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"

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);
  
    // do 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_;
    }
    
  }
  
}
Revision:	998
Committed:	Mon Jul 3 13:18:43 2006 UTC (18 years, 10 months ago) by chrisfen
Original Path:	*trunk/src/restraints/ThermoIntegrationForceManager.cpp*
File size:	5843 byte(s)
Log Message:	Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
#	User	Rev	Content
1	gezelter	507	/*
2	chrisfen	417	* 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	423	#include "math/SquareMatrix3.hpp"
46	chrisfen	417	#include "primitives/Molecule.hpp"
47			#include "utils/simError.h"
48			#include "utils/OOPSEConstant.hpp"
49			#include "utils/StringUtils.hpp"
50
51			namespace oopse {
52
53			ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
54	gezelter	507	ForceManager(info){
55			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
56			simParam = info_->getSimParams();
57	chrisfen	417
58	tim	665	if (simParam->haveThermodynamicIntegrationLambda()){
59			tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
60	gezelter	507	}
61			else{
62			tIntLambda_ = 1.0;
63			sprintf(painCave.errMsg,
64	chrisfen	998	"ThermoIntegration error: the transformation parameter\n"
65			"\t(lambda) was not specified. OOPSE will use a default\n"
66			"\tvalue of %f. To set lambda, use the \n"
67			"\tthermodynamicIntegrationLambda variable.\n",
68	gezelter	507	tIntLambda_);
69			painCave.isFatal = 0;
70			simError();
71			}
72	chrisfen	417
73	tim	665	if (simParam->haveThermodynamicIntegrationK()){
74			tIntK_ = simParam->getThermodynamicIntegrationK();
75	gezelter	507	}
76			else{
77			tIntK_ = 1.0;
78			sprintf(painCave.errMsg,
79	chrisfen	998	"ThermoIntegration Warning: the tranformation parameter\n"
80			"\texponent (k) was not specified. OOPSE will use a default\n"
81			"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
82			"\tvariable.\n",
83	gezelter	507	tIntK_);
84			painCave.isFatal = 0;
85			simError();
86			}
87	chrisfen	417
88	gezelter	507	if (simParam->getUseSolidThermInt()) {
89			// build a restraint object
90			restraint_ = new Restraints(info_, tIntLambda_, tIntK_);
91	chrisfen	417
92	gezelter	507	}
93	chrisfen	417
94	gezelter	507	// build the scaling factor used to modulate the forces and torques
95			factor_ = pow(tIntLambda_, tIntK_);
96	chrisfen	419
97	gezelter	507	}
98	chrisfen	417
99			ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
100			}
101
102			void ThermoIntegrationForceManager::calcForces(bool needPotential,
103			bool needStress){
104			Snapshot* curSnapshot;
105			SimInfo::MoleculeIterator mi;
106			Molecule* mol;
107			Molecule::IntegrableObjectIterator ii;
108			StuntDouble* integrableObject;
109			Vector3d frc;
110			Vector3d trq;
111	chrisfen	423	Mat3x3d tempTau;
112	chrisfen	417
113			// perform the standard calcForces first
114			ForceManager::calcForces(needPotential, needStress);
115
116	chrisfen	419	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
117
118	chrisfen	417	// now scale forces and torques of all the integrableObjects
119
120			for (mol = info_->beginMolecule(mi); mol != NULL;
121			mol = info_->nextMolecule(mi)) {
122			for (integrableObject = mol->beginIntegrableObject(ii);
123			integrableObject != NULL;
124			integrableObject = mol->nextIntegrableObject(ii)) {
125			frc = integrableObject->getFrc();
126			frc *= factor_;
127			integrableObject->setFrc(frc);
128
129			if (integrableObject->isDirectional()){
130			trq = integrableObject->getTrq();
131			trq *= factor_;
132			integrableObject->setTrq(trq);
133			}
134			}
135			}
136	chrisfen	420
137			// set vraw to be the unmodulated potential
138			lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
139			curSnapshot->statData[Stats::VRAW] = lrPot_;
140	chrisfen	417
141	chrisfen	420	// modulate the potential and update the snapshot
142			lrPot_ *= factor_;
143			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
144
145	chrisfen	423	// scale the pressure tensor
146			tempTau = curSnapshot->statData.getTau();
147			tempTau *= factor_;
148			curSnapshot->statData.setTau(tempTau);
149	chrisfen	990
150	chrisfen	417	// do crystal restraint forces for thermodynamic integration
151			if (simParam->getUseSolidThermInt()) {
152
153			lrPot_ += restraint_->Calc_Restraint_Forces();
154	chrisfen	419	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
155	chrisfen	417
156			vHarm_ = restraint_->getVharm();
157			curSnapshot->statData[Stats::VHARM] = vHarm_;
158			}
159
160			}
161
162			}