applications/dynamicProps/StressCorrFunc.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/StressCorrFunc.hpp"
#include "utils/PhysicalConstants.hpp"
#include "brains/ForceManager.hpp"
#include "brains/Thermo.hpp"

namespace OpenMD {

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

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

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


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


  void StressCorrFunc::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,
              "StressCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
      painCave.isFatal = 1;
      simError();        
    }

    ofs.close();    
  }

}
Revision:	1596
Committed:	Mon Jul 25 17:30:53 2011 UTC (14 years, 1 month ago) by gezelter
File size:	8282 byte(s)
Log Message:	Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
#	User	Rev	Content
1	chuckv	1565	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* 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			*
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			*/
41
42			#include "applications/dynamicProps/StressCorrFunc.hpp"
43			#include "utils/PhysicalConstants.hpp"
44			#include "brains/ForceManager.hpp"
45			#include "brains/Thermo.hpp"
46
47			namespace OpenMD {
48
49			// We need all of the positions, velocities, etc. so that we can
50			// recalculate pressures and actions on the fly:
51			StressCorrFunc::StressCorrFunc(SimInfo* info, const std::string& filename,
52			const std::string& sele1,
53	gezelter	1596	const std::string& sele2,
54			long long int memSize)
55	chuckv	1565	: FrameTimeCorrFunc(info, filename, sele1, sele2,
56			DataStorage::dslPosition \|
57			DataStorage::dslVelocity \|
58	gezelter	1596	DataStorage::dslForce,
59			memSize){
60	chuckv	1565
61			setCorrFuncType("StressCorrFunc");
62			setOutputName(getPrefix(dumpFilename_) + ".action");
63			histogram_.resize(nTimeBins_);
64			count_.resize(nTimeBins_);
65			}
66
67			void StressCorrFunc::correlateFrames(int frame1, int frame2) {
68			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
69			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
70			assert(snapshot1 && snapshot2);
71
72			RealType time1 = snapshot1->getTime();
73			RealType time2 = snapshot2->getTime();
74			RealType vol1 = snapshot1->getVolume();
75			RealType vol2 = snapshot2->getVolume();
76
77			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
78
79			//std::cerr << "times = " << time1 << " " << time2 << "\n";
80			//std::cerr << "vols = " << vol1 << " " << vol2 << "\n";
81
82			int i;
83			int j;
84
85			StuntDouble* sd1;
86
87			Mat3x3d actionTensor1(0.0);
88			//std::cerr << "at1 = " << actionTensor1 << "\n";
89			Mat3x3d actionTensor2(0.0);
90			//std::cerr << "at2 = " << actionTensor2 << "\n";
91
92			for (sd1 = seleMan1_.beginSelected(i); sd1 != NULL;
93			sd1 = seleMan1_.nextSelected(i)) {
94			//std::cerr << "found a SD\n";
95			Vector3d r1 = sd1->getPos(frame1);
96			//std::cerr << "r1 = " << r1 << "\n";
97			Vector3d v1 = sd1->getVel(frame1);
98			//std::cerr << "v1 = " << v1 << "\n";
99			Vector3d r2 = sd1->getPos(frame2);
100			//std::cerr << "r2 = " << r2 << "\n";
101			Vector3d v2 = sd1->getVel(frame2);
102			//std::cerr << "v2 = " << v2 << "\n";
103
104			RealType m = sd1->getMass();
105
106			//std::cerr << "m = " << m << "\n";
107
108			actionTensor1 += m*outProduct(r1, v1);
109			actionTensor2 += m*outProduct(r2, v2);
110			}
111
112			actionTensor1 /= vol1;
113			//std::cerr << "at1 = " << actionTensor1 << "\n";
114			actionTensor2 /= vol2;
115			//std::cerr << "at2 = " << actionTensor2 << "\n";
116
117			Mat3x3d corrTensor(0.0);
118			//std::cerr << "ct = " << corrTensor << "\n";
