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_);

    //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 Fixed 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) {
    
    //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 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:	2017
Committed:	Mon Feb 14 17:35:25 2005 UTC (20 years, 8 months ago) by tim
File size:	8785 byte(s)
Log Message:	refactory CorrelationFunction
#	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/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	//if selection is static, we only need to evaluate it once
83	if (!evaluator1_.isDynamic()) {
84	seleMan1_.setSelectionSet(evaluator1_.evaluate());
85	validateSelection(seleMan1_);
86	} else {
87	sprintf(painCave.errMsg,
88	"TimeCorrFunc Error: dynamic selection is not supported\n");
89	painCave.isFatal = 1;
90	simError();
91	}
92
93	if (!evaluator2_.isDynamic()) {
94	seleMan2_.setSelectionSet(evaluator2_.evaluate());
95	validateSelection(seleMan2_);
96	} else {
97	sprintf(painCave.errMsg,
98	"TimeCorrFunc Error: dynamic selection is not supported\n");
99	painCave.isFatal = 1;
100	simError();
101	}
102
103
104
105	/*@todo Fixed Me /
106	Globals* simParams = info_->getSimParams();
107	if (simParams->haveSampleTime()){
108	deltaTime_ = simParams->getSampleTime();
109	} else {
110	sprintf(painCave.errMsg,
111	"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
112	painCave.isFatal = 1;
113	simError();
114	}
115
116	int nframes = bsMan_->getNFrames();
117	nTimeBins_ = nframes;
118	histogram_.resize(nTimeBins_);
119	count_.resize(nTimeBins_);
120	time_.resize(nTimeBins_);
121
122	for (int i = 0; i < nTimeBins_; ++i) {
123	time_[i] = i * deltaTime_;
124	}
125
126	}
127
128
129	void TimeCorrFunc::doCorrelate() {
130	preCorrelate();
131
132	int nblocks = bsMan_->getNBlocks();
133
134	for (int i = 0; i < nblocks; ++i) {
135	bsMan_->loadBlock(i);
136	for (int j = i; j < nblocks; ++j) {
137	bsMan_->loadBlock(j);
138	correlateBlocks(i, j);
139
140	if (i != j) {
141	//if i equals to j, the block is still used, should not unload it
142	bsMan_->unloadBlock(j);
143	}
144	}
145	bsMan_->unloadBlock(i);
146	}
147
148	postCorrelate();
149
150	writeCorrelate();
151	}
152
153	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
154
155	int jstart, jend;
156
157	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
158
159	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
160	SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
161
162	jend = snapshotBlock2.second;
163
164	for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
165
166	//evaluate selection if it is dynamic
167	if (evaluator1_.isDynamic()) {
168	seleMan1_.setSelectionSet(evaluator1_.evaluate());
169	validateSelection(seleMan1_);
170	}
171
172	//update the position or velocity of the atoms belong to rigid bodies
173	updateFrame(i);
174
175	// if the two blocks are the same, we don't want to correlate
176	// backwards in time, so start j at the same frame as i
177
178	if (block1 == block2)
179	jstart = i;
180	else
181	jstart = snapshotBlock2.first;
182
183	for(int j = jstart; j < jend; ++j) {
184	//evaluate selection
185	if (!evaluator2_.isDynamic()) {
186	seleMan2_.setSelectionSet(evaluator2_.evaluate());
187	validateSelection(seleMan2_);
188	}
189	//update the position or velocity of the atoms belong to rigid bodies
190	updateFrame(j);
191
192	correlateFrames(i, j);
193	}
194	}
195	}
196
197	void TimeCorrFunc::updateFrame(int frame){
198	Molecule* mol;
199	RigidBody* rb;
200	SimInfo::MoleculeIterator mi;
201	Molecule::RigidBodyIterator rbIter;
202
203	/** @todo need improvement */
204	if (storageLayout_ & DataStorage::dslPosition) {
205	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
206
207	//change the positions of atoms which belong to the rigidbodies
208	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
209	rb->updateAtoms(frame);
210	}
211	}
212	}
213
214	if (storageLayout_ & DataStorage::dslVelocity) {
215	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
216
217	//change the positions of atoms which belong to the rigidbodies
218	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
219	rb->updateAtomVel(frame);
220	}
221	}
222
223	}
224
225	}
226
227
228	void TimeCorrFunc::preCorrelate() {
229	std::fill(histogram_.begin(), histogram_.end(), 0.0);
230	std::fill(count_.begin(), count_.end(), 0);
231	}
232
233	void TimeCorrFunc::postCorrelate() {
234	for (int i =0 ; i < nTimeBins_; ++i) {
235	if (count_[i] > 0) {
236	histogram_[i] /= count_[i];
237	}
238	}
239	}
240
241
242	void TimeCorrFunc::writeCorrelate() {
243	std::ofstream ofs(outputFilename_.c_str());
244
245	if (ofs.is_open()) {
246
247	ofs << "#" << getCorrFuncType() << "\n";
248	ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
249	ofs << "#extra information: " << extra_ << "\n";
250	ofs << "#time\tcorrVal\n";
251
252	for (int i = 0; i < nTimeBins_; ++i) {
253	ofs << time_[i] << "\t" << histogram_[i] << "\n";
254	}
255
256	} else {
257	sprintf(painCave.errMsg,
258	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
259	painCave.isFatal = 1;
260	simError();
261	}
262
263	ofs.close();
264	}
265
266	}