src/integrators/SMIPDynamics.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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @file LangevinDynamics.cpp
 * @author tlin
 * @date 11/08/2004
 * @time 15:13am
 * @version 1.0
 */

#include "integrators/SMIPDynamics.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "integrators/SMIPDForceManager.hpp"
namespace OpenMD {

  
   SMIPDynamics::SMIPDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
    setForceManager(new SMIPDForceManager(info));
  }
  
  void SMIPDynamics::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 SMIPDynamics::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 SMIPDynamics::calcConservedQuantity() {
    return 0.0;
  }

} //end namespace OpenMD

Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	5184 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	chuckv	1294	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1294	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1294	* 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			* [4] Vardeman & Gezelter, in progress (2009).
40	chuckv	1294	*/
41
42			/**
43			* @file LangevinDynamics.cpp
44			* @author tlin
45			* @date 11/08/2004
46			* @time 15:13am
47			* @version 1.0
48			*/
49
50			#include "integrators/SMIPDynamics.hpp"
51			#include "primitives/Molecule.hpp"
52	gezelter	1390	#include "utils/PhysicalConstants.hpp"
53	chuckv	1294	#include "integrators/SMIPDForceManager.hpp"
54	gezelter	1390	namespace OpenMD {
55	chuckv	1294
56
57			SMIPDynamics::SMIPDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58			setForceManager(new SMIPDForceManager(info));
59			}
60
61			void SMIPDynamics::moveA(){
62			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			RealType mass;
72
73			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
74			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	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
84	chuckv	1294
85			// position whole step
86			pos += dt * vel;
87
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	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
102	chuckv	1294
103			rotAlgo->rotate(integrableObject, ji, dt);
104
105			integrableObject->setJ(ji);
106			}
107
108
109			}
110			} //end for(mol = info_->beginMolecule(i))
111
112			rattle->constraintA();
113
114			}
115
116			void SMIPDynamics::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	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
137	chuckv	1294
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	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
151	chuckv	1294
152			integrableObject->setJ(ji);
153			}
154
155
156			}
157			} //end for(mol = info_->beginMolecule(i))
158
159
160			rattle->constraintB();
161
162			}
163
164
165			RealType SMIPDynamics::calcConservedQuantity() {
166			return 0.0;
167			}
168
169	gezelter	1390	} //end namespace OpenMD
170	chuckv	1294