119			RealType thisTerm;
120
121			for (i = 0; i < 3; i++) {
122			for (j = 0; j < 3; j++) {
123
124			//std::cerr << "i, j = " << i << " " << j << "\n";
125			if (i == j) {
126			thisTerm = (actionTensor2(i, j) - actionTensor1(i, j) - avePress_ *(time2-time1));
127			std::cerr << "at1, at2 = " << actionTensor1(i,j) << " " << actionTensor2(i,j) << " p = " << avePress_ << "\n";
128			} else {
129			thisTerm = (actionTensor2(i, j) - actionTensor1(i, j));
130			}
131
132			//std::cerr << "thisTerm = " << thisTerm << "\n";
133			corrTensor(i, j) += thisTerm * thisTerm;
134			}
135			}
136
137			//std::cerr << "ct = " << corrTensor << "\n";
138			//std::cerr << "hist = " << histogram_[timeBin] << "\n";
139			histogram_[timeBin] += corrTensor;
140			count_[timeBin]++;
141
142			}
143
144			void StressCorrFunc::postCorrelate() {
145			for (int i =0 ; i < nTimeBins_; ++i) {
146			if (count_[i] > 0) {
147			histogram_[i] /= count_[i];
148			}
149			}
150			}
151
152
153			void StressCorrFunc::preCorrelate() {
154			// Fill the histogram with empty 3x3 matrices:
155			std::fill(histogram_.begin(), histogram_.end(), Mat3x3d(0.0));
156			// count array set to zero
157			std::fill(count_.begin(), count_.end(), 0);
158
159			SimInfo::MoleculeIterator mi;
160			Molecule* mol;
161			Molecule::AtomIterator ai;
162			Atom* atom;
163
164			// We'll need the force manager to compute forces for the average pressure
165			ForceManager* forceMan = new ForceManager(info_);
166			forceMan->init();
167
168			// We'll need thermo to compute the pressures from the virial
169			Thermo* thermo = new Thermo(info_);
170
171			// prepare the averages
172			RealType pSum = 0.0;
173			RealType vSum = 0.0;
174			int nsamp = 0;
175
176			// dump files can be enormous, so read them in block-by-block:
177			int nblocks = bsMan_->getNBlocks();
178			for (int i = 0; i < nblocks; ++i) {
179			std::cerr << "block = " << i << "\n";
180			bsMan_->loadBlock(i);
181			assert(bsMan_->isBlockActive(i));
182			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
183			for (int j = block1.first; j < block1.second; ++j) {
184
185			// go snapshot-by-snapshot through this block:
186			Snapshot* snap = bsMan_->getSnapshot(j);
187
188			// update the positions and velocities of the atoms belonging
189			// to rigid bodies:
190
191			updateFrame(j);
192
193			// do the forces:
194	chuckv	1566	//forceMan->calcForces(true, true);
195	chuckv	1565	// call thermo to get the pressure and volume.
196			pSum += thermo->getPressure();
197			vSum += thermo->getVolume();
198			nsamp++;
199
200			}
201			bsMan_->unloadBlock(i);
202			}
203
204			avePress_ = pSum / ( PhysicalConstants::pressureConvert * (RealType)nsamp);
205			aveVol_ = vSum / (RealType)nsamp;
206			std::cout << "pAve = " << avePress_ << " vAve = " << aveVol_ << "\n";
207			}
208
209
210			void StressCorrFunc::writeCorrelate() {
211			std::ofstream ofs(getOutputFileName().c_str());
212
213			if (ofs.is_open()) {
214
215			ofs << "#" << getCorrFuncType() << "\n";
216			ofs << "#time\tcorrTensor\txx\txy\txz\tyx\tyy\tyz\tzx\tzy\tzz\n";
217
218			for (int i = 0; i < nTimeBins_; ++i) {
219			ofs << time_[i] << "\t" <<
220			histogram_[i](0,0) << "\t" <<
221			histogram_[i](0,1) << "\t" <<
222			histogram_[i](0,2) << "\t" <<
223			histogram_[i](1,0) << "\t" <<
224			histogram_[i](1,1) << "\t" <<
225			histogram_[i](1,2) << "\t" <<
226			histogram_[i](2,0) << "\t" <<
227			histogram_[i](2,1) << "\t" <<
228			histogram_[i](2,2) << "\t" << "\n";
229			}
230
231			} else {
232			sprintf(painCave.errMsg,
233			"StressCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
234			painCave.isFatal = 1;
235			simError();
236			}
237
238			ofs.close();
239			}
240
241			}