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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years, 6 months ago) by gezelter
File size:	4964 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
43			* @file NVE.cpp
44			* @author tlin
45			* @date 11/08/2004
46			* @time 15:13am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#include "integrators/NVE.hpp"
51			#include "primitives/Molecule.hpp"
52			#include "utils/OOPSEConstant.hpp"
53
54			namespace oopse {
55
56
57	gezelter	2204	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
58	gezelter	1930
59	gezelter	2204	}
60	gezelter	1930
61	gezelter	2204	void NVE::moveA(){
62	gezelter	1930	SimInfo::MoleculeIterator i;
63			Molecule::IntegrableObjectIterator j;
64			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			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
74	gezelter	2204	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
75			integrableObject = mol->nextIntegrableObject(j)) {
76	gezelter	1930
77	gezelter	2204	vel =integrableObject->getVel();
78			pos = integrableObject->getPos();
79			frc = integrableObject->getFrc();
80			mass = integrableObject->getMass();
81	gezelter	1930
82	gezelter	2204	// velocity half step
83			vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
84	gezelter	1930
85	gezelter	2204	// position whole step
86			pos += dt * vel;
87	gezelter	1930
88	gezelter	2204	integrableObject->setVel(vel);
89			integrableObject->setPos(pos);
90	gezelter	1930
91	gezelter	2204	if (integrableObject->isDirectional()){
92	gezelter	1930
93	gezelter	2204	// get and convert the torque to body frame
94	gezelter	1930
95	gezelter	2204	Tb = integrableObject->lab2Body(integrableObject->getTrq());
96	gezelter	1930
97	gezelter	2204	// get the angular momentum, and propagate a half step
98	gezelter	1930
99	gezelter	2204	ji = integrableObject->getJ();
100	gezelter	1930
101	gezelter	2204	ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
102	gezelter	1930
103	gezelter	2204	rotAlgo->rotate(integrableObject, ji, dt);
104	gezelter	1930
105	gezelter	2204	integrableObject->setJ(ji);
106			}
107	gezelter	1930
108
109	gezelter	2204	}
110	gezelter	1930	} //end for(mol = info_->beginMolecule(i))
111
112			rattle->constraintA();
113
114	gezelter	2204	}
115	gezelter	1930
116	gezelter	2204	void NVE::moveB(){
117	gezelter	1930	SimInfo::MoleculeIterator i;
118			Molecule::IntegrableObjectIterator j;
119			Molecule* mol;
120			StuntDouble* integrableObject;
121			Vector3d vel;
122			Vector3d frc;
123			Vector3d Tb;
124			Vector3d ji;
125			double mass;
126
127			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
128	gezelter	2204	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
129			integrableObject = mol->nextIntegrableObject(j)) {
130	gezelter	1930
131	gezelter	2204	vel =integrableObject->getVel();
132			frc = integrableObject->getFrc();
133			mass = integrableObject->getMass();
134	gezelter	1930
135	gezelter	2204	// velocity half step
136			vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
137	gezelter	1930
138	gezelter	2204	integrableObject->setVel(vel);
139	gezelter	1930
140	gezelter	2204	if (integrableObject->isDirectional()){
141	gezelter	1930
142	gezelter	2204	// get and convert the torque to body frame
143	gezelter	1930
144	gezelter	2204	Tb = integrableObject->lab2Body(integrableObject->getTrq());
145	gezelter	1930
146	gezelter	2204	// get the angular momentum, and propagate a half step
147	gezelter	1930
148	gezelter	2204	ji = integrableObject->getJ();
149	gezelter	1930
150	gezelter	2204	ji += (dt2 * OOPSEConstant::energyConvert) * Tb;
151	gezelter	1930
152	gezelter	2204	integrableObject->setJ(ji);
153			}
154	gezelter	1930
155
156	gezelter	2204	}
157	gezelter	1930	} //end for(mol = info_->beginMolecule(i))
158
159
160			rattle->constraintB();
161
162	gezelter	2204	}
163	gezelter	1930
164
165	gezelter	2204	double NVE::calcConservedQuantity() {
166	gezelter	1930	return thermo.getTotalE();
167	gezelter	2204	}
168	gezelter	1930
169			} //end namespace oopse