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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 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
# Line 14 | Line 16 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
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 +  // retrieve chi and integralOfChidt from simInfo
33 +  data = info->getProperty(CHIVALUE_ID);
34 +  if(data){
35 +    chiValue = dynamic_cast<DoubleData*>(data);
36 +  }
37 +
38 +  data = info->getProperty(INTEGRALOFCHIDT_ID);
39 +  if(data){
40 +    integralOfChidtValue = dynamic_cast<DoubleData*>(data);
41 +  }
42 +
43 +  // chi and integralOfChidt should appear by pair
44 +  if(chiValue && integralOfChidtValue){
45 +    chi = chiValue->getData();
46 +    integralOfChidt = integralOfChidtValue->getData();
47 +  }
48 +
49 +  oldVel = new double[3*nAtoms];
50 +  oldJi = new double[3*nAtoms];
51   }
52  
53 + template<typename T> NVT<T>::~NVT() {
54 +  delete[] oldVel;
55 +  delete[] oldJi;
56 + }
57 +
58   template<typename T> void NVT<T>::moveA() {
59 <  
59 >
60    int i, j;
61    DirectionalAtom* dAtom;
62    double Tb[3], ji[3];
63 <  double A[3][3], I[3][3];
28 <  double angle, mass;
63 >  double mass;
64    double vel[3], pos[3], frc[3];
65  
66    double instTemp;
67  
68 +  // We need the temperature at time = t for the chi update below:
69 +
70    instTemp = tStats->getTemperature();
71  
35 –  // first evolve chi a half step
36 –  
37 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
38 –
72    for( i=0; i<nAtoms; i++ ){
73  
74      atoms[i]->getVel( vel );
# Line 45 | Line 78 | template<typename T> void NVT<T>::moveA() {
78      mass = atoms[i]->getMass();
79  
80      for (j=0; j < 3; j++) {
81 <      // velocity half step
81 >      // velocity half step  (use chi from previous step here):
82        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
83        // position whole step
84        pos[j] += dt * vel[j];
# Line 53 | Line 86 | template<typename T> void NVT<T>::moveA() {
86  
87      atoms[i]->setVel( vel );
88      atoms[i]->setPos( pos );
89 <  
89 >
90      if( atoms[i]->isDirectional() ){
91  
92        dAtom = (DirectionalAtom *)atoms[i];
93 <          
93 >
94        // get and convert the torque to body frame
95 <      
95 >
96        dAtom->getTrq( Tb );
97        dAtom->lab2Body( Tb );
98 <      
98 >
99        // get the angular momentum, and propagate a half step
100  
101        dAtom->getJ( ji );
102  
103 <      for (j=0; j < 3; j++)
103 >      for (j=0; j < 3; j++)
104          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
105  
106 <      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 );
106 >      this->rotationPropagation( dAtom, ji );
107  
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 –      
108        dAtom->setJ( ji );
109 <      dAtom->setA( A  );    
101 <    }    
109 >    }
110    }
111 +
112 +  if (nConstrained){
113 +    constrainA();
114 +  }
115 +
116 +  // Finally, evolve chi a half step (just like a velocity) using
117 +  // temperature at time t, not time t+dt/2
118 +
119 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
120 +  integralOfChidt += chi*dt2;
121 +
122   }
123  
124   template<typename T> void NVT<T>::moveB( void ){
125 <  int i, j;
125 >  int i, j, k;
126    DirectionalAtom* dAtom;
127    double Tb[3], ji[3];
128    double vel[3], frc[3];
129    double mass;
111 –
130    double instTemp;
131 <  
132 <  instTemp = tStats->getTemperature();
133 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
134 <  
131 >  double oldChi, prevChi;
132 >
133 >  // Set things up for the iteration:
134 >
135 >  oldChi = chi;
136 >
137    for( i=0; i<nAtoms; i++ ){
138  
139      atoms[i]->getVel( vel );
120 –    atoms[i]->getFrc( frc );
140  
141 <    mass = atoms[i]->getMass();
141 >    for (j=0; j < 3; j++)
142 >      oldVel[3*i + j]  = vel[j];
143  
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 –
144      if( atoms[i]->isDirectional() ){
145  
146        dAtom = (DirectionalAtom *)atoms[i];
147  
148 <      // get and convert the torque to body frame      
