src/integrators/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

#define HONKING_LARGE_VALUE 1.0e10

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;

#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;
            }
          }       
        }
      }
    }

#ifdef IS_MPI
    int nProc, worldRank;

    nProc = MPI::COMM_WORLD.Get_size();
    worldRank = MPI::COMM_WORLD.Get_rank();

    bool my_min_found = min_found;
    bool my_max_found = max_found;

    // Even if we didn't find a minimum, did someone else?
    MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found, 
                              1, MPI::BOOL, MPI::LAND);
    
    // Even if we didn't find a maximum, did someone else?
    MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found, 
                              1, MPI::BOOL, MPI::LAND);
    
    struct {
      RealType val;
      int rank;
    } max_vals, min_vals;
    
    if (min_found) {
      if (my_min_found) 
        min_vals.val = min_val;
      else 
        min_vals.val = HONKING_LARGE_VALUE;
      
      min_vals.rank = worldRank;    
      
      // Who had the minimum?
      MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals, 
                                1, MPI::REALTYPE_INT, MPI::MINLOC);
      min_val = min_vals.val;
    }
      
    if (max_found) {
      if (my_max_found) 
        max_vals.val = max_val;
      else 
        max_vals.val = -HONKING_LARGE_VALUE;
      
      max_vals.rank = worldRank;    
      
      // Who had the maximum?
      MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals, 
                                1, MPI::REALTYPE_INT, MPI::MAXLOC);
      max_val = max_vals.val;
    }
#endif

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

#ifdef IS_MPI       
        if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
          // I have both maximum and minimum, so proceed like a single
          // processor version:
#endif
          // objects to be swapped: velocity & angular velocity
          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;
          }
#ifdef IS_MPI
          // the rest of the cases only apply in parallel simulations:
        } else if (max_vals.rank == worldRank) {
          // I had the max, but not the minimum
          
          Vector3d min_vel;
          Vector3d max_vel = max_sd->getVel();
          MPI::Status status;

          // point-to-point swap of the velocity vector
          MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
                                   min_vals.rank, 0, 
                                   min_vel.getArrayPointer(), 3, MPI::REALTYPE,
                                   min_vals.rank, 0, status);
          
          switch(rnemdType_) {
          case rnemdKinetic :
            max_sd->setVel(min_vel);
            
            if (max_sd->isDirectional()) {
              Vector3d min_angMom;
              Vector3d max_angMom = max_sd->getJ();

              // point-to-point swap of the angular momentum vector
              MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3, 
                                       MPI::REALTYPE, min_vals.rank, 1, 
                                       min_angMom.getArrayPointer(), 3, 
                                       MPI::REALTYPE, min_vals.rank, 1, 
                                       status);

              max_sd->setJ(min_angMom);
            }
            break;
          case rnemdPx :
            max_vel.x() = min_vel.x();
            max_sd->setVel(max_vel);
            break;
          case rnemdPy :
            max_vel.y() = min_vel.y();
            max_sd->setVel(max_vel);
            break;
          case rnemdPz :
            max_vel.z() = min_vel.z();
            max_sd->setVel(max_vel);
            break;
          case rnemdUnknown : 
          default :
            break;
          }
        } else if (min_vals.rank == worldRank) {
          // I had the minimum but not the maximum:
          
          Vector3d max_vel;
          Vector3d min_vel = min_sd->getVel();
          MPI::Status status;
          
          // point-to-point swap of the velocity vector
          MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
                                   max_vals.rank, 0, 
                                   max_vel.getArrayPointer(), 3, MPI::REALTYPE,
                                   max_vals.rank, 0, status);
          
          switch(rnemdType_) {
          case rnemdKinetic :
            min_sd->setVel(max_vel);
            
            if (min_sd->isDirectional()) {
              Vector3d min_angMom = min_sd->getJ();
              Vector3d max_angMom;

