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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC vs.
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC

# Line 6 | Line 6
6   #include "Thermo.hpp"
7   #include "ReadWrite.hpp"
8   #include "Integrator.hpp"
9 < #include "simError.h"
9 > #include "simError.h"
10  
11  
12   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
# Line 14 | Line 14 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
14   template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15    T( theInfo, the_ff )
16   {
17 +  GenericData* data;
18 +  DoubleData * chiValue;
19 +  DoubleData * integralOfChidtValue;
20 +
21 +  chiValue = NULL;
22 +  integralOfChidtValue = NULL;
23 +
24    chi = 0.0;
25    have_tau_thermostat = 0;
26    have_target_temp = 0;
27 +  have_chi_tolerance = 0;
28 +  integralOfChidt = 0.0;
29 +
30 +  // retrieve chi and integralOfChidt from simInfo
31 +  data = info->getProperty(CHIVALUE_ID);
32 +  if(data){
33 +    chiValue = dynamic_cast<DoubleData*>(data);
34 +  }
35 +
36 +  data = info->getProperty(INTEGRALOFCHIDT_ID);
37 +  if(data){
38 +    integralOfChidtValue = dynamic_cast<DoubleData*>(data);
39 +  }
40 +
41 +  // chi and integralOfChidt should appear by pair
42 +  if(chiValue && integralOfChidtValue){
43 +    chi = chiValue->getData();
44 +    integralOfChidt = integralOfChidtValue->getData();
45 +  }
46 +
47 +  oldVel = new double[3*nAtoms];
48 +  oldJi = new double[3*nAtoms];
49   }
50  
51 + template<typename T> NVT<T>::~NVT() {
52 +  delete[] oldVel;
53 +  delete[] oldJi;
54 + }
55 +
56   template<typename T> void NVT<T>::moveA() {
57 <  
57 >
58    int i, j;
59    DirectionalAtom* dAtom;
60    double Tb[3], ji[3];
61 <  double A[3][3], I[3][3];
28 <  double angle, mass;
61 >  double mass;
62    double vel[3], pos[3], frc[3];
63  
64    double instTemp;
65  
66 +  // We need the temperature at time = t for the chi update below:
67 +
68    instTemp = tStats->getTemperature();
69  
35 –  // first evolve chi a half step
36 –  
37 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
38 –
70    for( i=0; i<nAtoms; i++ ){
71  
72      atoms[i]->getVel( vel );
# Line 45 | Line 76 | template<typename T> void NVT<T>::moveA() {
76      mass = atoms[i]->getMass();
77  
78      for (j=0; j < 3; j++) {
79 <      // velocity half step
79 >      // velocity half step  (use chi from previous step here):
80        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
81        // position whole step
82        pos[j] += dt * vel[j];
# Line 53 | Line 84 | template<typename T> void NVT<T>::moveA() {
84  
85      atoms[i]->setVel( vel );
86      atoms[i]->setPos( pos );
87 <  
87 >
88      if( atoms[i]->isDirectional() ){
89  
90        dAtom = (DirectionalAtom *)atoms[i];
91 <          
91 >
92        // get and convert the torque to body frame
93 <      
93 >
94        dAtom->getTrq( Tb );
95        dAtom->lab2Body( Tb );
96 <      
96 >
97        // get the angular momentum, and propagate a half step
98  
99        dAtom->getJ( ji );
100  
101 <      for (j=0; j < 3; j++)
101 >      for (j=0; j < 3; j++)
102          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
72 –      
73 –      // use the angular velocities to propagate the rotation matrix a
74 –      // full time step
103  
104 <      dAtom->getA(A);
77 <      dAtom->getI(I);
78 <    
79 <      // rotate about the x-axis      
80 <      angle = dt2 * ji[0] / I[0][0];
81 <      this->rotate( 1, 2, angle, ji, A );
104 >      this->rotationPropagation( dAtom, ji );
105  
83 –      // rotate about the y-axis
84 –      angle = dt2 * ji[1] / I[1][1];
85 –      this->rotate( 2, 0, angle, ji, A );
86 –      
87 –      // rotate about the z-axis
88 –      angle = dt * ji[2] / I[2][2];
89 –      this->rotate( 0, 1, angle, ji, A);
90 –      
91 –      // rotate about the y-axis
92 –      angle = dt2 * ji[1] / I[1][1];
93 –      this->rotate( 2, 0, angle, ji, A );
94 –      
95 –       // rotate about the x-axis
96 –      angle = dt2 * ji[0] / I[0][0];
97 –      this->rotate( 1, 2, angle, ji, A );
98 –      
106        dAtom->setJ( ji );
107 <      dAtom->setA( A  );    
101 <    }    
107 >    }
108    }
109 +
110 +  if (nConstrained){
111 +    constrainA();
112 +  }
113 +
114 +  // Finally, evolve chi a half step (just like a velocity) using
115 +  // temperature at time t, not time t+dt/2
116 +
117 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
118 +  integralOfChidt += chi*dt2;
119 +
120   }
121  
122   template<typename T> void NVT<T>::moveB( void ){
123 <  int i, j;
123 >  int i, j, k;
124    DirectionalAtom* dAtom;
125    double Tb[3], ji[3];
126    double vel[3], frc[3];
127    double mass;
111 –
128    double instTemp;
129 <  
130 <  instTemp = tStats->getTemperature();
