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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include "applications/dynamicProps/TimeCorrFunc.hpp"
#include "utils/simError.h"
#include "primitives/Molecule.hpp"
namespace oopse {

  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 (hasMultipole) {
        storageLayout_ |= DataStorage::dslElectroFrame;
        if (nRigidBodies > 0) { 
          storageLayout_ |= DataStorage::dslAngularMomentum;        
        }
      }
      if(nRigidBodies > 0 && storageLayout_ & DataStorage::dslVelocity) {
        storageLayout_ |= DataStorage::dslAngularMomentum;
      }
        
      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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 3 months ago) by gezelter
File size:	8348 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	tim	2017	/*
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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "applications/dynamicProps/TimeCorrFunc.hpp"
43			#include "utils/simError.h"
44			#include "primitives/Molecule.hpp"
45			namespace oopse {
46
47	gezelter	2204	TimeCorrFunc::TimeCorrFunc(SimInfo* info, const std::string& filename,
48			const std::string& sele1, const std::string& sele2, int storageLayout)
49	tim	2017	: info_(info), storageLayout_(storageLayout), dumpFilename_(filename), selectionScript1_(sele1),
50			selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
51
52	gezelter	2204	int nAtoms = info->getNGlobalAtoms();
53			int nRigidBodies = info->getNGlobalRigidBodies();
54			int nStuntDoubles = nAtoms + nRigidBodies;
55	tim	2017
56	gezelter	2204	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	2017	if ((*i)->isDirectional()){
62	gezelter	2204	hasDirectionalAtom = true;
63	tim	2017	}
64			if ((*i)->isMultipole()){
65	gezelter	2204	hasMultipole = true;
66	tim	2017	}
67	gezelter	2204	}
68	tim	2017
69	gezelter	2204	if (nRigidBodies > 0 \|\| hasDirectionalAtom) {
70	tim	2017	storageLayout_ \|= DataStorage::dslAmat;
71	gezelter	2204	}
72			if (hasMultipole) {
73	tim	2017	storageLayout_ \|= DataStorage::dslElectroFrame;
74			if (nRigidBodies > 0) {
75	gezelter	2204	storageLayout_ \|= DataStorage::dslAngularMomentum;
76	tim	2017	}
77	gezelter	2204	}
78			if(nRigidBodies > 0 && storageLayout_ & DataStorage::dslVelocity) {
79	tim	2037	storageLayout_ \|= DataStorage::dslAngularMomentum;
80	gezelter	2204	}
81	tim	2017
82	gezelter	2204	bsMan_ = new BlockSnapshotManager(info, dumpFilename_, storageLayout_);
83			info_->setSnapshotManager(bsMan_);
84	tim	2017
85	gezelter	2204	evaluator1_.loadScriptString(selectionScript1_);
86			evaluator2_.loadScriptString(selectionScript2_);
87	tim	2018
88	gezelter	2204	//if selection is static, we only need to evaluate it once
89			if (!evaluator1_.isDynamic()) {
90	tim	2017	seleMan1_.setSelectionSet(evaluator1_.evaluate());
91			validateSelection(seleMan1_);
92	gezelter	2204	} else {
93			sprintf(painCave.errMsg,
94	tim	2017	"TimeCorrFunc Error: dynamic selection is not supported\n");
95	gezelter	2204	painCave.isFatal = 1;
96			simError();
97			}
98	tim	2017
99	gezelter	2204	if (!evaluator2_.isDynamic()) {
100	tim	2017	seleMan2_.setSelectionSet(evaluator2_.evaluate());
101			validateSelection(seleMan2_);
102	gezelter	2204	} else {
103			sprintf(painCave.errMsg,
104	tim	2017	"TimeCorrFunc Error: dynamic selection is not supported\n");
105	gezelter	2204	painCave.isFatal = 1;
106			simError();
107			}
108	tim	2017
109
110
111	gezelter	2204	/*@todo Fix Me /
112			Globals* simParams = info_->getSimParams();
113			if (simParams->haveSampleTime()){
114	tim	2017	deltaTime_ = simParams->getSampleTime();
115	gezelter	2204	} else {
116			sprintf(painCave.errMsg,
117	tim	2017	"TimeCorrFunc::writeCorrelate Error: can not figure out deltaTime\n");
118	gezelter	2204	painCave.isFatal = 1;
119			simError();
120			}
121	tim	2017
122	gezelter	2204	int nframes = bsMan_->getNFrames();
123			nTimeBins_ = nframes;
