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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 768 by mmeineke, Wed Sep 17 14:22:15 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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 >
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 30 | Line 62 | template<typename T> void NVT<T>::moveA() {
62   }
63  
64   template<typename T> void NVT<T>::moveA() {
65 <  
65 >
66    int i, j;
67    DirectionalAtom* dAtom;
68    double Tb[3], ji[3];
69 <  double A[3][3], I[3][3];
38 <  double angle, mass;
69 >  double mass;
70    double vel[3], pos[3], frc[3];
71  
72    double instTemp;
# Line 43 | Line 74 | template<typename T> void NVT<T>::moveA() {
74    // We need the temperature at time = t for the chi update below:
75  
76    instTemp = tStats->getTemperature();
46 –  
47 –  for( i=0; i<nAtoms; i++ ){
77  
78 <    atoms[i]->getVel( vel );
50 <    atoms[i]->getPos( pos );
51 <    atoms[i]->getFrc( frc );
78 >  for( i=0; i < integrableObjects.size(); i++ ){
79  
80 <    mass = atoms[i]->getMass();
80 >    integrableObjects[i]->getVel( vel );
81 >    integrableObjects[i]->getPos( pos );
82 >    integrableObjects[i]->getFrc( frc );
83  
84 +    mass = integrableObjects[i]->getMass();
85 +
86      for (j=0; j < 3; j++) {
87        // velocity half step  (use chi from previous step here):
88        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
# Line 59 | 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 );
64 <  
65 <    if( atoms[i]->isDirectional() ){
93 >    integrableObjects[i]->setVel( vel );
94 >    integrableObjects[i]->setPos( pos );
95  
96 <      dAtom = (DirectionalAtom *)atoms[i];
97 <          
96 >    if( integrableObjects[i]->isDirectional() ){
97 >
98        // get and convert the torque to body frame
99 <      
100 <      dAtom->getTrq( Tb );
101 <      dAtom->lab2Body( Tb );
102 <      
99 >
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++)
107 >      for (j=0; j < 3; j++)
108          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
80 –      
81 –      // use the angular velocities to propagate the rotation matrix a
82 –      // full time step
109  
110 <      dAtom->getA(A);
85 <      dAtom->getI(I);
86 <    
87 <      // rotate about the x-axis      
88 <      angle = dt2 * ji[0] / I[0][0];
89 <      this->rotate( 1, 2, angle, ji, A );
110 >      this->rotationPropagation( integrableObjects[i], ji );
111  
112 <      // rotate about the y-axis
113 <      angle = dt2 * ji[1] / I[1][1];
93 <      this->rotate( 2, 0, angle, ji, A );
94 <      
95 <      // rotate about the z-axis
96 <      angle = dt * ji[2] / I[2][2];
97 <      this->rotate( 0, 1, angle, ji, A);
98 <      
99 <      // rotate about the y-axis
100 <      angle = dt2 * ji[1] / I[1][1];
101 <      this->rotate( 2, 0, angle, ji, A );
102 <      
103 <       // rotate about the x-axis
104 <      angle = dt2 * ji[0] / I[0][0];
105 <      this->rotate( 1, 2, angle, ji, A );
106 <      
107 <      dAtom->setJ( ji );
108 <      dAtom->setA( A  );    
109 <    }    
112 >      integrableObjects[i]->setJ( ji );
113 >    }
114    }
115 <  
115 >
116    if (nConstrained){
117      constrainA();
118    }
119  
120 <  // Finally, evolve chi a half step (just like a velocity) using
120 >  // Finally, evolve chi a half step (just like a velocity) using
121    // temperature at time t, not time t+dt/2
122  
123    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
# Line 123 | Line 127 | template<typename T> void NVT<T>::moveB( void ){
127  
128   template<typename T> void NVT<T>::moveB( void ){
129    int i, j, k;
126 –  DirectionalAtom* dAtom;
130    double Tb[3], ji[3];
131    double vel[3], frc[3];
132    double mass;
# Line 134 | Line 137 | template<typename T> void NVT<T>::moveB( void ){
137  
138    oldChi = chi;
139  
140 <  for( i=0; i<nAtoms; i++ ){
140 >  for( i=0; i < integrableObjects.size(); i++ ){
141  
142 <    atoms[i]->getVel( vel );
142 >    integrableObjects[i]->getVel( vel );
143  
144      for (j=0; j < 3; j++)
145        oldVel[3*i + j]  = vel[j];
146  
147 <    if( atoms[i]->isDirectional() ){
147 >    if( integrableObjects[i]->isDirectional() ){
148  
149 <      dAtom = (DirectionalAtom *)atoms[i];
149 >      integrableObjects[i]->getJ( ji );
150  
148 –      dAtom->getJ( ji );
149 –
151        for (j=0; j < 3; j++)
152          oldJi[3*i + j] = ji[j];
153  
# Line 156 | Line 157 | template<typename T> void NVT<T>::moveB( void ){
157    // do the iteration:
158  
159    for (k=0; k < 4; k++) {
160 <    
160 >
161      instTemp = tStats->getTemperature();
162  
163      // evolve chi another half step using the temperature at t + dt/2
164  
