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

/* Remove me after testing*/
/*
#include <cstdio>
#include <iostream>
*/
/*End remove me*/

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();

    std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
    evaluator_.loadScriptString(rnemdObjectSelection_);
    std::cerr << "done\n";
    
    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
    //profile_.open("profile", std::ios::out);

#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_;
    //profile_.close();
  }

  void RNEMD::doSwap() {
    //std::cerr << "in RNEMD!\n";   
    //std::cerr << "nBins = " << nBins_ << "\n";
    int midBin = nBins_ / 2;
    //std::cerr << "midBin = " << midBin << "\n";
    //std::cerr << "swapTime = " << swapTime_ << "\n";
    //std::cerr << "swapType = " << rnemdType_ << "\n";
    //std::cerr << "selection = " << rnemdObjectSelection_ << "\n";

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

    //std::cerr << "hmat = " << hmat << "\n";

    seleMan_.setSelectionSet(evaluator_.evaluate());

    //std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";

    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_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2));

      //std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";

      // 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;
            }
          }       
        }
      }
    }
    //std::cerr << "smallest value = " << min_val  << "\n";
    //std::cerr << "largest value = " << max_val << "\n";
    
    // 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";
    }
    std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
  }

  void RNEMD::getStatus() {
    //std::cerr << "in RNEMD!\n";   
    //std::cerr << "nBins = " << nBins_ << "\n";
    int midBin = nBins_ / 2;
    //std::cerr << "midBin = " << midBin << "\n";
    //std::cerr << "swapTime = " << swapTime_ << "\n";
    //std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
    //std::cerr << "swapType = " << rnemdType_ << "\n";
    //std::cerr << "selection = " << rnemdObjectSelection_ << "\n";

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

    //std::cerr << "hmat = " << hmat << "\n";

    seleMan_.setSelectionSet(evaluator_.evaluate());

    //std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";

    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;
    */
    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_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2));
      
      //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;

        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);

            valueCount[binNo] +=2;

