src/rnemd/RNEMD.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 "integrators/RNEMD.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/StuntDouble.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/Tuple.hpp"

#ifndef IS_MPI
#include "math/SeqRandNumGen.hpp"
#else
#include "math/ParallelRandNumGen.hpp"
#endif


namespace oopse {
  
  RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
    
    int seedValue;
    Globals * simParams = info->getSimParams();

    stringToEnumMap_["Kinetic"] = rnemdKinetic;
    stringToEnumMap_["Px"] = rnemdPx;
    stringToEnumMap_["Py"] = rnemdPy;
    stringToEnumMap_["Pz"] = rnemdPz;
    stringToEnumMap_["Unknown"] = rnemdUnknown;

    rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
    evaluator_.loadScriptString(rnemdObjectSelection_);
    seleMan_.setSelectionSet(evaluator_.evaluate());


    // do some sanity checking

    int selectionCount = seleMan_.getSelectionCount();
    int nIntegrable = info->getNGlobalIntegrableObjects();

    if (selectionCount > nIntegrable) {
      sprintf(painCave.errMsg, 
              "RNEMD warning: The current RNEMD_objectSelection,\n"
              "\t\t%s\n"
              "\thas resulted in %d selected objects.  However,\n"
              "\tthe total number of integrable objects in the system\n"
              "\tis only %d.  This is almost certainly not what you want\n"
              "\tto do.  A likely cause of this is forgetting the _RB_0\n"
              "\tselector in the selection script!\n", 
              rnemdObjectSelection_.c_str(), 
              selectionCount, nIntegrable);
      painCave.isFatal = 0;
      simError();

    }
    
    const std::string st = simParams->getRNEMD_swapType();

    std::map<std::string, RNEMDTypeEnum>::iterator i;
    i = stringToEnumMap_.find(st);
    rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;

    set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
    set_RNEMD_nBins(simParams->getRNEMD_nBins());
    exchangeSum_ = 0.0;
    counter_ = 0; //added by shenyu

#ifndef IS_MPI
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      randNumGen_ = new SeqRandNumGen(seedValue);
    }else {
      randNumGen_ = new SeqRandNumGen();
    }    
#else
    if (simParams->haveSeed()) {
      seedValue = simParams->getSeed();
      randNumGen_ = new ParallelRandNumGen(seedValue);
    }else {
      randNumGen_ = new ParallelRandNumGen();
    }    
#endif 
  }
  
  RNEMD::~RNEMD() {
    delete randNumGen_;
  }

  void RNEMD::doSwap() {
    int midBin = nBins_ / 2;

    Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
    Mat3x3d hmat = currentSnap_->getHmat();

    seleMan_.setSelectionSet(evaluator_.evaluate());

    int selei;
    StuntDouble* sd;
    int idx;

    RealType min_val;
    bool min_found = false;   
    StuntDouble* min_sd;

    RealType max_val;
    bool max_found = false;
    StuntDouble* max_sd;

    for (sd = seleMan_.beginSelected(selei); sd != NULL; 
         sd = seleMan_.nextSelected(selei)) {

      idx = sd->getLocalIndex();

      Vector3d pos = sd->getPos();

      // wrap the stuntdouble's position back into the box:

      if (usePeriodicBoundaryConditions_)
        currentSnap_->wrapVector(pos);

      // which bin is this stuntdouble in?
      // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]

      int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;


      // if we're in bin 0 or the middleBin
      if (binNo == 0 || binNo == midBin) {
        
        RealType mass = sd->getMass();
        Vector3d vel = sd->getVel();
        RealType value;

        switch(rnemdType_) {
        case rnemdKinetic :
          
          value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + 
                          vel[2]*vel[2]);
          if (sd->isDirectional()) {
            Vector3d angMom = sd->getJ();
            Mat3x3d I = sd->getI();
            
            if (sd->isLinear()) {
              int i = sd->linearAxis();
              int j = (i + 1) % 3;
              int k = (i + 2) % 3;
              value += angMom[j] * angMom[j] / I(j, j) + 
                angMom[k] * angMom[k] / I(k, k);
            } else {                        
              value += angMom[0]*angMom[0]/I(0, 0) 
                + angMom[1]*angMom[1]/I(1, 1) 
                + angMom[2]*angMom[2]/I(2, 2);
            }
          }
          value = value * 0.5 / OOPSEConstant::energyConvert;
          break;
        case rnemdPx :
          value = mass * vel[0];
          break;
        case rnemdPy :
          value = mass * vel[1];
          break;
        case rnemdPz :
          value = mass * vel[2];
          break;
        case rnemdUnknown : 
        default :
          break;
        }
        
        if (binNo == 0) {
          if (!min_found) {
            min_val = value;
            min_sd = sd;
            min_found = true;
          } else {
            if (min_val > value) {
              min_val = value;
              min_sd = sd;
            }
          }
        } else {
          if (!max_found) {
            max_val = value;
            max_sd = sd;
            max_found = true;
          } else {
            if (max_val < value) {
              max_val = value;
              max_sd = sd;
            }
          }       
        }
      }
    }

