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root/group/branches/new-templateless/OOPSE/libmdtools/NVT.cpp
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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.
branches/new-templateless/OOPSE/libmdtools/NVT.cpp (file contents), Revision 851 by mmeineke, Wed Nov 5 19:18:17 2003 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
15  
16 < template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 <  T( theInfo, the_ff )
16 > NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 >  Integrator( theInfo, the_ff )
18   {
19 +  GenericData* data;
20 +
21    chi = 0.0;
22    have_tau_thermostat = 0;
23    have_target_temp = 0;
24    have_chi_tolerance = 0;
25    integralOfChidt = 0.0;
26  
27 +  // retrieve chi and integralOfChidt from simInfo
28 +  data = info->getProperty(CHIVALUE_ID);
29 +  if(data != NULL ){
30 +    chi = data->getDval();
31 +  }
32 +
33 +  data = info->getProperty(INTEGRALOFCHIDT_ID);
34 +  if(data != NULL ){
35 +    integralOfChidt = data->getDval();
36 +  }
37 +
38    oldVel = new double[3*nAtoms];
39    oldJi = new double[3*nAtoms];
40   }
41  
42 < template<typename T> NVT<T>::~NVT() {
42 > NVT::~NVT() {
43    delete[] oldVel;
44    delete[] oldJi;
45   }
46  
47 < template<typename T> void NVT<T>::moveA() {
48 <  
47 > void NVT::moveA() {
48 >
49    int i, j;
50    DirectionalAtom* dAtom;
51    double Tb[3], ji[3];
# Line 42 | Line 57 | template<typename T> void NVT<T>::moveA() {
57    // We need the temperature at time = t for the chi update below:
58  
59    instTemp = tStats->getTemperature();
60 <  
60 >
61    for( i=0; i<nAtoms; i++ ){
62  
63      atoms[i]->getVel( vel );
# Line 60 | Line 75 | template<typename T> void NVT<T>::moveA() {
75  
76      atoms[i]->setVel( vel );
77      atoms[i]->setPos( pos );
78 <  
78 >
79      if( atoms[i]->isDirectional() ){
80  
81        dAtom = (DirectionalAtom *)atoms[i];
82 <          
82 >
83        // get and convert the torque to body frame
84 <      
84 >
85        dAtom->getTrq( Tb );
86        dAtom->lab2Body( Tb );
87 <      
87 >
88        // get the angular momentum, and propagate a half step
89  
90        dAtom->getJ( ji );
91  
92 <      for (j=0; j < 3; j++)
92 >      for (j=0; j < 3; j++)
93          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
94 <      
94 >
95        this->rotationPropagation( dAtom, ji );
96 <      
96 >
97        dAtom->setJ( ji );
98 <    }    
98 >    }
99    }
100 <  
100 >
101    if (nConstrained){
102      constrainA();
103    }
104  
105 <  // Finally, evolve chi a half step (just like a velocity) using
105 >  // Finally, evolve chi a half step (just like a velocity) using
106    // temperature at time t, not time t+dt/2
107  
108    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
# Line 95 | Line 110 | template<typename T> void NVT<T>::moveA() {
110  
111   }
112  
113 < template<typename T> void NVT<T>::moveB( void ){
113 > void NVT::moveB( void ){
114    int i, j, k;
115    DirectionalAtom* dAtom;
116    double Tb[3], ji[3];
# Line 130 | Line 145 | template<typename T> void NVT<T>::moveB( void ){
145    // do the iteration:
146  
147    for (k=0; k < 4; k++) {
148 <    
148 >
149      instTemp = tStats->getTemperature();
150  
151      // evolve chi another half step using the temperature at t + dt/2
152  
153      prevChi = chi;
154 <    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
154 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
155        (tauThermostat*tauThermostat);
156 <  
156 >
157      for( i=0; i<nAtoms; i++ ){
158  
159        atoms[i]->getFrc( frc );
160        atoms[i]->getVel(vel);
161 <      
161 >
162        mass = atoms[i]->getMass();
163 <      
163 >
164        // velocity half step
165 <      for (j=0; j < 3; j++)
165 >      for (j=0; j < 3; j++)
