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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 53 | Line 53 | namespace oopse {
53  
54   namespace oopse {
55  
56 < double Thermo::getKinetic() {
56 >  RealType Thermo::getKinetic() {
57      SimInfo::MoleculeIterator miter;
58      std::vector<StuntDouble*>::iterator iiter;
59      Molecule* mol;
# Line 64 | Line 64 | double Thermo::getKinetic() {
64      int i;
65      int j;
66      int k;
67 <    double kinetic = 0.0;
68 <    double kinetic_global = 0.0;
67 >    RealType kinetic = 0.0;
68 >    RealType kinetic_global = 0.0;
69      
70      for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
71 <        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
72 <               integrableObject = mol->nextIntegrableObject(iiter)) {
71 >      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
72 >           integrableObject = mol->nextIntegrableObject(iiter)) {
73 >        
74 >        RealType mass = integrableObject->getMass();
75 >        Vector3d vel = integrableObject->getVel();
76 >        
77 >        kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
78 >        
79 >        if (integrableObject->isDirectional()) {
80 >          angMom = integrableObject->getJ();
81 >          I = integrableObject->getI();
82  
83 <            double mass = integrableObject->getMass();
84 <            Vector3d vel = integrableObject->getVel();
85 <
86 <            kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
87 <
88 <            if (integrableObject->isDirectional()) {
89 <                angMom = integrableObject->getJ();
90 <                I = integrableObject->getI();
91 <
92 <                if (integrableObject->isLinear()) {
84 <                    i = integrableObject->linearAxis();
85 <                    j = (i + 1) % 3;
86 <                    k = (i + 2) % 3;
87 <                    kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
88 <                } else {                        
89 <                    kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
90 <                                    + angMom[2]*angMom[2]/I(2, 2);
91 <                }
92 <            }
83 >          if (integrableObject->isLinear()) {
84 >            i = integrableObject->linearAxis();
85 >            j = (i + 1) % 3;
86 >            k = (i + 2) % 3;
87 >            kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
88 >          } else {                        
89 >            kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
90 >              + angMom[2]*angMom[2]/I(2, 2);
91 >          }
92 >        }
93              
94 <        }
94 >      }
95      }
96      
97   #ifdef IS_MPI
98  
99 <    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
99 >    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
100                    MPI_COMM_WORLD);
101      kinetic = kinetic_global;
102  
# Line 105 | Line 105 | double Thermo::getKinetic() {
105      kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
106  
107      return kinetic;
108 < }
108 >  }
109  
110 < double Thermo::getPotential() {
111 <    double potential = 0.0;
110 >  RealType Thermo::getPotential() {
111 >    RealType potential = 0.0;
112      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113 <    double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114 <                                             curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
113 >    RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
114  
115      // Get total potential for entire system from MPI.
116  
117   #ifdef IS_MPI
118  
119 <    MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
119 >    MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
120                    MPI_COMM_WORLD);
121 +    potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
122  
123   #else
124  
125 <    potential = potential_local;
125 >    potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
126  
127   #endif // is_mpi
128  
129      return potential;
130 < }
130 >  }
131  
132 < double Thermo::getTotalE() {
133 <    double total;
132 >  RealType Thermo::getTotalE() {
133 >    RealType total;
134  
135      total = this->getKinetic() + this->getPotential();
136      return total;
137 < }
137 >  }
138  
139 < double Thermo::getTemperature() {
139 >  RealType Thermo::getTemperature() {
140      
141 <    double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
141 >    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142      return temperature;
143 < }
143 >  }
144  
145 < double Thermo::getVolume() {
145 >  RealType Thermo::getVolume() {
146      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
147      return curSnapshot->getVolume();
148 < }
148 >  }
149  
150 < double Thermo::getPressure() {
150 >  RealType Thermo::getPressure() {
151  
152      // Relies on the calculation of the full molecular pressure tensor
153  
154  
155      Mat3x3d tensor;
156 <    double pressure;
156 >    RealType pressure;
157  
158      tensor = getPressureTensor();
159  
160      pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
161  
162      return pressure;
163 < }
163 >  }
164  
165 < Mat3x3d Thermo::getPressureTensor() {
165 >  RealType Thermo::getPressure(int direction) {
166 >
167 >    // Relies on the calculation of the full molecular pressure tensor
168 >
169 >          
170 >    Mat3x3d tensor;
171 >    RealType pressure;
172 >
173 >    tensor = getPressureTensor();
174 >
175 >    pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
176 >
177 >    return pressure;
178 >  }
179 >
180 >
181 >
182 >  Mat3x3d Thermo::getPressureTensor() {
183      // returns pressure tensor in units amu*fs^-2*Ang^-1
184      // routine derived via viral theorem description in:
185      // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
# Line 175 | Line 192 | Mat3x3d Thermo::getPressureTensor() {
192      Molecule* mol;
193      StuntDouble* integrableObject;    
194      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
195 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
196 <               integrableObject = mol->nextIntegrableObject(j)) {
195 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
196 >           integrableObject = mol->nextIntegrableObject(j)) {
197  
198 <            double mass = integrableObject->getMass();
199 <            Vector3d vcom = integrableObject->getVel();
200 <            p_local += mass * outProduct(vcom, vcom);        
201 <        }
198 >        RealType mass = integrableObject->getMass();
199 >        Vector3d vcom = integrableObject->getVel();
200 >        p_local += mass * outProduct(vcom, vcom);        
201 >      }
202      }
203      
204   #ifdef IS_MPI
205 <    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
205 >    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
206   #else
207      p_global = p_local;
208   #endif // is_mpi
209  
210 <    double volume = this->getVolume();
210 >    RealType volume = this->getVolume();
211      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212      Mat3x3d tau = curSnapshot->statData.getTau();
213  
214      pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
215  
216      return pressureTensor;
217 < }
217 >  }
218  
219 < void Thermo::saveStat(){
219 >  void Thermo::saveStat(){
220      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221      Stats& stat = currSnapshot->statData;
222      
# Line 210 | Line 227 | void Thermo::saveStat(){
227      stat[Stats::PRESSURE] = getPressure();
228      stat[Stats::VOLUME] = getVolume();      
229  
230 +    Mat3x3d tensor =getPressureTensor();
231 +    stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);      
232 +    stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);      
233 +    stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);      
234 +
235 +
236      /**@todo need refactorying*/
237      //Conserved Quantity is set by integrator and time is set by setTime
238      
239 < }
239 >  }
240  
241   } //end namespace oopse

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