              // point-to-point swap of the angular momentum vector
              MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3, 
                                       MPI::REALTYPE, max_vals.rank, 1, 
                                       max_angMom.getArrayPointer(), 3, 
                                       MPI::REALTYPE, max_vals.rank, 1, 
                                       status);

              min_sd->setJ(max_angMom);
            }
            break;
          case rnemdPx :
            min_vel.x() = max_vel.x();
            min_sd->setVel(min_vel);
            break;
          case rnemdPy :
            min_vel.y() = max_vel.y();
            min_sd->setVel(min_vel);
            break;
          case rnemdPz :
            min_vel.z() = max_vel.z();
            min_sd->setVel(min_vel);
            break;
          case rnemdUnknown : 
          default :
            break;
          }
        }
#endif
        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;
    RealType time = currentSnap_->getTime();

    stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;

    seleMan_.setSelectionSet(evaluator_.evaluate());

    int selei;
    StuntDouble* sd;
    int idx;

    std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's 
                                                  // being averaged
    std::vector<int> valueCount(nBins_, 0);       // keeps track of the 
                                                  // number of degrees of 
                                                  // freedom being averaged

    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_;     
      
      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]);
        
        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;
          }
        }
        value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;

        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;
      }
      valueHist[binNo] += value;
    }

#ifdef IS_MPI

    // all processors have the same number of bins, and STL vectors pack their 
    // arrays, so in theory, this should be safe:

    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
                              nBins_, MPI::REALTYPE, MPI::SUM);
    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
                              nBins_, MPI::INT, MPI::SUM);

    // If we're the root node, should we print out the results
    int worldRank = MPI::COMM_WORLD.Get_rank();
    if (worldRank == 0) {
#endif
       
      std::cout << time;
      for (int j = 0; j < nBins_; j++)
        std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
      std::cout << "\n";
      
