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:	2917
Committed:	Mon Jul 3 13:18:43 2006 UTC (18 years ago) by chrisfen
File size:	5843 byte(s)
Log Message:	Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
#	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->haveThermodynamicIntegrationLambda()){
59	tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
60	}
61	else{
62	tIntLambda_ = 1.0;
63	sprintf(painCave.errMsg,
64	"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	tIntLambda_);
69	painCave.isFatal = 0;
70	simError();
71	}
72
73	if (simParam->haveThermodynamicIntegrationK()){
74	tIntK_ = simParam->getThermodynamicIntegrationK();
75	}
76	else{
77	tIntK_ = 1.0;
78	sprintf(painCave.errMsg,
79	"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	tIntK_);
84	painCave.isFatal = 0;
85	simError();
86	}
87
88	if (simParam->getUseSolidThermInt()) {
89	// build a restraint object
90	restraint_ = new Restraints(info_, tIntLambda_, tIntK_);
91
92	}
93
94	// build the scaling factor used to modulate the forces and torques
95	factor_ = pow(tIntLambda_, tIntK_);
96
97	}
98
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	Mat3x3d tempTau;
112
113	// perform the standard calcForces first
114	ForceManager::calcForces(needPotential, needStress);
115
116	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
117
118	// 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
137	// set vraw to be the unmodulated potential
138	lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
139	curSnapshot->statData[Stats::VRAW] = lrPot_;
140
141	// modulate the potential and update the snapshot
142	lrPot_ *= factor_;
143	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
144
145	// scale the pressure tensor
146	tempTau = curSnapshot->statData.getTau();
147	tempTau *= factor_;
148	curSnapshot->statData.setTau(tempTau);
149
150	// do crystal restraint forces for thermodynamic integration
151	if (simParam->getUseSolidThermInt()) {
152
153	lrPot_ += restraint_->Calc_Restraint_Forces();
154	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
155
156	vHarm_ = restraint_->getVharm();
157	curSnapshot->statData[Stats::VHARM] = vHarm_;
158	}
159
160	}
161
162	}