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

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

namespace OpenMD {


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

} //end namespace OpenMD
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5100 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file NVE.cpp
45			* @author tlin
46			* @date 11/08/2004
47			* @time 15:13am
48			* @version 1.0
49			*/
50	gezelter	246
51			#include "integrators/NVE.hpp"
52			#include "primitives/Molecule.hpp"
53	gezelter	1390	#include "utils/PhysicalConstants.hpp"
54	gezelter	246
55	gezelter	1390	namespace OpenMD {
56	gezelter	246
57
58	gezelter	507	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
59	gezelter	246
60	gezelter	507	}
61	gezelter	246
62	gezelter	507	void NVE::moveA(){
63	gezelter	246	SimInfo::MoleculeIterator i;
64			Molecule::IntegrableObjectIterator j;
65			Molecule* mol;
66			StuntDouble* integrableObject;
67			Vector3d vel;
68			Vector3d pos;
69			Vector3d frc;
70			Vector3d Tb;
71			Vector3d ji;
72	tim	963	RealType mass;
73	gezelter	246
74			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
75	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
76			integrableObject = mol->nextIntegrableObject(j)) {
77	gezelter	246
78	gezelter	507	vel =integrableObject->getVel();
79			pos = integrableObject->getPos();
80			frc = integrableObject->getFrc();
81			mass = integrableObject->getMass();
82	gezelter	246
83	gezelter	507	// velocity half step
84	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
85	gezelter	246
86	gezelter	507	// position whole step
87			pos += dt * vel;
88	gezelter	246
89	gezelter	507	integrableObject->setVel(vel);
90			integrableObject->setPos(pos);
91	gezelter	246
92	gezelter	507	if (integrableObject->isDirectional()){
93	gezelter	246
94	gezelter	507	// get and convert the torque to body frame
95	gezelter	246
96	gezelter	507	Tb = integrableObject->lab2Body(integrableObject->getTrq());
97	gezelter	246
98	gezelter	507	// get the angular momentum, and propagate a half step
99	gezelter	246
100	gezelter	507	ji = integrableObject->getJ();
101	gezelter	246
102	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
103	gezelter	246
104	gezelter	507	rotAlgo->rotate(integrableObject, ji, dt);
105	gezelter	246
106	gezelter	507	integrableObject->setJ(ji);
107			}
108	gezelter	246
109
110	gezelter	507	}
111	gezelter	246	} //end for(mol = info_->beginMolecule(i))
112
113			rattle->constraintA();
114
115	gezelter	507	}
116	gezelter	246
117	gezelter	507	void NVE::moveB(){
118	gezelter	246	SimInfo::MoleculeIterator i;
119			Molecule::IntegrableObjectIterator j;
120			Molecule* mol;
121			StuntDouble* integrableObject;
122			Vector3d vel;
123			Vector3d frc;
124			Vector3d Tb;
125			Vector3d ji;
126	tim	963	RealType mass;
127	gezelter	246
128			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
129	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
130			integrableObject = mol->nextIntegrableObject(j)) {
131	gezelter	246
132	gezelter	507	vel =integrableObject->getVel();
133			frc = integrableObject->getFrc();
134			mass = integrableObject->getMass();
135	gezelter	246
136	gezelter	507	// velocity half step
137	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
138	gezelter	246
139	chuckv	1306	integrableObject->setVel(vel);
140	gezelter	246
141	gezelter	507	if (integrableObject->isDirectional()){
142	gezelter	246
143	gezelter	507	// get and convert the torque to body frame
144	gezelter	246
145	gezelter	507	Tb = integrableObject->lab2Body(integrableObject->getTrq());
146	gezelter	246
147	gezelter	507	// get the angular momentum, and propagate a half step
148	gezelter	246
149	gezelter	507	ji = integrableObject->getJ();
150	gezelter	246
151	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
152	gezelter	246
153	gezelter	507	integrableObject->setJ(ji);
154			}
155	gezelter	246
156
157	gezelter	507	}
158	gezelter	246	} //end for(mol = info_->beginMolecule(i))
159
160
161			rattle->constraintB();
162
163	gezelter	507	}
164	gezelter	246
165
166	tim	963	RealType NVE::calcConservedQuantity() {
167	chuckv	1306	return thermo.getTotalE() ;
168	gezelter	507	}
169	gezelter	246
170	gezelter	1390	} //end namespace OpenMD