#ifdef IS_MPI
    }
#endif
  }
}
Revision:	1350
Committed:	Thu May 21 18:56:45 2009 UTC (16 years, 5 months ago) by gezelter
File size:	17543 byte(s)
Log Message:	Parallel version of 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	gezelter	1350	#define HONKING_LARGE_VALUE 1.0e10
57	gezelter	1329
58			namespace oopse {
59
60	gezelter	1334	RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
61	gezelter	1329
62			int seedValue;
63			Globals * simParams = info->getSimParams();
64	skuang	1330
65			stringToEnumMap_["Kinetic"] = rnemdKinetic;
66			stringToEnumMap_["Px"] = rnemdPx;
67			stringToEnumMap_["Py"] = rnemdPy;
68			stringToEnumMap_["Pz"] = rnemdPz;
69			stringToEnumMap_["Unknown"] = rnemdUnknown;
70
71	gezelter	1331	rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
72	skuang	1341	evaluator_.loadScriptString(rnemdObjectSelection_);
73			seleMan_.setSelectionSet(evaluator_.evaluate());
74	gezelter	1331
75	skuang	1341
76			// do some sanity checking
77
78			int selectionCount = seleMan_.getSelectionCount();
79			int nIntegrable = info->getNGlobalIntegrableObjects();
80
81			if (selectionCount > nIntegrable) {
82			sprintf(painCave.errMsg,
83			"RNEMD warning: The current RNEMD_objectSelection,\n"
84			"\t\t%s\n"
85			"\thas resulted in %d selected objects. However,\n"
86			"\tthe total number of integrable objects in the system\n"
87			"\tis only %d. This is almost certainly not what you want\n"
88			"\tto do. A likely cause of this is forgetting the _RB_0\n"
89			"\tselector in the selection script!\n",
90			rnemdObjectSelection_.c_str(),
91			selectionCount, nIntegrable);
92			painCave.isFatal = 0;
93			simError();
94
95			}
96	gezelter	1331
97	skuang	1330	const std::string st = simParams->getRNEMD_swapType();
98
99			std::map<std::string, RNEMDTypeEnum>::iterator i;
100			i = stringToEnumMap_.find(st);
101			rnemdType_ = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
102
103			set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
104			set_RNEMD_nBins(simParams->getRNEMD_nBins());
105			exchangeSum_ = 0.0;
106	skuang	1338
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	gezelter	1350	#ifdef IS_MPI
237			int nProc, worldRank;
238	skuang	1338
239	gezelter	1350	nProc = MPI::COMM_WORLD.Get_size();
240			worldRank = MPI::COMM_WORLD.Get_rank();
241
242			bool my_min_found = min_found;
243			bool my_max_found = max_found;
244
245			// Even if we didn't find a minimum, did someone else?
246			MPI::COMM_WORLD.Allreduce(&my_min_found, &min_found,
247			1, MPI::BOOL, MPI::LAND);
248
249			// Even if we didn't find a maximum, did someone else?
250			MPI::COMM_WORLD.Allreduce(&my_max_found, &max_found,
251			1, MPI::BOOL, MPI::LAND);
252
253			struct {
254			RealType val;
255			int rank;
256			} max_vals, min_vals;
257
258			if (min_found) {
259			if (my_min_found)
260			min_vals.val = min_val;
261			else
262			min_vals.val = HONKING_LARGE_VALUE;
263
264			min_vals.rank = worldRank;
265
266			// Who had the minimum?
267			MPI::COMM_WORLD.Allreduce(&min_vals, &min_vals,
268			1, MPI::REALTYPE_INT, MPI::MINLOC);
269			min_val = min_vals.val;
270			}
271
272			if (max_found) {
273			if (my_max_found)
274			max_vals.val = max_val;
275			else
276			max_vals.val = -HONKING_LARGE_VALUE;
277
278			max_vals.rank = worldRank;
279
280			// Who had the maximum?
281			MPI::COMM_WORLD.Allreduce(&max_vals, &max_vals,
282			1, MPI::REALTYPE_INT, MPI::MAXLOC);
283			max_val = max_vals.val;
284			}
285			#endif
286
287	skuang	1338	if (max_found && min_found) {
288			if (min_val< max_val) {
289	skuang	1341
290	gezelter	1350	#ifdef IS_MPI
291			if (max_vals.rank == worldRank && min_vals.rank == worldRank) {
292			// I have both maximum and minimum, so proceed like a single
293			// processor version:
294			#endif
295			// objects to be swapped: velocity & angular velocity
