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"
namespace OpenMD {

  TimeCorrFunc::TimeCorrFunc(SimInfo* info, const std::string& filename, 
                             const std::string& sele1, const std::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;

      std::set<AtomType*> atomTypes = info->getUniqueAtomTypes();
      std::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() {
    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::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() {
    std::ofstream ofs(outputFilename_.c_str());

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#selection script1: \"" << selectionScript1_ <<"\"\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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 10 months ago) by chuckv
File size:	8368 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	1390	namespace OpenMD {
46	tim	333
47	gezelter	507	TimeCorrFunc::TimeCorrFunc(SimInfo* info, const std::string& filename,
48			const std::string& sele1, const std::string& sele2, int storageLayout)
49	tim	333	: info_(info), storageLayout_(storageLayout), dumpFilename_(filename), selectionScript1_(sele1),
50			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
51
52	gezelter	507	int nAtoms = info->getNGlobalAtoms();
53			int nRigidBodies = info->getNGlobalRigidBodies();
54			int nStuntDoubles = nAtoms + nRigidBodies;
55	tim	333
56	gezelter	507	std::set<AtomType*> atomTypes = info->getUniqueAtomTypes();
57			std::set<AtomType*>::iterator i;
58			bool hasDirectionalAtom = false;
59			bool hasMultipole = false;
60			for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
61	tim	333	if ((*i)->isDirectional()){
62	gezelter	507	hasDirectionalAtom = true;
63	tim	333	}
64			if ((*i)->isMultipole()){
65	gezelter	507	hasMultipole = true;
66	tim	333	}
67	gezelter	507	}
68	tim	333
69	gezelter	507	if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
70	tim	333	storageLayout_ \|= DataStorage::dslAmat;
71	xsun	1183	if(storageLayout_ & DataStorage::dslVelocity) {
72			storageLayout_ \|= DataStorage::dslAngularMomentum;
73			}
74			if (storageLayout_ & DataStorage::dslForce) {
75			storageLayout_ \|= DataStorage::dslTorque;
76			}
77	gezelter	507	}
78			if (hasMultipole) {
79	tim	333	storageLayout_ \|= DataStorage::dslElectroFrame;
80	gezelter	507	}
81	tim	333
82	gezelter	507	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
83			info_->setSnapshotManager(bsMan_);
84	tim	333
85	gezelter	507	evaluator1_.loadScriptString(selectionScript1_);
86			evaluator2_.loadScriptString(selectionScript2_);
87	tim	334
88	gezelter	507	//if selection is static, we only need to evaluate it once
89			if (!evaluator1_.isDynamic()) {
90	tim	333	seleMan1_.setSelectionSet(evaluator1_.evaluate());
91			validateSelection(seleMan1_);
92	gezelter	507	} else {
93			sprintf(painCave.errMsg,
94	tim	333	"TimeCorrFunc Error: dynamic selection is not supported\n");
95	gezelter	507	painCave.isFatal = 1;
96			simError();
97			}
98	tim	333
99	gezelter	507	if (!evaluator2_.isDynamic()) {
100	tim	333	seleMan2_.setSelectionSet(evaluator2_.evaluate());
101			validateSelection(seleMan2_);
102	gezelter	507	} else {
103			sprintf(painCave.errMsg,
104	tim	333	"TimeCorrFunc Error: dynamic selection is not supported\n");
105	gezelter	507	painCave.isFatal = 1;
106			simError();
107			}
108	tim	333
109
110
111	gezelter	507	/*@todo Fix Me /
112			Globals* simParams = info_->getSimParams();
113			if (simParams->haveSampleTime()){
114	tim	333	deltaTime_ = simParams->getSampleTime();
115	gezelter	507	} else {
116			sprintf(painCave.errMsg,
