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, 234107 (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();

    // Request maximum needed storage for the simulation (including of
    // whatever was passed down by the individual correlation
    // function).

    storageLayout_ = info->getStorageLayout() | storageLayout;

    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;
    RealType i_t, j_t;

    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;
      }
      
      i_t = bsMan_->getSnapshot(i)->getTime();
              
      for(int j  = jstart; j < jend; ++j) {

        // Perform a sanity check on the actual configuration times to
        // make sure the configurations are spaced the same amount the
        // sample time said they were spaced:
               
        j_t = bsMan_->getSnapshot(j)->getTime(); 

        if ( fabs( (j_t - i_t) - (j-i)*deltaTime_ ) > 1.0e-4 ) {
          sprintf(painCave.errMsg,
                  "TimeCorrFunc::correlateBlocks Error: sampleTime (%f)\n"
                  "\tin %s does not match actual time-spacing between\n"
                  "\tconfigurations %d (t = %f) and %d (t = %f).\n",
                  deltaTime_, dumpFilename_.c_str(), i, i_t, j, j_t);
          painCave.isFatal = 1;
          simError();  
        }

        //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:	1937
Committed:	Tue Oct 29 16:02:58 2013 UTC (11 years, 10 months ago) by gezelter
File size:	8730 byte(s)
Log Message:	Fixed a few bugs and added some sanity checks in the analysis codes.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	1782	using namespace std;
47	gezelter	1390	namespace OpenMD {
48	tim	333
49	gezelter	1782	TimeCorrFunc::TimeCorrFunc(SimInfo* info, const string& filename,
50			const string& sele1, const string& sele2,
51	gezelter	1596	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	gezelter	1782	seleMan1_(info), seleMan2_(info) {
56	tim	333
57	gezelter	1782	int nAtoms = info->getNGlobalAtoms();
58			int nRigidBodies = info->getNGlobalRigidBodies();
59	gezelter	1879
60			// Request maximum needed storage for the simulation (including of
61			// whatever was passed down by the individual correlation
62			// function).
63
64			storageLayout_ = info->getStorageLayout() \| storageLayout;
65
66	gezelter	1811	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_,
67			memSize_);
68	gezelter	1782	info_->setSnapshotManager(bsMan_);
69
70			evaluator1_.loadScriptString(selectionScript1_);
71			evaluator2_.loadScriptString(selectionScript2_);
72
73			//if selection is static, we only need to evaluate it once
74			if (!evaluator1_.isDynamic()) {
75			seleMan1_.setSelectionSet(evaluator1_.evaluate());
76			validateSelection(seleMan1_);
77			}
78
79			if (!evaluator2_.isDynamic()) {
80			seleMan2_.setSelectionSet(evaluator2_.evaluate());
81			validateSelection(seleMan2_);
82			}
83
84			/*@todo Fix Me /
85			Globals* simParams = info_->getSimParams();
86			if (simParams->haveSampleTime()){
87			deltaTime_ = simParams->getSampleTime();
88			} else {
89			sprintf(painCave.errMsg,
90			"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
91			painCave.isFatal = 1;
92			simError();
93			}
94	tim	333
95	gezelter	1782	int nframes = bsMan_->getNFrames();
96			nTimeBins_ = nframes;
97			histogram_.resize(nTimeBins_);
98			count_.resize(nTimeBins_);
99			time_.resize(nTimeBins_);
100	tim	333
101	gezelter	1782	for (int i = 0; i < nTimeBins_; ++i) {
102			time_[i] = i * deltaTime_;
103	gezelter	1937	}
104	gezelter	1782	}
105	tim	333
106
107	gezelter	507	void TimeCorrFunc::doCorrelate() {
108	tim	333	preCorrelate();
109
110			int nblocks = bsMan_->getNBlocks();
111
112			for (int i = 0; i < nblocks; ++i) {
113	gezelter	507	bsMan_->loadBlock(i);
114	tim	351
115	gezelter	507	for (int j = i; j < nblocks; ++j) {
116			bsMan_->loadBlock(j);
117			correlateBlocks(i, j);
118			bsMan_->unloadBlock(j);
119			}
120	tim	351
121	gezelter	507	bsMan_->unloadBlock(i);
122	tim	333	}
123
124			postCorrelate();
125
126			writeCorrelate();
127	gezelter	507	}
128	tim	333
129	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
130	tim	333
131	tim	334	int jstart, jend;
132	gezelter	1937	RealType i_t, j_t;
133	tim	333
134	tim	334	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
135	tim	333
136	tim	334	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