          } else {                        
            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 <<"this value = " << value << "\n";
        value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
        value *= 2.0 / OOPSEConstant::kb;             // convert to temperature
        //std::cerr <<"this 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:	1339
Committed:	Thu Apr 23 18:31:05 2009 UTC (16 years ago) by gezelter
Original Path:	*trunk/src/integrators/RNEMD.cpp*
File size:	12603 byte(s)
Log Message:	bug fix in DLM, added temperature profiles and uniform bins to RNEMD
#	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			/* Remove me after testing*/
57			/*
58			#include <cstdio>
59			#include <iostream>
60			*/
61			/End remove me/
62
63			namespace oopse {
64
65	gezelter	1334	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
66	gezelter	1329
67			int seedValue;
68			Globals * simParams = info->getSimParams();
69	skuang	1330
70			stringToEnumMap_["Kinetic"] = rnemdKinetic;
71			stringToEnumMap_["Px"] = rnemdPx;
72			stringToEnumMap_["Py"] = rnemdPy;
73			stringToEnumMap_["Pz"] = rnemdPz;
74			stringToEnumMap_["Unknown"] = rnemdUnknown;
75
76	gezelter	1331	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
77
78			std::cerr << "calling evaluator with " << rnemdObjectSelection_ << "\n";
79			evaluator_.loadScriptString(rnemdObjectSelection_);
80	skuang	1338	std::cerr << "done\n";
81	gezelter	1331
82	skuang	1330	const std::string st = simParams->getRNEMD_swapType();
83
84			std::map<std::string, RNEMDTypeEnum>::iterator i;
85			i = stringToEnumMap_.find(st);
86			rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
87
88			set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
89			set_RNEMD_nBins(simParams->getRNEMD_nBins());
90			exchangeSum_ = 0.0;
91	skuang	1338	counter_ = 0; //added by shenyu
92			//profile_.open("profile", std::ios::out);
93
94	gezelter	1329	#ifndef IS_MPI
95			if (simParams->haveSeed()) {
96			seedValue = simParams->getSeed();
97			randNumGen_ = new SeqRandNumGen(seedValue);
98			}else {
99			randNumGen_ = new SeqRandNumGen();
100			}
101			#else
102			if (simParams->haveSeed()) {
103			seedValue = simParams->getSeed();
104			randNumGen_ = new ParallelRandNumGen(seedValue);
105			}else {
106			randNumGen_ = new ParallelRandNumGen();
107			}
108			#endif
109			}
110
111			RNEMD::~RNEMD() {
112			delete randNumGen_;
113	skuang	1338	//profile_.close();
114	gezelter	1329	}
115	skuang	1330
116	gezelter	1329	void RNEMD::doSwap() {
117	skuang	1338	//std::cerr << "in RNEMD!\n";
118			//std::cerr << "nBins = " << nBins_ << "\n";
119	gezelter	1332	int midBin = nBins_ / 2;
120	skuang	1338	//std::cerr << "midBin = " << midBin << "\n";
121			//std::cerr << "swapTime = " << swapTime_ << "\n";
122			//std::cerr << "swapType = " << rnemdType_ << "\n";
123			//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
124	gezelter	1331
125	gezelter	1332	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
126			Mat3x3d hmat = currentSnap_->getHmat();
127
128	skuang	1338	//std::cerr << "hmat = " << hmat << "\n";
129	gezelter	1333
130	gezelter	1331	seleMan_.setSelectionSet(evaluator_.evaluate());
131
132	skuang	1338	//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
133	gezelter	1331
134	gezelter	1333	int selei;
135	gezelter	1331	StuntDouble* sd;
136	gezelter	1333	int idx;
137	gezelter	1331
138	skuang	1338	RealType min_val;
139			bool min_found = false;
140			StuntDouble* min_sd;
141
142			RealType max_val;
143			bool max_found = false;
144			StuntDouble* max_sd;
145
146	gezelter	1333	for (sd = seleMan_.beginSelected(selei); sd != NULL;
147			sd = seleMan_.nextSelected(selei)) {
148	gezelter	1332
149	gezelter	1333	idx = sd->getLocalIndex();
150
151	gezelter	1331	Vector3d pos = sd->getPos();
152	gezelter	1332
153			// wrap the stuntdouble's position back into the box:
154
155	gezelter	1331	if (usePeriodicBoundaryConditions_)
156	gezelter	1332	currentSnap_->wrapVector(pos);
157
158			// which bin is this stuntdouble in?
159	gezelter	1334	// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
160	gezelter	1332
161	gezelter	1339	int binNo = int((nBins_-1) * (pos.z() + 0.5*hmat(2,2)) / hmat(2,2));
162	gezelter	1332
163	skuang	1338	//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
164	gezelter	1333
165	gezelter	1332	// if we're in bin 0 or the middleBin
166			if (binNo == 0 \|\| binNo == midBin) {
167
168			RealType mass = sd->getMass();
169			Vector3d vel = sd->getVel();
170			RealType value;
171
172			switch(rnemdType_) {
173			case rnemdKinetic :
174
175			value = mass * (vel[0]vel[0] + vel[1]vel[1] +
176			vel[2]*vel[2]);
177
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	1338	//std::cerr << "smallest value = " << min_val << "\n";
236			//std::cerr << "largest value = " << max_val << "\n";
237	gezelter	1334
238	skuang	1338	// missing: swap information in parallel
239
240			if (max_found && min_found) {
241			if (min_val< max_val) {
242			Vector3d min_vel = min_sd->getVel();
243			Vector3d max_vel = max_sd->getVel();
244			RealType temp_vel;
245			switch(rnemdType_) {
246			case rnemdKinetic :
