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root/OpenMD/branches/development/src/brains/Thermo.cpp
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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 541 by tim, Sun May 22 21:05:15 2005 UTC vs.
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC

# 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 | namespace oopse {
64      int i;
65      int j;
66      int k;
67 <    double kinetic = 0.0;
68 <    double kinetic_global = 0.0;
67 >    RealType mass;
68 >    RealType kinetic = 0.0;
69 >    RealType kinetic_global = 0.0;
70      
71      for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73             integrableObject = mol->nextIntegrableObject(iiter)) {
74 <
75 <        double mass = integrableObject->getMass();
76 <        Vector3d vel = integrableObject->getVel();
77 <
74 >        
75 >        mass = integrableObject->getMass();
76 >        vel = integrableObject->getVel();
77 >        
78          kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
79 <
79 >        
80          if (integrableObject->isDirectional()) {
81            angMom = integrableObject->getJ();
82            I = integrableObject->getI();
# Line 96 | Line 97 | namespace oopse {
97      
98   #ifdef IS_MPI
99  
100 <    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
100 >    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101                    MPI_COMM_WORLD);
102      kinetic = kinetic_global;
103  
# Line 107 | Line 108 | namespace oopse {
108      return kinetic;
109    }
110  
111 <  double Thermo::getPotential() {
112 <    double potential = 0.0;
111 >  RealType Thermo::getPotential() {
112 >    RealType potential = 0.0;
113      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114 <    double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114 <      curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
114 >    RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115  
116      // Get total potential for entire system from MPI.
117  
118   #ifdef IS_MPI
119  
120 <    MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
120 >    MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121                    MPI_COMM_WORLD);
122 +    potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123  
124   #else
125  
126 <    potential = potential_local;
126 >    potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127  
128   #endif // is_mpi
129  
130      return potential;
131    }
132  
133 <  double Thermo::getTotalE() {
134 <    double total;
133 >  RealType Thermo::getTotalE() {
134 >    RealType total;
135  
136      total = this->getKinetic() + this->getPotential();
137      return total;
138    }
139  
140 <  double Thermo::getTemperature() {
140 >  RealType Thermo::getTemperature() {
141      
142 <    double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142 >    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
143      return temperature;
144    }
145  
146 <  double Thermo::getVolume() {
146 >  RealType Thermo::getVolume() {
147      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148      return curSnapshot->getVolume();
149    }
150  
151 <  double Thermo::getPressure() {
151 >  RealType Thermo::getPressure() {
152  
153      // Relies on the calculation of the full molecular pressure tensor
154  
155  
156      Mat3x3d tensor;
157 <    double pressure;
157 >    RealType pressure;
158  
159      tensor = getPressureTensor();
160  
# Line 162 | Line 163 | namespace oopse {
163      return pressure;
164    }
165  
166 <  double Thermo::getPressure(int direction) {
166 >  RealType Thermo::getPressure(int direction) {
167  
168      // Relies on the calculation of the full molecular pressure tensor
169  
170            
171      Mat3x3d tensor;
172 <    double pressure;
172 >    RealType pressure;
173  
174      tensor = getPressureTensor();
175  
# Line 177 | Line 178 | namespace oopse {
178      return pressure;
179    }
180  
180 –
181 –
181    Mat3x3d Thermo::getPressureTensor() {
182      // returns pressure tensor in units amu*fs^-2*Ang^-1
183      // routine derived via viral theorem description in:
# Line 195 | Line 194 | namespace oopse {
194        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195             integrableObject = mol->nextIntegrableObject(j)) {
196  
197 <        double mass = integrableObject->getMass();
197 >        RealType mass = integrableObject->getMass();
198          Vector3d vcom = integrableObject->getVel();
199          p_local += mass * outProduct(vcom, vcom);        
200        }
201      }
202      
203   #ifdef IS_MPI
204 <    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
204 >    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205   #else
206      p_global = p_local;
207   #endif // is_mpi
208  
209 <    double volume = this->getVolume();
209 >    RealType volume = this->getVolume();
210      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211      Mat3x3d tau = curSnapshot->statData.getTau();
212 <
212 >    
213      pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
214 <
214 >    
215      return pressureTensor;
216    }
217  
218 +
219    void Thermo::saveStat(){
220      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221      Stats& stat = currSnapshot->statData;

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