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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 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
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    }
115 +
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 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
124 +  integralOfChidt += chi*dt2;
125 +
126   }
127  
128 < void NVT::moveB( void ){
129 <  int i,j,k;
130 <  int atomIndex;
131 <  DirectionalAtom* dAtom;
132 <  double Tb[3];
109 <  double ji[3];
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 <  
135 <  instTemp = tStats->getTemperature();
136 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
137 <  
138 <  for( i=0; i<nAtoms; i++ ){
139 <    atomIndex = i * 3;
140 <    
141 <    // velocity half step
142 <    for( j=atomIndex; j<(atomIndex+3); j++ )
143 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
144 <    
145 <    if( atoms[i]->isDirectional() ){
146 <      
147 <      dAtom = (DirectionalAtom *)atoms[i];
148 <      
149 <      // get and convert the torque to body frame
150 <      
151 <      Tb[0] = dAtom->getTx();
152 <      Tb[1] = dAtom->getTy();
153 <      Tb[2] = dAtom->getTz();
131 <      
132 <      dAtom->lab2Body( Tb );
133 <      
134 <      // get the angular momentum, and complete the angular momentum
135 <      // half step
136 <      
137 <      ji[0] = dAtom->getJx();
138 <      ji[1] = dAtom->getJy();
139 <      ji[2] = dAtom->getJz();
140 <      
141 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
142 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
143 <      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] );
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() {
207 <
208 <  // First check to see if we have a target temperature.
209 <  // Not having one is fatal.
210 <  
206 > template<typename T> void NVT<T>::resetIntegrator( void ){
207 >
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 162 | Line 226 | int NVT::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 172 | Line 236 | int NVT::readyCheck() {
236      painCave.isFatal = 1;
237      simError();
238      return -1;
239 <  }    
239 >  }
240 >
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 >
250    return 1;
251 +
252   }
253  
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->getNDF()    ) * 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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