src/restraints/ThermoIntegrationForceManager.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 <cmath>
#include "restraints/ThermoIntegrationForceManager.hpp"
#include "integrators/Integrator.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/OOPSEConstant.hpp"
#include "utils/StringUtils.hpp"

#ifdef IS_MPI
#include <mpi.h>
#define TAKE_THIS_TAG_REAL 2
#endif //is_mpi

namespace oopse {
  
  ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info): 
    ForceManager(info){
      currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      simParam = info_->getSimParams();
    
      if (simParam->haveThermodynamicIntegrationLambda()){
        tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
      }
      else{
        tIntLambda_ = 1.0;
        sprintf(painCave.errMsg,
                "ThermoIntegration error: the transformation parameter\n"
                "\t(lambda) was not specified. OOPSE will use a default\n"
                "\tvalue of %f. To set lambda, use the \n"
                "\tthermodynamicIntegrationLambda variable.\n",
                tIntLambda_);
        painCave.isFatal = 0;
        simError();
      }
    
      if (simParam->haveThermodynamicIntegrationK()){
        tIntK_ = simParam->getThermodynamicIntegrationK();
      }
      else{
        tIntK_ = 1.0;
        sprintf(painCave.errMsg,
                "ThermoIntegration Warning: the tranformation parameter\n"
                "\texponent (k) was not specified. OOPSE will use a default\n"
                "\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
                "\tvariable.\n",
                tIntK_);
        painCave.isFatal = 0;
        simError();      
      }
    
      if (simParam->getUseSolidThermInt()) {
        // build a restraint object
        restraint_ =  new Restraints(info_, tIntLambda_, tIntK_);
      
      }
    
      // build the scaling factor used to modulate the forces and torques
      factor_ = pow(tIntLambda_, tIntK_);

    }
  
  ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
  }
  
  void ThermoIntegrationForceManager::calcForces(bool needPotential, 
                                                 bool needStress){
    Snapshot* curSnapshot;
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::IntegrableObjectIterator ii;
    StuntDouble* integrableObject;
    Vector3d frc;
    Vector3d trq;
    Mat3x3d tempTau;
    
    // perform the standard calcForces first
    ForceManager::calcForces(needPotential, needStress);
    
    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();

    // now scale forces and torques of all the integrableObjects
      
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (integrableObject = mol->beginIntegrableObject(ii); 
           integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(ii)) {
        frc = integrableObject->getFrc();
        frc *= factor_;
        integrableObject->setFrc(frc);
        
        if (integrableObject->isDirectional()){
          trq = integrableObject->getTrq();
          trq *= factor_;
          integrableObject->setTrq(trq);
        }
      }
    }
  
    // set vraw to be the unmodulated potential
    lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
    curSnapshot->statData[Stats::VRAW] = lrPot_;
    
    // modulate the potential and update the snapshot
    lrPot_ *= factor_;
    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
    
    // scale the pressure tensor
    tempTau = curSnapshot->statData.getTau();
    tempTau *= factor_;
    curSnapshot->statData.setTau(tempTau);
#ifndef IS_MPI
    // do the single processor crystal restraint forces for 
    // thermodynamic integration
    if (simParam->getUseSolidThermInt()) {
      
      lrPot_ += restraint_->Calc_Restraint_Forces();
      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
      
      vHarm_ = restraint_->getVharm();
      curSnapshot->statData[Stats::VHARM] = vHarm_;
    }
#else
    double tempLRPot = 0.0;
    double tempVHarm = 0.0;
    MPI_Status ierr;
    int nproc;
    MPI_Comm_size(MPI_COMM_WORLD, &nproc);

    // do the MPI crystal restraint forces for each processor
    if (simParam->getUseSolidThermInt()) {
      tempLRPot = restraint_->Calc_Restraint_Forces();
      tempVHarm = restraint_->getVharm();
    }

