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))
    flucQ_->moveA();
    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))
  
    flucQ_->moveB();
    rattle_->constraintB();
  }


  RealType NVE::calcConservedQuantity() {
    return thermo.getTotalEnergy();
  }

} //end namespace OpenMD
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 9 months ago) by gezelter
File size:	5141 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	Content
1	/*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file NVE.cpp
45	* @author tlin
46	* @date 11/08/2004
47	* @time 15:13am
48	* @version 1.0
49	*/
50
51	#include "integrators/NVE.hpp"
52	#include "primitives/Molecule.hpp"
53	#include "utils/PhysicalConstants.hpp"
54
55	namespace OpenMD {
56
57
58	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
59
60	}
61
62	void NVE::moveA(){
63	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	RealType mass;
73
74	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
75	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
76	integrableObject = mol->nextIntegrableObject(j)) {
77
78	vel =integrableObject->getVel();
79	pos = integrableObject->getPos();
80	frc = integrableObject->getFrc();
81	mass = integrableObject->getMass();
82
83	// velocity half step
84	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
85
86	// position whole step
87	pos += dt * vel;
88
89	integrableObject->setVel(vel);
90	integrableObject->setPos(pos);
91
92	if (integrableObject->isDirectional()){
93
94	// get and convert the torque to body frame
95
96	Tb = integrableObject->lab2Body(integrableObject->getTrq());
97
98	// get the angular momentum, and propagate a half step
99
100	ji = integrableObject->getJ();
101
102	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
103
104	rotAlgo_->rotate(integrableObject, ji, dt);
105
106	integrableObject->setJ(ji);
107	}
108
109
110	}
111	} //end for(mol = info_->beginMolecule(i))
112	flucQ_->moveA();
113	rattle_->constraintA();
114	}
115
116	void NVE::moveB(){
117	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	RealType mass;
126
127	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
128	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	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
137
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	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
151
152	integrableObject->setJ(ji);
153	}
154
155
156	}
157	} //end for(mol = info_->beginMolecule(i))
158
159	flucQ_->moveB();
160	rattle_->constraintB();
161	}
162
163
164	RealType NVE::calcConservedQuantity() {
165	return thermo.getTotalEnergy();
166	}
167
168	} //end namespace OpenMD