    // missing:  swap information in parallel

    if (max_found && min_found) {
      if (min_val< max_val) {

        Vector3d min_vel = min_sd->getVel();
        Vector3d max_vel = max_sd->getVel();
        RealType temp_vel;

        switch(rnemdType_) {
        case rnemdKinetic :
          min_sd->setVel(max_vel);
          max_sd->setVel(min_vel);

          if (min_sd->isDirectional() && max_sd->isDirectional()) {
            Vector3d min_angMom = min_sd->getJ();
            Vector3d max_angMom = max_sd->getJ();
            min_sd->setJ(max_angMom);
            max_sd->setJ(min_angMom);
          }
          break;
        case rnemdPx :
          temp_vel = min_vel.x();
          min_vel.x() = max_vel.x();
          max_vel.x() = temp_vel;
          min_sd->setVel(min_vel);
          max_sd->setVel(max_vel);
          break;
        case rnemdPy :
          temp_vel = min_vel.y();
          min_vel.y() = max_vel.y();
          max_vel.y() = temp_vel;
          min_sd->setVel(min_vel);
          max_sd->setVel(max_vel);
          break;
        case rnemdPz :
          temp_vel = min_vel.z();
          min_vel.z() = max_vel.z();
          max_vel.z() = temp_vel;
          min_sd->setVel(min_vel);
          max_sd->setVel(max_vel);
          break;
        case rnemdUnknown : 
        default :
          break;
        }
      exchangeSum_ += max_val - min_val;
      } else {
        std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
      }
    } else {
      std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
    }
  }

  void RNEMD::getStatus() {

    Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
    Mat3x3d hmat = currentSnap_->getHmat();
    Stats& stat = currentSnap_->statData;

    stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;

    seleMan_.setSelectionSet(evaluator_.evaluate());

    int selei;
    StuntDouble* sd;
    int idx;

    std::vector<RealType> valueHist;  // keeps track of what's being averaged
    std::vector<int> valueCount; // keeps track of the number of degrees of 
                                 // freedom being averaged
    valueHist.resize(nBins_);
    valueCount.resize(nBins_);
    //do they initialize themselves to zero automatically?
    for (sd = seleMan_.beginSelected(selei); sd != NULL; 
         sd = seleMan_.nextSelected(selei)) {
      
      idx = sd->getLocalIndex();
      
      Vector3d pos = sd->getPos();

      // wrap the stuntdouble's position back into the box:
      
      if (usePeriodicBoundaryConditions_)
        currentSnap_->wrapVector(pos);
      
      // which bin is this stuntdouble in?
      // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
      
      int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
      
      //std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
      
      RealType mass = sd->getMass();
      Vector3d vel = sd->getVel();
      //std::cerr << "mass = " << mass << " vel = " << vel << "\n";
      RealType value;

      switch(rnemdType_) {
      case rnemdKinetic :
        
        value = mass * (vel[0]*vel[0] + vel[1]*vel[1] + 
                        vel[2]*vel[2]);
        
        valueCount[binNo] += 3;
        //std::cerr <<"starting value = " << value << "\n";
        if (sd->isDirectional()) {
          //std::cerr << "angMom calculated.\n";
          Vector3d angMom = sd->getJ();
          //std::cerr << "current angMom: " << angMom << "\n";
          Mat3x3d I = sd->getI();
          
          if (sd->isLinear()) {
            int i = sd->linearAxis();
            int j = (i + 1) % 3;
            int k = (i + 2) % 3;
            value += angMom[j] * angMom[j] / I(j, j) + 
              angMom[k] * angMom[k] / I(k, k);

            valueCount[binNo] +=2;

          } else {
            //std::cerr << "non-linear molecule.\n";
            value += angMom[0]*angMom[0]/I(0, 0) 
              + angMom[1]*angMom[1]/I(1, 1) 
              + angMom[2]*angMom[2]/I(2, 2);
            valueCount[binNo] +=3;

