applications/dynamicProps/ActionCorrFunc.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/ActionCorrFunc.hpp"
#include "utils/OOPSEConstant.hpp"
#include "brains/ForceManager.hpp"
#include "brains/Thermo.hpp"

namespace oopse {

  // We need all of the positions, velocities, etc. so that we can
  // recalculate pressures and actions on the fly:
  ActionCorrFunc::ActionCorrFunc(SimInfo* info, const std::string& filename, 
                                 const std::string& sele1, 
                                 const std::string& sele2)
    : FrameTimeCorrFunc(info, filename, sele1, sele2, 
                        DataStorage::dslPosition | 
                        DataStorage::dslVelocity |
                        DataStorage::dslForce ){

      setCorrFuncType("ActionCorrFunc");
      setOutputName(getPrefix(dumpFilename_) + ".action");
      histogram_.resize(nTimeBins_); 
      count_.resize(nTimeBins_);
    }

  void ActionCorrFunc::correlateFrames(int frame1, int frame2) {
    Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
    Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
    assert(snapshot1 && snapshot2);

    RealType time1 = snapshot1->getTime();
    RealType time2 = snapshot2->getTime();
    RealType vol1 = snapshot1->getVolume();
    RealType vol2 = snapshot2->getVolume();
       
    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);

    //std::cerr << "times = " << time1 << " " << time2 << "\n";
    //std::cerr << "vols = " << vol1 << " " << vol2 << "\n";

    int i;
    int j;

    StuntDouble* sd1;

    Mat3x3d actionTensor1(0.0);
    //std::cerr << "at1 = " << actionTensor1 << "\n";
    Mat3x3d actionTensor2(0.0);
    //std::cerr << "at2 = " << actionTensor2 << "\n";

    for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL;
         sd1 = seleMan1_.nextSelected(i)) {
      //std::cerr << "found a SD\n";
      Vector3d r1 = sd1->getPos(frame1);
      //std::cerr << "r1 = " << r1 << "\n";
      Vector3d v1 = sd1->getVel(frame1);
      //std::cerr << "v1 = " << v1 << "\n";
      Vector3d r2 = sd1->getPos(frame2);
      //std::cerr << "r2 = " << r2 << "\n";
      Vector3d v2 = sd1->getVel(frame2);
      //std::cerr << "v2 = " << v2 << "\n";

      RealType m = sd1->getMass();

      //std::cerr << "m = " << m << "\n";

      actionTensor1 += m*outProduct(r1, v1);
      actionTensor2 += m*outProduct(r2, v2);
    }

    actionTensor1 /= vol1;
    //std::cerr << "at1 = " << actionTensor1 << "\n";
    actionTensor2 /= vol2;
    //std::cerr << "at2 = " << actionTensor2 << "\n";

    Mat3x3d corrTensor(0.0);
    //std::cerr << "ct = " << corrTensor << "\n";
    RealType thisTerm;

    for (i = 0; i < 3; i++) {
      for (j = 0; j < 3; j++) {
       
        //std::cerr << "i, j = " << i << " " << j << "\n"; 
        if (i == j) {
          thisTerm = (actionTensor2(i, j) - actionTensor1(i, j) - avePress_ *(time2-time1));
          std::cerr << "at1, at2 = " << actionTensor1(i,j) << " " << actionTensor2(i,j) << " p = " << avePress_ << "\n";
        } else {
          thisTerm = (actionTensor2(i, j) - actionTensor1(i, j));
        }
        
        //std::cerr << "thisTerm = " << thisTerm << "\n"; 
        corrTensor(i, j) += thisTerm * thisTerm;
      }
    }

    //std::cerr << "ct = " << corrTensor << "\n";
    //std::cerr << "hist = " << histogram_[timeBin] << "\n";
    histogram_[timeBin] += corrTensor;    
    count_[timeBin]++;    
    
  }

  void ActionCorrFunc::postCorrelate() {
    for (int i =0 ; i < nTimeBins_; ++i) {
      if (count_[i] > 0) {
        histogram_[i] /= count_[i];
      }
    }
  }


  void ActionCorrFunc::preCorrelate() {
    // Fill the histogram with empty 3x3 matrices:
    std::fill(histogram_.begin(), histogram_.end(), Mat3x3d(0.0));
    // count array set to zero
    std::fill(count_.begin(), count_.end(), 0);

    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;

    // We'll need the force manager to compute forces for the average pressure
    ForceManager* forceMan = new ForceManager(info_);
    forceMan->init();

    // We'll need thermo to compute the pressures from the virial
    Thermo* thermo =  new Thermo(info_);

    // prepare the averages
    RealType pSum = 0.0;
    RealType vSum = 0.0;
    int nsamp = 0;

    // dump files can be enormous, so read them in block-by-block:
    int nblocks = bsMan_->getNBlocks();
    for (int i = 0; i < nblocks; ++i) {
      std::cerr << "block = " << i << "\n";
      bsMan_->loadBlock(i);
      assert(bsMan_->isBlockActive(i));      
      SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
      for (int j = block1.first; j < block1.second; ++j) {

