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);


    // //std::cerr << "Correlating Frame" << std::endl; 
    //    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 eatom = (kinetic + atom->getParticlePot())/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:	3404
Committed:	Mon Jun 2 02:42:50 2008 UTC (16 years, 3 months ago) by gezelter
File size:	9420 byte(s)
Log Message:	Fixed a bug in BlockSnapshotManager.
#	User	Rev	Content
1	chuckv	3398	/*
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
88			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
89
90
91	chuckv	3400	// //std::cerr << "Correlating Frame" << std::endl;
92			// Vector3d G_t_frame1 = G_t_[frame1];
93			// Vector3d G_t_frame2 = G_t_[frame2];
94			//
95			//
96			// RealType diff_x = G_t_frame1.x()-G_t_frame2.x();
97			// RealType diff_x_sq = diff_x * diff_x;
98			//
99			// RealType diff_y = G_t_frame1.y()-G_t_frame2.y();
100			// RealType diff_y_sq = diff_y * diff_y;
101			//
102			// RealType diff_z = G_t_frame1.z()-G_t_frame2.z();
103			// RealType diff_z_sq = diff_z*diff_z;
104			//
105			//
106			//
107			//
108			// histogram_[timeBin][0] += diff_x_sq;
109			// histogram_[timeBin][1] += diff_y_sq;
110			// histogram_[timeBin][2] += diff_z_sq;
111			//
112			// count_[timeBin]++;
113	chuckv	3398
114			}
115
116			void EnergyCorrFunc::postCorrelate() {
117			for (int i =0 ; i < nTimeBins_; ++i) {
118			if (count_[i] > 0) {
119			histogram_[i] /= count_[i];
120			}
121			}
122			}
123
124
125
126			void EnergyCorrFunc::preCorrelate() {
127			// Fill the histogram with empty 3x3 matrices:
128			std::fill(histogram_.begin(), histogram_.end(), 0.0);
129			// count array set to zero
130			std::fill(count_.begin(), count_.end(), 0);
131
132			SimInfo::MoleculeIterator mi;
133			Molecule::IntegrableObjectIterator mj;
134			Molecule* mol;
135			Molecule::AtomIterator ai;
136			Atom* atom;
137			std::vector<RealType > particleEnergies;
138
139			// We'll need the force manager to compute forces for the average pressure
140			ForceManager* forceMan = new ForceManager(info_);
141
142			forceMan->init();
143
144
145			// We'll need thermo to compute the pressures from the virial
146			Thermo* thermo = new Thermo(info_);
147
148			// prepare the averages
149			RealType pSum = 0.0;
150			RealType vSum = 0.0;
151			int nsamp = 0;
152
153			// dump files can be enormous, so read them in block-by-block:
154			int nblocks = bsMan_->getNBlocks();
155			bool firsttime = true;
156	chuckv	3400	int junkframe = 0;
157	chuckv	3398	for (int i = 0; i < nblocks; ++i) {
158			bsMan_->loadBlock(i);
159			assert(bsMan_->isBlockActive(i));
160			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
161			for (int j = block1.first; j < block1.second; ++j) {
162
163			// go snapshot-by-snapshot through this block:
164			Snapshot* snap = bsMan_->getSnapshot(j);
165	gezelter	3404
166	chuckv	3398	// update the positions and velocities of the atoms belonging
167			// to rigid bodies:
168	gezelter	3404
169	chuckv	3398	updateFrame(j);
170	gezelter	3404
171	chuckv	3398	// do the forces:
172	gezelter	3404
173			forceMan->calcForces(true, true);
174
175	chuckv	3398	int index = 0;
176	gezelter	3404
177	chuckv	3398	for (mol = info_->beginMolecule(mi); mol != NULL;
178	gezelter	3404	mol = info_->nextMolecule(mi)) {
179	chuckv	3398	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
180			RealType mass = atom->getMass();
181			Vector3d vel = atom->getVel();
182	gezelter	3404	RealType kinetic = mass * (vel[0]vel[0] + vel[1]vel[1] +
183			vel[2]*vel[2]);
184	chuckv	3398	RealType eatom = (kinetic + atom->getParticlePot())/2.0;
185			particleEnergies.push_back(eatom);
186			if(firsttime)
187	gezelter	3404	{
188			AvgE_a_.push_back(eatom);
189			} else {
190	chuckv	3398	/* We assume the the number of atoms does not change.*/
191			AvgE_a_[index] += eatom;
192			}
193			index++;
194			}
195			}
196			firsttime = false;
197			E_a_.push_back(particleEnergies);
198			}
199	chuckv	3400
200	chuckv	3398	bsMan_->unloadBlock(i);
201			}
202
203	gezelter	3404	int nframes = bsMan_->getNFrames();
204			for (int i = 0; i < AvgE_a_.size(); i++){
205			AvgE_a_[i] /= nframes;
206			}
207	chuckv	3398
208	gezelter	3404	int frame = 0;
209	chuckv	3398
210	gezelter	3404	// Do it again to compute G^(kappa)(t) for x,y,z
211			for (int i = 0; i < nblocks; ++i) {
212			bsMan_->loadBlock(i);
213			assert(bsMan_->isBlockActive(i));
214			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
215			for (int j = block1.first; j < block1.second; ++j) {
216	chuckv	3398
217	gezelter	3404	// go snapshot-by-snapshot through this block:
218			Snapshot* snap = bsMan_->getSnapshot(j);
219
220			// update the positions and velocities of the atoms belonging
221			// to rigid bodies:
222
223			updateFrame(j);
224
225			// this needs to be updated to the frame value:
226			particleEnergies = E_a_[j];
227
228			int thisAtom = 0;
229			Vector3d G_t;
230
231			for (mol = info_->beginMolecule(mi); mol != NULL;
232			mol = info_->nextMolecule(mi)) {
233			for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
234
235			Vector3d pos = atom->getPos();
236
237			G_t[0] += pos.x()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
238			G_t[1] += pos.y()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
239			G_t[2] += pos.z()*(particleEnergies[thisAtom]-AvgE_a_[thisAtom]);
240
241			thisAtom++;
242			}
243			}
244
245			G_t_.push_back(G_t);
246			std::cerr <<"Frame: " << j <<"\t" << G_t << std::endl;
247			}
248			bsMan_->unloadBlock(i);
249			}
250	chuckv	3398	}
251
252
253			void EnergyCorrFunc::writeCorrelate() {
254			std::ofstream ofs(getOutputFileName().c_str());
255
256			if (ofs.is_open()) {
257
258			ofs << "#" << getCorrFuncType() << "\n";
259			ofs << "#time\tK_x\tK_y\tK_z\n";
260
261			for (int i = 0; i < nTimeBins_; ++i) {
262			ofs << time_[i] << "\t" <<
263			histogram_[i].x() << "\t" <<
264			histogram_[i].y() << "\t" <<
265			histogram_[i].z() << "\t" << "\n";
266			}
267
268			} else {
269			sprintf(painCave.errMsg,
270			"EnergyCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
271			painCave.isFatal = 1;
272			simError();
273			}
274
275			ofs.close();
276
277			}
278
279			}