165      prevChi = chi;
166 <    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
166 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
167        (tauThermostat*tauThermostat);
167 –  
168 –    for( i=0; i<nAtoms; i++ ){
168  
169 <      atoms[i]->getFrc( frc );
170 <      atoms[i]->getVel(vel);
171 <      
172 <      mass = atoms[i]->getMass();
173 <      
169 >    for( i=0; i < integrableObjects.size(); i++ ){
170 >
171 >      integrableObjects[i]->getFrc( frc );
172 >      integrableObjects[i]->getVel(vel);
173 >
174 >      mass = integrableObjects[i]->getMass();
175 >
176        // velocity half step
177 <      for (j=0; j < 3; j++)
177 >      for (j=0; j < 3; j++)
178          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
179 <      
180 <      atoms[i]->setVel( vel );
181 <      
182 <      if( atoms[i]->isDirectional() ){
183 <        
184 <        dAtom = (DirectionalAtom *)atoms[i];
185 <        
186 <        // get and convert the torque to body frame      
187 <        
188 <        dAtom->getTrq( Tb );
189 <        dAtom->lab2Body( Tb );      
189 <            
190 <        for (j=0; j < 3; j++)
179 >
180 >      integrableObjects[i]->setVel( vel );
181 >
182 >      if( integrableObjects[i]->isDirectional() ){
183 >
184 >        // get and convert the torque to body frame
185 >
186 >        integrableObjects[i]->getTrq( Tb );
187 >        integrableObjects[i]->lab2Body( Tb );
188 >
189 >        for (j=0; j < 3; j++)
190            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
191 <      
192 <        dAtom->setJ( ji );
191 >
192 >        integrableObjects[i]->setJ( ji );
193        }
194      }
195  
# Line 200 | Line 199 | template<typename T> void NVT<T>::moveB( void ){
199  
200      if (fabs(prevChi - chi) <= chiTolerance) break;
201    }
202 <  
202 >
203    integralOfChidt += dt2*chi;
204   }
205  
206   template<typename T> void NVT<T>::resetIntegrator( void ){
207 <  
207 >
208    chi = 0.0;
209    integralOfChidt = 0.0;
210   }
# Line 215 | Line 214 | template<typename T> int NVT<T>::readyCheck() {
214    //check parent's readyCheck() first
215    if (T::readyCheck() == -1)
216      return -1;
217 <  
218 <  // First check to see if we have a target temperature.
219 <  // Not having one is fatal.
220 <  
217 >
218 >  // First check to see if we have a target temperature.
219 >  // Not having one is fatal.
220 >
221    if (!have_target_temp) {
222      sprintf( painCave.errMsg,
223               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 227 | Line 226 | template<typename T> int NVT<T>::readyCheck() {
226      simError();
227      return -1;
228    }
229 <  
229 >
230    // We must set tauThermostat.
231 <  
231 >
232    if (!have_tau_thermostat) {
233      sprintf( painCave.errMsg,
234               "NVT error: If you use the constant temperature\n"
# Line 237 | Line 236 | template<typename T> int NVT<T>::readyCheck() {
236      painCave.isFatal = 1;
237      simError();
238      return -1;
239 <  }    
239 >  }
240  
241    if (!have_chi_tolerance) {
242      sprintf( painCave.errMsg,
# Line 246 | Line 245 | template<typename T> int NVT<T>::readyCheck() {
245      have_chi_tolerance = 1;
246      painCave.isFatal = 0;
247      simError();
248 <  }    
248 >  }
249  
250 <  return 1;    
250 >  return 1;
251  
252   }
253  
254   template<typename T> double NVT<T>::getConservedQuantity(void){
255  
256    double conservedQuantity;
257 <  double E_NVT;
257 >  double fkBT;
258 >  double Energy;
259 >  double thermostat_kinetic;
260 >  double thermostat_potential;
261  
262 <  //HNVE
261 <  conservedQuantity = tStats->getTotalE();
262 <  //HNVE
263 <  
264 <  E_NVT =  (info->getNDF() * kB * targetTemp *
265 <                (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert;
262 >  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
263  
264 <  conservedQuantity += E_NVT;
264 >  Energy = tStats->getTotalE();
265  
266 <  //cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl;
266 >  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
267 >    (2.0 * eConvert);
268  
269 <  return conservedQuantity;
269 >  thermostat_potential = fkBT * integralOfChidt / eConvert;
270 >
271 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
272 >
273 >  return conservedQuantity;
274   }
275 +
276 + template<typename T> string NVT<T>::getAdditionalParameters(void){
277 +  string parameters;
278 +  const int BUFFERSIZE = 2000; // size of the read buffer
279 +  char buffer[BUFFERSIZE];
280 +
281 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
282 +  parameters += buffer;
283 +
284 +  return parameters;
285 + }

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