166          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
167 <      
167 >
168        atoms[i]->setVel( vel );
169 <      
169 >
170        if( atoms[i]->isDirectional() ){
171 <        
171 >
172          dAtom = (DirectionalAtom *)atoms[i];
173 <        
174 <        // get and convert the torque to body frame      
175 <        
173 >
174 >        // get and convert the torque to body frame
175 >
176          dAtom->getTrq( Tb );
177 <        dAtom->lab2Body( Tb );      
178 <            
179 <        for (j=0; j < 3; j++)
177 >        dAtom->lab2Body( Tb );
178 >
179 >        for (j=0; j < 3; j++)
180            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
181 <      
181 >
182          dAtom->setJ( ji );
183        }
184      }
# Line 174 | Line 189 | template<typename T> void NVT<T>::moveB( void ){
189  
190      if (fabs(prevChi - chi) <= chiTolerance) break;
191    }
192 <  
192 >
193    integralOfChidt += dt2*chi;
194   }
195  
196 < template<typename T> void NVT<T>::resetIntegrator( void ){
197 <  
196 > void NVT::resetIntegrator( void ){
197 >
198    chi = 0.0;
199    integralOfChidt = 0.0;
200   }
201  
202 < template<typename T> int NVT<T>::readyCheck() {
202 > int NVT::readyCheck() {
203  
204    //check parent's readyCheck() first
205 <  if (T::readyCheck() == -1)
205 >  if (Integrator::readyCheck() == -1)
206      return -1;
207 <  
208 <  // First check to see if we have a target temperature.
209 <  // Not having one is fatal.
210 <  
207 >
208 >  // First check to see if we have a target temperature.
209 >  // Not having one is fatal.
210 >
211    if (!have_target_temp) {
212      sprintf( painCave.errMsg,
213               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 201 | Line 216 | template<typename T> int NVT<T>::readyCheck() {
216      simError();
217      return -1;
218    }
219 <  
219 >
220    // We must set tauThermostat.
221 <  
221 >
222    if (!have_tau_thermostat) {
223      sprintf( painCave.errMsg,
224               "NVT error: If you use the constant temperature\n"
# Line 211 | Line 226 | template<typename T> int NVT<T>::readyCheck() {
226      painCave.isFatal = 1;
227      simError();
228      return -1;
229 <  }    
229 >  }
230  
231    if (!have_chi_tolerance) {
232      sprintf( painCave.errMsg,
# Line 220 | Line 235 | template<typename T> int NVT<T>::readyCheck() {
235      have_chi_tolerance = 1;
236      painCave.isFatal = 0;
237      simError();
238 <  }    
238 >  }
239  
240 <  return 1;    
240 >  return 1;
241  
242   }
243  
244 < template<typename T> double NVT<T>::getConservedQuantity(void){
244 > double NVT::getConservedQuantity(void){
245  
246    double conservedQuantity;
247    double fkBT;
# Line 234 | Line 249 | template<typename T> double NVT<T>::getConservedQuanti
249    double thermostat_kinetic;
250    double thermostat_potential;
251  
252 <  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
253 <
252 >  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
253 >
254    Energy = tStats->getTotalE();
255  
256 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
256 >  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
257      (2.0 * eConvert);
258  
259    thermostat_potential = fkBT * integralOfChidt / eConvert;
260  
261    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
262 <  
263 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
262 >
263 >  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
264        "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
265  
266 <  return conservedQuantity;
266 >  return conservedQuantity;
267   }
268 +
269 + char* NVT::getAdditionalParameters(void){
270 +
271 +  sprintf(addParamBuffer,
272 +          "\t%G\t%G;",
273 +          chi, integralOfChidt
274 +          );
275 +
276 +  return addParamBuffer;
277 + }

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