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. 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

 /* 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/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:
  EnergyCorrFunc::EnergyCorrFunc(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 |
                        DataStorage::dslTorque |                        
                        DataStorage::dslParticlePot,
                        memSize){

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

  void EnergyCorrFunc::correlateFrames(int frame1, int frame2) {
    SimInfo::MoleculeIterator mi1;
    SimInfo::MoleculeIterator mi2;
    Molecule* mol1;
    Molecule* mol2;
    Molecule::AtomIterator ai1;
    Molecule::AtomIterator ai2;
    Atom* atom1;
    Atom* atom2;
    std::vector<RealType> particleEnergies1;
    std::vector<RealType> particleEnergies2;
    std::vector<Vector3d> atomPositions1;
    std::vector<Vector3d> atomPositions2;
    int thisAtom1, thisAtom2;

    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);

    // now do the correlation

    particleEnergies1 = E_a_[frame1];
    particleEnergies2 = E_a_[frame2];

    updateFrame(frame1);       
    atomPositions1.clear();
    for (mol1 = info_->beginMolecule(mi1); mol1 != NULL; 
         mol1 = info_->nextMolecule(mi1)) {
      for(atom1 = mol1->beginAtom(ai1); atom1 != NULL; 
          atom1 = mol1->nextAtom(ai1)) {        
        atomPositions1.push_back(atom1->getPos(frame1));
      }
    }
    updateFrame(frame2);       
    atomPositions2.clear();
    for (mol2 = info_->beginMolecule(mi2); mol2 != NULL; 
         mol2 = info_->nextMolecule(mi2)) {
      for(atom2 = mol2->beginAtom(ai2); atom2 != NULL; 
          atom2 = mol2->nextAtom(ai2)) {        
        atomPositions2.push_back(atom2->getPos(frame2));
      }
    }

    thisAtom1 = 0;

    for (mol1 = info_->beginMolecule(mi1); mol1 != NULL; 
         mol1 = info_->nextMolecule(mi1)) {
      for(atom1 = mol1->beginAtom(ai1); atom1 != NULL; 
          atom1 = mol1->nextAtom(ai1)) {
        
        Vector3d r1 = atomPositions1[thisAtom1];
        RealType energy1 = particleEnergies1[thisAtom1] - AvgE_a_[thisAtom1];

        thisAtom2 = 0;

        for (mol2 = info_->beginMolecule(mi2); mol2 != NULL; 
             mol2 = info_->nextMolecule(mi2)) {
          for(atom2 = mol2->beginAtom(ai2); atom2 != NULL; 
              atom2 = mol2->nextAtom(ai2)) {
            
            Vector3d r2 = atomPositions2[thisAtom2];
            RealType energy2 = particleEnergies2[thisAtom2] - AvgE_a_[thisAtom2];

            Vector3d deltaPos = (r2-r1);            
            RealType Eprod = energy2*energy1;
            
            histogram_[timeBin][0] += deltaPos.x()*deltaPos.x() * Eprod;
            histogram_[timeBin][1] += deltaPos.y()*deltaPos.y() * Eprod;
            histogram_[timeBin][2] += deltaPos.z()*deltaPos.z() * Eprod;
                                           
            thisAtom2++;                    
          }
        }
        
        thisAtom1++;
      } 
    }
    
    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* 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_);

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

    // dump files can be enormous, so read them in block-by-block:
    int nblocks = bsMan_->getNBlocks();
    bool firsttime = true;
    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(); 
        
        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(j);
            RealType kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + 
                                       vel[2]*vel[2]) / PhysicalConstants::energyConvert;
            RealType potential =  atom->getParticlePot(j);
            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 (unsigned int i = 0; i < AvgE_a_.size(); i++){
      AvgE_a_[i] /= nframes;
    }
    
