applications/dynamicProps/EnergyCorrFunc.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.
 */

 /* Uses the Helfand-moment method for calculating thermal
  * conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2*k_B*T^2*V*t) <[G_K(t)-G_K(0)]^2>
  * where G_K is the Helfand moment for thermal conductivity definded as
  * G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be
  *     E_a = p_2^2/(2*m)+1/2 sum_{b.ne.a} u(r_ab) where p is momentum and u is pot energy for the 
  * particle pair a-b. This routine calculates E_a, <E_a> and does the correlation
  * <[G_K(t)-G_K(0)]^2>.
  * See Viscardy et al. JCP 126, 184513 (2007)
  */


#include "applications/dynamicProps/EnergyCorrFunc.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:
  EnergyCorrFunc::EnergyCorrFunc(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 |
                        DataStorage::dslTorque |                        
                        DataStorage::dslParticlePot                     ){

      setCorrFuncType("EnergyCorrFunc");
      setOutputName(getPrefix(dumpFilename_) + ".moment");
      histogram_.resize(nTimeBins_); 
      count_.resize(nTimeBins_);
    }

  void EnergyCorrFunc::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();
       
    int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);

    Vector3d G_t_frame1 = G_t_[frame1];
    Vector3d G_t_frame2 = G_t_[frame2];
    
    
    RealType diff_x = G_t_frame1.x()-G_t_frame2.x();
    RealType diff_x_sq = diff_x * diff_x;
    
    RealType diff_y = G_t_frame1.y()-G_t_frame2.y();
    RealType diff_y_sq = diff_y * diff_y;
    
    RealType diff_z = G_t_frame1.z()-G_t_frame2.z();
    RealType diff_z_sq = diff_z*diff_z;    
    
    histogram_[timeBin][0] += diff_x_sq;
    histogram_[timeBin][1] += diff_y_sq;
    histogram_[timeBin][2] += diff_z_sq;
    
    count_[timeBin]++;
    
  }

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

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

    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator mj;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    std::vector<RealType > particleEnergies;

    // 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();
    bool firsttime = true;
    int junkframe = 0;
    for (int i = 0; i < nblocks; ++i) {
      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); 
        
        int index = 0;
        
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {
          for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            RealType mass = atom->getMass();
            Vector3d vel = atom->getVel();
            RealType kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + 
                                       vel[2]*vel[2]);
            RealType potential =  atom->getParticlePot();
            RealType eatom = (kinetic + potential)/2.0;
            particleEnergies.push_back(eatom);
            if(firsttime)
              {
                AvgE_a_.push_back(eatom);
              } else {
              /* We assume the the number of atoms does not change.*/
              AvgE_a_[index] += eatom;
            }
            index++;
          }      
        }
        firsttime = false;
        E_a_.push_back(particleEnergies);
      }
      
      bsMan_->unloadBlock(i);
    }
    
    int nframes =  bsMan_->getNFrames();
    for (int i = 0; i < AvgE_a_.size(); i++){
      AvgE_a_[i] /= nframes;
    }
    
    int frame = 0;
    
    // Do it again to compute G^(kappa)(t) for x,y,z
    for (int i = 0; i < nblocks; ++i) {
      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);        

        // this needs to be updated to the frame value:
        particleEnergies = E_a_[j];
        
        int thisAtom = 0;
        Vector3d G_t;
        
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {
          for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
                        
            Vector3d pos = atom->getPos();

            G_t[0] += pos.x()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
            G_t[1] += pos.y()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
            G_t[2] += pos.z()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
            
            thisAtom++;                    
          }
        }

        G_t_.push_back(G_t);
        //std::cerr <<"Frame: " << j <<"\t" << G_t << std::endl;
      } 
      bsMan_->unloadBlock(i);
    }
  }   


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

    if (ofs.is_open()) {

      ofs << "#" << getCorrFuncType() << "\n";
      ofs << "#time\tK_x\tK_y\tK_z\n";

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

    ofs.close();    
    