          }
        }
        //std::cerr <<"total value = " << value << "\n";
        //value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
        //value *= 2.0 / OOPSEConstant::kb;            // convert to temperature
        value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
        //std::cerr <<"value = " << value << "\n";
        break;
      case rnemdPx :
        value = mass * vel[0];
        valueCount[binNo]++;
        break;
      case rnemdPy :
        value = mass * vel[1];
        valueCount[binNo]++;
        break;
      case rnemdPz :
        value = mass * vel[2];
        valueCount[binNo]++;
        break;
      case rnemdUnknown : 
      default :
        break;
      }
      //std::cerr << "bin = " << binNo << " value = " << value ;
      valueHist[binNo] += value;
      //std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
    }
    
    std::cout << counter_++;
    for (int j = 0; j < nBins_; j++)
      std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
    std::cout << "\n";
  }
}
Revision:	1341
Committed:	Fri May 8 19:47:05 2009 UTC (16 years, 5 months ago) by skuang
Original Path:	*trunk/src/integrators/RNEMD.cpp*
File size:	12122 byte(s)
Log Message:	Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
#	User	Rev	Content
1	gezelter	1329	/*
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 "integrators/RNEMD.hpp"
43	gezelter	1332	#include "math/Vector3.hpp"
44	gezelter	1329	#include "math/SquareMatrix3.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "primitives/StuntDouble.hpp"
47	gezelter	1332	#include "utils/OOPSEConstant.hpp"
48			#include "utils/Tuple.hpp"
49	gezelter	1329
50			#ifndef IS_MPI
51			#include "math/SeqRandNumGen.hpp"
52			#else
53			#include "math/ParallelRandNumGen.hpp"
54			#endif
55
56
57			namespace oopse {
58
59	gezelter	1334	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
60	gezelter	1329
61			int seedValue;
62			Globals * simParams = info->getSimParams();
63	skuang	1330
64			stringToEnumMap_["Kinetic"] = rnemdKinetic;
65			stringToEnumMap_["Px"] = rnemdPx;
66			stringToEnumMap_["Py"] = rnemdPy;
67			stringToEnumMap_["Pz"] = rnemdPz;
68			stringToEnumMap_["Unknown"] = rnemdUnknown;
69
70	gezelter	1331	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
71	skuang	1341	evaluator_.loadScriptString(rnemdObjectSelection_);
72			seleMan_.setSelectionSet(evaluator_.evaluate());
73	gezelter	1331
74	skuang	1341
75			// do some sanity checking
76
77			int selectionCount = seleMan_.getSelectionCount();
78			int nIntegrable = info->getNGlobalIntegrableObjects();
79
80			if (selectionCount > nIntegrable) {
81			sprintf(painCave.errMsg,
82			"RNEMD warning: The current RNEMD_objectSelection,\n"
83			"\t\t%s\n"
84			"\thas resulted in %d selected objects. However,\n"
85			"\tthe total number of integrable objects in the system\n"
86			"\tis only %d. This is almost certainly not what you want\n"
87			"\tto do. A likely cause of this is forgetting the _RB_0\n"
88			"\tselector in the selection script!\n",
89			rnemdObjectSelection_.c_str(),
90			selectionCount, nIntegrable);
91			painCave.isFatal = 0;
92			simError();
93
94			}
95	gezelter	1331
96	skuang	1330	const std::string st = simParams->getRNEMD_swapType();
97
98			std::map<std::string, RNEMDTypeEnum>::iterator i;
99			i = stringToEnumMap_.find(st);
100			rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
101
102			set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
103			set_RNEMD_nBins(simParams->getRNEMD_nBins());
104			exchangeSum_ = 0.0;
105	skuang	1338	counter_ = 0; //added by shenyu
106
107	gezelter	1329	#ifndef IS_MPI
108			if (simParams->haveSeed()) {
109			seedValue = simParams->getSeed();
110			randNumGen_ = new SeqRandNumGen(seedValue);
111			}else {
112			randNumGen_ = new SeqRandNumGen();
113			}
114			#else
115			if (simParams->haveSeed()) {
116			seedValue = simParams->getSeed();
117			randNumGen_ = new ParallelRandNumGen(seedValue);
118			}else {
119			randNumGen_ = new ParallelRandNumGen();
120			}
121			#endif
122			}
123