        // go snapshot-by-snapshot through this block:
        Snapshot* snap = bsMan_->getSnapshot(j);
       
        // update the positions and velocities of the atoms belonging
        // to rigid bodies:

        updateFrame(j);

        // do the forces:
        forceMan->calcForces(true, true);
        // call thermo to get the pressure and volume.
        pSum += thermo->getPressure();
        vSum += thermo->getVolume();
        nsamp++;
        
      }
      bsMan_->unloadBlock(i);
    }

    avePress_ = pSum / ( OOPSEConstant::pressureConvert * (RealType)nsamp);
    aveVol_ = vSum / (RealType)nsamp;
    std::cout << "pAve = " << avePress_ << " vAve = " << aveVol_ << "\n";
  }   


  void ActionCorrFunc::writeCorrelate() {
    std::ofstream ofs(getOutputFileName().c_str());

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#time\tcorrTensor\txx\txy\txz\tyx\tyy\tyz\tzx\tzy\tzz\n";

      for (int i = 0; i < nTimeBins_; ++i) {
        ofs << time_[i] << "\t" << 
          histogram_[i](0,0) << "\t" <<
          histogram_[i](0,1) << "\t" <<
          histogram_[i](0,2) << "\t" <<
          histogram_[i](1,0) << "\t" <<
          histogram_[i](1,1) << "\t" <<
          histogram_[i](1,2) << "\t" <<
          histogram_[i](2,0) << "\t" <<
          histogram_[i](2,1) << "\t" <<
          histogram_[i](2,2) << "\t" << "\n";
      }
            
    } else {
      sprintf(painCave.errMsg,
              "ActionCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();        
    }

