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, 9 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
#	Content
1	/*
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 <cmath>
43	#include "restraints/ThermoIntegrationForceManager.hpp"
44	#include "integrators/Integrator.hpp"
45	#include "math/SquareMatrix3.hpp"
46	#include "primitives/Molecule.hpp"
47	#include "utils/simError.h"
48	#include "utils/OOPSEConstant.hpp"
49	#include "utils/StringUtils.hpp"
50
51	#ifdef IS_MPI
52	#include <mpi.h>
53	#define TAKE_THIS_TAG_REAL 2
54	#endif //is_mpi
55
56	namespace oopse {
57
58	ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
59	ForceManager(info){
60	currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
61	simParam = info_->getSimParams();
62
63	if (simParam->haveThermodynamicIntegrationLambda()){
64	tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
65	}
66	else{
67	tIntLambda_ = 1.0;
68	sprintf(painCave.errMsg,
69	"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	tIntLambda_);
74	painCave.isFatal = 0;
75	simError();
76	}
77
78	if (simParam->haveThermodynamicIntegrationK()){
79	tIntK_ = simParam->getThermodynamicIntegrationK();
80	}
81	else{
82	tIntK_ = 1.0;
83	sprintf(painCave.errMsg,
84	"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	tIntK_);
89	painCave.isFatal = 0;
90	simError();
91	}
92
93	if (simParam->getUseSolidThermInt()) {
94	// build a restraint object
95	restraint_ = new Restraints(info_, tIntLambda_, tIntK_);
96
97	}
98
99	// build the scaling factor used to modulate the forces and torques
100	factor_ = pow(tIntLambda_, tIntK_);
101
102	}
103
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	Mat3x3d tempTau;
117
118	// perform the standard calcForces first
119	ForceManager::calcForces(needPotential, needStress);
120
121	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
122
123	// 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
142	// set vraw to be the unmodulated potential
143	lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
144	curSnapshot->statData[Stats::VRAW] = lrPot_;
145
146	// modulate the potential and update the snapshot
147	lrPot_ *= factor_;
148	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
149
150	// scale the pressure tensor
151	tempTau = curSnapshot->statData.getTau();
152	tempTau *= factor_;
153	curSnapshot->statData.setTau(tempTau);
154	#ifndef IS_MPI
155	// do the single processor crystal restraint forces for
156	// thermodynamic integration
157	if (simParam->getUseSolidThermInt()) {
158
159	lrPot_ += restraint_->Calc_Restraint_Forces();
160	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
161
162	vHarm_ = restraint_->getVharm();
163	curSnapshot->statData[Stats::VHARM] = vHarm_;
164	}
165	#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	}
212
213	}