296			Vector3d min_vel = min_sd->getVel();
297			Vector3d max_vel = max_sd->getVel();
298			RealType temp_vel;
299
300			switch(rnemdType_) {
301			case rnemdKinetic :
302			min_sd->setVel(max_vel);
303			max_sd->setVel(min_vel);
304			if (min_sd->isDirectional() && max_sd->isDirectional()) {
305			Vector3d min_angMom = min_sd->getJ();
306			Vector3d max_angMom = max_sd->getJ();
307			min_sd->setJ(max_angMom);
308			max_sd->setJ(min_angMom);
309			}
310			break;
311			case rnemdPx :
312			temp_vel = min_vel.x();
313			min_vel.x() = max_vel.x();
314			max_vel.x() = temp_vel;
315			min_sd->setVel(min_vel);
316			max_sd->setVel(max_vel);
317			break;
318			case rnemdPy :
319			temp_vel = min_vel.y();
320			min_vel.y() = max_vel.y();
321			max_vel.y() = temp_vel;
322			min_sd->setVel(min_vel);
323			max_sd->setVel(max_vel);
324			break;
325			case rnemdPz :
326			temp_vel = min_vel.z();
327			min_vel.z() = max_vel.z();
328			max_vel.z() = temp_vel;
329			min_sd->setVel(min_vel);
330			max_sd->setVel(max_vel);
331			break;
332			case rnemdUnknown :
333			default :
334			break;
335			}
336			#ifdef IS_MPI
337			// the rest of the cases only apply in parallel simulations:
338			} else if (max_vals.rank == worldRank) {
339			// I had the max, but not the minimum
340
341			Vector3d min_vel;
342			Vector3d max_vel = max_sd->getVel();
343			MPI::Status status;
344	skuang	1341
345	gezelter	1350	// point-to-point swap of the velocity vector
346			MPI::COMM_WORLD.Sendrecv(max_vel.getArrayPointer(), 3, MPI::REALTYPE,
347			min_vals.rank, 0,
348			min_vel.getArrayPointer(), 3, MPI::REALTYPE,
349			min_vals.rank, 0, status);
350
351			switch(rnemdType_) {
352			case rnemdKinetic :
353			max_sd->setVel(min_vel);
354
355			if (max_sd->isDirectional()) {
356			Vector3d min_angMom;
357			Vector3d max_angMom = max_sd->getJ();
358	skuang	1341
359	gezelter	1350	// point-to-point swap of the angular momentum vector
360			MPI::COMM_WORLD.Sendrecv(max_angMom.getArrayPointer(), 3,
361			MPI::REALTYPE, min_vals.rank, 1,
362			min_angMom.getArrayPointer(), 3,
363			MPI::REALTYPE, min_vals.rank, 1,
364			status);
365
366			max_sd->setJ(min_angMom);
367			}
368			break;
369			case rnemdPx :
370			max_vel.x() = min_vel.x();
371			max_sd->setVel(max_vel);
372			break;
373			case rnemdPy :
374			max_vel.y() = min_vel.y();
375			max_sd->setVel(max_vel);
376			break;
377			case rnemdPz :
378			max_vel.z() = min_vel.z();
379			max_sd->setVel(max_vel);
380			break;
381			case rnemdUnknown :
382			default :
383			break;
384	skuang	1341	}
385	gezelter	1350	} else if (min_vals.rank == worldRank) {
386			// I had the minimum but not the maximum:
387
388			Vector3d max_vel;
389			Vector3d min_vel = min_sd->getVel();
390			MPI::Status status;
391
392			// point-to-point swap of the velocity vector
393			MPI::COMM_WORLD.Sendrecv(min_vel.getArrayPointer(), 3, MPI::REALTYPE,
394			max_vals.rank, 0,
395			max_vel.getArrayPointer(), 3, MPI::REALTYPE,
396			max_vals.rank, 0, status);
397
398			switch(rnemdType_) {
399			case rnemdKinetic :
400			min_sd->setVel(max_vel);
401
402			if (min_sd->isDirectional()) {
403			Vector3d min_angMom = min_sd->getJ();
404			Vector3d max_angMom;
405
406			// point-to-point swap of the angular momentum vector
407			MPI::COMM_WORLD.Sendrecv(min_angMom.getArrayPointer(), 3,
408			MPI::REALTYPE, max_vals.rank, 1,
409			max_angMom.getArrayPointer(), 3,
410			MPI::REALTYPE, max_vals.rank, 1,
411			status);
412
413			min_sd->setJ(max_angMom);
414			}
415			break;
416			case rnemdPx :
417			min_vel.x() = max_vel.x();
418			min_sd->setVel(min_vel);
419			break;
420			case rnemdPy :
421			min_vel.y() = max_vel.y();
422			min_sd->setVel(min_vel);
423			break;
424			case rnemdPz :
425			min_vel.z() = max_vel.z();
426			min_sd->setVel(min_vel);
427			break;
428			case rnemdUnknown :
