src/integrators/SMIPDynamics.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.
 */
 
/**
 * @file LangevinDynamics.cpp
 * @author tlin
 * @date 11/08/2004
 * @time 15:13am
 * @version 1.0
 */

#include "integrators/SMIPDynamics.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "integrators/SMIPDForceManager.hpp"
namespace oopse {

  
   SMIPDynamics::SMIPDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
    setForceManager(new SMIPDForceManager(info));

    // Langevin Dynamics Force Manager needs to know about the half-time step 
    // size to get convergence on the friction forces:
    dynamic_cast<SMIPDForceManager*>(forceMan_)->setDt2(dt2);

  }
  
  void SMIPDynamics::moveA(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

        vel =integrableObject->getVel();
        pos = integrableObject->getPos();
        frc = integrableObject->getFrc();
        mass = integrableObject->getMass();
                
        // velocity half step
        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;

        // position whole step
        pos += dt * vel;

        integrableObject->setVel(vel);
        integrableObject->setPos(pos);

        if (integrableObject->isDirectional()){

          // get and convert the torque to body frame

          Tb = integrableObject->lab2Body(integrableObject->getTrq());

          // get the angular momentum, and propagate a half step

          ji = integrableObject->getJ();

          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;

          rotAlgo->rotate(integrableObject, ji, dt);

          integrableObject->setJ(ji);
        }

            
      }
    } //end for(mol = info_->beginMolecule(i))
    
    rattle->constraintA();
    
  }    

  void SMIPDynamics::moveB(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {

        vel =integrableObject->getVel();
        frc = integrableObject->getFrc();
        mass = integrableObject->getMass();
                
        // velocity half step
        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
                
        integrableObject->setVel(vel);

        if (integrableObject->isDirectional()){

          // get and convert the torque to body frame

          Tb = integrableObject->lab2Body(integrableObject->getTrq());

          // get the angular momentum, and propagate a half step

          ji = integrableObject->getJ();

          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;

          integrableObject->setJ(ji);
        }

            
      }
    } //end for(mol = info_->beginMolecule(i))
  

    rattle->constraintB();

  }


  RealType SMIPDynamics::calcConservedQuantity() {
    return 0.0;
  }

} //end namespace oopse

Revision:	1294
Committed:	Wed Sep 17 00:23:39 2008 UTC (16 years, 7 months ago) by chuckv
Original Path:	*trunk/src/integrators/SMIPDynamics.cpp*
File size:	5319 byte(s)
Log Message:	Adding back more missing files.
#	User	Rev	Content
1	chuckv	1294	/*
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			/**
43			* @file LangevinDynamics.cpp
44			* @author tlin
45			* @date 11/08/2004
46			* @time 15:13am
47			* @version 1.0
48			*/
49
50			#include "integrators/SMIPDynamics.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "utils/OOPSEConstant.hpp"
53			#include "integrators/SMIPDForceManager.hpp"
54			namespace oopse {
55
56
57			SMIPDynamics::SMIPDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58			setForceManager(new SMIPDForceManager(info));
59
60			// Langevin Dynamics Force Manager needs to know about the half-time step
61			// size to get convergence on the friction forces:
62			dynamic_cast<SMIPDForceManager*>(forceMan_)->setDt2(dt2);
63
64			}
65
66			void SMIPDynamics::moveA(){
67			SimInfo::MoleculeIterator i;
68			Molecule::IntegrableObjectIterator j;
69			Molecule* mol;
70			StuntDouble* integrableObject;
71			Vector3d vel;
72			Vector3d pos;
73			Vector3d frc;
74			Vector3d Tb;
75			Vector3d ji;
76			RealType mass;
77
78			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
79			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
80			integrableObject = mol->nextIntegrableObject(j)) {
81
82			vel =integrableObject->getVel();
83			pos = integrableObject->getPos();
84			frc = integrableObject->getFrc();
85			mass = integrableObject->getMass();
86
87			// velocity half step
88			vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
89
90			// position whole step
91			pos += dt * vel;
92
93			integrableObject->setVel(vel);
94			integrableObject->setPos(pos);
95
96			if (integrableObject->isDirectional()){
97
98			// get and convert the torque to body frame
99
100			Tb = integrableObject->lab2Body(integrableObject->getTrq());
101
102			// get the angular momentum, and propagate a half step
103
104			ji = integrableObject->getJ();
105
106			ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
107
108			rotAlgo->rotate(integrableObject, ji, dt);
109
110			integrableObject->setJ(ji);
111			}
112
113
114			}
115			} //end for(mol = info_->beginMolecule(i))
116
117			rattle->constraintA();
118
119			}
120
121			void SMIPDynamics::moveB(){
122			SimInfo::MoleculeIterator i;
123			Molecule::IntegrableObjectIterator j;
124			Molecule* mol;
125			StuntDouble* integrableObject;
126			Vector3d vel;
127			Vector3d frc;
128			Vector3d Tb;
129			Vector3d ji;
130			RealType mass;
131
132			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
133			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
134			integrableObject = mol->nextIntegrableObject(j)) {
135
136			vel =integrableObject->getVel();
137			frc = integrableObject->getFrc();
138			mass = integrableObject->getMass();
139
140			// velocity half step
141			vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
142
143			integrableObject->setVel(vel);
144
145			if (integrableObject->isDirectional()){
146
147			// get and convert the torque to body frame
148
149			Tb = integrableObject->lab2Body(integrableObject->getTrq());
150
151			// get the angular momentum, and propagate a half step
152
153			ji = integrableObject->getJ();
154
155			ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
156
157			integrableObject->setJ(ji);
158			}
159
160
161			}
162			} //end for(mol = info_->beginMolecule(i))
163
164
165			rattle->constraintB();
166
167			}
168
169
170			RealType SMIPDynamics::calcConservedQuantity() {
171			return 0.0;
172			}
173
174			} //end namespace oopse
175