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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 565 by gezelter, Tue Jun 24 22:51:57 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 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 < NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 <  Integrator( theInfo, the_ff )
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 +
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 < void NVT::moveA() {
60 <  
61 <  int i,j,k;
62 <  int atomIndex, aMatIndex;
59 > template<typename T> NVT<T>::~NVT() {
60 >  delete[] oldVel;
61 >  delete[] oldJi;
62 > }
63 >
64 > template<typename T> void NVT<T>::moveA() {
65 >
66 >  int i, j;
67    DirectionalAtom* dAtom;
68 <  double Tb[3];
69 <  double ji[3];
68 >  double Tb[3], ji[3];
69 >  double mass;
70 >  double vel[3], pos[3], frc[3];
71 >
72    double instTemp;
30 –  double angle;
73  
74 +  // We need the temperature at time = t for the chi update below:
75 +
76    instTemp = tStats->getTemperature();
77  
78 <  // first evolve chi a half step
35 <  
36 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
78 >  for( i=0; i < integrableObjects.size(); i++ ){
79  
80 <  for( i=0; i<nAtoms; i++ ){
81 <    atomIndex = i * 3;
82 <    aMatIndex = i * 9;
41 <    
42 <    // velocity half step
43 <    for( j=atomIndex; j<(atomIndex+3); j++ )
44 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
80 >    integrableObjects[i]->getVel( vel );
81 >    integrableObjects[i]->getPos( pos );
82 >    integrableObjects[i]->getFrc( frc );
83  
84 <    // position whole step    
85 <    for( j=atomIndex; j<(atomIndex+3); j++ )
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);
89 >      // position whole step
90        pos[j] += dt * vel[j];
91 +    }
92  
93 <  
94 <    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 <      Tb[0] = dAtom->getTx();
101 <      Tb[1] = dAtom->getTy();
102 <      Tb[2] = dAtom->getTz();
60 <      
61 <      dAtom->lab2Body( Tb );
62 <      
99 >
100 >      integrableObjects[i]->getTrq( Tb );
101 >      integrableObjects[i]->lab2Body( Tb );
102 >
103        // get the angular momentum, and propagate a half step
104  
105 <      ji[0] = dAtom->getJx();
106 <      ji[1] = dAtom->getJy();
107 <      ji[2] = dAtom->getJz();
108 <      
109 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
110 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
111 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
112 <      
73 <      // use the angular velocities to propagate the rotation matrix a
74 <      // full time step
75 <      
76 <      // rotate about the x-axis      
77 <      angle = dt2 * ji[0] / dAtom->getIxx();
78 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
79 <      
80 <      // rotate about the y-axis
81 <      angle = dt2 * ji[1] / dAtom->getIyy();
82 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
83 <      
84 <      // rotate about the z-axis
85 <      angle = dt * ji[2] / dAtom->getIzz();
86 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
87 <      
88 <      // rotate about the y-axis
89 <      angle = dt2 * ji[1] / dAtom->getIyy();
90 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
91 <      
92 <       // rotate about the x-axis
93 <      angle = dt2 * ji[0] / dAtom->getIxx();
94 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
95 <      
96 <      dAtom->setJx( ji[0] );
97 <      dAtom->setJy( ji[1] );
98 <      dAtom->setJz( ji[2] );
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( integrableObjects[i], ji );
111 >
112 >      integrableObjects[i]->setJ( ji );
113      }
100 –    
114    }
102 – }
115  
116 < void NVT::moveB( void ){
117 <  int i,j,k;
118 <  int atomIndex;
119 <  DirectionalAtom* dAtom;
120 <  double Tb[3];
121 <  double ji[3];
122 <  double instTemp;
116 >  if (nConstrained){
117 >    constrainA();
118 >  }
119 >
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    
112 –  instTemp = tStats->getTemperature();
125    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
126 <  
127 <  for( i=0; i<nAtoms; i++ ){
128 <    atomIndex = i * 3;
129 <    
130 <    // velocity half step
131 <    for( j=atomIndex; j<(atomIndex+3); j++ )
132 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
133 <    
134 <    if( atoms[i]->isDirectional() ){
135 <      
136 <      dAtom = (DirectionalAtom *)atoms[i];
137 <      
138 <      // get and convert the torque to body frame
139 <      
140 <      Tb[0] = dAtom->getTx();
141 <      Tb[1] = dAtom->getTy();
142 <      Tb[2] = dAtom->getTz();
143 <      
144 <      dAtom->lab2Body( Tb );
145 <      
146 <      // get the angular momentum, and complete the angular momentum