247			min_sd->setVel(max_vel);
248			max_sd->setVel(min_vel);
249			if (min_sd->isDirectional() && max_sd->isDirectional()) {
250			Vector3d min_angMom = min_sd->getJ();
251			Vector3d max_angMom = max_sd->getJ();
252			min_sd->setJ(max_angMom);
253			max_sd->setJ(min_angMom);
254			}
255			break;
256			case rnemdPx :
257			temp_vel = min_vel.x();
258			min_vel.x() = max_vel.x();
259			max_vel.x() = temp_vel;
260			min_sd->setVel(min_vel);
261			max_sd->setVel(max_vel);
262			break;
263			case rnemdPy :
264			temp_vel = min_vel.y();
265			min_vel.y() = max_vel.y();
266			max_vel.y() = temp_vel;
267			min_sd->setVel(min_vel);
268			max_sd->setVel(max_vel);
269			break;
270			case rnemdPz :
271			temp_vel = min_vel.z();
272			min_vel.z() = max_vel.z();
273			max_vel.z() = temp_vel;
274			min_sd->setVel(min_vel);
275			max_sd->setVel(max_vel);
276			break;
277			case rnemdUnknown :
278			default :
279			break;
280			}
281			exchangeSum_ += max_val - min_val;
282			} else {
283			std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
284			}
285			} else {
286			std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
287			}
288			std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
289			}
290
291			void RNEMD::getStatus() {
292			//std::cerr << "in RNEMD!\n";
293			//std::cerr << "nBins = " << nBins_ << "\n";
294			int midBin = nBins_ / 2;
295			//std::cerr << "midBin = " << midBin << "\n";
296			//std::cerr << "swapTime = " << swapTime_ << "\n";
297			//std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
298			//std::cerr << "swapType = " << rnemdType_ << "\n";
299			//std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
300
301			Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
302			Mat3x3d hmat = currentSnap_->getHmat();
303
304			//std::cerr << "hmat = " << hmat << "\n";
305
306			seleMan_.setSelectionSet(evaluator_.evaluate());
307
308			//std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
309
310			int selei;
311			StuntDouble* sd;
312			int idx;
313			/*
314			RealType min_val;
315			bool min_found = false;
316			StuntDouble* min_sd;
317
318			RealType max_val;
319			bool max_found = false;
320			StuntDouble* max_sd;
321			*/
322	gezelter	1339	std::vector<RealType> valueHist; // keeps track of what's being averaged
323			std::vector<int> valueCount; // keeps track of the number of degrees of
324			// freedom being averaged
325	skuang	1338	valueHist.resize(nBins_);
326			valueCount.resize(nBins_);
327			//do they initialize themselves to zero automatically?
328			for (sd = seleMan_.beginSelected(selei); sd != NULL;
329			sd = seleMan_.nextSelected(selei)) {
330
331			idx = sd->getLocalIndex();
332
333			Vector3d pos = sd->getPos();
334
335			// wrap the stuntdouble's position back into the box:
336
337			if (usePeriodicBoundaryConditions_)
338			currentSnap_->wrapVector(pos);
339
340			// which bin is this stuntdouble in?
341			// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
342
343	gezelter	1339	int binNo = int((nBins_-1) * (pos.z()+0.5*hmat(2,2)) / hmat(2,2));
344	skuang	1338
345			//std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
346
347			RealType mass = sd->getMass();
348			Vector3d vel = sd->getVel();
349			//std::cerr << "mass = " << mass << " vel = " << vel << "\n";
350			RealType value;
351
352			switch(rnemdType_) {
353			case rnemdKinetic :
354
355			value = mass * (vel[0]vel[0] + vel[1]vel[1] +
356			vel[2]*vel[2]);
357
358	gezelter	1339	valueCount[binNo] += 3;
359
360	skuang	1338	if (sd->isDirectional()) {
361			Vector3d angMom = sd->getJ();
362			Mat3x3d I = sd->getI();
363
364			if (sd->isLinear()) {
365			int i = sd->linearAxis();
366			int j = (i + 1) % 3;
367			int k = (i + 2) % 3;
368			value += angMom[j] * angMom[j] / I(j, j) +
369			angMom[k] * angMom[k] / I(k, k);
370	gezelter	1339
371			valueCount[binNo] +=2;
372
373	skuang	1338	} else {
374			value += angMom[0]*angMom[0]/I(0, 0)
375			+ angMom[1]*angMom[1]/I(1, 1)
376			+ angMom[2]*angMom[2]/I(2, 2);
377	gezelter	1339	valueCount[binNo] +=3;
378
379	skuang	1338	}
380			}
381			//std::cerr <<"this value = " << value << "\n";
382	gezelter	1339	value *= 0.5 / OOPSEConstant::energyConvert; // get it in kcal / mol
383			value *= 2.0 / OOPSEConstant::kb; // convert to temperature
384	skuang	1338	//std::cerr <<"this value = " << value << "\n";
385			break;
386			case rnemdPx :
387			value = mass * vel[0];
388	gezelter	1339	valueCount[binNo]++;
389	skuang	1338	break;
390			case rnemdPy :
391			value = mass * vel[1];
392	gezelter	1339	valueCount[binNo]++;
393	skuang	1338	break;
394			case rnemdPz :
395			value = mass * vel[2];
396	gezelter	1339	valueCount[binNo]++;
397	skuang	1338	break;
398			case rnemdUnknown :
399			default :
400			break;
401			}
402			//std::cerr << "bin = " << binNo << " value = " << value ;
403			valueHist[binNo] += value;
404			//std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
405			}
406	gezelter	1334
407	skuang	1338	std::cout << counter_++;
408			for (int j = 0; j < nBins_; j++)
409			std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
410			std::cout << "\n";
411	gezelter	1334	}
412	skuang	1338	}