  }
  

  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:	1826
Committed:	Wed Jan 9 19:41:48 2013 UTC (12 years, 4 months ago) by gezelter
File size:	9781 byte(s)
Log Message:	Cleaning more cruft and unused variables.
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1246	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chuckv	1246	*/
42
43			/* Uses the Helfand-moment method for calculating thermal
44			* conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2k_BT^2Vt) <[G_K(t)-G_K(0)]^2>
45			* where G_K is the Helfand moment for thermal conductivity definded as
46			* G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be
47			* 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
48			* particle pair a-b. This routine calculates E_a, <E_a> and does the correlation
49			* <[G_K(t)-G_K(0)]^2>.
50			* See Viscardy et al. JCP 126, 184513 (2007)
51			*/
52
53
54
55			#include "applications/dynamicProps/EnergyCorrFunc.hpp"
56	gezelter	1390	#include "utils/PhysicalConstants.hpp"
57	chuckv	1246	#include "brains/ForceManager.hpp"
58			#include "brains/Thermo.hpp"
59
60	gezelter	1390	namespace OpenMD {
61	chuckv	1246
62			// We need all of the positions, velocities, etc. so that we can
63			// recalculate pressures and actions on the fly:
64			EnergyCorrFunc::EnergyCorrFunc(SimInfo* info, const std::string& filename,
65			const std::string& sele1,
66	gezelter	1629	const std::string& sele2,
67			long long int memSize)
68	chuckv	1246	: FrameTimeCorrFunc(info, filename, sele1, sele2,
69			DataStorage::dslPosition \|
70			DataStorage::dslVelocity \|
71			DataStorage::dslForce \|
72			DataStorage::dslTorque \|
73	gezelter	1629	DataStorage::dslParticlePot,
74			memSize){
75	chuckv	1246
76			setCorrFuncType("EnergyCorrFunc");
77			setOutputName(getPrefix(dumpFilename_) + ".moment");
78			histogram_.resize(nTimeBins_);
79			count_.resize(nTimeBins_);
80			}
81
82			void EnergyCorrFunc::correlateFrames(int frame1, int frame2) {
83	gezelter	1629	SimInfo::MoleculeIterator mi1;
84			SimInfo::MoleculeIterator mi2;
85			Molecule* mol1;
86			Molecule* mol2;
87			Molecule::AtomIterator ai1;
88			Molecule::AtomIterator ai2;
89			Atom* atom1;
90			Atom* atom2;
91			std::vector<RealType> particleEnergies1;
92			std::vector<RealType> particleEnergies2;
93			std::vector<Vector3d> atomPositions1;
94			std::vector<Vector3d> atomPositions2;
95			int thisAtom1, thisAtom2;
96
97	chuckv	1246	Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
98			Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
99			assert(snapshot1 && snapshot2);
100
101			RealType time1 = snapshot1->getTime();
102			RealType time2 = snapshot2->getTime();
103
104			int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
105
106	gezelter	1629	// now do the correlation
107
108			particleEnergies1 = E_a_[frame1];
109			particleEnergies2 = E_a_[frame2];
110
111			updateFrame(frame1);
112			atomPositions1.clear();
113			for (mol1 = info_->beginMolecule(mi1); mol1 != NULL;
114			mol1 = info_->nextMolecule(mi1)) {
115			for(atom1 = mol1->beginAtom(ai1); atom1 != NULL;
116			atom1 = mol1->nextAtom(ai1)) {
117			atomPositions1.push_back(atom1->getPos(frame1));
118			}
119			}
120			updateFrame(frame2);
121			atomPositions2.clear();
122			for (mol2 = info_->beginMolecule(mi2); mol2 != NULL;
123			mol2 = info_->nextMolecule(mi2)) {
124			for(atom2 = mol2->beginAtom(ai2); atom2 != NULL;
125			atom2 = mol2->nextAtom(ai2)) {
126			atomPositions2.push_back(atom2->getPos(frame2));
127			}
128			}
129
130			thisAtom1 = 0;
131
132			for (mol1 = info_->beginMolecule(mi1); mol1 != NULL;
133			mol1 = info_->nextMolecule(mi1)) {
134			for(atom1 = mol1->beginAtom(ai1); atom1 != NULL;
135			atom1 = mol1->nextAtom(ai1)) {
136
137			Vector3d r1 = atomPositions1[thisAtom1];
138			RealType energy1 = particleEnergies1[thisAtom1] - AvgE_a_[thisAtom1];
139
140			thisAtom2 = 0;
141
142			for (mol2 = info_->beginMolecule(mi2); mol2 != NULL;
143			mol2 = info_->nextMolecule(mi2)) {
144			for(atom2 = mol2->beginAtom(ai2); atom2 != NULL;
145			atom2 = mol2->nextAtom(ai2)) {
146
