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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 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 "NVT.hpp"
12 <
11 > #include "simError.h"
12 >
13 >
14   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
15  
16 < NVT::NVT() {
17 <  zeta = 0.0;
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_qmass = 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 >  oldVel = new double[3*nAtoms];
54 >  oldJi = new double[3*nAtoms];
55   }
56  
57 < void NVT::moveA() {
58 <  
59 <  int i,j,k;
60 <  int atomIndex, aMatIndex;
57 > template<typename T> NVT<T>::~NVT() {
58 >  delete[] oldVel;
59 >  delete[] oldJi;
60 > }
61 >
62 > template<typename T> void NVT<T>::moveA() {
63 >
64 >  int i, j;
65    DirectionalAtom* dAtom;
66 <  double Tb[3];
67 <  double ji[3];
66 >  double Tb[3], ji[3];
67 >  double mass;
68 >  double vel[3], pos[3], frc[3];
69  
70 <  ke = tStats->getKinetic() * eConvert;
29 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
70 >  double instTemp;
71  
72 +  // We need the temperature at time = t for the chi update below:
73 +
74 +  instTemp = tStats->getTemperature();
75 +
76    for( i=0; i<nAtoms; i++ ){
32 –    atomIndex = i * 3;
33 –    aMatIndex = i * 9;
34 –    
35 –    // velocity half step
36 –    for( j=atomIndex; j<(atomIndex+3); j++ )
37 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
77  
78 <    // position whole step    
79 <    for( j=atomIndex; j<(atomIndex+3); j++ )
78 >    atoms[i]->getVel( vel );
79 >    atoms[i]->getPos( pos );
80 >    atoms[i]->getFrc( frc );
81 >
82 >    mass = atoms[i]->getMass();
83 >
84 >    for (j=0; j < 3; j++) {
85 >      // velocity half step  (use chi from previous step here):
86 >      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
87 >      // position whole step
88        pos[j] += dt * vel[j];
89 +    }
90  
91 <  
91 >    atoms[i]->setVel( vel );
92 >    atoms[i]->setPos( pos );
93 >
94      if( atoms[i]->isDirectional() ){
95  
96        dAtom = (DirectionalAtom *)atoms[i];
97 <          
97 >
98        // get and convert the torque to body frame
99 <      
100 <      Tb[0] = dAtom->getTx();
51 <      Tb[1] = dAtom->getTy();
52 <      Tb[2] = dAtom->getTz();
53 <      
99 >
100 >      dAtom->getTrq( Tb );
101        dAtom->lab2Body( Tb );
102 <      
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]*zeta);
110 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
111 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
112 <      
66 <      // use the angular velocities to propagate the rotation matrix a
67 <      // full time step
68 <      
69 <      // rotate about the x-axis      
70 <      angle = dt2 * ji[0] / dAtom->getIxx();
71 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
72 <      
73 <      // rotate about the y-axis
74 <      angle = dt2 * ji[1] / dAtom->getIyy();
75 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
76 <      
77 <      // rotate about the z-axis
78 <      angle = dt * ji[2] / dAtom->getIzz();
79 <      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
80 <      
81 <      // rotate about the y-axis
82 <      angle = dt2 * ji[1] / dAtom->getIyy();
83 <      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
84 <      
85 <       // rotate about the x-axis
86 <      angle = dt2 * ji[0] / dAtom->getIxx();
87 <      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
88 <      
89 <      dAtom->setJx( ji[0] );
90 <      dAtom->setJy( ji[1] );
91 <      dAtom->setJz( ji[2] );
105 >      dAtom->getJ( ji );
106 >
107 >      for (j=0; j < 3; j++)
108 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
109 >
110 >      this->rotationPropagation( dAtom, ji );
111 >
112 >      dAtom->setJ( ji );
113      }
93 –    
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 Integrator::moveB( void ){
129 <  int i,j,k;
99 <  int atomIndex;
128 > template<typename T> void NVT<T>::moveB( void ){
129 >  int i, j, k;
130    DirectionalAtom* dAtom;
131 <  double Tb[3];
132 <  double ji[3];
131 >  double Tb[3], ji[3];
132 >  double vel[3], frc[3];
133 >  double mass;
134 >  double instTemp;
135 >  double oldChi, prevChi;
136  
137 <  ke = tStats->getKinetic() * eConvert;
138 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
139 <  
137 >  // Set things up for the iteration:
138 >
139 >  oldChi = chi;
140 >
141    for( i=0; i<nAtoms; i++ ){
142 <    atomIndex = i * 3;
143 <    
144 <    // velocity half step
145 <    for( j=atomIndex; j<(atomIndex+3); j++ )
146 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
147 <    
142 >
143 >    atoms[i]->getVel( vel );
144 >
145 >    for (j=0; j < 3; j++)
146 >      oldVel[3*i + j]  = vel[j];
147 >
148      if( atoms[i]->isDirectional() ){
149 <      
149 >
150        dAtom = (DirectionalAtom *)atoms[i];
151 <      
152 <      // get and convert the torque to body frame
153 <      
154 <      Tb[0] = dAtom->getTx();
155 <      Tb[1] = dAtom->getTy();
156 <      Tb[2] = dAtom->getTz();
123 <      
124 <      dAtom->lab2Body( Tb );
125 <      
126 <      // get the angular momentum, and complete the angular momentum
127 <      // half step
128 <      
129 <      ji[0] = dAtom->getJx();
130 <      ji[1] = dAtom->getJy();
131 <      ji[2] = dAtom->getJz();
132 <      
133 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
