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_);
    } 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);
        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() {
    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];
      }
    }
  }


  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:	1798
Committed:	Thu Sep 13 14:10:11 2012 UTC (12 years, 8 months ago) by gezelter
File size:	8658 byte(s)
Log Message:	Merged trunk changes into the 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	1629	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_, memSize_);
94	gezelter	1535	info_->setSnapshotManager(bsMan_);
95
96			evaluator1_.loadScriptString(selectionScript1_);
97			evaluator2_.loadScriptString(selectionScript2_);
98
99			//if selection is static, we only need to evaluate it once
100			if (!evaluator1_.isDynamic()) {
101			seleMan1_.setSelectionSet(evaluator1_.evaluate());
102			validateSelection(seleMan1_);
103			} else {
104			sprintf(painCave.errMsg,
105			"TimeCorrFunc Error: dynamic selection is not supported\n");
106			painCave.isFatal = 1;
107			simError();
108			}
109
110			if (!evaluator2_.isDynamic()) {
111			seleMan2_.setSelectionSet(evaluator2_.evaluate());
112			validateSelection(seleMan2_);
113			} else {
114			sprintf(painCave.errMsg,
115			"TimeCorrFunc Error: dynamic selection is not supported\n");
116			painCave.isFatal = 1;
117			simError();
118			}
119
120	tim	333
121
122	gezelter	1535	/*@todo Fix Me /
123			Globals* simParams = info_->getSimParams();
124			if (simParams->haveSampleTime()){
125			deltaTime_ = simParams->getSampleTime();
126			} else {
127			sprintf(painCave.errMsg,
128			"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
129			painCave.isFatal = 1;
130			simError();
131			}
132	tim	333
133	gezelter	1535	int nframes = bsMan_->getNFrames();
134			nTimeBins_ = nframes;
135			histogram_.resize(nTimeBins_);
136			count_.resize(nTimeBins_);
137			time_.resize(nTimeBins_);
138	tim	333
139	gezelter	1535	for (int i = 0; i < nTimeBins_; ++i) {
140			time_[i] = i * deltaTime_;
141			}
142	gezelter	507
143	gezelter	1535	}
144	tim	333
145
146	gezelter	507	void TimeCorrFunc::doCorrelate() {
147	tim	333	preCorrelate();
148
149			int nblocks = bsMan_->getNBlocks();
150
151			for (int i = 0; i < nblocks; ++i) {
152	gezelter	507	bsMan_->loadBlock(i);
153	tim	351
154	gezelter	507	for (int j = i; j < nblocks; ++j) {
155			bsMan_->loadBlock(j);
156			correlateBlocks(i, j);
157			bsMan_->unloadBlock(j);
158			}
159	tim	351
160	gezelter	507	bsMan_->unloadBlock(i);
161	tim	333	}
162
163			postCorrelate();
164
165			writeCorrelate();
166	gezelter	507	}
167	tim	333
168	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
169	tim	333
170	tim	334	int jstart, jend;
171	tim	333
172	tim	334	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
173	tim	333
174	tim	334	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
175			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
176	tim	333
177	tim	334	jend = snapshotBlock2.second;
178
179			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
180
181	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
182			updateFrame(i);
183	tim	334
184	gezelter	507	// if the two blocks are the same, we don't want to correlate
185			// backwards in time, so start j at the same frame as i
186			if (block1 == block2) {
187	tim	334	jstart = i;
188	gezelter	507	} else {
189			jstart = snapshotBlock2.first;
190			}
191	tim	334
192	gezelter	507	for(int j = jstart; j < jend; ++j) {
193			//update the position or velocity of the atoms belong to rigid bodies
194			updateFrame(j);
195	tim	334
196	gezelter	507	correlateFrames(i, j);
197			}
198	tim	333	}
199	gezelter	507	}
200	tim	333
201	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
202	tim	333	Molecule* mol;
203			RigidBody* rb;
204			SimInfo::MoleculeIterator mi;
205			Molecule::RigidBodyIterator rbIter;
206
207			/** @todo need improvement */
208			if (storageLayout_ & DataStorage::dslPosition) {
209	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
210			mol = info_->nextMolecule(mi)) {
211	tim	333
212	gezelter	507	//change the positions of atoms which belong to the rigidbodies
213	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
214			rb = mol->nextRigidBody(rbIter)) {
215	gezelter	507	rb->updateAtoms(frame);
216			}
217			}
218	tim	333	}
219
220			if (storageLayout_ & DataStorage::dslVelocity) {
221	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
222			mol = info_->nextMolecule(mi)) {
223
224	gezelter	507	//change the positions of atoms which belong to the rigidbodies
225	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
226			rb = mol->nextRigidBody(rbIter)) {
227	gezelter	507	rb->updateAtomVel(frame);
228			}
229	gezelter	1535	}
230			}
231	gezelter	507	}
232	tim	333
233
234	gezelter	507	void TimeCorrFunc::preCorrelate() {
235	gezelter	1535	fill(histogram_.begin(), histogram_.end(), 0.0);
236			fill(count_.begin(), count_.end(), 0);
237	gezelter	507	}
238	tim	333
239	gezelter	507	void TimeCorrFunc::postCorrelate() {
240	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
241	gezelter	507	if (count_[i] > 0) {
242			histogram_[i] /= count_[i];
243			}
244	tim	333	}
245	gezelter	507	}
246	tim	333
247
248	gezelter	507	void TimeCorrFunc::writeCorrelate() {
249	gezelter	1535	ofstream ofs(outputFilename_.c_str());
250	tim	333
251			if (ofs.is_open()) {
252
253	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
254	gezelter	1535	ofs << "#selection script1: \"" << selectionScript1_ ;
255			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
256	gezelter	507	ofs << "#extra information: " << extra_ << "\n";
257			ofs << "#time\tcorrVal\n";
258	tim	333
259	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
260			ofs << time_[i] << "\t" << histogram_[i] << "\n";
261			}
262	tim	333
263			} else {
264	gezelter	507	sprintf(painCave.errMsg,
265	gezelter	1535	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n",
266			outputFilename_.c_str());
267	gezelter	507	painCave.isFatal = 1;
268			simError();
269	tim	333	}
270
271			ofs.close();
272	gezelter	507	}
273	tim	333
274			}