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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "applications/dynamicProps/TimeCorrFunc.hpp"
#include "utils/simError.h"
#include "primitives/Molecule.hpp"
using namespace std;
namespace OpenMD {

  TimeCorrFunc::TimeCorrFunc(SimInfo* info, const string& filename, 
                             const string& sele1, const string& sele2,
                             int storageLayout, long long int memSize)
    : info_(info), storageLayout_(storageLayout), memSize_(memSize),
      dumpFilename_(filename), selectionScript1_(sele1), 
      selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), 
      seleMan1_(info), seleMan2_(info) {
    
    int nAtoms = info->getNGlobalAtoms();
    int nRigidBodies = info->getNGlobalRigidBodies();
    
    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
    set<AtomType*>::iterator i;
    bool hasDirectionalAtom = false;
    bool hasDipole = false;    
    bool hasQuadrupole = false;    
    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
      if ((*i)->isDirectional()){
        hasDirectionalAtom = true;
      }
      if ((*i)->isDipole()){
        hasDipole = true;
      }
      if ((*i)->isQuadrupole()){
        hasQuadrupole = true;
      }
    }
    
    if (nRigidBodies > 0 || hasDirectionalAtom) {
      storageLayout_ |= DataStorage::dslAmat;
      if(storageLayout_ & DataStorage::dslVelocity) {
        storageLayout_ |= DataStorage::dslAngularMomentum;
      }
      if (storageLayout_ & DataStorage::dslForce) {
        storageLayout_ |= DataStorage::dslTorque;
      }
      if (hasDipole) {
        storageLayout |= DataStorage::dslDipole;
      }
      if (hasQuadrupole) {
        storageLayout |= DataStorage::dslQuadrupole;
      }
    }

    bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_, 
                                      memSize_);
    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_);
    }
    
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
      validateSelection(seleMan2_);
    }
    
    /**@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);
        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 (evaluator1_.isDynamic()) {
        seleMan1_.clearSelection();
        seleMan1_.setSelectionSet(evaluator1_.evaluate(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);
        if (evaluator2_.isDynamic()) {
          seleMan2_.clearSelection();
          seleMan2_.setSelectionSet(evaluator2_.evaluate(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() {
    fill(histogram_.begin(), histogram_.end(), 0.0);
    fill(count_.begin(), count_.end(), 0);
  }