    // master receives and accumulates the restraint info
    if (worldRank == 0) {
      for(int i = 0 ; i < nproc; ++i) {
        if (i == worldRank) {
          lrPot_ += tempLRPot;
          vHarm_ += tempVHarm;
        } else {
          MPI_Recv(&tempLRPot, 1, MPI_REALTYPE, i, 
                   TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
          MPI_Recv(&tempVHarm, 1, MPI_REALTYPE, i, 
                   TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
          lrPot_ += tempLRPot;
          vHarm_ += tempVHarm;
        }
      }

      // give the final values to stats
      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
      curSnapshot->statData[Stats::VHARM] = vHarm_;

    } else {
      // pack up and send the appropriate info to the master node
      for(int j = 1; j < nproc; ++j) {
        if (worldRank == j) {

          MPI_Send(&tempLRPot, 1, MPI_REALTYPE, 0, 
                   TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
          MPI_Send(&tempVHarm, 1, MPI_REALTYPE, 0, 
                   TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
        }
      }
    }
#endif //is_mpi
  }
  
}
Revision:	2990
Committed:	Thu Aug 31 20:12:12 2006 UTC (17 years, 10 months ago) by chrisfen
File size:	7274 byte(s)
Log Message:	converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
#	User	Rev	Content
1	gezelter	2204	/*
2	chrisfen	2101	* 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 <cmath>
43			#include "restraints/ThermoIntegrationForceManager.hpp"
44			#include "integrators/Integrator.hpp"
45	chrisfen	2107	#include "math/SquareMatrix3.hpp"
46	chrisfen	2101	#include "primitives/Molecule.hpp"
47			#include "utils/simError.h"
48			#include "utils/OOPSEConstant.hpp"
49			#include "utils/StringUtils.hpp"
50
51	chrisfen	2990	#ifdef IS_MPI
52			#include <mpi.h>
53			#define TAKE_THIS_TAG_REAL 2
54			#endif //is_mpi
55
56	chrisfen	2101	namespace oopse {
57
58			ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
59	gezelter	2204	ForceManager(info){
60			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
61			simParam = info_->getSimParams();
62	chrisfen	2101
63	tim	2364	if (simParam->haveThermodynamicIntegrationLambda()){
64			tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
65	gezelter	2204	}
66			else{
67			tIntLambda_ = 1.0;
68			sprintf(painCave.errMsg,
69	chrisfen	2917	"ThermoIntegration error: the transformation parameter\n"
70			"\t(lambda) was not specified. OOPSE will use a default\n"
71			"\tvalue of %f. To set lambda, use the \n"
72			"\tthermodynamicIntegrationLambda variable.\n",
73	gezelter	2204	tIntLambda_);
74			painCave.isFatal = 0;
75			simError();
76			}
77	chrisfen	2101
78	tim	2364	if (simParam->haveThermodynamicIntegrationK()){
79			tIntK_ = simParam->getThermodynamicIntegrationK();
80	gezelter	2204	}
81			else{
82			tIntK_ = 1.0;
83			sprintf(painCave.errMsg,
84	chrisfen	2917	"ThermoIntegration Warning: the tranformation parameter\n"
85			"\texponent (k) was not specified. OOPSE will use a default\n"
86			"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
87			"\tvariable.\n",
88	gezelter	2204	tIntK_);
89			painCave.isFatal = 0;
90			simError();
91			}
92	chrisfen	2101
93	gezelter	2204	if (simParam->getUseSolidThermInt()) {
94			// build a restraint object
95			restraint_ = new Restraints(info_, tIntLambda_, tIntK_);
96	chrisfen	2101
97	gezelter	2204	}
98	chrisfen	2101
99	gezelter	2204	// build the scaling factor used to modulate the forces and torques
100			factor_ = pow(tIntLambda_, tIntK_);
101	chrisfen	2103
102	gezelter	2204	}
103	chrisfen	2101
104			ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