    ofs.close();    
  }

}
Revision:	1183
Committed:	Tue Oct 2 12:05:25 2007 UTC (18 years ago) by xsun
Original Path:	*trunk/src/applications/dynamicProps/ActionCorrFunc.cpp*
File size:	8141 byte(s)
Log Message:	Added: Action Correlation function (for viscosity), Directional RCorr (for non-spherical bodies) Modified: LCorr (for multiple axes)
#	User	Rev	Content
1	xsun	1183	/*
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/ActionCorrFunc.hpp"
43			#include "utils/OOPSEConstant.hpp"
44			#include "brains/ForceManager.hpp"
45			#include "brains/Thermo.hpp"
46
47			namespace oopse {
48
49			// We need all of the positions, velocities, etc. so that we can
50			// recalculate pressures and actions on the fly:
51			ActionCorrFunc::ActionCorrFunc(SimInfo* info, const std::string& filename,
52			const std::string& sele1,
53			const std::string& sele2)
54			: FrameTimeCorrFunc(info, filename, sele1, sele2,
55			DataStorage::dslPosition \|
56			DataStorage::dslVelocity \|
57			DataStorage::dslForce ){
58
59			setCorrFuncType("ActionCorrFunc");
60			setOutputName(getPrefix(dumpFilename_) + ".action");
61			histogram_.resize(nTimeBins_);
62			count_.resize(nTimeBins_);
63			}
64
65			void ActionCorrFunc::correlateFrames(int frame1, int frame2) {
66			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
67			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
68			assert(snapshot1 && snapshot2);
69
70			RealType time1 = snapshot1->getTime();
71			RealType time2 = snapshot2->getTime();
72			RealType vol1 = snapshot1->getVolume();
73			RealType vol2 = snapshot2->getVolume();
74
75			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
76
77			//std::cerr << "times = " << time1 << " " << time2 << "\n";
78			//std::cerr << "vols = " << vol1 << " " << vol2 << "\n";
79
80			int i;
81			int j;
82
83			StuntDouble* sd1;
84
85			Mat3x3d actionTensor1(0.0);
86			//std::cerr << "at1 = " << actionTensor1 << "\n";
87			Mat3x3d actionTensor2(0.0);
88			//std::cerr << "at2 = " << actionTensor2 << "\n";
89
90			for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL;
91			sd1 = seleMan1_.nextSelected(i)) {
92			//std::cerr << "found a SD\n";
93			Vector3d r1 = sd1->getPos(frame1);
94			//std::cerr << "r1 = " << r1 << "\n";
95			Vector3d v1 = sd1->getVel(frame1);
96			//std::cerr << "v1 = " << v1 << "\n";
97			Vector3d r2 = sd1->getPos(frame2);
98			//std::cerr << "r2 = " << r2 << "\n";
99			Vector3d v2 = sd1->getVel(frame2);
100			//std::cerr << "v2 = " << v2 << "\n";
101
102			RealType m = sd1->getMass();
103
104			//std::cerr << "m = " << m << "\n";
105
106			actionTensor1 += m*outProduct(r1, v1);
107			actionTensor2 += m*outProduct(r2, v2);
108			}
109
110			actionTensor1 /= vol1;
111			//std::cerr << "at1 = " << actionTensor1 << "\n";
112			actionTensor2 /= vol2;
113			//std::cerr << "at2 = " << actionTensor2 << "\n";
114
115			Mat3x3d corrTensor(0.0);
116			//std::cerr << "ct = " << corrTensor << "\n";
117			RealType thisTerm;
118
119			for (i = 0; i < 3; i++) {
120			for (j = 0; j < 3; j++) {
121
122			//std::cerr << "i, j = " << i << " " << j << "\n";
123			if (i == j) {
124			thisTerm = (actionTensor2(i, j) - actionTensor1(i, j) - avePress_ *(time2-time1));
125			std::cerr << "at1, at2 = " << actionTensor1(i,j) << " " << actionTensor2(i,j) << " p = " << avePress_ << "\n";
126			} else {
127			thisTerm = (actionTensor2(i, j) - actionTensor1(i, j));
128			}
129
130			//std::cerr << "thisTerm = " << thisTerm << "\n";
131			corrTensor(i, j) += thisTerm * thisTerm;
132			}
133			}
134
135			//std::cerr << "ct = " << corrTensor << "\n";
136			//std::cerr << "hist = " << histogram_[timeBin] << "\n";
137			histogram_[timeBin] += corrTensor;
138			count_[timeBin]++;
139
140			}
141
142			void ActionCorrFunc::postCorrelate() {
143			for (int i =0 ; i < nTimeBins_; ++i) {
144			if (count_[i] > 0) {
145			histogram_[i] /= count_[i];
146			}
147			}
148			}
149
150
151			void ActionCorrFunc::preCorrelate() {
152			// Fill the histogram with empty 3x3 matrices:
153			std::fill(histogram_.begin(), histogram_.end(), Mat3x3d(0.0));
154			// count array set to zero
155			std::fill(count_.begin(), count_.end(), 0);
156
157			SimInfo::MoleculeIterator mi;
158			Molecule* mol;
159			Molecule::AtomIterator ai;
160			Atom* atom;
161
162			// We'll need the force manager to compute forces for the average pressure
163			ForceManager* forceMan = new ForceManager(info_);
164			forceMan->init();
165
166			// We'll need thermo to compute the pressures from the virial
167			Thermo* thermo = new Thermo(info_);
168
169			// prepare the averages
170			RealType pSum = 0.0;
171			RealType vSum = 0.0;
172			int nsamp = 0;
173
174			// dump files can be enormous, so read them in block-by-block:
175			int nblocks = bsMan_->getNBlocks();
176			for (int i = 0; i < nblocks; ++i) {
177			std::cerr << "block = " << i << "\n";
178			bsMan_->loadBlock(i);
179			assert(bsMan_->isBlockActive(i));
180			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
181			for (int j = block1.first; j < block1.second; ++j) {
182
183			// go snapshot-by-snapshot through this block:
184			Snapshot* snap = bsMan_->getSnapshot(j);
185
186			// update the positions and velocities of the atoms belonging
187			// to rigid bodies:
188
189			updateFrame(j);
190
191			// do the forces:
192			forceMan->calcForces(true, true);
193			// call thermo to get the pressure and volume.
194			pSum += thermo->getPressure();
195			vSum += thermo->getVolume();
196			nsamp++;
197
198			}
199			bsMan_->unloadBlock(i);
200			}
201
202			avePress_ = pSum / ( OOPSEConstant::pressureConvert * (RealType)nsamp);
203			aveVol_ = vSum / (RealType)nsamp;
204			std::cout << "pAve = " << avePress_ << " vAve = " << aveVol_ << "\n";
205			}
206
207
208			void ActionCorrFunc::writeCorrelate() {
209			std::ofstream ofs(getOutputFileName().c_str());
210
211			if (ofs.is_open()) {
212
213			ofs << "#" << getCorrFuncType() << "\n";
214			ofs << "#time\tcorrTensor\txx\txy\txz\tyx\tyy\tyz\tzx\tzy\tzz\n";
215
216			for (int i = 0; i < nTimeBins_; ++i) {
217			ofs << time_[i] << "\t" <<
218			histogram_[i](0,0) << "\t" <<
219			histogram_[i](0,1) << "\t" <<
220			histogram_[i](0,2) << "\t" <<
221			histogram_[i](1,0) << "\t" <<
222			histogram_[i](1,1) << "\t" <<
223			histogram_[i](1,2) << "\t" <<
224			histogram_[i](2,0) << "\t" <<
225			histogram_[i](2,1) << "\t" <<
226			histogram_[i](2,2) << "\t" << "\n";
227			}
228
229			} else {
230			sprintf(painCave.errMsg,
231			"ActionCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
232			painCave.isFatal = 1;
233			simError();
234			}
235
236			ofs.close();
237			}
238
239			}