147 <      // half step
148 <      
149 <      ji[0] = dAtom->getJx();
150 <      ji[1] = dAtom->getJy();
151 <      ji[2] = dAtom->getJz();
152 <      
153 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
154 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
155 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
144 <      
145 <      dAtom->setJx( ji[0] );
146 <      dAtom->setJy( ji[1] );
147 <      dAtom->setJz( ji[2] );
126 >  integralOfChidt += chi*dt2;
127 >
128 > }
129 >
130 > template<typename T> void NVT<T>::moveB( void ){
131 >  int i, j, k;
132 >  double Tb[3], ji[3];
133 >  double vel[3], frc[3];
134 >  double mass;
135 >  double instTemp;
136 >  double oldChi, prevChi;
137 >
138 >  // Set things up for the iteration:
139 >
140 >  oldChi = chi;
141 >
142 >  for( i=0; i < integrableObjects.size(); i++ ){
143 >
144 >    integrableObjects[i]->getVel( vel );
145 >
146 >    for (j=0; j < 3; j++)
147 >      oldVel[3*i + j]  = vel[j];
148 >
149 >    if( integrableObjects[i]->isDirectional() ){
150 >
151 >      integrableObjects[i]->getJ( ji );
152 >
153 >      for (j=0; j < 3; j++)
154 >        oldJi[3*i + j] = ji[j];
155 >
156      }
157    }
158 +
159 +  // do the iteration:
160 +
161 +  for (k=0; k < 4; k++) {
162 +
163 +    instTemp = tStats->getTemperature();
164 +
165 +    // evolve chi another half step using the temperature at t + dt/2
166 +
167 +    prevChi = chi;
168 +    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
169 +      (tauThermostat*tauThermostat);
170 +
171 +    for( i=0; i < integrableObjects.size(); i++ ){
172 +
173 +      integrableObjects[i]->getFrc( frc );
174 +      integrableObjects[i]->getVel(vel);
175 +
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 +      integrableObjects[i]->setVel( vel );
183 +
184 +      if( integrableObjects[i]->isDirectional() ){
185 +
186 +        // get and convert the torque to body frame
187 +
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 +        integrableObjects[i]->setJ( ji );
195 +      }
196 +    }
197 +
198 +    if (nConstrained){
199 +      constrainB();
200 +    }
201 +
202 +    if (fabs(prevChi - chi) <= chiTolerance) break;
203 +  }
204 +
205 +  integralOfChidt += dt2*chi;
206   }
207  
208 < int NVT::readyCheck() {
209 <
210 <  // First check to see if we have a target temperature.
211 <  // Not having one is fatal.
212 <  
208 > template<typename T> void NVT<T>::resetIntegrator( void ){
209 >
210 >  chi = 0.0;
211 >  integralOfChidt = 0.0;
212 > }
213 >
214 > template<typename T> int NVT<T>::readyCheck() {
215 >
216 >  //check parent's readyCheck() first
217 >  if (T::readyCheck() == -1)
218 >    return -1;
219 >
220 >  // First check to see if we have a target temperature.
221 >  // Not having one is fatal.
222 >
223    if (!have_target_temp) {
224      sprintf( painCave.errMsg,
225               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 162 | Line 228 | int NVT::readyCheck() {
228      simError();
229      return -1;
230    }
231 <  
231 >
232    // We must set tauThermostat.
233 <  
233 >
234    if (!have_tau_thermostat) {
235      sprintf( painCave.errMsg,
236               "NVT error: If you use the constant temperature\n"
# Line 172 | Line 238 | int NVT::readyCheck() {
238      painCave.isFatal = 1;
239      simError();
240      return -1;
241 <  }    
241 >  }
242 >
243 >  if (!have_chi_tolerance) {
244 >    sprintf( painCave.errMsg,
245 >             "NVT warning: setting chi tolerance to 1e-6\n");
246 >    chiTolerance = 1e-6;
247 >    have_chi_tolerance = 1;
248 >    painCave.isFatal = 0;
249 >    simError();
250 >  }
251 >
252    return 1;
253 +
254   }
255  
256 + template<typename T> double NVT<T>::getConservedQuantity(void){
257 +
258 +  double conservedQuantity;
259 +  double fkBT;
260 +  double Energy;
261 +  double thermostat_kinetic;
262 +  double thermostat_potential;
263 +
264 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
265 +
266 +  Energy = tStats->getTotalE();
267 +
268 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
269 +    (2.0 * eConvert);
270 +
271 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
272 +
273 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
274 +
275 +  return conservedQuantity;
276 + }
277 +
278 + template<typename T> string NVT<T>::getAdditionalParameters(void){
279 +  string parameters;
280 +  const int BUFFERSIZE = 2000; // size of the read buffer
281 +  char buffer[BUFFERSIZE];
282 +
283 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
284 +  parameters += buffer;
285 +
286 +  return parameters;
287 + }

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