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


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

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#selection script1: \"" << selectionScript1_ ;
      ofs << "\"\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:	1831
Committed:	Thu Jan 10 14:06:34 2013 UTC (12 years, 4 months ago) by gezelter
File size:	8697 byte(s)
Log Message:	Merging trunk changes 1812:1830 into development branch.
#	User	Rev	Content
1	tim	333	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	333	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	333	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	333	*/
42
43			#include "applications/dynamicProps/TimeCorrFunc.hpp"
44			#include "utils/simError.h"
45			#include "primitives/Molecule.hpp"
46	gezelter	1535	using namespace std;
47	gezelter	1390	namespace OpenMD {
48	tim	333
49	gezelter	1535	TimeCorrFunc::TimeCorrFunc(SimInfo* info, const string& filename,
50			const string& sele1, const string& sele2,
51	gezelter	1629	int storageLayout, long long int memSize)
52			: info_(info), storageLayout_(storageLayout), memSize_(memSize),
53			dumpFilename_(filename), selectionScript1_(sele1),
54			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
55			seleMan1_(info), seleMan2_(info) {
56	tim	333
57	gezelter	1535	int nAtoms = info->getNGlobalAtoms();
58			int nRigidBodies = info->getNGlobalRigidBodies();
59
60			set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
61			set<AtomType*>::iterator i;
62			bool hasDirectionalAtom = false;
63	gezelter	1787	bool hasDipole = false;
64			bool hasQuadrupole = false;
65	gezelter	1535	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
66			if ((*i)->isDirectional()){
67			hasDirectionalAtom = true;
68	gezelter	507	}
69	gezelter	1787	if ((*i)->isDipole()){
70			hasDipole = true;
71	gezelter	507	}
72	gezelter	1787	if ((*i)->isQuadrupole()){
73			hasQuadrupole = true;
74			}
75	gezelter	1535	}
76	tim	334
77	gezelter	1535	if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
78			storageLayout_ \|= DataStorage::dslAmat;
79			if(storageLayout_ & DataStorage::dslVelocity) {
80			storageLayout_ \|= DataStorage::dslAngularMomentum;
81	gezelter	507	}
82	gezelter	1535	if (storageLayout_ & DataStorage::dslForce) {
83			storageLayout_ \|= DataStorage::dslTorque;
84	gezelter	507	}
85	gezelter	1787	if (hasDipole) {
86			storageLayout \|= DataStorage::dslDipole;
87			}
88			if (hasQuadrupole) {
89			storageLayout \|= DataStorage::dslQuadrupole;
90			}
91	gezelter	1535	}
92	gezelter	1787
93	gezelter	1812	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_,
94			memSize_);
95	gezelter	1535	info_->setSnapshotManager(bsMan_);
96
97			evaluator1_.loadScriptString(selectionScript1_);
98			evaluator2_.loadScriptString(selectionScript2_);
99
100			//if selection is static, we only need to evaluate it once
101			if (!evaluator1_.isDynamic()) {
102			seleMan1_.setSelectionSet(evaluator1_.evaluate());
103			validateSelection(seleMan1_);
104			}
105
106			if (!evaluator2_.isDynamic()) {
107			seleMan2_.setSelectionSet(evaluator2_.evaluate());
108			validateSelection(seleMan2_);
109			}
110
111			/*@todo Fix Me /
112			Globals* simParams = info_->getSimParams();
113			if (simParams->haveSampleTime()){
114			deltaTime_ = simParams->getSampleTime();
115			} else {
116			sprintf(painCave.errMsg,
117			"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
118			painCave.isFatal = 1;
119			simError();
120			}
121	tim	333
122	gezelter	1535	int nframes = bsMan_->getNFrames();
123			nTimeBins_ = nframes;
124			histogram_.resize(nTimeBins_);
125			count_.resize(nTimeBins_);
126			time_.resize(nTimeBins_);
127	tim	333
128	gezelter	1535	for (int i = 0; i < nTimeBins_; ++i) {
129			time_[i] = i * deltaTime_;
130			}
131	gezelter	507
132	gezelter	1535	}
133	tim	333
134
135	gezelter	507	void TimeCorrFunc::doCorrelate() {
136	tim	333	preCorrelate();
137
138			int nblocks = bsMan_->getNBlocks();
139
140			for (int i = 0; i < nblocks; ++i) {
141	gezelter	507	bsMan_->loadBlock(i);
142	tim	351
143	gezelter	507	for (int j = i; j < nblocks; ++j) {
144			bsMan_->loadBlock(j);
145			correlateBlocks(i, j);
146			bsMan_->unloadBlock(j);
147			}
148	tim	351
149	gezelter	507	bsMan_->unloadBlock(i);
150	tim	333	}
151
152			postCorrelate();
153
154			writeCorrelate();
155	gezelter	507	}
156	tim	333
157	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
158	tim	333
159	tim	334	int jstart, jend;
160	tim	333
161	tim	334	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
162	tim	333
163	tim	334	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
164			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
165	tim	333
166	tim	334	jend = snapshotBlock2.second;
167
168			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
169
170	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
171			updateFrame(i);
172	tim	334
173	gezelter	1812	if (evaluator1_.isDynamic()) {
174	gezelter	1831	seleMan1_.clearSelection();
175			seleMan1_.setSelectionSet(evaluator1_.evaluate(i));
176	gezelter	1812	}
177
178	gezelter	507	// if the two blocks are the same, we don't want to correlate
179			// backwards in time, so start j at the same frame as i
180			if (block1 == block2) {
181	tim	334	jstart = i;
182	gezelter	507	} else {
183			jstart = snapshotBlock2.first;
184			}
185	tim	334
186	gezelter	507	for(int j = jstart; j < jend; ++j) {
187			//update the position or velocity of the atoms belong to rigid bodies
188			updateFrame(j);
189	gezelter	1812	if (evaluator2_.isDynamic()) {
190	gezelter	1831	seleMan2_.clearSelection();
191			seleMan2_.setSelectionSet(evaluator2_.evaluate(j));
192	gezelter	1812	}
193
194	gezelter	507	correlateFrames(i, j);
195			}
196	tim	333	}
197	gezelter	507	}
198	tim	333
199	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
200	tim	333	Molecule* mol;
201			RigidBody* rb;
202			SimInfo::MoleculeIterator mi;
203			Molecule::RigidBodyIterator rbIter;
204			/** @todo need improvement */
205			if (storageLayout_ & DataStorage::dslPosition) {
206	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
207			mol = info_->nextMolecule(mi)) {
208	tim	333
209	gezelter	507	//change the positions of atoms which belong to the rigidbodies
210	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
211			rb = mol->nextRigidBody(rbIter)) {
212	gezelter	507	rb->updateAtoms(frame);
213			}
214			}
215	tim	333	}
216
217			if (storageLayout_ & DataStorage::dslVelocity) {
218	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
219			mol = info_->nextMolecule(mi)) {
220
221	gezelter	507	//change the positions of atoms which belong to the rigidbodies
222	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
223			rb = mol->nextRigidBody(rbIter)) {
224	gezelter	507	rb->updateAtomVel(frame);
225			}
226	gezelter	1535	}
227			}
228	gezelter	507	}
229	tim	333
230
231	gezelter	507	void TimeCorrFunc::preCorrelate() {
232	gezelter	1535	fill(histogram_.begin(), histogram_.end(), 0.0);
233			fill(count_.begin(), count_.end(), 0);
234	gezelter	507	}
235	tim	333
236	gezelter	507	void TimeCorrFunc::postCorrelate() {
237	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
238	gezelter	507	if (count_[i] > 0) {
239			histogram_[i] /= count_[i];
240	gezelter	1831	} else {
241			histogram_[i] = 0;
242	gezelter	507	}
243	tim	333	}
244	gezelter	507	}
245	tim	333
246
247	gezelter	507	void TimeCorrFunc::writeCorrelate() {
248	gezelter	1535	ofstream ofs(outputFilename_.c_str());
249	tim	333
250			if (ofs.is_open()) {
251
252	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
253	gezelter	1535	ofs << "#selection script1: \"" << selectionScript1_ ;
254			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
255	gezelter	507	ofs << "#extra information: " << extra_ << "\n";
256			ofs << "#time\tcorrVal\n";
257	tim	333
258	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
259			ofs << time_[i] << "\t" << histogram_[i] << "\n";
260			}
261	tim	333
262			} else {
263	gezelter	507	sprintf(painCave.errMsg,
264	gezelter	1535	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n",
265			outputFilename_.c_str());
266	gezelter	507	painCave.isFatal = 1;
267			simError();
268	tim	333	}
269
270			ofs.close();
271	gezelter	507	}
272	tim	333
273			}