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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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)
    : info_(info), storageLayout_(storageLayout), dumpFilename_(filename), 
      selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), 
      evaluator2_(info), seleMan1_(info), seleMan2_(info) {
    
    int nAtoms = info->getNGlobalAtoms();
    int nRigidBodies = info->getNGlobalRigidBodies();
    int nStuntDoubles =   nAtoms + nRigidBodies;
    
    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
    set<AtomType*>::iterator i;
    bool hasDirectionalAtom = false;
    bool hasMultipole = false;    
    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
      if ((*i)->isDirectional()){
        hasDirectionalAtom = true;
      }
      if ((*i)->isMultipole()){
        hasMultipole = true;
      }
    }
    
    if (nRigidBodies > 0 || hasDirectionalAtom) {
      storageLayout_ |= DataStorage::dslAmat;
      if(storageLayout_ & DataStorage::dslVelocity) {
        storageLayout_ |= DataStorage::dslAngularMomentum;
      }
      if (storageLayout_ & DataStorage::dslForce) {
        storageLayout_ |= DataStorage::dslTorque;
      }
    }
    if (hasMultipole) {
      storageLayout_ |= DataStorage::dslElectroFrame;
    }
    
    bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
    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:	1535
Committed:	Fri Dec 31 18:31:56 2010 UTC (14 years, 4 months ago) by gezelter
File size:	8405 byte(s)
Log Message:	Well, it compiles and builds, but still has a bus error at runtime.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	333	*/
41
42			#include "applications/dynamicProps/TimeCorrFunc.hpp"
43			#include "utils/simError.h"
44			#include "primitives/Molecule.hpp"
45	gezelter	1535	using namespace std;
46	gezelter	1390	namespace OpenMD {
47	tim	333
48	gezelter	1535	TimeCorrFunc::TimeCorrFunc(SimInfo* info, const string& filename,
49			const string& sele1, const string& sele2,
50			int storageLayout)
51			: info_(info), storageLayout_(storageLayout), dumpFilename_(filename),
52			selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info),
53			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
54	tim	333
55	gezelter	1535	int nAtoms = info->getNGlobalAtoms();
56			int nRigidBodies = info->getNGlobalRigidBodies();
57			int nStuntDoubles = nAtoms + nRigidBodies;
58
59			set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
60			set<AtomType*>::iterator i;
61			bool hasDirectionalAtom = false;
62			bool hasMultipole = false;
63			for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
64			if ((*i)->isDirectional()){
65			hasDirectionalAtom = true;
66	gezelter	507	}
67	gezelter	1535	if ((*i)->isMultipole()){
68			hasMultipole = true;
69	gezelter	507	}
70	gezelter	1535	}
71	tim	334
72	gezelter	1535	if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
73			storageLayout_ \|= DataStorage::dslAmat;
74			if(storageLayout_ & DataStorage::dslVelocity) {
75			storageLayout_ \|= DataStorage::dslAngularMomentum;
76	gezelter	507	}
77	gezelter	1535	if (storageLayout_ & DataStorage::dslForce) {
78			storageLayout_ \|= DataStorage::dslTorque;
79	gezelter	507	}
80	gezelter	1535	}
81			if (hasMultipole) {
82			storageLayout_ \|= DataStorage::dslElectroFrame;
83			}
84	tim	333
85	gezelter	1535	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
86			info_->setSnapshotManager(bsMan_);
87
88			evaluator1_.loadScriptString(selectionScript1_);
89			evaluator2_.loadScriptString(selectionScript2_);
90
91			//if selection is static, we only need to evaluate it once
92			if (!evaluator1_.isDynamic()) {
93			seleMan1_.setSelectionSet(evaluator1_.evaluate());
94			validateSelection(seleMan1_);
95			} else {
96			sprintf(painCave.errMsg,
97			"TimeCorrFunc Error: dynamic selection is not supported\n");
98			painCave.isFatal = 1;
99			simError();
100			}
101
102			if (!evaluator2_.isDynamic()) {
103			seleMan2_.setSelectionSet(evaluator2_.evaluate());
104			validateSelection(seleMan2_);
105			} else {
106			sprintf(painCave.errMsg,
107			"TimeCorrFunc Error: dynamic selection is not supported\n");
108			painCave.isFatal = 1;
109			simError();
110			}
111
112	tim	333
113
114	gezelter	1535	/*@todo Fix Me /
115			Globals* simParams = info_->getSimParams();
116			if (simParams->haveSampleTime()){
117			deltaTime_ = simParams->getSampleTime();
118			} else {
119			sprintf(painCave.errMsg,
