src/integrators/LangevinHullDynamics.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, 234107 (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/LangevinHullDynamics.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "integrators/LangevinHullForceManager.hpp"
namespace OpenMD {

   LangevinHullDynamics::LangevinHullDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
    setForceManager(new LangevinHullForceManager(info));
  }
  
  void LangevinHullDynamics::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 LangevinHullDynamics::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 LangevinHullDynamics::calcConservedQuantity() {
    return 0.0;
  }

} //end namespace OpenMD

Revision:	1858
Committed:	Wed Apr 3 21:32:13 2013 UTC (12 years, 1 month ago) by gezelter
File size:	4948 byte(s)
Log Message:	Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
#	User	Rev	Content
1	gezelter	1629	/*
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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1629	*/
42
43			/**
44			* @file LangevinDynamics.cpp
45			* @author tlin
46			* @date 11/08/2004
47			* @version 1.0
48			*/
49
50			#include "integrators/LangevinHullDynamics.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "utils/PhysicalConstants.hpp"
53			#include "integrators/LangevinHullForceManager.hpp"
54			namespace OpenMD {
55
56			LangevinHullDynamics::LangevinHullDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
57			setForceManager(new LangevinHullForceManager(info));
58			}
59
60			void LangevinHullDynamics::moveA(){
61			SimInfo::MoleculeIterator i;
62			Molecule::IntegrableObjectIterator j;
63			Molecule* mol;
64	gezelter	1769	StuntDouble* sd;
65	gezelter	1629	Vector3d vel;
66			Vector3d pos;
67			Vector3d frc;
68			Vector3d Tb;
69			Vector3d ji;
70			RealType mass;
71
72	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
73			mol = info_->nextMolecule(i)) {
74	gezelter	1629
75	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
76			sd = mol->nextIntegrableObject(j)) {
77
78			vel = sd->getVel();
79			pos = sd->getPos();
80			frc = sd->getFrc();
81			mass = sd->getMass();
82	gezelter	1629
83			// velocity half step
84			vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
85
86			// position whole step
87			pos += dt * vel;
88
89	gezelter	1769	sd->setVel(vel);
90			sd->setPos(pos);
91	gezelter	1629
92	gezelter	1769	if (sd->isDirectional()){
93	gezelter	1629
94			// get and convert the torque to body frame
95
96	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
97	gezelter	1629
98			// get the angular momentum, and propagate a half step
99
100	gezelter	1769	ji = sd->getJ();
101	gezelter	1629
102			ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
103
104	gezelter	1769	rotAlgo_->rotate(sd, ji, dt);
105	gezelter	1629
106	gezelter	1769	sd->setJ(ji);
107	gezelter	1629	}
108
109
110			}
111			} //end for(mol = info_->beginMolecule(i))
112
113	gezelter	1715	flucQ_->moveA();
114			rattle_->constraintA();
115	gezelter	1629	}
116
117			void LangevinHullDynamics::moveB(){
118			SimInfo::MoleculeIterator i;
119			Molecule::IntegrableObjectIterator j;
120			Molecule* mol;
121	gezelter	1769	StuntDouble* sd;
122	gezelter	1629	Vector3d vel;
123			Vector3d frc;
124			Vector3d Tb;
125			Vector3d ji;
126			RealType mass;
127
128	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
129			mol = info_->nextMolecule(i)) {
130	gezelter	1629
131	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
132			sd = mol->nextIntegrableObject(j)) {
133
134			vel = sd->getVel();
135			frc = sd->getFrc();
136			mass = sd->getMass();
137	gezelter	1629
138			// velocity half step
139			vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
140
141	gezelter	1769	sd->setVel(vel);
142	gezelter	1629
143	gezelter	1769	if (sd->isDirectional()){
144	gezelter	1629
145			// get and convert the torque to body frame
146
147	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
148	gezelter	1629
149			// get the angular momentum, and propagate a half step
150
151	gezelter	1769	ji = sd->getJ();
152	gezelter	1629
153			ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
154
155	gezelter	1769	sd->setJ(ji);
156	gezelter	1629	}
157
158
159			}
160			} //end for(mol = info_->beginMolecule(i))
161
162	gezelter	1715	flucQ_->moveB();
163			rattle_->constraintB();
164	gezelter	1629	}
165
166			RealType LangevinHullDynamics::calcConservedQuantity() {
167			return 0.0;
168			}
169
170			} //end namespace OpenMD
171