124			RNEMD::~RNEMD() {
125			delete randNumGen_;
126			}
127	skuang	1330
128	gezelter	1329	void RNEMD::doSwap() {
129	gezelter	1332	int midBin = nBins_ / 2;
130	gezelter	1331
131	gezelter	1332	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
132			Mat3x3d hmat = currentSnap_->getHmat();
133
134	gezelter	1331	seleMan_.setSelectionSet(evaluator_.evaluate());
135
136	gezelter	1333	int selei;
137	gezelter	1331	StuntDouble* sd;
138	gezelter	1333	int idx;
139	gezelter	1331
140	skuang	1338	RealType min_val;
141			bool min_found = false;
142			StuntDouble* min_sd;
143
144			RealType max_val;
145			bool max_found = false;
146			StuntDouble* max_sd;
147
148	gezelter	1333	for (sd = seleMan_.beginSelected(selei); sd != NULL;
149			sd = seleMan_.nextSelected(selei)) {
150	gezelter	1332
151	gezelter	1333	idx = sd->getLocalIndex();
152
153	gezelter	1331	Vector3d pos = sd->getPos();
154	gezelter	1332
155			// wrap the stuntdouble's position back into the box:
156
157	gezelter	1331	if (usePeriodicBoundaryConditions_)
158	gezelter	1332	currentSnap_->wrapVector(pos);
159
160			// which bin is this stuntdouble in?
161	gezelter	1334	// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
162	gezelter	1332
163	skuang	1341	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
164	gezelter	1332
165	gezelter	1333
166	gezelter	1332	// if we're in bin 0 or the middleBin
167			if (binNo == 0 \|\| binNo == midBin) {
168
169			RealType mass = sd->getMass();
170			Vector3d vel = sd->getVel();
171			RealType value;
172
173			switch(rnemdType_) {
174			case rnemdKinetic :
175
176			value = mass * (vel[0]vel[0] + vel[1]vel[1] +
177			vel[2]*vel[2]);
178			if (sd->isDirectional()) {
179			Vector3d angMom = sd->getJ();
180			Mat3x3d I = sd->getI();
181
182			if (sd->isLinear()) {
183			int i = sd->linearAxis();
184			int j = (i + 1) % 3;
185			int k = (i + 2) % 3;
186			value += angMom[j] * angMom[j] / I(j, j) +
187			angMom[k] * angMom[k] / I(k, k);
188			} else {
189			value += angMom[0]*angMom[0]/I(0, 0)
190			+ angMom[1]*angMom[1]/I(1, 1)
191			+ angMom[2]*angMom[2]/I(2, 2);
192			}
193			}
194			value = value * 0.5 / OOPSEConstant::energyConvert;
195			break;
196			case rnemdPx :
197			value = mass * vel[0];
198			break;
199			case rnemdPy :
200			value = mass * vel[1];
201			break;
202			case rnemdPz :
203			value = mass * vel[2];
204			break;
205			case rnemdUnknown :
206			default :
207			break;
208			}
209
210	skuang	1338	if (binNo == 0) {
211			if (!min_found) {
212			min_val = value;
213			min_sd = sd;
214			min_found = true;
215			} else {
216			if (min_val > value) {
217			min_val = value;
218			min_sd = sd;
219			}
220			}
221			} else {
222			if (!max_found) {
223			max_val = value;
224			max_sd = sd;
225			max_found = true;
226			} else {
227			if (max_val < value) {
228			max_val = value;
229			max_sd = sd;
230			}
231			}
232			}
233	gezelter	1332	}
234	gezelter	1331	}
235	skuang	1341
236	skuang	1338	// missing: swap information in parallel
237
238			if (max_found && min_found) {
239			if (min_val< max_val) {
240	skuang	1341
241	skuang	1338	Vector3d min_vel = min_sd->getVel();
242			Vector3d max_vel = max_sd->getVel();
243			RealType temp_vel;
244	skuang	1341
245	skuang	1338	switch(rnemdType_) {
246			case rnemdKinetic :
247			min_sd->setVel(max_vel);
248	skuang	1341	max_sd->setVel(min_vel);
249
250	skuang	1338	if (min_sd->isDirectional() && max_sd->isDirectional()) {
251			Vector3d min_angMom = min_sd->getJ();
252			Vector3d max_angMom = max_sd->getJ();
253			min_sd->setJ(max_angMom);
254			max_sd->setJ(min_angMom);
255	skuang	1341	}
256	skuang	1338	break;
257			case rnemdPx :
258			temp_vel = min_vel.x();
259			min_vel.x() = max_vel.x();
260			max_vel.x() = temp_vel;
261			min_sd->setVel(min_vel);
262			max_sd->setVel(max_vel);
263			break;
264			case rnemdPy :
265			temp_vel = min_vel.y();
266			min_vel.y() = max_vel.y();
267			max_vel.y() = temp_vel;
268			min_sd->setVel(min_vel);
269			max_sd->setVel(max_vel);
270			break;
271			case rnemdPz :
272			temp_vel = min_vel.z();
273			min_vel.z() = max_vel.z();
