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;

    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:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 3 months ago) by gezelter
File size:	7926 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1787
60	gezelter	1838	// 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	1812	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_,
67			memSize_);
68	gezelter	1535	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	1535	int nframes = bsMan_->getNFrames();
96			nTimeBins_ = nframes;
97			histogram_.resize(nTimeBins_);
98			count_.resize(nTimeBins_);
99			time_.resize(nTimeBins_);
100	tim	333
101	gezelter	1535	for (int i = 0; i < nTimeBins_; ++i) {
102			time_[i] = i * deltaTime_;
103			}
104	gezelter	507
105	gezelter	1535	}
106	tim	333
107
108	gezelter	507	void TimeCorrFunc::doCorrelate() {
109	tim	333	preCorrelate();
110
111			int nblocks = bsMan_->getNBlocks();
112
113			for (int i = 0; i < nblocks; ++i) {
114	gezelter	507	bsMan_->loadBlock(i);
115	tim	351
116	gezelter	507	for (int j = i; j < nblocks; ++j) {
117			bsMan_->loadBlock(j);
118			correlateBlocks(i, j);
119			bsMan_->unloadBlock(j);
120			}
121	tim	351
122	gezelter	507	bsMan_->unloadBlock(i);
123	tim	333	}
124
125			postCorrelate();
126
127			writeCorrelate();
128	gezelter	507	}
129	tim	333
130	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
131	tim	333
132	tim	334	int jstart, jend;
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
143	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
144			updateFrame(i);
145	tim	334
146	gezelter	1812	if (evaluator1_.isDynamic()) {
147	gezelter	1831	seleMan1_.clearSelection();
148			seleMan1_.setSelectionSet(evaluator1_.evaluate(i));
149	gezelter	1812	}
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	tim	334
159	gezelter	507	for(int j = jstart; j < jend; ++j) {
160			//update the position or velocity of the atoms belong to rigid bodies
161			updateFrame(j);
162	gezelter	1812	if (evaluator2_.isDynamic()) {
163	gezelter	1831	seleMan2_.clearSelection();
164			seleMan2_.setSelectionSet(evaluator2_.evaluate(j));
165	gezelter	1812	}
166
167	gezelter	507	correlateFrames(i, j);
168			}
169	tim	333	}
170	gezelter	507	}
171	tim	333
172	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
173	tim	333	Molecule* mol;
174			RigidBody* rb;
175			SimInfo::MoleculeIterator mi;
176			Molecule::RigidBodyIterator rbIter;
177			/** @todo need improvement */
178			if (storageLayout_ & DataStorage::dslPosition) {
179	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
180			mol = info_->nextMolecule(mi)) {
181	tim	333
182	gezelter	507	//change the positions of atoms which belong to the rigidbodies
183	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
184			rb = mol->nextRigidBody(rbIter)) {
185	gezelter	507	rb->updateAtoms(frame);
186			}
187			}
188	tim	333	}
189
190			if (storageLayout_ & DataStorage::dslVelocity) {
191	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
192			mol = info_->nextMolecule(mi)) {
193
194	gezelter	507	//change the positions of atoms which belong to the rigidbodies
195	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
196			rb = mol->nextRigidBody(rbIter)) {
197	gezelter	507	rb->updateAtomVel(frame);
198			}
199	gezelter	1535	}
200			}
201	gezelter	507	}
202	tim	333
203
204	gezelter	507	void TimeCorrFunc::preCorrelate() {
205	gezelter	1535	fill(histogram_.begin(), histogram_.end(), 0.0);
206			fill(count_.begin(), count_.end(), 0);
207	gezelter	507	}
208	tim	333
209	gezelter	507	void TimeCorrFunc::postCorrelate() {
210	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
211	gezelter	507	if (count_[i] > 0) {
212			histogram_[i] /= count_[i];
213	gezelter	1831	} else {
214			histogram_[i] = 0;
215	gezelter	507	}
216	tim	333	}
217	gezelter	507	}
218	tim	333
219
220	gezelter	507	void TimeCorrFunc::writeCorrelate() {
221	gezelter	1535	ofstream ofs(outputFilename_.c_str());
222	tim	333
223			if (ofs.is_open()) {
224
225	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
226	gezelter	1535	ofs << "#selection script1: \"" << selectionScript1_ ;
227			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
228	gezelter	507	ofs << "#extra information: " << extra_ << "\n";
229			ofs << "#time\tcorrVal\n";
230	tim	333
231	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
232			ofs << time_[i] << "\t" << histogram_[i] << "\n";
233			}
234	tim	333
235			} else {
236	gezelter	507	sprintf(painCave.errMsg,
237	gezelter	1535	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n",
238			outputFilename_.c_str());
239	gezelter	507	painCave.isFatal = 1;
240			simError();
241	tim	333	}
242
243			ofs.close();
244	gezelter	507	}
245	tim	333
246			}