105			}
106
107			void ThermoIntegrationForceManager::calcForces(bool needPotential,
108			bool needStress){
109			Snapshot* curSnapshot;
110			SimInfo::MoleculeIterator mi;
111			Molecule* mol;
112			Molecule::IntegrableObjectIterator ii;
113			StuntDouble* integrableObject;
114			Vector3d frc;
115			Vector3d trq;
116	chrisfen	2107	Mat3x3d tempTau;
117	chrisfen	2101
118			// perform the standard calcForces first
119			ForceManager::calcForces(needPotential, needStress);
120
121	chrisfen	2103	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
122
123	chrisfen	2101	// now scale forces and torques of all the integrableObjects
124
125			for (mol = info_->beginMolecule(mi); mol != NULL;
126			mol = info_->nextMolecule(mi)) {
127			for (integrableObject = mol->beginIntegrableObject(ii);
128			integrableObject != NULL;
129			integrableObject = mol->nextIntegrableObject(ii)) {
130			frc = integrableObject->getFrc();
131			frc *= factor_;
132			integrableObject->setFrc(frc);
133
134			if (integrableObject->isDirectional()){
135			trq = integrableObject->getTrq();
136			trq *= factor_;
137			integrableObject->setTrq(trq);
138			}
139			}
140			}
141	chrisfen	2104
142			// set vraw to be the unmodulated potential
143			lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
144			curSnapshot->statData[Stats::VRAW] = lrPot_;
145	chrisfen	2101
146	chrisfen	2104	// modulate the potential and update the snapshot
147			lrPot_ *= factor_;
148			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
149
150	chrisfen	2107	// scale the pressure tensor
151			tempTau = curSnapshot->statData.getTau();
152			tempTau *= factor_;
153			curSnapshot->statData.setTau(tempTau);
154	chrisfen	2990	#ifndef IS_MPI
155			// do the single processor crystal restraint forces for
156			// thermodynamic integration
157	chrisfen	2101	if (simParam->getUseSolidThermInt()) {
158
159			lrPot_ += restraint_->Calc_Restraint_Forces();
160	chrisfen	2103	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
161	chrisfen	2101
162			vHarm_ = restraint_->getVharm();
163			curSnapshot->statData[Stats::VHARM] = vHarm_;
164			}
165	chrisfen	2990	#else
166			double tempLRPot = 0.0;
167			double tempVHarm = 0.0;
168			MPI_Status ierr;
169			int nproc;
170			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
171
172			// do the MPI crystal restraint forces for each processor
173			if (simParam->getUseSolidThermInt()) {
174			tempLRPot = restraint_->Calc_Restraint_Forces();
175			tempVHarm = restraint_->getVharm();
176			}
177
178			// master receives and accumulates the restraint info
179			if (worldRank == 0) {
180			for(int i = 0 ; i < nproc; ++i) {
181			if (i == worldRank) {
182			lrPot_ += tempLRPot;
183			vHarm_ += tempVHarm;
184			} else {
185			MPI_Recv(&tempLRPot, 1, MPI_REALTYPE, i,
186			TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
187			MPI_Recv(&tempVHarm, 1, MPI_REALTYPE, i,
188			TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
189			lrPot_ += tempLRPot;
190			vHarm_ += tempVHarm;
191			}
192			}
193
194			// give the final values to stats
195			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
196			curSnapshot->statData[Stats::VHARM] = vHarm_;
197
198			} else {
199			// pack up and send the appropriate info to the master node
200			for(int j = 1; j < nproc; ++j) {
201			if (worldRank == j) {
202
203			MPI_Send(&tempLRPot, 1, MPI_REALTYPE, 0,
204			TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
205			MPI_Send(&tempVHarm, 1, MPI_REALTYPE, 0,
206			TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
207			}
208			}
209			}
210			#endif //is_mpi
211	chrisfen	2101	}
212
213			}