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root/group/trunk/OOPSE/libmdtools/NVT.cpp
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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 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
13  
14 < NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15 <  Integrator( theInfo, the_ff )
14 > template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
15 >  T( theInfo, the_ff )
16   {
17 <  zeta = 0.0;
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_qmass = 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 < void NVT::moveA() {
52 <  
53 <  int i,j,k;
54 <  int atomIndex, aMatIndex;
51 > template<typename T> NVT<T>::~NVT() {
52 >  delete[] oldVel;
53 >  delete[] oldJi;
54 > }
55 >
56 > template<typename T> void NVT<T>::moveA() {
57 >
58 >  int i, j;
59    DirectionalAtom* dAtom;
60 <  double Tb[3];
61 <  double ji[3];
62 <  double ke;
31 <  double angle;
60 >  double Tb[3], ji[3];
61 >  double mass;
62 >  double vel[3], pos[3], frc[3];
63  
64 +  double instTemp;
65  
66 <  ke = tStats->getKinetic() * eConvert;
35 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
66 >  // We need the temperature at time = t for the chi update below:
67  
68 +  instTemp = tStats->getTemperature();
69 +
70    for( i=0; i<nAtoms; i++ ){
38 –    atomIndex = i * 3;
39 –    aMatIndex = i * 9;
40 –    
41 –    // velocity half step
42 –    for( j=atomIndex; j<(atomIndex+3); j++ )
43 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
71  
72 <    // position whole step    
73 <    for( j=atomIndex; j<(atomIndex+3); j++ )
72 >    atoms[i]->getVel( vel );
73 >    atoms[i]->getPos( pos );
74 >    atoms[i]->getFrc( frc );
75 >
76 >    mass = atoms[i]->getMass();
77 >
78 >    for (j=0; j < 3; j++) {
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];
83 +    }
84  
85 <  
85 >    atoms[i]->setVel( vel );
86 >    atoms[i]->setPos( pos );
87 >
88      if( atoms[i]->isDirectional() ){
89  
90        dAtom = (DirectionalAtom *)atoms[i];
91 <          
91 >
92        // get and convert the torque to body frame
93 <      
94 <      Tb[0] = dAtom->getTx();
57 <      Tb[1] = dAtom->getTy();
58 <      Tb[2] = dAtom->getTz();
59 <      
93 >
94 >      dAtom->getTrq( Tb );
95        dAtom->lab2Body( Tb );
96 <      
96 >
97        // get the angular momentum, and propagate a half step
98  
99 <      ji[0] = dAtom->getJx();
100 <      ji[1] = dAtom->getJy();
101 <      ji[2] = dAtom->getJz();
102 <      
103 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
104 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
105 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
106 <      
72 <      // use the angular velocities to propagate the rotation matrix a
73 <      // full time step
74 <      
75 <      // rotate about the x-axis      
76 <      angle = dt2 * ji[0] / dAtom->getIxx();
77 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
78 <      
79 <      // rotate about the y-axis
80 <      angle = dt2 * ji[1] / dAtom->getIyy();
81 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
82 <      
83 <      // rotate about the z-axis
84 <      angle = dt * ji[2] / dAtom->getIzz();
85 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
86 <      
87 <      // rotate about the y-axis
88 <      angle = dt2 * ji[1] / dAtom->getIyy();
89 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
90 <      
91 <       // rotate about the x-axis
92 <      angle = dt2 * ji[0] / dAtom->getIxx();
93 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
94 <      
95 <      dAtom->setJx( ji[0] );
96 <      dAtom->setJy( ji[1] );
97 <      dAtom->setJz( ji[2] );
99 >      dAtom->getJ( ji );
100 >
101 >      for (j=0; j < 3; j++)
102 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
103 >
104 >      this->rotationPropagation( dAtom, ji );
105 >
106 >      dAtom->setJ( ji );
107      }
99 –    
