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->haveThermIntLambda()){
      tIntLambda_ = simParam->getThermIntLambda();
    }
    else{
      tIntLambda_ = 1.0;
      sprintf(painCave.errMsg,
              "ThermoIntegration error: the transformation parameter (lambda) was\n"
              "\tnot specified. OOPSE will use a default value of %f. To set\n"
              "\tlambda, use the thermodynamicIntegrationLambda variable.\n",
              tIntLambda_);
      painCave.isFatal = 0;
      simError();
    }
    
    if (simParam->haveThermIntK()){
      tIntK_ = simParam->getThermIntK();
    }
    else{
      tIntK_ = 1.0;
      sprintf(painCave.errMsg,
              "ThermoIntegration Warning: the tranformation parameter exponent\n"
              "\t(k) was not specified. OOPSE will use a default value of %f.\n"
              "\tTo set k, use the thermodynamicIntegrationK variable.\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:	437
Committed:	Sat Mar 12 19:05:16 2005 UTC (20 years, 7 months ago) by chrisfen
File size:	5885 byte(s)
Log Message:	added some samples
#	User	Rev	Content
1	chrisfen	417	/*
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	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			ForceManager(info){
55			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
56			simParam = info_->getSimParams();
57
58			if (simParam->haveThermIntLambda()){
59			tIntLambda_ = simParam->getThermIntLambda();
60			}
61			else{
62			tIntLambda_ = 1.0;
63			sprintf(painCave.errMsg,
64			"ThermoIntegration error: the transformation parameter (lambda) was\n"
65			"\tnot specified. OOPSE will use a default value of %f. To set\n"
66			"\tlambda, use the thermodynamicIntegrationLambda variable.\n",
67			tIntLambda_);
68			painCave.isFatal = 0;
69			simError();
70			}
71
72			if (simParam->haveThermIntK()){
73			tIntK_ = simParam->getThermIntK();
74			}
75			else{
76			tIntK_ = 1.0;
77			sprintf(painCave.errMsg,
78			"ThermoIntegration Warning: the tranformation parameter exponent\n"
79			"\t(k) was not specified. OOPSE will use a default value of %f.\n"
80			"\tTo set k, use the thermodynamicIntegrationK variable.\n",
81			tIntK_);
82			painCave.isFatal = 0;
83			simError();
84			}
85
86			if (simParam->getUseSolidThermInt()) {
87			// build a restraint object
88			restraint_ = new Restraints(info_, tIntLambda_, tIntK_);
89
90			}
91
92			// build the scaling factor used to modulate the forces and torques
93			factor_ = pow(tIntLambda_, tIntK_);
94	chrisfen	419
95	chrisfen	417	}
96
97			ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
98			}
99
100			void ThermoIntegrationForceManager::calcForces(bool needPotential,
101			bool needStress){
102			Snapshot* curSnapshot;
103			SimInfo::MoleculeIterator mi;
104			Molecule* mol;
105			Molecule::IntegrableObjectIterator ii;
106			StuntDouble* integrableObject;
107			Vector3d frc;
108			Vector3d trq;
109	chrisfen	423	Mat3x3d tempTau;
110	chrisfen	417
111			// perform the standard calcForces first
112			ForceManager::calcForces(needPotential, needStress);
113
114	chrisfen	419	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
115
116	chrisfen	417	// now scale forces and torques of all the integrableObjects
117
118			for (mol = info_->beginMolecule(mi); mol != NULL;
119			mol = info_->nextMolecule(mi)) {
120			for (integrableObject = mol->beginIntegrableObject(ii);
121			integrableObject != NULL;
122			integrableObject = mol->nextIntegrableObject(ii)) {
123			frc = integrableObject->getFrc();
124			frc *= factor_;
125			integrableObject->setFrc(frc);
126
127			if (integrableObject->isDirectional()){
128			trq = integrableObject->getTrq();
129			trq *= factor_;
130			integrableObject->setTrq(trq);
131			}
132			}
133			}
134	chrisfen	420
135			// set vraw to be the unmodulated potential
136			lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
137			curSnapshot->statData[Stats::VRAW] = lrPot_;
138	chrisfen	417
139	chrisfen	420	// modulate the potential and update the snapshot
140			lrPot_ *= factor_;
141			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
142
143	chrisfen	423	// scale the pressure tensor
144			tempTau = curSnapshot->statData.getTau();
145			tempTau *= factor_;
146			curSnapshot->statData.setTau(tempTau);
147
148	chrisfen	417	// do crystal restraint forces for thermodynamic integration
149			if (simParam->getUseSolidThermInt()) {
150
151			lrPot_ += restraint_->Calc_Restraint_Forces();
152	chrisfen	419	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
153	chrisfen	417
154			vHarm_ = restraint_->getVharm();
155			curSnapshot->statData[Stats::VHARM] = vHarm_;
156			}
157
158			}
159
160			}