148 >      dAtom->getJ( ji );
149  
150 <      dAtom->getTrq( Tb );
151 <      dAtom->lab2Body( Tb );
150 >      for (j=0; j < 3; j++)
151 >        oldJi[3*i + j] = ji[j];
152  
153 <      // get the angular momentum, and propagate a half step
153 >    }
154 >  }
155  
156 <      dAtom->getJ( ji );
156 >  // do the iteration:
157  
158 <      for (j=0; j < 3; j++)
144 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
145 <      
158 >  for (k=0; k < 4; k++) {
159  
160 <      dAtom->setJ( ji );
160 >    instTemp = tStats->getTemperature();
161 >
162 >    // evolve chi another half step using the temperature at t + dt/2
163 >
164 >    prevChi = chi;
165 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
166 >      (tauThermostat*tauThermostat);
167 >
168 >    for( i=0; i<nAtoms; i++ ){
169 >
170 >      atoms[i]->getFrc( frc );
171 >      atoms[i]->getVel(vel);
172 >
173 >      mass = atoms[i]->getMass();
174 >
175 >      // velocity half step
176 >      for (j=0; j < 3; j++)
177 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
178 >
179 >      atoms[i]->setVel( vel );
180 >
181 >      if( atoms[i]->isDirectional() ){
182 >
183 >        dAtom = (DirectionalAtom *)atoms[i];
184 >
185 >        // get and convert the torque to body frame
186 >
187 >        dAtom->getTrq( Tb );
188 >        dAtom->lab2Body( Tb );
189 >
190 >        for (j=0; j < 3; j++)
191 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
192 >
193 >        dAtom->setJ( ji );
194 >      }
195      }
196 +
197 +    if (nConstrained){
198 +      constrainB();
199 +    }
200 +
201 +    if (fabs(prevChi - chi) <= chiTolerance) break;
202    }
203 +
204 +  integralOfChidt += dt2*chi;
205   }
206  
207 + template<typename T> void NVT<T>::resetIntegrator( void ){
208 +
209 +  chi = 0.0;
210 +  integralOfChidt = 0.0;
211 + }
212 +
213   template<typename T> int NVT<T>::readyCheck() {
214  
215    //check parent's readyCheck() first
216    if (T::readyCheck() == -1)
217      return -1;
218 <  
219 <  // First check to see if we have a target temperature.
220 <  // Not having one is fatal.
221 <  
218 >
219 >  // First check to see if we have a target temperature.
220 >  // Not having one is fatal.
221 >
222    if (!have_target_temp) {
223      sprintf( painCave.errMsg,
224               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 166 | Line 227 | template<typename T> int NVT<T>::readyCheck() {
227      simError();
228      return -1;
229    }
230 <  
230 >
231    // We must set tauThermostat.
232 <  
232 >
233    if (!have_tau_thermostat) {
234      sprintf( painCave.errMsg,
235               "NVT error: If you use the constant temperature\n"
# Line 176 | Line 237 | template<typename T> int NVT<T>::readyCheck() {
237      painCave.isFatal = 1;
238      simError();
239      return -1;
240 <  }    
240 >  }
241 >
242 >  if (!have_chi_tolerance) {
243 >    sprintf( painCave.errMsg,
244 >             "NVT warning: setting chi tolerance to 1e-6\n");
245 >    chiTolerance = 1e-6;
246 >    have_chi_tolerance = 1;
247 >    painCave.isFatal = 0;
248 >    simError();
249 >  }
250 >
251    return 1;
252 +
253   }
254 +
255 + template<typename T> double NVT<T>::getConservedQuantity(void){
256 +
257 +  double conservedQuantity;
258 +  double fkBT;
259 +  double Energy;
260 +  double thermostat_kinetic;
261 +  double thermostat_potential;
262 +
263 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
264 +
265 +  Energy = tStats->getTotalE();
266 +
267 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
268 +    (2.0 * eConvert);
269 +
270 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
271 +
272 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
273 +
274 +  return conservedQuantity;
275 + }
276 +
277 + template<typename T> string NVT<T>::getAdditionalParameters(void){
278 +  string parameters;
279 +  const int BUFFERSIZE = 2000; // size of the read buffer
280 +  char buffer[BUFFERSIZE];
281 +
282 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
283 +  parameters += buffer;
284 +
285 +  return parameters;
286 + }

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