131 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
132 <  
129 >  double oldChi, prevChi;
130 >
131 >  // Set things up for the iteration:
132 >
133 >  oldChi = chi;
134 >
135    for( i=0; i<nAtoms; i++ ){
136  
137      atoms[i]->getVel( vel );
120 –    atoms[i]->getFrc( frc );
138  
139 <    mass = atoms[i]->getMass();
139 >    for (j=0; j < 3; j++)
140 >      oldVel[3*i + j]  = vel[j];
141  
124 –    // velocity half step
125 –    for (j=0; j < 3; j++)
126 –      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
127 –    
128 –    atoms[i]->setVel( vel );
129 –
142      if( atoms[i]->isDirectional() ){
143  
144        dAtom = (DirectionalAtom *)atoms[i];
145  
146 <      // get and convert the torque to body frame      
146 >      dAtom->getJ( ji );
147  
148 <      dAtom->getTrq( Tb );
149 <      dAtom->lab2Body( Tb );
148 >      for (j=0; j < 3; j++)
149 >        oldJi[3*i + j] = ji[j];
150  
151 <      // get the angular momentum, and propagate a half step
151 >    }
152 >  }
153  
154 <      dAtom->getJ( ji );
154 >  // do the iteration:
155  
156 <      for (j=0; j < 3; j++)
144 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
145 <      
156 >  for (k=0; k < 4; k++) {
157  
158 <      dAtom->setJ( ji );
158 >    instTemp = tStats->getTemperature();
159 >
160 >    // evolve chi another half step using the temperature at t + dt/2
161 >
162 >    prevChi = chi;
163 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
164 >      (tauThermostat*tauThermostat);
165 >
166 >    for( i=0; i<nAtoms; i++ ){
167 >
168 >      atoms[i]->getFrc( frc );
169 >      atoms[i]->getVel(vel);
170 >
171 >      mass = atoms[i]->getMass();
172 >
173 >      // velocity half step
174 >      for (j=0; j < 3; j++)
175 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
176 >
177 >      atoms[i]->setVel( vel );
178 >
179 >      if( atoms[i]->isDirectional() ){
180 >
181 >        dAtom = (DirectionalAtom *)atoms[i];
182 >
183 >        // get and convert the torque to body frame
184 >
185 >        dAtom->getTrq( Tb );
186 >        dAtom->lab2Body( Tb );
187 >
188 >        for (j=0; j < 3; j++)
189 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
190 >
191 >        dAtom->setJ( ji );
192 >      }
193      }
194 +
195 +    if (nConstrained){
196 +      constrainB();
197 +    }
198 +
199 +    if (fabs(prevChi - chi) <= chiTolerance) break;
200    }
201 +
202 +  integralOfChidt += dt2*chi;
203   }
204  
205   template<typename T> void NVT<T>::resetIntegrator( void ){
206 <  
206 >
207    chi = 0.0;
208 +  integralOfChidt = 0.0;
209   }
210  
211   template<typename T> int NVT<T>::readyCheck() {
# Line 159 | Line 213 | template<typename T> int NVT<T>::readyCheck() {
213    //check parent's readyCheck() first
214    if (T::readyCheck() == -1)
215      return -1;
216 <  
217 <  // First check to see if we have a target temperature.
218 <  // Not having one is fatal.
219 <  
216 >
217 >  // First check to see if we have a target temperature.
218 >  // Not having one is fatal.
219 >
220    if (!have_target_temp) {
221      sprintf( painCave.errMsg,
222               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 171 | Line 225 | template<typename T> int NVT<T>::readyCheck() {
225      simError();
226      return -1;
227    }
228 <  
228 >
229    // We must set tauThermostat.
230 <  
230 >
231    if (!have_tau_thermostat) {
232      sprintf( painCave.errMsg,
233               "NVT error: If you use the constant temperature\n"
# Line 181 | Line 235 | template<typename T> int NVT<T>::readyCheck() {
235      painCave.isFatal = 1;
236      simError();
237      return -1;
238 <  }    
238 >  }
239 >
240 >  if (!have_chi_tolerance) {
241 >    sprintf( painCave.errMsg,
242 >             "NVT warning: setting chi tolerance to 1e-6\n");
243 >    chiTolerance = 1e-6;
244 >    have_chi_tolerance = 1;
245 >    painCave.isFatal = 0;
246 >    simError();
247 >  }
248 >
249    return 1;
250 +
251   }
252 +
253 + template<typename T> double NVT<T>::getConservedQuantity(void){
254 +
255 +  double conservedQuantity;
256 +  double fkBT;
257 +  double Energy;
258 +  double thermostat_kinetic;
259 +  double thermostat_potential;
260 +
261 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
262 +
263 +  Energy = tStats->getTotalE();
264 +
265 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
266 +    (2.0 * eConvert);
267 +
268 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
269 +
270 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
271 +
272 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
273 +      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
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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