src/integrators/LangevinDynamics.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/LangevinDynamics.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "integrators/LDForceManager.hpp"
namespace oopse {

  
  LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
    setForceManager(new LDForceManager(info));

    // Langevin Dynamics Force Manager needs to know about the half-time step 
    // size to get convergence on the friction forces:
    dynamic_cast<LDForceManager*>(forceMan_)->setDt2(dt2);
  }
  
  void LangevinDynamics::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 LangevinDynamics::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 LangevinDynamics::calcConservedQuantity() {
    return 0.0;
  }

} //end namespace oopse

Revision:	3384
Committed:	Fri Apr 18 16:55:15 2008 UTC (16 years, 3 months ago) by gezelter
File size:	5332 byte(s)
Log Message:	Adding iterative looping to get better estimates of friction forces from full-step velocities
#	User	Rev	Content
1	tim	2611	/*
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/LangevinDynamics.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "utils/OOPSEConstant.hpp"
53			#include "integrators/LDForceManager.hpp"
54			namespace oopse {
55
56	gezelter	2733
57	tim	2611	LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58			setForceManager(new LDForceManager(info));
59	gezelter	3384
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<LDForceManager*>(forceMan_)->setDt2(dt2);
63	tim	2611	}
64	gezelter	2733
65	tim	2611	void LangevinDynamics::moveA(){
66			SimInfo::MoleculeIterator i;
67			Molecule::IntegrableObjectIterator j;
68			Molecule* mol;
69			StuntDouble* integrableObject;
70			Vector3d vel;
71			Vector3d pos;
72			Vector3d frc;
73			Vector3d Tb;
74			Vector3d ji;
75	tim	2759	RealType mass;
76	tim	2611
77			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
78			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
79			integrableObject = mol->nextIntegrableObject(j)) {
80
81			vel =integrableObject->getVel();
82			pos = integrableObject->getPos();
83			frc = integrableObject->getFrc();
84			mass = integrableObject->getMass();
85
86			// velocity half step
87			vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
88
89			// position whole step
90			pos += dt * vel;
91
92			integrableObject->setVel(vel);
93			integrableObject->setPos(pos);
94
95			if (integrableObject->isDirectional()){
96
97			// get and convert the torque to body frame
98
99			Tb = integrableObject->lab2Body(integrableObject->getTrq());
100
101			// get the angular momentum, and propagate a half step
102
103			ji = integrableObject->getJ();
104
105			ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
106
107			rotAlgo->rotate(integrableObject, ji, dt);
108
109			integrableObject->setJ(ji);
110			}
111
112
113			}
114			} //end for(mol = info_->beginMolecule(i))
115
116			rattle->constraintA();
117
118			}
119
120			void LangevinDynamics::moveB(){
121			SimInfo::MoleculeIterator i;
122			Molecule::IntegrableObjectIterator j;
123			Molecule* mol;
124			StuntDouble* integrableObject;
125			Vector3d vel;
126			Vector3d frc;
127			Vector3d Tb;
128			Vector3d ji;
129	tim	2759	RealType mass;
130	tim	2611
131			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
132			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
133			integrableObject = mol->nextIntegrableObject(j)) {
134
135			vel =integrableObject->getVel();
136			frc = integrableObject->getFrc();
137			mass = integrableObject->getMass();
138
139			// velocity half step
140			vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
141
142			integrableObject->setVel(vel);
143
144			if (integrableObject->isDirectional()){
145
146			// get and convert the torque to body frame
147
148			Tb = integrableObject->lab2Body(integrableObject->getTrq());
149
150			// get the angular momentum, and propagate a half step
151
152			ji = integrableObject->getJ();
153
154			ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
155
156			integrableObject->setJ(ji);
157			}
158
159
160			}
161			} //end for(mol = info_->beginMolecule(i))
162
163
164			rattle->constraintB();
165
166			}
167
168
169	tim	2759	RealType LangevinDynamics::calcConservedQuantity() {
170	tim	2611	return 0.0;
171			}
172
173			} //end namespace oopse
174