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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 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 "NVT.hpp"
12 <
11 > #include "simError.h"
12 >
13 >
14   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
15  
16 < NVT::NVT() {
17 <  zeta = 0.0;
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_qmass = 0;
29 >  have_chi_tolerance = 0;
30 >  integralOfChidt = 0.0;
31 >
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 < void NVT::moveA() {
58 <  
59 <  int i,j,k;
60 <  int atomIndex, aMatIndex;
57 > template<typename T> NVT<T>::~NVT() {
58 >  delete[] oldVel;
59 >  delete[] oldJi;
60 > }
61 >
62 > template<typename T> void NVT<T>::moveA() {
63 >
64 >  int i, j;
65    DirectionalAtom* dAtom;
66 <  double Tb[3];
67 <  double ji[3];
66 >  double Tb[3], ji[3];
67 >  double mass;
68 >  double vel[3], pos[3], frc[3];
69  
70 <  ke = tStats->getKinetic() * eConvert;
29 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
70 >  double instTemp;
71  
72 <  for( i=0; i<nAtoms; i++ ){
32 <    atomIndex = i * 3;
33 <    aMatIndex = i * 9;
34 <    
35 <    // velocity half step
36 <    for( j=atomIndex; j<(atomIndex+3); j++ )
37 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
72 >  // We need the temperature at time = t for the chi update below:
73  
74 <    // position whole step    
75 <    for( j=atomIndex; j<(atomIndex+3); j++ )
74 >  instTemp = tStats->getTemperature();
75 >
76 >  for( i=0; i < integrableObjects.size(); i++ ){
77 >
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);
87 >      // position whole step
88        pos[j] += dt * vel[j];
89 +    }
90  
91 <  
92 <    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 <      Tb[0] = dAtom->getTx();
99 <      Tb[1] = dAtom->getTy();
100 <      Tb[2] = dAtom->getTz();
53 <      
54 <      dAtom->lab2Body( Tb );
55 <      
97 >
98 >      integrableObjects[i]->getTrq( Tb );
99 >      integrableObjects[i]->lab2Body( Tb );
100 >
101        // get the angular momentum, and propagate a half step
102  
103 <      ji[0] = dAtom->getJx();
104 <      ji[1] = dAtom->getJy();
105 <      ji[2] = dAtom->getJz();
106 <      
107 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
108 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
109 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
110 <      
66 <      // use the angular velocities to propagate the rotation matrix a
67 <      // full time step
68 <      
69 <      // rotate about the x-axis      
70 <      angle = dt2 * ji[0] / dAtom->getIxx();
71 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
72 <      
73 <      // rotate about the y-axis
74 <      angle = dt2 * ji[1] / dAtom->getIyy();
75 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
76 <      
77 <      // rotate about the z-axis
78 <      angle = dt * ji[2] / dAtom->getIzz();
79 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
80 <      
81 <      // rotate about the y-axis
82 <      angle = dt2 * ji[1] / dAtom->getIyy();
83 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
84 <      
85 <       // rotate about the x-axis
86 <      angle = dt2 * ji[0] / dAtom->getIxx();
87 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
88 <      
89 <      dAtom->setJx( ji[0] );
90 <      dAtom->setJy( ji[1] );
91 <      dAtom->setJz( ji[2] );
103 >      integrableObjects[i]->getJ( ji );
104 >
105 >      for (j=0; j < 3; j++)
106 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
107 >
108 >      this->rotationPropagation( integrableObjects[i], ji );
109 >
110 >      integrableObjects[i]->setJ( ji );
111      }
93 –    
112    }
95 – }
113  
114 < void Integrator::moveB( void ){
115 <  int i,j,k;
116 <  int atomIndex;
100 <  DirectionalAtom* dAtom;
101 <  double Tb[3];
102 <  double ji[3];
114 >  if (nConstrained){
115 >    constrainA();
116 >  }
117  
118 <  ke = tStats->getKinetic() * eConvert;
119 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
118 >  // Finally, evolve chi a half step (just like a velocity) using
119 >  // temperature at time t, not time t+dt/2
120 >
121 >  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
122    
123 <  for( i=0; i<nAtoms; i++ ){
124 <    atomIndex = i * 3;
125 <    
126 <    // velocity half step
127 <    for( j=atomIndex; j<(atomIndex+3); j++ )
128 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
129 <    
130 <    if( atoms[i]->isDirectional() ){
131 <      
132 <      dAtom = (DirectionalAtom *)atoms[i];
133 <      
134 <      // get and convert the torque to body frame
135 <      
136 <      Tb[0] = dAtom->getTx();
137 <      Tb[1] = dAtom->getTy();
138 <      Tb[2] = dAtom->getTz();
139 <      
140 <      dAtom->lab2Body( Tb );
141 <      
142 <      // get the angular momentum, and complete the angular momentum
143 <      // half step
144 <      
