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* 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);
        }

            
      }
    }
    flucQ_->moveA();
    rattle_->constraintA();    
  }    

  void NVE::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);
        }

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


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

} //end namespace OpenMD
Revision:	1769
Committed:	Mon Jul 9 14:15:52 2012 UTC (12 years, 9 months ago) by gezelter
File size:	4677 byte(s)
Log Message:	Code readability updates.
#	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	gezelter	1769	StuntDouble* sd;
67	gezelter	246	Vector3d vel;
68			Vector3d pos;
69			Vector3d frc;
70			Vector3d Tb;
71			Vector3d ji;
72	tim	963	RealType mass;
73	gezelter	246
74	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
75			mol = info_->nextMolecule(i)) {
76	gezelter	246
77	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
78			sd = mol->nextIntegrableObject(j)) {
79
80			vel = sd->getVel();
81			pos = sd->getPos();
82			frc = sd->getFrc();
83			mass = sd->getMass();
84	gezelter	246
85	gezelter	507	// velocity half step
86	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
87	gezelter	246
88	gezelter	507	// position whole step
89			pos += dt * vel;
90	gezelter	246
91	gezelter	1769	sd->setVel(vel);
92			sd->setPos(pos);
93	gezelter	246
94	gezelter	1769	if (sd->isDirectional()){
95	gezelter	246
96	gezelter	507	// get and convert the torque to body frame
97	gezelter	246
98	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
99	gezelter	246
100	gezelter	507	// get the angular momentum, and propagate a half step
101	gezelter	246
102	gezelter	1769	ji = sd->getJ();
103	gezelter	246
104	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
105	gezelter	246
106	gezelter	1769	rotAlgo_->rotate(sd, ji, dt);
107	gezelter	246
108	gezelter	1769	sd->setJ(ji);
109	gezelter	507	}
110	gezelter	246
111
112	gezelter	507	}
113	gezelter	1769	}
114	gezelter	1715	flucQ_->moveA();
115			rattle_->constraintA();
116	gezelter	507	}
117	gezelter	246
118	gezelter	507	void NVE::moveB(){
119	gezelter	246	SimInfo::MoleculeIterator i;
120			Molecule::IntegrableObjectIterator j;
121			Molecule* mol;
122	gezelter	1769	StuntDouble* sd;
123	gezelter	246	Vector3d vel;
124			Vector3d frc;
125			Vector3d Tb;
126			Vector3d ji;
127	tim	963	RealType mass;
128	gezelter	246
129	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
130			mol = info_->nextMolecule(i)) {
131	gezelter	246
132	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
133			sd = mol->nextIntegrableObject(j)) {
134
135			vel = sd->getVel();
136			frc = sd->getFrc();
137			mass = sd->getMass();
138	gezelter	246
139	gezelter	507	// velocity half step
140	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
141	gezelter	246
142	gezelter	1769	sd->setVel(vel);
143	gezelter	246
144	gezelter	1769	if (sd->isDirectional()){
145	gezelter	246
146	gezelter	507	// get and convert the torque to body frame
147	gezelter	246
148	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
149	gezelter	246
150	gezelter	507	// get the angular momentum, and propagate a half step
151	gezelter	246
152	gezelter	1769	ji = sd->getJ();
153	gezelter	246
154	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
155	gezelter	246
156	gezelter	1769	sd->setJ(ji);
157	gezelter	507	}
158	gezelter	246
159
160	gezelter	507	}
161	gezelter	1769	}
162	gezelter	246
163	gezelter	1715	flucQ_->moveB();
164			rattle_->constraintB();
165	gezelter	507	}
166	gezelter	246
167
168	tim	963	RealType NVE::calcConservedQuantity() {
169	gezelter	1764	return thermo.getTotalEnergy();
170	gezelter	507	}
171	gezelter	246
172	gezelter	1390	} //end namespace OpenMD