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";
    
    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() {
    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;

    std::vector<tuple3<RealType, int, StuntDouble* > > endSlice;
    std::vector<tuple3<RealType, int, StuntDouble* > > midSlice;
    
    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 = midBin + int(nBins_ * (pos.z()) / 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)
          endSlice.push_back( make_tuple3(value, idx, sd));
        
        if (binNo == midBin) 
          midSlice.push_back( make_tuple3(value, idx, sd));               
      }
    }
    
    // find smallest value in endSlice:
    std::sort(endSlice.begin(), endSlice.end());     
    RealType min_val = endSlice[0].first;
    int min_idx = endSlice[0].second;
    StuntDouble* min_sd = endSlice[0].third;
    
    std::cerr << "smallest value = " << min_val << " idx = " << min_idx << "\n";
    
    // find largest value in midSlice:
    std::sort(midSlice.rbegin(), midSlice.rend());
    RealType max_val = midSlice[0].first;
    int max_idx = midSlice[0].second;
    StuntDouble* max_sd = midSlice[0].third;
    
    std::cerr << "largest value = " << max_val << " idx = " << max_idx << "\n";
    
  }
}   
Revision:	1334
Committed:	Thu Apr 2 19:55:37 2009 UTC (16 years, 7 months ago) by gezelter
Original Path:	*trunk/src/integrators/RNEMD.cpp*
File size:	7723 byte(s)
Log Message:	Bug fix
#	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			std::cerr << "done";
81
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	gezelter	1329
92			#ifndef IS_MPI
93			if (simParams->haveSeed()) {
94			seedValue = simParams->getSeed();
95			randNumGen_ = new SeqRandNumGen(seedValue);
96			}else {
97			randNumGen_ = new SeqRandNumGen();
98			}
99			#else
100			if (simParams->haveSeed()) {
101			seedValue = simParams->getSeed();
102			randNumGen_ = new ParallelRandNumGen(seedValue);
103			}else {
104			randNumGen_ = new ParallelRandNumGen();
105			}
106			#endif
107			}
108
109			RNEMD::~RNEMD() {
110			delete randNumGen_;
111			}
112	skuang	1330
113	gezelter	1329	void RNEMD::doSwap() {
114			std::cerr << "in RNEMD!\n";
115	skuang	1330	std::cerr << "nBins = " << nBins_ << "\n";
116	gezelter	1332	int midBin = nBins_ / 2;
117			std::cerr << "midBin = " << midBin << "\n";
118	skuang	1330	std::cerr << "swapTime = " << swapTime_ << "\n";
119			std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
120			std::cerr << "swapType = " << rnemdType_ << "\n";
121	gezelter	1331	std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
122
123	gezelter	1332	Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
124			Mat3x3d hmat = currentSnap_->getHmat();
125
126	gezelter	1333	std::cerr << "hmat = " << hmat << "\n";
127
128	gezelter	1331	seleMan_.setSelectionSet(evaluator_.evaluate());
129
130			std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
131
132	gezelter	1333	int selei;
133	gezelter	1331	StuntDouble* sd;
134	gezelter	1333	int idx;
135	gezelter	1331
136	gezelter	1332	std::vector<tuple3<RealType, int, StuntDouble* > > endSlice;
137			std::vector<tuple3<RealType, int, StuntDouble* > > midSlice;
138
139	gezelter	1333	for (sd = seleMan_.beginSelected(selei); sd != NULL;
140			sd = seleMan_.nextSelected(selei)) {
141	gezelter	1332
142	gezelter	1333	idx = sd->getLocalIndex();
143
144	gezelter	1331	Vector3d pos = sd->getPos();
145	gezelter	1332
146			// wrap the stuntdouble's position back into the box:
147
148	gezelter	1331	if (usePeriodicBoundaryConditions_)
149	gezelter	1332	currentSnap_->wrapVector(pos);
150
151			// which bin is this stuntdouble in?
152	gezelter	1334	// wrapped positions are in the range [-0.5hmat(2,2), +0.5hmat(2,2)]
153	gezelter	1332
154	gezelter	1334	int binNo = midBin + int(nBins_ * (pos.z()) / hmat(2,2));
155	gezelter	1332
156	gezelter	1334	std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
157	gezelter	1333
158	gezelter	1332	// if we're in bin 0 or the middleBin
159			if (binNo == 0 \|\| binNo == midBin) {
160
161			RealType mass = sd->getMass();
162			Vector3d vel = sd->getVel();
163			RealType value;
164
165			switch(rnemdType_) {
166			case rnemdKinetic :
167
168			value = mass * (vel[0]vel[0] + vel[1]vel[1] +
169			vel[2]*vel[2]);
170
171			if (sd->isDirectional()) {
172			Vector3d angMom = sd->getJ();
173			Mat3x3d I = sd->getI();
174
175			if (sd->isLinear()) {
176			int i = sd->linearAxis();
177			int j = (i + 1) % 3;
178			int k = (i + 2) % 3;
179			value += angMom[j] * angMom[j] / I(j, j) +
180			angMom[k] * angMom[k] / I(k, k);
181			} else {
182			value += angMom[0]*angMom[0]/I(0, 0)
183			+ angMom[1]*angMom[1]/I(1, 1)
184			+ angMom[2]*angMom[2]/I(2, 2);
185			}
186			}
187			value = value * 0.5 / OOPSEConstant::energyConvert;
188			break;
189			case rnemdPx :
190			value = mass * vel[0];
191			break;
192			case rnemdPy :
193			value = mass * vel[1];
194			break;
195			case rnemdPz :
196			value = mass * vel[2];
197			break;
198			case rnemdUnknown :
199			default :
200			break;
201			}
202
203			if (binNo == 0)
204			endSlice.push_back( make_tuple3(value, idx, sd));
205
206			if (binNo == midBin)
207			midSlice.push_back( make_tuple3(value, idx, sd));
208			}
209	gezelter	1331	}
210	gezelter	1334
211			// find smallest value in endSlice:
212			std::sort(endSlice.begin(), endSlice.end());
213			RealType min_val = endSlice[0].first;
214			int min_idx = endSlice[0].second;
215			StuntDouble* min_sd = endSlice[0].third;
216
217			std::cerr << "smallest value = " << min_val << " idx = " << min_idx << "\n";
218
219			// find largest value in midSlice:
220			std::sort(midSlice.rbegin(), midSlice.rend());
221			RealType max_val = midSlice[0].first;
222			int max_idx = midSlice[0].second;
223			StuntDouble* max_sd = midSlice[0].third;
224
225			std::cerr << "largest value = " << max_val << " idx = " << max_idx << "\n";
226
227			}
228			}