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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file LangevinDynamics.cpp
 * @author tlin
 * @date 11/08/2004
 * @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* sd;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

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

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

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

        if (sd->isDirectional()){

          // get and convert the torque to body frame

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

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

          ji = sd->getJ();

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

          rotAlgo_->rotate(sd, ji, dt);

          sd->setJ(ji);
        }

            
      }
    } //end for(mol = info_->beginMolecule(i))
    
    flucQ_->moveA();
    rattle_->constraintA();    
  }    

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

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

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

        if (sd->isDirectional()){

          // get and convert the torque to body frame

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

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

          ji = sd->getJ();

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

          sd->setJ(ji);
        }

            
      }
    } //end for(mol = info_->beginMolecule(i))
  
    flucQ_->moveB();
    rattle_->constraintB();
  }


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

} //end namespace OpenMD

Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	5104 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	User	Rev	Content
1	tim	895	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	895	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	895	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	895	*/
42
43			/**
44			* @file LangevinDynamics.cpp
45			* @author tlin
46			* @date 11/08/2004
47			* @version 1.0
48			*/
49
50			#include "integrators/LangevinDynamics.hpp"
51			#include "primitives/Molecule.hpp"
52	gezelter	1390	#include "utils/PhysicalConstants.hpp"
53	tim	895	#include "integrators/LDForceManager.hpp"
54	gezelter	1390	namespace OpenMD {
55	tim	895
56	gezelter	945
57	tim	895	LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58			setForceManager(new LDForceManager(info));
59	gezelter	1237
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	895	}
64	gezelter	945
65	tim	895	void LangevinDynamics::moveA(){
66			SimInfo::MoleculeIterator i;
67			Molecule::IntegrableObjectIterator j;
68			Molecule* mol;
69	gezelter	1769	StuntDouble* sd;
70	tim	895	Vector3d vel;
71			Vector3d pos;
72			Vector3d frc;
73			Vector3d Tb;
74			Vector3d ji;
75	tim	963	RealType mass;
76	tim	895
77	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
78			mol = info_->nextMolecule(i)) {
79	tim	895
80	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
81			sd = mol->nextIntegrableObject(j)) {
82
83			vel = sd->getVel();
84			pos = sd->getPos();
85			frc = sd->getFrc();
86			mass = sd->getMass();
87	tim	895
88			// velocity half step
89	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
90	tim	895
91			// position whole step
92			pos += dt * vel;
93
94	gezelter	1769	sd->setVel(vel);
95			sd->setPos(pos);
96	tim	895
97	gezelter	1769	if (sd->isDirectional()){
98	tim	895
99			// get and convert the torque to body frame
100
101	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
102	tim	895
103			// get the angular momentum, and propagate a half step
104
105	gezelter	1769	ji = sd->getJ();
106	tim	895
107	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
108	tim	895
109	gezelter	1769	rotAlgo_->rotate(sd, ji, dt);
110	tim	895
111	gezelter	1769	sd->setJ(ji);
112	tim	895	}
113
114
115			}
116			} //end for(mol = info_->beginMolecule(i))
117
118	gezelter	1715	flucQ_->moveA();
119			rattle_->constraintA();
120	tim	895	}
121
122			void LangevinDynamics::moveB(){
123			SimInfo::MoleculeIterator i;
124			Molecule::IntegrableObjectIterator j;
125			Molecule* mol;
126	gezelter	1769	StuntDouble* sd;
127	tim	895	Vector3d vel;
128			Vector3d frc;
129			Vector3d Tb;
130			Vector3d ji;
131	tim	963	RealType mass;
132	tim	895
133	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
134			mol = info_->nextMolecule(i)) {
135	tim	895
136	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
137			sd = mol->nextIntegrableObject(j)) {
138
139			vel = sd->getVel();
140			frc = sd->getFrc();
141			mass = sd->getMass();
142	tim	895
143			// velocity half step
144	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
145	tim	895
146	gezelter	1769	sd->setVel(vel);
147	tim	895
148	gezelter	1769	if (sd->isDirectional()){
149	tim	895
150			// get and convert the torque to body frame
151
152	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
153	tim	895
154			// get the angular momentum, and propagate a half step
155
156	gezelter	1769	ji = sd->getJ();
157	tim	895
158	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
159	tim	895
160	gezelter	1769	sd->setJ(ji);
161	tim	895	}
162
163
164			}
165			} //end for(mol = info_->beginMolecule(i))
166
167	gezelter	1715	flucQ_->moveB();
168			rattle_->constraintB();
169	tim	895	}
170
171
172	tim	963	RealType LangevinDynamics::calcConservedQuantity() {
173	tim	895	return 0.0;
174			}
175
176	gezelter	1390	} //end namespace OpenMD
177	tim	895