120			"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
121			painCave.isFatal = 1;
122			simError();
123			}
124	tim	333
125	gezelter	1535	int nframes = bsMan_->getNFrames();
126			nTimeBins_ = nframes;
127			histogram_.resize(nTimeBins_);
128			count_.resize(nTimeBins_);
129			time_.resize(nTimeBins_);
130	tim	333
131	gezelter	1535	for (int i = 0; i < nTimeBins_; ++i) {
132			time_[i] = i * deltaTime_;
133			}
134	gezelter	507
135	gezelter	1535	}
136	tim	333
137
138	gezelter	507	void TimeCorrFunc::doCorrelate() {
139	tim	333	preCorrelate();
140
141			int nblocks = bsMan_->getNBlocks();
142
143			for (int i = 0; i < nblocks; ++i) {
144	gezelter	507	bsMan_->loadBlock(i);
145	tim	351
146	gezelter	507	for (int j = i; j < nblocks; ++j) {
147			bsMan_->loadBlock(j);
148			correlateBlocks(i, j);
149			bsMan_->unloadBlock(j);
150			}
151	tim	351
152	gezelter	507	bsMan_->unloadBlock(i);
153	tim	333	}
154
155			postCorrelate();
156
157			writeCorrelate();
158	gezelter	507	}
159	tim	333
160	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
161	tim	333
162	tim	334	int jstart, jend;
163	tim	333
164	tim	334	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
165	tim	333
166	tim	334	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
167			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
168	tim	333
169	tim	334	jend = snapshotBlock2.second;
170
171			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
172
173	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
174			updateFrame(i);
175	tim	334
176	gezelter	507	// if the two blocks are the same, we don't want to correlate
177			// backwards in time, so start j at the same frame as i
178			if (block1 == block2) {
179	tim	334	jstart = i;
180	gezelter	507	} else {
181			jstart = snapshotBlock2.first;
182			}
183	tim	334
184	gezelter	507	for(int j = jstart; j < jend; ++j) {
185			//update the position or velocity of the atoms belong to rigid bodies
186			updateFrame(j);
187	tim	334
188	gezelter	507	correlateFrames(i, j);
189			}
190	tim	333	}
191	gezelter	507	}
192	tim	333
193	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
194	tim	333	Molecule* mol;
195			RigidBody* rb;
196			SimInfo::MoleculeIterator mi;
197			Molecule::RigidBodyIterator rbIter;
198
199			/** @todo need improvement */
200			if (storageLayout_ & DataStorage::dslPosition) {
201	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
202			mol = info_->nextMolecule(mi)) {
203	tim	333
204	gezelter	507	//change the positions of atoms which belong to the rigidbodies
205	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
206			rb = mol->nextRigidBody(rbIter)) {
207	gezelter	507	rb->updateAtoms(frame);
208			}
209			}
210	tim	333	}
211
212			if (storageLayout_ & DataStorage::dslVelocity) {
213	xsun	1183	for (mol = info_->beginMolecule(mi); mol != NULL;
214			mol = info_->nextMolecule(mi)) {
215
216	gezelter	507	//change the positions of atoms which belong to the rigidbodies
217	xsun	1183	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
218			rb = mol->nextRigidBody(rbIter)) {
219	gezelter	507	rb->updateAtomVel(frame);
220			}
221	gezelter	1535	}
222			}
223	gezelter	507	}
224	tim	333
225
226	gezelter	507	void TimeCorrFunc::preCorrelate() {
227	gezelter	1535	fill(histogram_.begin(), histogram_.end(), 0.0);
228			fill(count_.begin(), count_.end(), 0);
229	gezelter	507	}
230	tim	333
231	gezelter	507	void TimeCorrFunc::postCorrelate() {
232	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
233	gezelter	507	if (count_[i] > 0) {
234			histogram_[i] /= count_[i];
235			}
236	tim	333	}
237	gezelter	507	}
238	tim	333
239
240	gezelter	507	void TimeCorrFunc::writeCorrelate() {
241	gezelter	1535	ofstream ofs(outputFilename_.c_str());
242	tim	333
243			if (ofs.is_open()) {
244
245	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
246	gezelter	1535	ofs << "#selection script1: \"" << selectionScript1_ ;
247			ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
248	gezelter	507	ofs << "#extra information: " << extra_ << "\n";
249			ofs << "#time\tcorrVal\n";
250	tim	333
251	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
252			ofs << time_[i] << "\t" << histogram_[i] << "\n";
253			}
254	tim	333
255			} else {
256	gezelter	507	sprintf(painCave.errMsg,
257	gezelter	1535	"TimeCorrFunc::writeCorrelate Error: fail to open %s\n",
258			outputFilename_.c_str());
259	gezelter	507	painCave.isFatal = 1;
260			simError();
261	tim	333	}
262
263			ofs.close();
264	gezelter	507	}
265	tim	333
266			}