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), seleMan1_(info_), seleMan2_(info_),
      selectionScript1_(sele1), selectionScript2_(sele2), 
      evaluator1_(info_), evaluator2_(info_) {
    
    // 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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 5 months ago) by gezelter
File size:	8635 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	gezelter	2071	dumpFilename_(filename), seleMan1_(info_), seleMan2_(info_),
54			selectionScript1_(sele1), selectionScript2_(sele2),
55			evaluator1_(info_), evaluator2_(info_) {
56	tim	333
57	gezelter	1879	// Request maximum needed storage for the simulation (including of
58			// whatever was passed down by the individual correlation
59			// function).
60
61			storageLayout_ = info->getStorageLayout() \| storageLayout;
62
63	gezelter	1811	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_,
64			memSize_);
65	gezelter	1782	info_->setSnapshotManager(bsMan_);
66
67			evaluator1_.loadScriptString(selectionScript1_);
68			evaluator2_.loadScriptString(selectionScript2_);
69
70			//if selection is static, we only need to evaluate it once
71			if (!evaluator1_.isDynamic()) {
72			seleMan1_.setSelectionSet(evaluator1_.evaluate());
73			validateSelection(seleMan1_);
74			}
75
76			if (!evaluator2_.isDynamic()) {
77			seleMan2_.setSelectionSet(evaluator2_.evaluate());
78			validateSelection(seleMan2_);
79			}
80
81			/*@todo Fix Me /
82			Globals* simParams = info_->getSimParams();
83			if (simParams->haveSampleTime()){
84			deltaTime_ = simParams->getSampleTime();
85			} else {
86			sprintf(painCave.errMsg,
87			"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
88			painCave.isFatal = 1;
89			simError();
90			}
91	tim	333
92	gezelter	1782	int nframes = bsMan_->getNFrames();
93			nTimeBins_ = nframes;
94			histogram_.resize(nTimeBins_);
95			count_.resize(nTimeBins_);
96			time_.resize(nTimeBins_);
97	tim	333
98	gezelter	1782	for (int i = 0; i < nTimeBins_; ++i) {
99			time_[i] = i * deltaTime_;
100	gezelter	1937	}
101	gezelter	1782	}
102	tim	333
103	gezelter	507	void TimeCorrFunc::doCorrelate() {
104	tim	333	preCorrelate();
105
106			int nblocks = bsMan_->getNBlocks();
107
108			for (int i = 0; i < nblocks; ++i) {
109	gezelter	507	bsMan_->loadBlock(i);
110	tim	351
111	gezelter	507	for (int j = i; j < nblocks; ++j) {
112			bsMan_->loadBlock(j);
113			correlateBlocks(i, j);
114			bsMan_->unloadBlock(j);
115			}
116	tim	351
117	gezelter	507	bsMan_->unloadBlock(i);
118	tim	333	}
119
120			postCorrelate();
121
122			writeCorrelate();
123	gezelter	507	}
124	tim	333
125	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
126	tim	333
127	tim	334	int jstart, jend;
128	gezelter	1937	RealType i_t, j_t;
129	tim	333
130	tim	334	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
131	tim	333
132	tim	334	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
133			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
134	tim	333
135	tim	334	jend = snapshotBlock2.second;
136
137			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
138	gezelter	1937
139	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
140			updateFrame(i);
141	tim	334
142	gezelter	1811	if (evaluator1_.isDynamic()) {
143	gezelter	1816	seleMan1_.clearSelection();
144			seleMan1_.setSelectionSet(evaluator1_.evaluate(i));
145	gezelter	1811	}
146
147	gezelter	507	// if the two blocks are the same, we don't want to correlate
148			// backwards in time, so start j at the same frame as i
149			if (block1 == block2) {
150	tim	334	jstart = i;
151	gezelter	507	} else {
152			jstart = snapshotBlock2.first;
153			}
154	gezelter	1937
155			i_t = bsMan_->getSnapshot(i)->getTime();
156
157	gezelter	507	for(int j = jstart; j < jend; ++j) {
158	gezelter	1937
159			// Perform a sanity check on the actual configuration times to
160			// make sure the configurations are spaced the same amount the
161			// sample time said they were spaced:
162
163			j_t = bsMan_->getSnapshot(j)->getTime();
164
165			if ( fabs( (j_t - i_t) - (j-i)*deltaTime_ ) > 1.0e-4 ) {
166			sprintf(painCave.errMsg,
167			"TimeCorrFunc::correlateBlocks Error: sampleTime (%f)\n"
168			"\tin %s does not match actual time-spacing between\n"
169			"\tconfigurations %d (t = %f) and %d (t = %f).\n",
170			deltaTime_, dumpFilename_.c_str(), i, i_t, j, j_t);
171			painCave.isFatal = 1;
172			simError();
173			}
174
175	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
176			updateFrame(j);
177	gezelter	1811	if (evaluator2_.isDynamic()) {
178	gezelter	1816	seleMan2_.clearSelection();
179			seleMan2_.setSelectionSet(evaluator2_.evaluate(j));
180	gezelter	1811	}
181
182	gezelter	507	correlateFrames(i, j);
183			}
184	tim	333	}
185	gezelter	507	}
186	tim	333
187	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
188	tim	333	Molecule* mol;
189			RigidBody* rb;
190			SimInfo::MoleculeIterator mi;
191			Molecule::RigidBodyIterator rbIter;
192			/** @todo need improvement */
193			if (storageLayout_ & DataStorage::dslPosition) {
194	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
195			mol = info_->nextMolecule(mi)) {
196	tim	333
197	gezelter	507	//change the positions of atoms which belong to the rigidbodies
198	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
199			rb = mol->nextRigidBody(rbIter)) {
200	gezelter	507	rb->updateAtoms(frame);
201			}
202			}
203	tim	333	}
204
205			if (storageLayout_ & DataStorage::dslVelocity) {
206	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
207			mol = info_->nextMolecule(mi)) {
208
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->updateAtomVel(frame);
213			}
214	gezelter	1782	}
215			}
216	gezelter	507	}
217	tim	333
218
219	gezelter	507	void TimeCorrFunc::preCorrelate() {
220	gezelter	1782	fill(histogram_.begin(), histogram_.end(), 0.0);
221			fill(count_.begin(), count_.end(), 0);
222	gezelter	507	}
223	tim	333
224	gezelter	507	void TimeCorrFunc::postCorrelate() {
225	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
226	gezelter	507	if (count_[i] > 0) {
227			histogram_[i] /= count_[i];
228	gezelter	1815	} else {
229			histogram_[i] = 0;
230	gezelter	507	}
231	tim	333	}
232	gezelter	507	}
233	tim	333
234
235	gezelter	507	void TimeCorrFunc::writeCorrelate() {
236	gezelter	1782	ofstream ofs(outputFilename_.c_str());
237	tim	333
238			if (ofs.is_open()) {
239
240	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
241	gezelter	1782	ofs << "#selection script1: \"" << selectionScript1_ ;
242			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
243	gezelter	507	ofs << "#extra information: " << extra_ << "\n";
244			ofs << "#time\tcorrVal\n";
245	tim	333
246	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
247			ofs << time_[i] << "\t" << histogram_[i] << "\n";
248			}
249	tim	333
250			} else {
251	gezelter	507	sprintf(painCave.errMsg,
252	gezelter	1782	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n",
253			outputFilename_.c_str());
254	gezelter	507	painCave.isFatal = 1;
255			simError();
256	tim	333	}
257
258			ofs.close();
259	gezelter	507	}
260	tim	333
261			}