147			Vector3d r2 = atomPositions2[thisAtom2];
148			RealType energy2 = particleEnergies2[thisAtom2] - AvgE_a_[thisAtom2];
149
150			Vector3d deltaPos = (r2-r1);
151			RealType Eprod = energy2*energy1;
152
153			histogram_[timeBin][0] += deltaPos.x()deltaPos.x() Eprod;
154			histogram_[timeBin][1] += deltaPos.y()deltaPos.y() Eprod;
155			histogram_[timeBin][2] += deltaPos.z()deltaPos.z() Eprod;
156
157			thisAtom2++;
158			}
159			}
160
161			thisAtom1++;
162			}
163			}
164	gezelter	1313
165			count_[timeBin]++;
166
167	chuckv	1246	}
168
169			void EnergyCorrFunc::postCorrelate() {
170			for (int i =0 ; i < nTimeBins_; ++i) {
171			if (count_[i] > 0) {
172			histogram_[i] /= count_[i];
173			}
174			}
175			}
176
177			void EnergyCorrFunc::preCorrelate() {
178			// Fill the histogram with empty 3x3 matrices:
179			std::fill(histogram_.begin(), histogram_.end(), 0.0);
180			// count array set to zero
181			std::fill(count_.begin(), count_.end(), 0);
182
183			SimInfo::MoleculeIterator mi;
184			Molecule* mol;
185			Molecule::AtomIterator ai;
186			Atom* atom;
187			std::vector<RealType > particleEnergies;
188
189			// We'll need the force manager to compute forces for the average pressure
190			ForceManager* forceMan = new ForceManager(info_);
191
192			// We'll need thermo to compute the pressures from the virial
193			Thermo* thermo = new Thermo(info_);
194
195			// dump files can be enormous, so read them in block-by-block:
196			int nblocks = bsMan_->getNBlocks();
197			bool firsttime = true;
198			for (int i = 0; i < nblocks; ++i) {
199			bsMan_->loadBlock(i);
200			assert(bsMan_->isBlockActive(i));
201			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
202			for (int j = block1.first; j < block1.second; ++j) {
203
204			// go snapshot-by-snapshot through this block:
205			Snapshot* snap = bsMan_->getSnapshot(j);
206	gezelter	1249
207	chuckv	1246	// update the positions and velocities of the atoms belonging
208			// to rigid bodies:
209	gezelter	1249
210	chuckv	1246	updateFrame(j);
211	gezelter	1249
212	chuckv	1246	// do the forces:
213	gezelter	1249
214	gezelter	1464	forceMan->calcForces();
215	gezelter	1249
216	chuckv	1246	int index = 0;
217	gezelter	1249
218	chuckv	1246	for (mol = info_->beginMolecule(mi); mol != NULL;
219	gezelter	1249	mol = info_->nextMolecule(mi)) {
220	chuckv	1246	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
221			RealType mass = atom->getMass();
222	gezelter	1629	Vector3d vel = atom->getVel(j);
223	gezelter	1249	RealType kinetic = mass * (vel[0]vel[0] + vel[1]vel[1] +
224	gezelter	1390	vel[2]*vel[2]) / PhysicalConstants::energyConvert;
225	gezelter	1629	RealType potential = atom->getParticlePot(j);
226	gezelter	1313	RealType eatom = (kinetic + potential)/2.0;
227	chuckv	1246	particleEnergies.push_back(eatom);
228			if(firsttime)
229	gezelter	1249	{
230			AvgE_a_.push_back(eatom);
231			} else {
232	chuckv	1246	/* We assume the the number of atoms does not change.*/
233			AvgE_a_[index] += eatom;
234			}
235			index++;
236			}
237			}
238			firsttime = false;
239			E_a_.push_back(particleEnergies);
240			}
241	chuckv	1247
242	chuckv	1246	bsMan_->unloadBlock(i);
243			}
244
245	gezelter	1249	int nframes = bsMan_->getNFrames();
246	gezelter	1767	for (unsigned int i = 0; i < AvgE_a_.size(); i++){
247	gezelter	1249	AvgE_a_[i] /= nframes;
248			}
249	chuckv	1246
250	gezelter	1629	}
251
252	chuckv	1246
253	gezelter	1249
254	chuckv	1246	void EnergyCorrFunc::writeCorrelate() {
255			std::ofstream ofs(getOutputFileName().c_str());
256
257			if (ofs.is_open()) {
258
259			ofs << "#" << getCorrFuncType() << "\n";
260			ofs << "#time\tK_x\tK_y\tK_z\n";
261
262			for (int i = 0; i < nTimeBins_; ++i) {
263			ofs << time_[i] << "\t" <<
264			histogram_[i].x() << "\t" <<
265			histogram_[i].y() << "\t" <<
266			histogram_[i].z() << "\t" << "\n";
267			}
268
269			} else {
270			sprintf(painCave.errMsg,
271			"EnergyCorrFunc::writeCorrelate Error: fail to open %s\n", getOutputFileName().c_str());
272			painCave.isFatal = 1;
273			simError();
274			}
275
276			ofs.close();
277
278			}
279
280			}