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

#include "integrators/NVE.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"

namespace oopse {


NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){

}

void NVE::moveA(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    double 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 NVE::moveB(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    double 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();

}


double NVE::calcConservedQuantity() {
    return thermo.getTotalE();
}

} //end namespace oopse
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (21 years, 4 months ago) by tim
File size:	5507 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1722	*
4	tim	1927	* 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	tim	1722	*/
41
42			/**
43			* @file NVE.cpp
44			* @author tlin
45			* @date 11/08/2004
46			* @time 15:13am
47			* @version 1.0
48			*/
49	tim	1837
50	tim	1820	#include "integrators/NVE.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "utils/OOPSEConstant.hpp"
53	tim	1722
54			namespace oopse {
55
56	tim	1758
57	tim	1756	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
58	tim	1722
59			}
60
61	tim	1756	void NVE::moveA(){
62	tim	1820	SimInfo::MoleculeIterator i;
63			Molecule::IntegrableObjectIterator j;
64	tim	1722	Molecule* mol;
65			StuntDouble* integrableObject;
66			Vector3d vel;
67			Vector3d pos;
68			Vector3d frc;
69			Vector3d Tb;
70			Vector3d ji;
71			double mass;
72
73	tim	1756	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
74	tim	1722	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
75			integrableObject = mol->nextIntegrableObject(j)) {
76
77			vel =integrableObject->getVel();
78			pos = integrableObject->getPos();
79			frc = integrableObject->getFrc();
80			mass = integrableObject->getMass();
81
82			// velocity half step
83	tim	1820	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
84	tim	1722
85			// position whole step
86	tim	1774	pos += dt * vel;
87	tim	1722
88			integrableObject->setVel(vel);
89			integrableObject->setPos(pos);
90
91			if (integrableObject->isDirectional()){
92
93			// get and convert the torque to body frame
94
95			Tb = integrableObject->lab2Body(integrableObject->getTrq());
96
97			// get the angular momentum, and propagate a half step
98
99			ji = integrableObject->getJ();
100
101	tim	1820	ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
102	tim	1722
103	tim	1820	rotAlgo->rotate(integrableObject, ji, dt);
104	tim	1722
105			integrableObject->setJ(ji);
106			}
107
108
109			}
110	tim	1756	} //end for(mol = info_->beginMolecule(i))
111	tim	1722
112	tim	1901	rattle->constraintA();
113	tim	1722
114			}
115
116	tim	1756	void NVE::moveB(){
117	tim	1820	SimInfo::MoleculeIterator i;
118			Molecule::IntegrableObjectIterator j;
119	tim	1722	Molecule* mol;
120			StuntDouble* integrableObject;
121			Vector3d vel;
122			Vector3d frc;
123			Vector3d Tb;
124			Vector3d ji;
125			double mass;
126
127	tim	1756	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
128	tim	1722	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
129			integrableObject = mol->nextIntegrableObject(j)) {
130
131			vel =integrableObject->getVel();
132			frc = integrableObject->getFrc();
133			mass = integrableObject->getMass();
134
135			// velocity half step
136	tim	1820	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
137	tim	1722
138			integrableObject->setVel(vel);
139
140			if (integrableObject->isDirectional()){
141
142			// get and convert the torque to body frame
143
144			Tb = integrableObject->lab2Body(integrableObject->getTrq());
145
146			// get the angular momentum, and propagate a half step
147
148			ji = integrableObject->getJ();
149
150	tim	1820	ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
151	tim	1722
152			integrableObject->setJ(ji);
153			}
154
155
156			}
157	tim	1756	} //end for(mol = info_->beginMolecule(i))
158	tim	1722
159
160	tim	1901	rattle->constraintB();
161	tim	1722
162			}
163
164	tim	1756
165	tim	1774	double NVE::calcConservedQuantity() {
166	tim	1820	return thermo.getTotalE();
167	tim	1756	}
168
169	tim	1722	} //end namespace oopse