137			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
138	tim	333
139	tim	334	jend = snapshotBlock2.second;
140
141			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
142	gezelter	1937
143	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
144			updateFrame(i);
145	tim	334
146	gezelter	1811	if (evaluator1_.isDynamic()) {
147	gezelter	1816	seleMan1_.clearSelection();
148			seleMan1_.setSelectionSet(evaluator1_.evaluate(i));
149	gezelter	1811	}
150
151	gezelter	507	// if the two blocks are the same, we don't want to correlate
152			// backwards in time, so start j at the same frame as i
153			if (block1 == block2) {
154	tim	334	jstart = i;
155	gezelter	507	} else {
156			jstart = snapshotBlock2.first;
157			}
158	gezelter	1937
159			i_t = bsMan_->getSnapshot(i)->getTime();
160
161	gezelter	507	for(int j = jstart; j < jend; ++j) {
162	gezelter	1937
163			// Perform a sanity check on the actual configuration times to
164			// make sure the configurations are spaced the same amount the
165			// sample time said they were spaced:
166
167			j_t = bsMan_->getSnapshot(j)->getTime();
168
169			if ( fabs( (j_t - i_t) - (j-i)*deltaTime_ ) > 1.0e-4 ) {
170			sprintf(painCave.errMsg,
171			"TimeCorrFunc::correlateBlocks Error: sampleTime (%f)\n"
172			"\tin %s does not match actual time-spacing between\n"
173			"\tconfigurations %d (t = %f) and %d (t = %f).\n",
174			deltaTime_, dumpFilename_.c_str(), i, i_t, j, j_t);
175			painCave.isFatal = 1;
176			simError();
177			}
178
179	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
180			updateFrame(j);
181	gezelter	1811	if (evaluator2_.isDynamic()) {
182	gezelter	1816	seleMan2_.clearSelection();
183			seleMan2_.setSelectionSet(evaluator2_.evaluate(j));
184	gezelter	1811	}
185
186	gezelter	507	correlateFrames(i, j);
187			}
188	tim	333	}
189	gezelter	507	}
190	tim	333
191	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
192	tim	333	Molecule* mol;
193			RigidBody* rb;
194			SimInfo::MoleculeIterator mi;
195			Molecule::RigidBodyIterator rbIter;
196			/** @todo need improvement */
197			if (storageLayout_ & DataStorage::dslPosition) {
198	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
199			mol = info_->nextMolecule(mi)) {
200	tim	333
201	gezelter	507	//change the positions of atoms which belong to the rigidbodies
202	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
203			rb = mol->nextRigidBody(rbIter)) {
204	gezelter	507	rb->updateAtoms(frame);
205			}
206			}
207	tim	333	}
208
209			if (storageLayout_ & DataStorage::dslVelocity) {
210	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
211			mol = info_->nextMolecule(mi)) {
212
213	gezelter	507	//change the positions of atoms which belong to the rigidbodies
214	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
215			rb = mol->nextRigidBody(rbIter)) {
216	gezelter	507	rb->updateAtomVel(frame);
217			}
218	gezelter	1782	}
219			}
220	gezelter	507	}
221	tim	333
222
223	gezelter	507	void TimeCorrFunc::preCorrelate() {
224	gezelter	1782	fill(histogram_.begin(), histogram_.end(), 0.0);
225			fill(count_.begin(), count_.end(), 0);
226	gezelter	507	}
227	tim	333
228	gezelter	507	void TimeCorrFunc::postCorrelate() {
229	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
230	gezelter	507	if (count_[i] > 0) {
231			histogram_[i] /= count_[i];
232	gezelter	1815	} else {
233			histogram_[i] = 0;
234	gezelter	507	}
235	tim	333	}
236	gezelter	507	}
237	tim	333
238
239	gezelter	507	void TimeCorrFunc::writeCorrelate() {
240	gezelter	1782	ofstream ofs(outputFilename_.c_str());
241	tim	333
242			if (ofs.is_open()) {
243
244	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
245	gezelter	1782	ofs << "#selection script1: \"" << selectionScript1_ ;
246			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
247	gezelter	507	ofs << "#extra information: " << extra_ << "\n";
248			ofs << "#time\tcorrVal\n";
249	tim	333
250	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
251			ofs << time_[i] << "\t" << histogram_[i] << "\n";
252			}
253	tim	333
254			} else {
255	gezelter	507	sprintf(painCave.errMsg,
256	gezelter	1782	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n",
257			outputFilename_.c_str());
258	gezelter	507	painCave.isFatal = 1;
259			simError();
260	tim	333	}
261
262			ofs.close();
263	gezelter	507	}
264	tim	333
265			}