145 <      ji[0] = dAtom->getJx();
146 <      ji[1] = dAtom->getJy();
147 <      ji[2] = dAtom->getJz();
148 <      
149 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
150 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
151 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
152 <      
153 <      jx2 = ji[0] * ji[0];
138 <      jy2 = ji[1] * ji[1];
139 <      jz2 = ji[2] * ji[2];
140 <      
141 <      dAtom->setJx( ji[0] );
142 <      dAtom->setJy( ji[1] );
143 <      dAtom->setJz( ji[2] );
123 >  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
124 >  integralOfChidt += chi*dt2;
125 >
126 > }
127 >
128 > template<typename T> void NVT<T>::moveB( void ){
129 >  int i, j, k;
130 >  double Tb[3], ji[3];
131 >  double vel[3], frc[3];
132 >  double mass;
133 >  double instTemp;
134 >  double oldChi, prevChi;
135 >
136 >  // Set things up for the iteration:
137 >
138 >  oldChi = chi;
139 >
140 >  for( i=0; i < integrableObjects.size(); i++ ){
141 >
142 >    integrableObjects[i]->getVel( vel );
143 >
144 >    for (j=0; j < 3; j++)
145 >      oldVel[3*i + j]  = vel[j];
146 >
147 >    if( integrableObjects[i]->isDirectional() ){
148 >
149 >      integrableObjects[i]->getJ( ji );
150 >
151 >      for (j=0; j < 3; j++)
152 >        oldJi[3*i + j] = ji[j];
153 >
154      }
155    }
156 +
157 +  // do the iteration:
158 +
159 +  for (k=0; k < 4; k++) {
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) /
167 +      (tauThermostat*tauThermostat);
168 +
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++)
178 +        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
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 +        integrableObjects[i]->setJ( ji );
193 +      }
194 +    }
195 +
196 +    if (nConstrained){
197 +      constrainB();
198 +    }
199 +
200 +    if (fabs(prevChi - chi) <= chiTolerance) break;
201 +  }
202 +
203 +  integralOfChidt += dt2*chi;
204   }
205  
206 < int NVT::readyCheck() {
149 <  double NkBT;
206 > template<typename T> void NVT<T>::resetIntegrator( void ){
207  
208 <  // First check to see if we have a target temperature.
209 <  // Not having one is fatal.
210 <  
208 >  chi = 0.0;
209 >  integralOfChidt = 0.0;
210 > }
211 >
212 > template<typename T> int NVT<T>::readyCheck() {
213 >
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 >
221    if (!have_target_temp) {
222      sprintf( painCave.errMsg,
223               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 159 | Line 226 | int NVT::readyCheck() {
226      simError();
227      return -1;
228    }
162 –    
163 –  // Next check to see that we have a reasonable number of degrees of freedom
164 –  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
165 –  // are also fatal.
229  
230 <  if (entry_plug->ndf > 0) {
231 <    NkBT = (double)entry_plug->ndf * kB * targetTemp;
232 <  } else {
230 >  // We must set tauThermostat.
231 >
232 >  if (!have_tau_thermostat) {
233      sprintf( painCave.errMsg,
234 <             "NVT error: We got a silly number of degrees of freedom!\n"
235 <             );
234 >             "NVT error: If you use the constant temperature\n"
235 >             "   integrator, you must set tauThermostat.\n");
236      painCave.isFatal = 1;
237      simError();
238      return -1;
239    }
177 –    
178 –  // We have our choice on setting qmass or tauThermostat.  One of them
179 –  // must be set.
240  
241 <  if (!have_qmass) {
242 <    if (have_tau_thermostat) {
243 <      sprintf( painCave.errMsg,
244 <               "NVT info: Setting qMass = %d\n", tauThermostat * NkBT);
245 <      this->setQmass(tauThermostat * NkBT);      
246 <      painCave.isFatal = 0;
247 <      simError();
188 <    } else {
189 <      sprintf( painCave.errMsg,
190 <               "NVT error: If you use the constant temperature\n"
191 <               "   integrator, you must set either tauThermostat or qMass.\n");
192 <      painCave.isFatal = 1;
193 <      simError();
194 <      return -1;
195 <    }
241 >  if (!have_chi_tolerance) {
242 >    sprintf( painCave.errMsg,
243 >             "NVT warning: setting chi tolerance to 1e-6\n");
244 >    chiTolerance = 1e-6;
245 >    have_chi_tolerance = 1;
246 >    painCave.isFatal = 0;
247 >    simError();
248    }
249 <  
249 >
250    return 1;
251 +
252   }
253  
254 < #endif
254 > template<typename T> double NVT<T>::getConservedQuantity(void){
255 >
256 >  double conservedQuantity;
257 >  double fkBT;
258 >  double Energy;
259 >  double thermostat_kinetic;
260 >  double thermostat_potential;
261 >
262 >  fkBT = (double)(info->ndf) * kB * targetTemp;
263 >
264 >  Energy = tStats->getTotalE();
265 >
266 >  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
267 >    (2.0 * eConvert);
268 >
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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