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Comparing branches/development/src/integrators/LangevinDynamics.cpp (file contents):
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

# Line 67 | Line 67 | namespace OpenMD {
67      SimInfo::MoleculeIterator i;
68      Molecule::IntegrableObjectIterator  j;
69      Molecule* mol;
70 <    StuntDouble* integrableObject;
70 >    StuntDouble* sd;
71      Vector3d vel;
72      Vector3d pos;
73      Vector3d frc;
# Line 75 | Line 75 | namespace OpenMD {
75      Vector3d ji;
76      RealType mass;
77      
78 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
79 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
80 <           integrableObject = mol->nextIntegrableObject(j)) {
78 >    for (mol = info_->beginMolecule(i); mol != NULL;
79 >         mol = info_->nextMolecule(i)) {
80  
81 <        vel =integrableObject->getVel();
82 <        pos = integrableObject->getPos();
83 <        frc = integrableObject->getFrc();
84 <        mass = integrableObject->getMass();
81 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
82 >           sd = mol->nextIntegrableObject(j)) {
83 >
84 >        vel = sd->getVel();
85 >        pos = sd->getPos();
86 >        frc = sd->getFrc();
87 >        mass = sd->getMass();
88                  
89          // velocity half step
90          vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
# Line 90 | Line 92 | namespace OpenMD {
92          // position whole step
93          pos += dt * vel;
94  
95 <        integrableObject->setVel(vel);
96 <        integrableObject->setPos(pos);
95 >        sd->setVel(vel);
96 >        sd->setPos(pos);
97  
98 <        if (integrableObject->isDirectional()){
98 >        if (sd->isDirectional()){
99  
100            // get and convert the torque to body frame
101  
102 <          Tb = integrableObject->lab2Body(integrableObject->getTrq());
102 >          Tb = sd->lab2Body(sd->getTrq());
103  
104            // get the angular momentum, and propagate a half step
105  
106 <          ji = integrableObject->getJ();
106 >          ji = sd->getJ();
107  
108            ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
109  
110 <          rotAlgo_->rotate(integrableObject, ji, dt);
110 >          rotAlgo_->rotate(sd, ji, dt);
111  
112 <          integrableObject->setJ(ji);
112 >          sd->setJ(ji);
113          }
114  
115              
# Line 122 | Line 124 | namespace OpenMD {
124      SimInfo::MoleculeIterator i;
125      Molecule::IntegrableObjectIterator  j;
126      Molecule* mol;
127 <    StuntDouble* integrableObject;
127 >    StuntDouble* sd;
128      Vector3d vel;
129      Vector3d frc;
130      Vector3d Tb;
131      Vector3d ji;
132      RealType mass;
133      
134 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
135 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
134 <           integrableObject = mol->nextIntegrableObject(j)) {
134 >    for (mol = info_->beginMolecule(i); mol != NULL;
135 >         mol = info_->nextMolecule(i)) {
136  
137 <        vel =integrableObject->getVel();
138 <        frc = integrableObject->getFrc();
139 <        mass = integrableObject->getMass();
137 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
138 >           sd = mol->nextIntegrableObject(j)) {
139 >
140 >        vel = sd->getVel();
141 >        frc = sd->getFrc();
142 >        mass = sd->getMass();
143                  
144          // velocity half step
145          vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
146                  
147 <        integrableObject->setVel(vel);
147 >        sd->setVel(vel);
148  
149 <        if (integrableObject->isDirectional()){
149 >        if (sd->isDirectional()){
150  
151            // get and convert the torque to body frame
152  
153 <          Tb = integrableObject->lab2Body(integrableObject->getTrq());
153 >          Tb = sd->lab2Body(sd->getTrq());
154  
155            // get the angular momentum, and propagate a half step
156  
157 <          ji = integrableObject->getJ();
157 >          ji = sd->getJ();
158  
159            ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
160  
161 <          integrableObject->setJ(ji);
161 >          sd->setJ(ji);
162          }
163  
164              

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