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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1125 by gezelter, Mon Apr 19 22:13:01 2004 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 27 | Line 29 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
29    have_chi_tolerance = 0;
30    integralOfChidt = 0.0;
31  
30 –  // retrieve chi and integralOfChidt from simInfo
31 –  data = info->getProperty(CHIVALUE_ID);
32 –  if(data){
33 –    chiValue = dynamic_cast<DoubleData*>(data);
34 –  }
32  
33 <  data = info->getProperty(INTEGRALOFCHIDT_ID);
37 <  if(data){
38 <    integralOfChidtValue = dynamic_cast<DoubleData*>(data);
39 <  }
33 >  if( theInfo->useInitXSstate ){
34  
35 <  // chi and integralOfChidt should appear by pair
36 <  if(chiValue && integralOfChidtValue){
37 <    chi = chiValue->getData();
38 <    integralOfChidt = integralOfChidtValue->getData();
35 >    // retrieve chi and integralOfChidt from simInfo
36 >    data = info->getProperty(CHIVALUE_ID);
37 >    if(data){
38 >      chiValue = dynamic_cast<DoubleData*>(data);
39 >    }
40 >    
41 >    data = info->getProperty(INTEGRALOFCHIDT_ID);
42 >    if(data){
43 >      integralOfChidtValue = dynamic_cast<DoubleData*>(data);
44 >    }
45 >    
46 >    // chi and integralOfChidt should appear by pair
47 >    if(chiValue && integralOfChidtValue){
48 >      chi = chiValue->getData();
49 >      integralOfChidt = integralOfChidtValue->getData();
50 >    }
51    }
52  
53 <  oldVel = new double[3*nAtoms];
54 <  oldJi = new double[3*nAtoms];
53 >
54 >  std::cerr << "building oldVel with \t" << integrableObjects.size() << "\n";
55 >  oldVel = new double[3*integrableObjects.size()];
56 >  oldJi = new double[3*integrableObjects.size()];
57   }
58  
59   template<typename T> NVT<T>::~NVT() {
# Line 67 | Line 75 | template<typename T> void NVT<T>::moveA() {
75  
76    instTemp = tStats->getTemperature();
77  
78 <  for( i=0; i<nAtoms; i++ ){
78 >  for( i=0; i < integrableObjects.size(); i++ ){
79  
80 <    atoms[i]->getVel( vel );
81 <    atoms[i]->getPos( pos );
82 <    atoms[i]->getFrc( frc );
80 >    integrableObjects[i]->getVel( vel );
81 >    integrableObjects[i]->getPos( pos );
82 >    integrableObjects[i]->getFrc( frc );
83  
84 <    mass = atoms[i]->getMass();
84 >    mass = integrableObjects[i]->getMass();
85  
86      for (j=0; j < 3; j++) {
87        // velocity half step  (use chi from previous step here):
# Line 82 | Line 90 | template<typename T> void NVT<T>::moveA() {
90        pos[j] += dt * vel[j];
91      }
92  
93 <    atoms[i]->setVel( vel );
94 <    atoms[i]->setPos( pos );
93 >    integrableObjects[i]->setVel( vel );
94 >    integrableObjects[i]->setPos( pos );
95  
96 <    if( atoms[i]->isDirectional() ){
96 >    if( integrableObjects[i]->isDirectional() ){
97  
90 –      dAtom = (DirectionalAtom *)atoms[i];
91 –
98        // get and convert the torque to body frame
99  
100 <      dAtom->getTrq( Tb );
101 <      dAtom->lab2Body( Tb );
100 >      integrableObjects[i]->getTrq( Tb );
101 >      integrableObjects[i]->lab2Body( Tb );
102  
103        // get the angular momentum, and propagate a half step
104  
105 <      dAtom->getJ( ji );
105 >      integrableObjects[i]->getJ( ji );
106  
107        for (j=0; j < 3; j++)
108          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
109  
110 <      this->rotationPropagation( dAtom, ji );
110 >      this->rotationPropagation( integrableObjects[i], ji );
111  
112 <      dAtom->setJ( ji );
112 >      integrableObjects[i]->setJ( ji );
113      }
114    }
115  
# Line 114 | Line 120 | template<typename T> void NVT<T>::moveA() {
120    // Finally, evolve chi a half step (just like a velocity) using
121    // temperature at time t, not time t+dt/2
122  
123 +  std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
124 +  
125    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
126    integralOfChidt += chi*dt2;
127  
# Line 121 | Line 129 | template<typename T> void NVT<T>::moveB( void ){
129  
130   template<typename T> void NVT<T>::moveB( void ){
131    int i, j, k;
124 –  DirectionalAtom* dAtom;
132    double Tb[3], ji[3];
133    double vel[3], frc[3];
134    double mass;
# Line 132 | Line 139 | template<typename T> void NVT<T>::moveB( void ){
139  
140    oldChi = chi;
141  
142 <  for( i=0; i<nAtoms; i++ ){
142 >  for( i=0; i < integrableObjects.size(); i++ ){
143  
144 <    atoms[i]->getVel( vel );
144 >    integrableObjects[i]->getVel( vel );
145  
146      for (j=0; j < 3; j++)
147        oldVel[3*i + j]  = vel[j];
148  
149 <    if( atoms[i]->isDirectional() ){
149 >    if( integrableObjects[i]->isDirectional() ){
150  
151 <      dAtom = (DirectionalAtom *)atoms[i];
151 >      integrableObjects[i]->getJ( ji );
152  
146 –      dAtom->getJ( ji );
147 –
153        for (j=0; j < 3; j++)
154          oldJi[3*i + j] = ji[j];
155  
# Line 163 | Line 168 | template<typename T> void NVT<T>::moveB( void ){
168      chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
169        (tauThermostat*tauThermostat);
170  
171 <    for( i=0; i<nAtoms; i++ ){
171 >    for( i=0; i < integrableObjects.size(); i++ ){
172  
173 <      atoms[i]->getFrc( frc );
174 <      atoms[i]->getVel(vel);
173 >      integrableObjects[i]->getFrc( frc );
174 >      integrableObjects[i]->getVel(vel);
175  
176 <      mass = atoms[i]->getMass();
176 >      mass = integrableObjects[i]->getMass();
177  
178        // velocity half step
179        for (j=0; j < 3; j++)
180          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
181  
182 <      atoms[i]->setVel( vel );
182 >      integrableObjects[i]->setVel( vel );
183  
184 <      if( atoms[i]->isDirectional() ){
184 >      if( integrableObjects[i]->isDirectional() ){
185  
181 –        dAtom = (DirectionalAtom *)atoms[i];
182 –
186          // get and convert the torque to body frame
187  
188 <        dAtom->getTrq( Tb );
189 <        dAtom->lab2Body( Tb );
188 >        integrableObjects[i]->getTrq( Tb );
189 >        integrableObjects[i]->lab2Body( Tb );
190  
191          for (j=0; j < 3; j++)
192            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
193  
194 <        dAtom->setJ( ji );
194 >        integrableObjects[i]->setJ( ji );
195        }
196      }
197  
# Line 269 | Line 272 | template<typename T> double NVT<T>::getConservedQuanti
272  
273    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
274  
272 –  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
273 –      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
274 –
275    return conservedQuantity;
276   }
277  
# Line 280 | Line 280 | template<typename T> string NVT<T>::getAdditionalParam
280    const int BUFFERSIZE = 2000; // size of the read buffer
281    char buffer[BUFFERSIZE];
282  
283 <  sprintf(buffer,"\t%g\t%g;", chi, integralOfChidt);
283 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
284    parameters += buffer;
285  
286    return parameters;

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