
139			for (int j = i; j < nblocks; ++j) {
140			bsMan_->loadBlock(j);
141			correlateBlocks(i, j);
142
143			if (i != j) {
144			//if i equals to j, the block is still used, should not unload it
145			bsMan_->unloadBlock(j);
146			}
147			}
148			bsMan_->unloadBlock(i);
149			}
150
151			postCorrelate();
152
153			writeCorrelate();
154			}
155
156			void TimeCorrFunc::correlateBlocks(int block1, int block2) {
157
158	tim	2018	int jstart, jend;
159	tim	2017
160	tim	2018	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
161	tim	2017
162	tim	2018	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
163			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
164	tim	2017
165	tim	2018	jend = snapshotBlock2.second;
166
167			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
168
169			//update the position or velocity of the atoms belong to rigid bodies
170			updateFrame(i);
171
172			// if the two blocks are the same, we don't want to correlate
173			// backwards in time, so start j at the same frame as i
174			if (block1 == block2) {
175			jstart = i;
176			} else {
177			jstart = snapshotBlock2.first;
178			}
179
180			for(int j = jstart; j < jend; ++j) {
181			//update the position or velocity of the atoms belong to rigid bodies
182			updateFrame(j);
183
184			correlateFrames(i, j);
185			}
186	tim	2017	}
187			}
188
189			void TimeCorrFunc::updateFrame(int frame){
190			Molecule* mol;
191			RigidBody* rb;
192			SimInfo::MoleculeIterator mi;
193			Molecule::RigidBodyIterator rbIter;
194
195			/** @todo need improvement */
196			if (storageLayout_ & DataStorage::dslPosition) {
197			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
198
199			//change the positions of atoms which belong to the rigidbodies
200			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
201			rb->updateAtoms(frame);
202			}
203			}
204			}
205
206			if (storageLayout_ & DataStorage::dslVelocity) {
207			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
208
209			//change the positions of atoms which belong to the rigidbodies
210			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
211			rb->updateAtomVel(frame);
212			}
213			}
214
215			}
216
217			}
218
219
220			void TimeCorrFunc::preCorrelate() {
221			std::fill(histogram_.begin(), histogram_.end(), 0.0);
222			std::fill(count_.begin(), count_.end(), 0);
223			}
224
225			void TimeCorrFunc::postCorrelate() {
226			for (int i =0 ; i < nTimeBins_; ++i) {
227			if (count_[i] > 0) {
228			histogram_[i] /= count_[i];
229			}
230			}
231			}
232
233
234			void TimeCorrFunc::writeCorrelate() {
235			std::ofstream ofs(outputFilename_.c_str());
236
237			if (ofs.is_open()) {
238
239			ofs << "#" << getCorrFuncType() << "\n";
240			ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
241			ofs << "#extra information: " << extra_ << "\n";
242			ofs << "#time\tcorrVal\n";
243
244			for (int i = 0; i < nTimeBins_; ++i) {
245			ofs << time_[i] << "\t" << histogram_[i] << "\n";
246			}
247
248			} else {
249			sprintf(painCave.errMsg,
250			"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
251			painCave.isFatal = 1;
252			simError();
253			}
254
255			ofs.close();
256			}
257
258			}