429			default :
430			break;
431			}
432			}
433			#endif
434			exchangeSum_ += max_val - min_val;
435	skuang	1338	} else {
436	gezelter	1350	std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
437	skuang	1338	}
438			} else {
439			std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
440			}
441	gezelter	1350
442	skuang	1338	}
443	gezelter	1350
444	skuang	1338	void RNEMD::getStatus() {
445
446			Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
447			Mat3x3d hmat = currentSnap_->getHmat();
448	skuang	1341	Stats& stat = currentSnap_->statData;
449	gezelter	1350	RealType time = currentSnap_->getTime();
450	skuang	1338
451	skuang	1341	stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
452	skuang	1338
453			seleMan_.setSelectionSet(evaluator_.evaluate());
454
455			int selei;
456			StuntDouble* sd;
457			int idx;
458
459	gezelter	1350	std::vector<RealType> valueHist(nBins_, 0.0); // keeps track of what's
460			// being averaged
461			std::vector<int> valueCount(nBins_, 0); // keeps track of the
462			// number of degrees of
463			// freedom being averaged
464
465	skuang	1338	for (sd = seleMan_.beginSelected(selei); sd != NULL;
466			sd = seleMan_.nextSelected(selei)) {
467
468			idx = sd->getLocalIndex();
469
470			Vector3d pos = sd->getPos();
471
472			// wrap the stuntdouble's position back into the box:
473
474			if (usePeriodicBoundaryConditions_)
475			currentSnap_->wrapVector(pos);
476
477			// which bin is this stuntdouble in?
478			// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
479
480	gezelter	1350	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
481	skuang	1338
482			RealType mass = sd->getMass();
483			Vector3d vel = sd->getVel();
484			RealType value;
485
486			switch(rnemdType_) {
487			case rnemdKinetic :
488
489			value = mass * (vel[0]vel[0] + vel[1]vel[1] +
490			vel[2]*vel[2]);
491
492	gezelter	1339	valueCount[binNo] += 3;
493	skuang	1338	if (sd->isDirectional()) {
494			Vector3d angMom = sd->getJ();
495			Mat3x3d I = sd->getI();
496
497			if (sd->isLinear()) {
498			int i = sd->linearAxis();
499			int j = (i + 1) % 3;
500			int k = (i + 2) % 3;
501			value += angMom[j] * angMom[j] / I(j, j) +
502			angMom[k] * angMom[k] / I(k, k);
503	gezelter	1339
504			valueCount[binNo] +=2;
505
506	skuang	1341	} else {
507	skuang	1338	value += angMom[0]*angMom[0]/I(0, 0)
508			+ angMom[1]*angMom[1]/I(1, 1)
509			+ angMom[2]*angMom[2]/I(2, 2);
510	gezelter	1339	valueCount[binNo] +=3;
511	skuang	1338	}
512			}
513	skuang	1341	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
514	gezelter	1350
515	skuang	1338	break;
516			case rnemdPx :
517			value = mass * vel[0];
518	gezelter	1339	valueCount[binNo]++;
519	skuang	1338	break;
520			case rnemdPy :
521			value = mass * vel[1];
522	gezelter	1339	valueCount[binNo]++;
523	skuang	1338	break;
524			case rnemdPz :
525			value = mass * vel[2];
526	gezelter	1339	valueCount[binNo]++;
527	skuang	1338	break;
528			case rnemdUnknown :
529			default :
530			break;
531			}
532			valueHist[binNo] += value;
533			}
534	gezelter	1350
535			#ifdef IS_MPI
536
537			// all processors have the same number of bins, and STL vectors pack their
538			// arrays, so in theory, this should be safe:
539
540			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueHist[0],
541			nBins_, MPI::REALTYPE, MPI::SUM);
542			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &valueCount[0],
543			nBins_, MPI::INT, MPI::SUM);
544
545			// If we're the root node, should we print out the results
546			int worldRank = MPI::COMM_WORLD.Get_rank();
547			if (worldRank == 0) {
548			#endif
549
550			std::cout << time;
551			for (int j = 0; j < nBins_; j++)
552			std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
553			std::cout << "\n";
554
555			#ifdef IS_MPI
556			}
557			#endif
558	gezelter	1334	}
559	skuang	1338	}