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 < void NVT::moveB( void ){
123 <  int i,j,k;
105 <  int atomIndex;
122 > template<typename T> void NVT<T>::moveB( void ){
123 >  int i, j, k;
124    DirectionalAtom* dAtom;
125 <  double Tb[3];
126 <  double ji[3];
127 <  double ke;
128 <  
125 >  double Tb[3], ji[3];
126 >  double vel[3], frc[3];
127 >  double mass;
128 >  double instTemp;
129 >  double oldChi, prevChi;
130  
131 <  ke = tStats->getKinetic() * eConvert;
132 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
133 <  
131 >  // Set things up for the iteration:
132 >
133 >  oldChi = chi;
134 >
135    for( i=0; i<nAtoms; i++ ){
136 <    atomIndex = i * 3;
137 <    
138 <    // velocity half step
139 <    for( j=atomIndex; j<(atomIndex+3); j++ )
140 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
141 <    
136 >
137 >    atoms[i]->getVel( vel );
138 >
139 >    for (j=0; j < 3; j++)
140 >      oldVel[3*i + j]  = vel[j];
141 >
142      if( atoms[i]->isDirectional() ){
143 <      
143 >
144        dAtom = (DirectionalAtom *)atoms[i];
145 <      
146 <      // get and convert the torque to body frame
147 <      
148 <      Tb[0] = dAtom->getTx();
149 <      Tb[1] = dAtom->getTy();
150 <      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]*zeta);
142 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
143 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
144 <      
145 <      dAtom->setJx( ji[0] );
146 <      dAtom->setJy( ji[1] );
147 <      dAtom->setJz( ji[2] );
145 >
146 >      dAtom->getJ( ji );
147 >
148 >      for (j=0; j < 3; j++)
149 >        oldJi[3*i + j] = ji[j];
150 >
151      }
152    }
153 +
154 +  // do the iteration:
155 +
156 +  for (k=0; k < 4; k++) {
157 +
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 < int NVT::readyCheck() {
206 <
207 <  // First check to see if we have a target temperature.
208 <  // Not having one is fatal.
209 <  
205 > template<typename T> void NVT<T>::resetIntegrator( void ){
206 >
207 >  chi = 0.0;
208 >  integralOfChidt = 0.0;
209 > }
210 >
211 > template<typename T> int NVT<T>::readyCheck() {
212 >
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 >
220    if (!have_target_temp) {
221      sprintf( painCave.errMsg,
222               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 162 | Line 225 | int NVT::readyCheck() {
225      simError();
226      return -1;
227    }
165 –    
166 –  // Next check to see that we have a reasonable number of degrees of freedom
167 –  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
168 –  // are also fatal.
228  
229 <  if (info->ndf > 0) {
230 <    NkBT = (double)info->ndf * kB * targetTemp;
231 <  } else {
229 >  // We must set tauThermostat.
230 >
231 >  if (!have_tau_thermostat) {
232      sprintf( painCave.errMsg,
233 <             "NVT error: We got a silly number of degrees of freedom!\n"
234 <             );
233 >             "NVT error: If you use the constant temperature\n"
234 >             "   integrator, you must set tauThermostat.\n");
235      painCave.isFatal = 1;
236      simError();
237      return -1;
238    }
180 –    
181 –  // We have our choice on setting qmass or tauThermostat.  One of them
182 –  // must be set.
239  
240 <  if (!have_qmass) {
241 <    if (have_tau_thermostat) {
242 <      sprintf( painCave.errMsg,
243 <               "NVT info: Setting qMass = %lf\n", tauThermostat * NkBT);
244 <      this->setQmass(tauThermostat * NkBT);      
245 <      painCave.isFatal = 0;
246 <      simError();
191 <    } else {
192 <      sprintf( painCave.errMsg,
193 <               "NVT error: If you use the constant temperature\n"
194 <               "   integrator, you must set either tauThermostat or qMass.\n");
195 <      painCave.isFatal = 1;
196 <      simError();
197 <      return -1;
198 <    }
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 <  
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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