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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 6 | Line 8
8   #include "Thermo.hpp"
9   #include "ReadWrite.hpp"
10   #include "Integrator.hpp"
11 < #include "simError.h"
11 > #include "simError.h"
12  
13  
14   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
# Line 14 | Line 16 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
16   template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17    T( theInfo, the_ff )
18   {
19 +  GenericData* data;
20 +  DoubleData * chiValue;
21 +  DoubleData * integralOfChidtValue;
22 +
23 +  chiValue = NULL;
24 +  integralOfChidtValue = NULL;
25 +
26    chi = 0.0;
27    have_tau_thermostat = 0;
28    have_target_temp = 0;
29    have_chi_tolerance = 0;
30    integralOfChidt = 0.0;
31  
32 <  oldVel = new double[3*nAtoms];
33 <  oldJi = new double[3*nAtoms];
32 >
33 >  if( theInfo->useInitXSstate ){
34 >
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*integrableObjects.size()];
54 >  oldJi = new double[3*integrableObjects.size()];
55   }
56  
57   template<typename T> NVT<T>::~NVT() {
# Line 30 | Line 60 | template<typename T> void NVT<T>::moveA() {
60   }
61  
62   template<typename T> void NVT<T>::moveA() {
63 <  
63 >
64    int i, j;
65    DirectionalAtom* dAtom;
66    double Tb[3], ji[3];
# Line 42 | Line 72 | template<typename T> void NVT<T>::moveA() {
72    // We need the temperature at time = t for the chi update below:
73  
74    instTemp = tStats->getTemperature();
45 –  
46 –  for( i=0; i<nAtoms; i++ ){
75  
76 <    atoms[i]->getVel( vel );
49 <    atoms[i]->getPos( pos );
50 <    atoms[i]->getFrc( frc );
76 >  for( i=0; i < integrableObjects.size(); i++ ){
77  
78 <    mass = atoms[i]->getMass();
78 >    integrableObjects[i]->getVel( vel );
79 >    integrableObjects[i]->getPos( pos );
80 >    integrableObjects[i]->getFrc( frc );
81  
82 +    mass = integrableObjects[i]->getMass();
83 +
84      for (j=0; j < 3; j++) {
85        // velocity half step  (use chi from previous step here):
86        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
# Line 58 | Line 88 | template<typename T> void NVT<T>::moveA() {
88        pos[j] += dt * vel[j];
89      }
90  
91 <    atoms[i]->setVel( vel );
92 <    atoms[i]->setPos( pos );
63 <  
64 <    if( atoms[i]->isDirectional() ){
91 >    integrableObjects[i]->setVel( vel );
92 >    integrableObjects[i]->setPos( pos );
93  
94 <      dAtom = (DirectionalAtom *)atoms[i];
95 <          
94 >    if( integrableObjects[i]->isDirectional() ){
95 >
96        // get and convert the torque to body frame
97 <      
98 <      dAtom->getTrq( Tb );
99 <      dAtom->lab2Body( Tb );
100 <      
97 >
98 >      integrableObjects[i]->getTrq( Tb );
99 >      integrableObjects[i]->lab2Body( Tb );
100 >
101        // get the angular momentum, and propagate a half step
102  
103 <      dAtom->getJ( ji );
103 >      integrableObjects[i]->getJ( ji );
104  
105 <      for (j=0; j < 3; j++)
105 >      for (j=0; j < 3; j++)
106          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
107 <      
108 <      this->rotationPropagation( dAtom, ji );
109 <      
110 <      dAtom->setJ( ji );
111 <    }    
107 >
108 >      this->rotationPropagation( integrableObjects[i], ji );
109 >
110 >      integrableObjects[i]->setJ( ji );
111 >    }
112    }
85 –  
86 –  if (nConstrained){
87 –    constrainA();
88 –  }
113  
114 <  // Finally, evolve chi a half step (just like a velocity) using
114 >  consFramework->doConstrainA();
115 >
116 >  // Finally, evolve chi a half step (just like a velocity) using
117    // temperature at time t, not time t+dt/2
118  
119 +  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
120 +  
121    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
122    integralOfChidt += chi*dt2;
123  
# Line 97 | Line 125 | template<typename T> void NVT<T>::moveB( void ){
125  
126   template<typename T> void NVT<T>::moveB( void ){
127    int i, j, k;
100 –  DirectionalAtom* dAtom;
128    double Tb[3], ji[3];
129    double vel[3], frc[3];
130    double mass;
# Line 108 | Line 135 | template<typename T> void NVT<T>::moveB( void ){
135  
136    oldChi = chi;
137  
138 <  for( i=0; i<nAtoms; i++ ){
138 >  for( i=0; i < integrableObjects.size(); i++ ){
139  
140 <    atoms[i]->getVel( vel );
140 >    integrableObjects[i]->getVel( vel );
141  
142      for (j=0; j < 3; j++)
143        oldVel[3*i + j]  = vel[j];
144  
145 <    if( atoms[i]->isDirectional() ){
145 >    if( integrableObjects[i]->isDirectional() ){
146  
147 <      dAtom = (DirectionalAtom *)atoms[i];
147 >      integrableObjects[i]->getJ( ji );
148  
122 –      dAtom->getJ( ji );
123 –
149        for (j=0; j < 3; j++)
150          oldJi[3*i + j] = ji[j];
151  
# Line 130 | Line 155 | template<typename T> void NVT<T>::moveB( void ){
155    // do the iteration:
156  
157    for (k=0; k < 4; k++) {
158 <    
158 >
159      instTemp = tStats->getTemperature();
160  
161      // evolve chi another half step using the temperature at t + dt/2