134 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
135 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
136 <      
137 <      jx2 = ji[0] * ji[0];
138 <      jy2 = ji[1] * ji[1];
139 <      jz2 = ji[2] * ji[2];
140 <      
141 <      dAtom->setJx( ji[0] );
142 <      dAtom->setJy( ji[1] );
143 <      dAtom->setJz( ji[2] );
151 >
152 >      dAtom->getJ( ji );
153 >
154 >      for (j=0; j < 3; j++)
155 >        oldJi[3*i + j] = ji[j];
156 >
157      }
158    }
159 +
160 +  // do the iteration:
161 +
162 +  for (k=0; k < 4; k++) {
163 +
164 +    instTemp = tStats->getTemperature();
165 +
166 +    // evolve chi another half step using the temperature at t + dt/2
167 +
168 +    prevChi = chi;
169 +    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
170 +      (tauThermostat*tauThermostat);
171 +
172 +    for( i=0; i<nAtoms; i++ ){
173 +
174 +      atoms[i]->getFrc( frc );
175 +      atoms[i]->getVel(vel);
176 +
177 +      mass = atoms[i]->getMass();
178 +
179 +      // velocity half step
180 +      for (j=0; j < 3; j++)
181 +        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
182 +
183 +      atoms[i]->setVel( vel );
184 +
185 +      if( atoms[i]->isDirectional() ){
186 +
187 +        dAtom = (DirectionalAtom *)atoms[i];
188 +
189 +        // get and convert the torque to body frame
190 +
191 +        dAtom->getTrq( Tb );
192 +        dAtom->lab2Body( Tb );
193 +
194 +        for (j=0; j < 3; j++)
195 +          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
196 +
197 +        dAtom->setJ( ji );
198 +      }
199 +    }
200 +
201 +    if (nConstrained){
202 +      constrainB();
203 +    }
204 +
205 +    if (fabs(prevChi - chi) <= chiTolerance) break;
206 +  }
207 +
208 +  integralOfChidt += dt2*chi;
209   }
210  
211 < int NVT::readyCheck() {
149 <  double NkBT;
211 > template<typename T> void NVT<T>::resetIntegrator( void ){
212  
213 <  // First check to see if we have a target temperature.
214 <  // Not having one is fatal.
215 <  
213 >  chi = 0.0;
214 >  integralOfChidt = 0.0;
215 > }
216 >
217 > template<typename T> int NVT<T>::readyCheck() {
218 >
219 >  //check parent's readyCheck() first
220 >  if (T::readyCheck() == -1)
221 >    return -1;
222 >
223 >  // First check to see if we have a target temperature.
224 >  // Not having one is fatal.
225 >
226    if (!have_target_temp) {
227      sprintf( painCave.errMsg,
228               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 159 | Line 231 | int NVT::readyCheck() {
231      simError();
232      return -1;
233    }
162 –    
163 –  // Next check to see that we have a reasonable number of degrees of freedom
164 –  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
165 –  // are also fatal.
234  
235 <  if (entry_plug->ndf > 0) {
236 <    NkBT = (double)entry_plug->ndf * kB * targetTemp;
237 <  } else {
235 >  // We must set tauThermostat.
236 >
237 >  if (!have_tau_thermostat) {
238      sprintf( painCave.errMsg,
239 <             "NVT error: We got a silly number of degrees of freedom!\n"
240 <             );
239 >             "NVT error: If you use the constant temperature\n"
240 >             "   integrator, you must set tauThermostat.\n");
241      painCave.isFatal = 1;
242      simError();
243      return -1;
244    }
177 –    
178 –  // We have our choice on setting qmass or tauThermostat.  One of them
179 –  // must be set.
245  
246 <  if (!have_qmass) {
247 <    if (have_tau_thermostat) {
248 <      sprintf( painCave.errMsg,
249 <               "NVT info: Setting qMass = %d\n", tauThermostat * NkBT);
250 <      this->setQmass(tauThermostat * NkBT);      
251 <      painCave.isFatal = 0;
252 <      simError();
188 <    } else {
189 <      sprintf( painCave.errMsg,
190 <               "NVT error: If you use the constant temperature\n"
191 <               "   integrator, you must set either tauThermostat or qMass.\n");
192 <      painCave.isFatal = 1;
193 <      simError();
194 <      return -1;
195 <    }
246 >  if (!have_chi_tolerance) {
247 >    sprintf( painCave.errMsg,
248 >             "NVT warning: setting chi tolerance to 1e-6\n");
249 >    chiTolerance = 1e-6;
250 >    have_chi_tolerance = 1;
251 >    painCave.isFatal = 0;
252 >    simError();
253    }
254 <  
254 >
255    return 1;
256 +
257   }
258  
259 < #endif
259 > template<typename T> double NVT<T>::getConservedQuantity(void){
260 >
261 >  double conservedQuantity;
262 >  double fkBT;
263 >  double Energy;
264 >  double thermostat_kinetic;
265 >  double thermostat_potential;
266 >
267 >  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
268 >
269 >  Energy = tStats->getTotalE();
270 >
271 >  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
272 >    (2.0 * eConvert);
273 >
274 >  thermostat_potential = fkBT * integralOfChidt / eConvert;
275 >
276 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
277 >
278 >  return conservedQuantity;
279 > }
280 >
281 > template<typename T> string NVT<T>::getAdditionalParameters(void){
282 >  string parameters;
283 >  const int BUFFERSIZE = 2000; // size of the read buffer
284 >  char buffer[BUFFERSIZE];
285 >
286 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
287 >  parameters += buffer;
288 >
289 >  return parameters;
290 > }

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