  }

}
Revision:	1313
Committed:	Wed Oct 22 20:01:49 2008 UTC (16 years, 7 months ago) by gezelter
Original Path:	*trunk/src/applications/dynamicProps/EnergyCorrFunc.cpp*
File size:	9264 byte(s)
Log Message:	General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
#	User	Rev	Content
1	chuckv	1246	/*
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			/* Uses the Helfand-moment method for calculating thermal
43			* conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2k_BT^2Vt) <[G_K(t)-G_K(0)]^2>
44			* where G_K is the Helfand moment for thermal conductivity definded as
45			* G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be
46			* E_a = p_2^2/(2*m)+1/2 sum_{b.ne.a} u(r_ab) where p is momentum and u is pot energy for the
47			* particle pair a-b. This routine calculates E_a, <E_a> and does the correlation
48			* <[G_K(t)-G_K(0)]^2>.
49			* See Viscardy et al. JCP 126, 184513 (2007)
50			*/
51
52
53
54			#include "applications/dynamicProps/EnergyCorrFunc.hpp"
55			#include "utils/OOPSEConstant.hpp"
56			#include "brains/ForceManager.hpp"
57			#include "brains/Thermo.hpp"
58
59			namespace oopse {
60
61			// We need all of the positions, velocities, etc. so that we can
62			// recalculate pressures and actions on the fly:
63			EnergyCorrFunc::EnergyCorrFunc(SimInfo* info, const std::string& filename,
64			const std::string& sele1,
65			const std::string& sele2)
66			: FrameTimeCorrFunc(info, filename, sele1, sele2,
67			DataStorage::dslPosition \|
68			DataStorage::dslVelocity \|
69			DataStorage::dslForce \|
70			DataStorage::dslTorque \|
71			DataStorage::dslParticlePot ){
72
73			setCorrFuncType("EnergyCorrFunc");
74			setOutputName(getPrefix(dumpFilename_) + ".moment");
75			histogram_.resize(nTimeBins_);
76			count_.resize(nTimeBins_);
77			}
78
79			void EnergyCorrFunc::correlateFrames(int frame1, int frame2) {
80			Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
81			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
82			assert(snapshot1 && snapshot2);
83
84			RealType time1 = snapshot1->getTime();
85			RealType time2 = snapshot2->getTime();
86
87			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
88
89	gezelter	1313	Vector3d G_t_frame1 = G_t_[frame1];
90			Vector3d G_t_frame2 = G_t_[frame2];
91
92
93			RealType diff_x = G_t_frame1.x()-G_t_frame2.x();
94			RealType diff_x_sq = diff_x * diff_x;
95
96			RealType diff_y = G_t_frame1.y()-G_t_frame2.y();
97			RealType diff_y_sq = diff_y * diff_y;
98
99			RealType diff_z = G_t_frame1.z()-G_t_frame2.z();
100			RealType diff_z_sq = diff_z*diff_z;
101
102			histogram_[timeBin][0] += diff_x_sq;
103			histogram_[timeBin][1] += diff_y_sq;
104			histogram_[timeBin][2] += diff_z_sq;
105
106			count_[timeBin]++;
107
108	chuckv	1246	}
109
110			void EnergyCorrFunc::postCorrelate() {
111			for (int i =0 ; i < nTimeBins_; ++i) {
112			if (count_[i] > 0) {
113			histogram_[i] /= count_[i];
114			}
115			}
116			}
117
118			void EnergyCorrFunc::preCorrelate() {
119			// Fill the histogram with empty 3x3 matrices:
120			std::fill(histogram_.begin(), histogram_.end(), 0.0);
121			// count array set to zero
122			std::fill(count_.begin(), count_.end(), 0);
123
124			SimInfo::MoleculeIterator mi;
125			Molecule::IntegrableObjectIterator mj;
126			Molecule* mol;
127			Molecule::AtomIterator ai;
128			Atom* atom;
129			std::vector<RealType > particleEnergies;
130
131			// We'll need the force manager to compute forces for the average pressure
132			ForceManager* forceMan = new ForceManager(info_);
133
134			forceMan->init();
135	gezelter	1313
136	chuckv	1246	// We'll need thermo to compute the pressures from the virial
137			Thermo* thermo = new Thermo(info_);
138
139			// prepare the averages
140			RealType pSum = 0.0;
141			RealType vSum = 0.0;
142			int nsamp = 0;
143
144			// dump files can be enormous, so read them in block-by-block:
145			int nblocks = bsMan_->getNBlocks();
146			bool firsttime = true;
147	chuckv	1247	int junkframe = 0;
148	chuckv	1246	for (int i = 0; i < nblocks; ++i) {
149			bsMan_->loadBlock(i);
150			assert(bsMan_->isBlockActive(i));
151			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
152			for (int j = block1.first; j < block1.second; ++j) {
153
154			// go snapshot-by-snapshot through this block:
155			Snapshot* snap = bsMan_->getSnapshot(j);
156	gezelter	1249
157	chuckv	1246	// update the positions and velocities of the atoms belonging
158			// to rigid bodies:
159	gezelter	1249
160	chuckv	1246	updateFrame(j);
161	gezelter	1249
162	chuckv	1246	// do the forces:
163	gezelter	1249
164			forceMan->calcForces(true, true);
165
166	chuckv	1246	int index = 0;
167	gezelter	1249
168	chuckv	1246	for (mol = info_->beginMolecule(mi); mol != NULL;
169	gezelter	1249	mol = info_->nextMolecule(mi)) {
170	chuckv	1246	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
171			RealType mass = atom->getMass();
172			Vector3d vel = atom->getVel();
173	gezelter	1249	RealType kinetic = mass * (vel[0]vel[0] + vel[1]vel[1] +
174			vel[2]*vel[2]);
175	gezelter	1313	RealType potential = atom->getParticlePot();
176			RealType eatom = (kinetic + potential)/2.0;
177	chuckv	1246	particleEnergies.push_back(eatom);
178			if(firsttime)
179	gezelter	1249	{
180			AvgE_a_.push_back(eatom);
181			} else {
182	chuckv	1246	/* We assume the the number of atoms does not change.*/
183			AvgE_a_[index] += eatom;
184			}
185			index++;
186			}
187			}
188			firsttime = false;
189			E_a_.push_back(particleEnergies);
190			}
191	chuckv	1247
192	chuckv	1246	bsMan_->unloadBlock(i);
193			}
194
195	gezelter	1249	int nframes = bsMan_->getNFrames();
196			for (int i = 0; i < AvgE_a_.size(); i++){
197			AvgE_a_[i] /= nframes;
198			}
199	chuckv	1246
200	gezelter	1249	int frame = 0;
201	chuckv	1246
202	gezelter	1249	// Do it again to compute G^(kappa)(t) for x,y,z
203			for (int i = 0; i < nblocks; ++i) {
204			bsMan_->loadBlock(i);
205			assert(bsMan_->isBlockActive(i));
206			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
207			for (int j = block1.first; j < block1.second; ++j) {
208	chuckv	1246
209	gezelter	1249	// go snapshot-by-snapshot through this block:
210			Snapshot* snap = bsMan_->getSnapshot(j);
211
212			// update the positions and velocities of the atoms belonging
213			// to rigid bodies:
214
215			updateFrame(j);
216
217			// this needs to be updated to the frame value:
218			particleEnergies = E_a_[j];
219
220			int thisAtom = 0;
221			Vector3d G_t;
222
223			for (mol = info_->beginMolecule(mi); mol != NULL;
224			mol = info_->nextMolecule(mi)) {
225			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
226
227			Vector3d pos = atom->getPos();
228
229			G_t[0] += pos.x()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
230			G_t[1] += pos.y()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
231			G_t[2] += pos.z()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
232
233			thisAtom++;
234			}
235			}
236
237			G_t_.push_back(G_t);
238	gezelter	1313	//std::cerr <<"Frame: " << j <<"\t" << G_t << std::endl;
239	gezelter	1249	}
240			bsMan_->unloadBlock(i);
241			}
242	chuckv	1246	}
243
244
245			void EnergyCorrFunc::writeCorrelate() {
246			std::ofstream ofs(getOutputFileName().c_str());
247
248			if (ofs.is_open()) {
249
250			ofs << "#" << getCorrFuncType() << "\n";
251			ofs << "#time\tK_x\tK_y\tK_z\n";
252
253			for (int i = 0; i < nTimeBins_; ++i) {
254			ofs << time_[i] << "\t" <<
255			histogram_[i].x() << "\t" <<
256			histogram_[i].y() << "\t" <<
257			histogram_[i].z() << "\t" << "\n";
258			}
259
260			} else {
261			sprintf(painCave.errMsg,
262			"EnergyCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
263			painCave.isFatal = 1;
264			simError();
265			}
266
267			ofs.close();
268
269			}
270
271			}