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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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/PhysicalConstants.hpp"
#include "integrators/LDForceManager.hpp"
namespace OpenMD {

  
  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 * PhysicalConstants::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  * PhysicalConstants::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 * PhysicalConstants::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  * PhysicalConstants::energyConvert) * Tb;

          integrableObject->setJ(ji);
        }

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

    rattle->constraintB();

  }


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

} //end namespace OpenMD

Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	5395 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
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/PhysicalConstants.hpp"
53	#include "integrators/LDForceManager.hpp"
54	namespace OpenMD {
55
56
57	LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58	setForceManager(new LDForceManager(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<LDForceManager*>(forceMan_)->setDt2(dt2);
63	}
64
65	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	RealType mass;
76
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 * PhysicalConstants::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 * PhysicalConstants::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	RealType mass;
130
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 * PhysicalConstants::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 * PhysicalConstants::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	RealType LangevinDynamics::calcConservedQuantity() {
170	return 0.0;
171	}
172
173	} //end namespace OpenMD
174