117	tim	333	"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
118	gezelter	507	painCave.isFatal = 1;
119			simError();
120			}
121	tim	333
122	gezelter	507	int nframes = bsMan_->getNFrames();
123			nTimeBins_ = nframes;
124			histogram_.resize(nTimeBins_);
125			count_.resize(nTimeBins_);
126			time_.resize(nTimeBins_);
127	tim	333
128	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
129	tim	333	time_[i] = i * deltaTime_;
130	gezelter	507	}
131
132	tim	333	}
133
134
135	gezelter	507	void TimeCorrFunc::doCorrelate() {
136	tim	333	preCorrelate();
137
138			int nblocks = bsMan_->getNBlocks();
139
140			for (int i = 0; i < nblocks; ++i) {
141	gezelter	507	bsMan_->loadBlock(i);
142	tim	351
143	gezelter	507	for (int j = i; j < nblocks; ++j) {
144			bsMan_->loadBlock(j);
145			correlateBlocks(i, j);
146			bsMan_->unloadBlock(j);
147			}
148	tim	351
149	gezelter	507	bsMan_->unloadBlock(i);
150	tim	333	}
151
152			postCorrelate();
153
154			writeCorrelate();
155	gezelter	507	}
156	tim	333
157	gezelter	507	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
158	tim	333
159	tim	334	int jstart, jend;
160	tim	333
161	tim	334	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
162	tim	333
163	tim	334	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
164			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
165	tim	333
166	tim	334	jend = snapshotBlock2.second;
167
168			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
169
170	gezelter	507	//update the position or velocity of the atoms belong to rigid bodies
171			updateFrame(i);
172	tim	334
173	gezelter	507	// if the two blocks are the same, we don't want to correlate
174			// backwards in time, so start j at the same frame as i
175			if (block1 == block2) {
176	tim	334	jstart = i;
177	gezelter	507	} else {
178			jstart = snapshotBlock2.first;
179			}
180	tim	334
181	gezelter	507	for(int j = jstart; j < jend; ++j) {
182			//update the position or velocity of the atoms belong to rigid bodies
183			updateFrame(j);
184	tim	334
185	gezelter	507	correlateFrames(i, j);
186			}
187	tim	333	}
188	gezelter	507	}
189	tim	333
190	gezelter	507	void TimeCorrFunc::updateFrame(int frame){
191	tim	333	Molecule* mol;
192			RigidBody* rb;
193			SimInfo::MoleculeIterator mi;
194			Molecule::RigidBodyIterator rbIter;
195
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			}
219	xsun	1183
220	tim	333	}
221
222	gezelter	507	}
223	tim	333
224
225	gezelter	507	void TimeCorrFunc::preCorrelate() {
226	tim	333	std::fill(histogram_.begin(), histogram_.end(), 0.0);
227			std::fill(count_.begin(), count_.end(), 0);
228	gezelter	507	}
229	tim	333
230	gezelter	507	void TimeCorrFunc::postCorrelate() {
231	tim	333	for (int i =0 ; i < nTimeBins_; ++i) {
232	gezelter	507	if (count_[i] > 0) {
233			histogram_[i] /= count_[i];
234			}
235	tim	333	}
236	gezelter	507	}
237	tim	333
238
239	gezelter	507	void TimeCorrFunc::writeCorrelate() {
240	tim	333	std::ofstream ofs(outputFilename_.c_str());
241
242			if (ofs.is_open()) {
243
244	gezelter	507	ofs << "#" << getCorrFuncType() << "\n";
245			ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
246			ofs << "#extra information: " << extra_ << "\n";
247			ofs << "#time\tcorrVal\n";
248	tim	333
249	gezelter	507	for (int i = 0; i < nTimeBins_; ++i) {
250			ofs << time_[i] << "\t" << histogram_[i] << "\n";
251			}
252	tim	333
253			} else {
254	gezelter	507	sprintf(painCave.errMsg,
255			"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
256			painCave.isFatal = 1;
257			simError();
258	tim	333	}
259
260			ofs.close();
261	gezelter	507	}
262	tim	333
263			}