124			histogram_.resize(nTimeBins_);
125			count_.resize(nTimeBins_);
126			time_.resize(nTimeBins_);
127	tim	2017
128	gezelter	2204	for (int i = 0; i < nTimeBins_; ++i) {
129	tim	2017	time_[i] = i * deltaTime_;
130	gezelter	2204	}
131
132	tim	2017	}
133
134
135	gezelter	2204	void TimeCorrFunc::doCorrelate() {
136	tim	2017	preCorrelate();
137
138			int nblocks = bsMan_->getNBlocks();
139
140			for (int i = 0; i < nblocks; ++i) {
141	gezelter	2204	bsMan_->loadBlock(i);
142	tim	2035
143	gezelter	2204	for (int j = i; j < nblocks; ++j) {
144			bsMan_->loadBlock(j);
145			correlateBlocks(i, j);
146			bsMan_->unloadBlock(j);
147			}
148	tim	2035
149	gezelter	2204	bsMan_->unloadBlock(i);
150	tim	2017	}
151
152			postCorrelate();
153
154			writeCorrelate();
155	gezelter	2204	}
156	tim	2017
157	gezelter	2204	void TimeCorrFunc::correlateBlocks(int block1, int block2) {
158	tim	2017
159	tim	2018	int jstart, jend;
160	tim	2017
161	tim	2018	assert(bsMan_->isBlockActive(block1) && bsMan_->isBlockActive(block2));
162	tim	2017
163	tim	2018	SnapshotBlock snapshotBlock1 = bsMan_->getSnapshotBlock(block1);
164			SnapshotBlock snapshotBlock2 = bsMan_->getSnapshotBlock(block2);
165	tim	2017
166	tim	2018	jend = snapshotBlock2.second;
167
168			for (int i = snapshotBlock1.first; i < snapshotBlock1.second; ++i) {
169
170	gezelter	2204	//update the position or velocity of the atoms belong to rigid bodies
171			updateFrame(i);
172	tim	2018
173	gezelter	2204	// 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	2018	jstart = i;
177	gezelter	2204	} else {
178			jstart = snapshotBlock2.first;
179			}
180	tim	2018
181	gezelter	2204	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	2018
185	gezelter	2204	correlateFrames(i, j);
186			}
187	tim	2017	}
188	gezelter	2204	}
189	tim	2017
190	gezelter	2204	void TimeCorrFunc::updateFrame(int frame){
191	tim	2017	Molecule* mol;
192			RigidBody* rb;
193			SimInfo::MoleculeIterator mi;
194			Molecule::RigidBodyIterator rbIter;
195
196			/** @todo need improvement */
197			if (storageLayout_ & DataStorage::dslPosition) {
198	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
199	tim	2017
200	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
201			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
202			rb->updateAtoms(frame);
203			}
204			}
205	tim	2017	}
206
207			if (storageLayout_ & DataStorage::dslVelocity) {
208	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
209	tim	2017
210	gezelter	2204	//change the positions of atoms which belong to the rigidbodies
211			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
212			rb->updateAtomVel(frame);
213			}
214			}
215	tim	2017
216			}
217
218	gezelter	2204	}
219	tim	2017
220
221	gezelter	2204	void TimeCorrFunc::preCorrelate() {
222	tim	2017	std::fill(histogram_.begin(), histogram_.end(), 0.0);
223			std::fill(count_.begin(), count_.end(), 0);
224	gezelter	2204	}
225	tim	2017
226	gezelter	2204	void TimeCorrFunc::postCorrelate() {
227	tim	2017	for (int i =0 ; i < nTimeBins_; ++i) {
228	gezelter	2204	if (count_[i] > 0) {
229			histogram_[i] /= count_[i];
230			}
231	tim	2017	}
232	gezelter	2204	}
233	tim	2017
234
235	gezelter	2204	void TimeCorrFunc::writeCorrelate() {
236	tim	2017	std::ofstream ofs(outputFilename_.c_str());
237
238			if (ofs.is_open()) {
239
240	gezelter	2204	ofs << "#" << getCorrFuncType() << "\n";
241			ofs << "#selection script1: \"" << selectionScript1_ <<"\"\tselection script2: \"" << selectionScript2_ << "\"\n";
242			ofs << "#extra information: " << extra_ << "\n";
243			ofs << "#time\tcorrVal\n";
244	tim	2017
245	gezelter	2204	for (int i = 0; i < nTimeBins_; ++i) {
246			ofs << time_[i] << "\t" << histogram_[i] << "\n";
247			}
248	tim	2017
249			} else {
250	gezelter	2204	sprintf(painCave.errMsg,
251			"TimeCorrFunc::writeCorrelate Error: fail to open %s\n", outputFilename_.c_str());
252			painCave.isFatal = 1;
253			simError();
254	tim	2017	}
255
256			ofs.close();
257	gezelter	2204	}
258	tim	2017
259			}