274			max_vel.z() = temp_vel;
275			min_sd->setVel(min_vel);
276			max_sd->setVel(max_vel);
277			break;
278			case rnemdUnknown :
279			default :
280			break;
281			}
282			exchangeSum_ += max_val - min_val;
283			} else {
284			std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
285			}
286			} else {
287			std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
288			}
289			}
290
291			void RNEMD::getStatus() {
292
293			Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
294			Mat3x3d hmat = currentSnap_->getHmat();
295	skuang	1341	Stats& stat = currentSnap_->statData;
296	skuang	1338
297	skuang	1341	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
298	skuang	1338
299			seleMan_.setSelectionSet(evaluator_.evaluate());
300
301			int selei;
302			StuntDouble* sd;
303			int idx;
304
305	gezelter	1339	std::vector<RealType> valueHist; // keeps track of what's being averaged
306			std::vector<int> valueCount; // keeps track of the number of degrees of
307			// freedom being averaged
308	skuang	1338	valueHist.resize(nBins_);
309			valueCount.resize(nBins_);
310			//do they initialize themselves to zero automatically?
311			for (sd = seleMan_.beginSelected(selei); sd != NULL;
312			sd = seleMan_.nextSelected(selei)) {
313
314			idx = sd->getLocalIndex();
315
316			Vector3d pos = sd->getPos();
317
318			// wrap the stuntdouble's position back into the box:
319
320			if (usePeriodicBoundaryConditions_)
321			currentSnap_->wrapVector(pos);
322
323			// which bin is this stuntdouble in?
324			// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
325
326	skuang	1341	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
327	skuang	1338
328			//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
329
330			RealType mass = sd->getMass();
331			Vector3d vel = sd->getVel();
332			//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
333			RealType value;
334
335			switch(rnemdType_) {
336			case rnemdKinetic :
337
338			value = mass * (vel[0]vel[0] + vel[1]vel[1] +
339			vel[2]*vel[2]);
340
341	gezelter	1339	valueCount[binNo] += 3;
342	skuang	1341	//std::cerr <<"starting value = " << value << "\n";
343	skuang	1338	if (sd->isDirectional()) {
344	skuang	1341	//std::cerr << "angMom calculated.\n";
345	skuang	1338	Vector3d angMom = sd->getJ();
346	skuang	1341	//std::cerr << "current angMom: " << angMom << "\n";
347	skuang	1338	Mat3x3d I = sd->getI();
348
349			if (sd->isLinear()) {
350			int i = sd->linearAxis();
351			int j = (i + 1) % 3;
352			int k = (i + 2) % 3;
353			value += angMom[j] * angMom[j] / I(j, j) +
354			angMom[k] * angMom[k] / I(k, k);
355	gezelter	1339
356			valueCount[binNo] +=2;
357
358	skuang	1341	} else {
359			//std::cerr << "non-linear molecule.\n";
360	skuang	1338	value += angMom[0]*angMom[0]/I(0, 0)
361			+ angMom[1]*angMom[1]/I(1, 1)
362			+ angMom[2]*angMom[2]/I(2, 2);
363	gezelter	1339	valueCount[binNo] +=3;
364
365	skuang	1338	}
366			}
367	skuang	1341	//std::cerr <<"total value = " << value << "\n";
368			//value *= 0.5 / OOPSEConstant::energyConvert; // get it in kcal / mol
369			//value *= 2.0 / OOPSEConstant::kb; // convert to temperature
370			value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
371			//std::cerr <<"value = " << value << "\n";
372	skuang	1338	break;
373			case rnemdPx :
374			value = mass * vel[0];
375	gezelter	1339	valueCount[binNo]++;
376	skuang	1338	break;
377			case rnemdPy :
378			value = mass * vel[1];
379	gezelter	1339	valueCount[binNo]++;
380	skuang	1338	break;
381			case rnemdPz :
382			value = mass * vel[2];
383	gezelter	1339	valueCount[binNo]++;
384	skuang	1338	break;
385			case rnemdUnknown :
386			default :
387			break;
388			}
389			//std::cerr << "bin = " << binNo << " value = " << value ;
390			valueHist[binNo] += value;
391			//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
392			}
393	gezelter	1334
394	skuang	1338	std::cout << counter_++;
395			for (int j = 0; j < nBins_; j++)
396			std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
397			std::cout << "\n";
398	gezelter	1334	}
399	skuang	1338	}