162  
163      prevChi = chi;
164 <    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
164 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
165        (tauThermostat*tauThermostat);
141 –  
142 –    for( i=0; i<nAtoms; i++ ){
166  
167 <      atoms[i]->getFrc( frc );
168 <      atoms[i]->getVel(vel);
169 <      
170 <      mass = atoms[i]->getMass();
171 <      
167 >    for( i=0; i < integrableObjects.size(); i++ ){
168 >
169 >      integrableObjects[i]->getFrc( frc );
170 >      integrableObjects[i]->getVel(vel);
171 >
172 >      mass = integrableObjects[i]->getMass();
173 >
174        // velocity half step
175 <      for (j=0; j < 3; j++)
175 >      for (j=0; j < 3; j++)
176          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
177 <      
178 <      atoms[i]->setVel( vel );
179 <      
180 <      if( atoms[i]->isDirectional() ){
181 <        
182 <        dAtom = (DirectionalAtom *)atoms[i];
183 <        
184 <        // get and convert the torque to body frame      
185 <        
186 <        dAtom->getTrq( Tb );
187 <        dAtom->lab2Body( Tb );      
163 <            
164 <        for (j=0; j < 3; j++)
177 >
178 >      integrableObjects[i]->setVel( vel );
179 >
180 >      if( integrableObjects[i]->isDirectional() ){
181 >
182 >        // get and convert the torque to body frame
183 >
184 >        integrableObjects[i]->getTrq( Tb );
185 >        integrableObjects[i]->lab2Body( Tb );
186 >
187 >        for (j=0; j < 3; j++)
188            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
189 <      
190 <        dAtom->setJ( ji );
189 >
190 >        integrableObjects[i]->setJ( ji );
191        }
192      }
193  
194 <    if (nConstrained){
172 <      constrainB();
173 <    }
194 >    consFramework->doConstrainB();
195  
196      if (fabs(prevChi - chi) <= chiTolerance) break;
197    }
198 <  
198 >
199    integralOfChidt += dt2*chi;
200   }
201  
202   template<typename T> void NVT<T>::resetIntegrator( void ){
203 <  
203 >
204    chi = 0.0;
205    integralOfChidt = 0.0;
206   }
# Line 189 | Line 210 | template<typename T> int NVT<T>::readyCheck() {
210    //check parent's readyCheck() first
211    if (T::readyCheck() == -1)
212      return -1;
213 <  
214 <  // First check to see if we have a target temperature.
215 <  // Not having one is fatal.
216 <  
213 >
214 >  // First check to see if we have a target temperature.
215 >  // Not having one is fatal.
216 >
217    if (!have_target_temp) {
218      sprintf( painCave.errMsg,
219 <             "NVT error: You can't use the NVT integrator without a targetTemp!\n"
219 >             "You can't use the NVT integrator without a targetTemp!\n"
220               );
221      painCave.isFatal = 1;
222 +    painCave.severity = OOPSE_ERROR;
223      simError();
224      return -1;
225    }
226 <  
226 >
227    // We must set tauThermostat.
228 <  
228 >
229    if (!have_tau_thermostat) {
230      sprintf( painCave.errMsg,
231 <             "NVT error: If you use the constant temperature\n"
232 <             "   integrator, you must set tauThermostat.\n");
231 >             "If you use the constant temperature\n"
232 >             "\tintegrator, you must set tauThermostat.\n");
233 >    painCave.severity = OOPSE_ERROR;
234      painCave.isFatal = 1;
235      simError();
236      return -1;
237 <  }    
237 >  }
238  
239    if (!have_chi_tolerance) {
240      sprintf( painCave.errMsg,
241 <             "NVT warning: setting chi tolerance to 1e-6\n");
241 >             "In NVT integrator: setting chi tolerance to 1e-6\n");
242      chiTolerance = 1e-6;
243      have_chi_tolerance = 1;
244 +    painCave.severity = OOPSE_INFO;
245      painCave.isFatal = 0;
246      simError();
247 <  }    
247 >  }
248  
249 <  return 1;    
249 >  return 1;
250  
251   }
252  
# Line 234 | Line 258 | template<typename T> double NVT<T>::getConservedQuanti
258    double thermostat_kinetic;
259    double thermostat_potential;
260  
261 <  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
262 <
261 >  fkBT = (double)(info->ndf) * kB * targetTemp;
262 >
263    Energy = tStats->getTotalE();
264  
265 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
265 >  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
266      (2.0 * eConvert);
267  
268    thermostat_potential = fkBT * integralOfChidt / eConvert;
269  
270    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
247 –  
248 –  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
249 –      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
271  
272 <  return conservedQuantity;
272 >  return conservedQuantity;
273   }
274 +
275 + template<typename T> string NVT<T>::getAdditionalParameters(void){
276 +  string parameters;
277 +  const int BUFFERSIZE = 2000; // size of the read buffer
278 +  char buffer[BUFFERSIZE];
279 +
280 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
281 +  parameters += buffer;
282 +
283 +  return parameters;
284 + }

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