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:	423
Committed:	Thu Mar 10 19:11:02 2005 UTC (20 years, 7 months ago) by chrisfen
File size:	5885 byte(s)
Log Message:	Oops... MPI now builds...
#	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	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
95	}
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	Mat3x3d tempTau;
110
111	// perform the standard calcForces first
112	ForceManager::calcForces(needPotential, needStress);
113
114	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
115
116	// 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
135	// set vraw to be the unmodulated potential
136	lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
137	curSnapshot->statData[Stats::VRAW] = lrPot_;
138
139	// modulate the potential and update the snapshot
140	lrPot_ *= factor_;
141	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
142
143	// scale the pressure tensor
144	tempTau = curSnapshot->statData.getTau();
145	tempTau *= factor_;
146	curSnapshot->statData.setTau(tempTau);
147
148	// do crystal restraint forces for thermodynamic integration
149	if (simParam->getUseSolidThermInt()) {
150
151	lrPot_ += restraint_->Calc_Restraint_Forces();
152	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
153
154	vHarm_ = restraint_->getVharm();
155	curSnapshot->statData[Stats::VHARM] = vHarm_;
156	}
157
158	}
159
160	}