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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC vs.
Revision 772 by gezelter, Fri Sep 19 16:01:07 2003 UTC

# Line 9 | Line 9
9   #include "Integrator.hpp"
10   #include "simError.h"
11  
12 + #ifdef IS_MPI
13 + #include "mpiSimulation.hpp"
14 + #endif
15  
16   // Basic isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
# Line 25 | Line 28 | template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo,
28   {
29    chi = 0.0;
30    eta = 0.0;
31 +  integralOfChidt = 0.0;
32    have_tau_thermostat = 0;
33    have_tau_barostat = 0;
34    have_target_temp = 0;
35    have_target_pressure = 0;
36 +  have_chi_tolerance = 0;
37 +  have_eta_tolerance = 0;
38 +  have_pos_iter_tolerance = 0;
39 +
40 +  oldPos = new double[3*nAtoms];
41 +  oldVel = new double[3*nAtoms];
42 +  oldJi = new double[3*nAtoms];
43 + #ifdef IS_MPI
44 +  Nparticles = mpiSim->getTotAtoms();
45 + #else
46 +  Nparticles = theInfo->n_atoms;
47 + #endif
48 +
49   }
50  
51 + template<typename T> NPTi<T>::~NPTi() {
52 +  delete[] oldPos;
53 +  delete[] oldVel;
54 +  delete[] oldJi;
55 + }
56 +
57   template<typename T> void NPTi<T>::moveA() {
58 <  
59 <  int i, j;
58 >
59 >  //new version of NPTi
60 >  int i, j, k;
61    DirectionalAtom* dAtom;
62    double Tb[3], ji[3];
63    double A[3][3], I[3][3];
# Line 43 | Line 67 | template<typename T> void NPTi<T>::moveA() {
67    double rj[3];
68    double instaTemp, instaPress, instaVol;
69    double tt2, tb2, scaleFactor;
70 +  double COM[3];
71  
72    tt2 = tauThermostat * tauThermostat;
73    tb2 = tauBarostat * tauBarostat;
# Line 50 | Line 75 | template<typename T> void NPTi<T>::moveA() {
75    instaTemp = tStats->getTemperature();
76    instaPress = tStats->getPressure();
77    instaVol = tStats->getVolume();
53 –  
54 –   // first evolve chi a half step
78    
79 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
80 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
81 <                 (p_convert*NkBT*tb2));
59 <
79 >  tStats->getCOM(COM);
80 >  
81 >  //evolve velocity half step
82    for( i=0; i<nAtoms; i++ ){
83 +
84      atoms[i]->getVel( vel );
62 –    atoms[i]->getPos( pos );
85      atoms[i]->getFrc( frc );
86  
87      mass = atoms[i]->getMass();
88  
89      for (j=0; j < 3; j++) {
90 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
91 <      rj[j] = pos[j];
90 >      // velocity half step
91 >      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
92      }
93  
94      atoms[i]->setVel( vel );
95 <
74 <    info->wrapVector(rj);
75 <
76 <    for (j = 0; j < 3; j++)
77 <      pos[j] += dt * (vel[j] + eta*rj[j]);
78 <
79 <    atoms[i]->setPos( pos );
80 <
95 >  
96      if( atoms[i]->isDirectional() ){
97  
98        dAtom = (DirectionalAtom *)atoms[i];
99 <          
99 >
100        // get and convert the torque to body frame
101        
102        dAtom->getTrq( Tb );
# Line 122 | Line 137 | template<typename T> void NPTi<T>::moveA() {
137        
138        dAtom->setJ( ji );
139        dAtom->setA( A  );    
140 <    }                
140 >    }    
141 >  }
142  
143 +  // advance chi half step
144 +  
145 +  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
146 +
147 +  // calculate the integral of chidt
148 +
149 +  integralOfChidt += dt2*chi;
150 +
151 +  // advance eta half step
152 +
153 +  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2));
154 +
155 +  //save the old positions
156 +  for(i = 0; i < nAtoms; i++){
157 +    atoms[i]->getPos(pos);
158 +    for(j = 0; j < 3; j++)
159 +      oldPos[i*3 + j] = pos[j];
160    }
161 +  
162 +  //the first estimation of r(t+dt) is equal to  r(t)
163 +    
164 +  for(k = 0; k < 4; k ++){
165  
166 +    for(i =0 ; i < nAtoms; i++){
167 +
168 +      atoms[i]->getVel(vel);
169 +      atoms[i]->getPos(pos);
170 +
171 +      for(j = 0; j < 3; j++)
172 +        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];    
173 +      
174 +      for(j = 0; j < 3; j++)
175 +        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]);
176 +
177 +      atoms[i]->setPos( pos );
178 +    }
179 +    
180 +    if (nConstrained){
181 +      constrainA();
182 +    }
183 +  }
184 +    
185 +
186    // Scale the box after all the positions have been moved:
187    
188    scaleFactor = exp(dt*eta);
# Line 139 | Line 196 | template<typename T> void NPTi<T>::moveA() {
196      painCave.isFatal = 1;
197      simError();
198    } else {        
199 <    info->scaleBox(exp(dt*eta));      
200 <  }
199 >    info->scaleBox(scaleFactor);      
200 >  }  
201  
202   }
203  
204   template<typename T> void NPTi<T>::moveB( void ){
205 <
206 <  int i, j;
205 >  
206 >  //new version of NPTi
207 >  int i, j, k;
208    DirectionalAtom* dAtom;
209    double Tb[3], ji[3];
210    double vel[3], frc[3];
# Line 154 | Line 212 | template<typename T> void NPTi<T>::moveB( void ){
212  
213    double instaTemp, instaPress, instaVol;
214    double tt2, tb2;
215 +  double oldChi, prevChi;
216 +  double oldEta, prevEta;
217    
218    tt2 = tauThermostat * tauThermostat;
219    tb2 = tauBarostat * tauBarostat;
220  
221 <  instaTemp = tStats->getTemperature();
162 <  instaPress = tStats->getPressure();
163 <  instaVol = tStats->getVolume();
221 >  // Set things up for the iteration:
222  
223 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
224 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
225 <                 (p_convert*NkBT*tb2));
168 <  
223 >  oldChi = chi;
224 >  oldEta = eta;
225 >
226    for( i=0; i<nAtoms; i++ ){
227  
228      atoms[i]->getVel( vel );
172 –    atoms[i]->getFrc( frc );
229  
230 <    mass = atoms[i]->getMass();
230 >    for (j=0; j < 3; j++)
231 >      oldVel[3*i + j]  = vel[j];
232  
176 –    // velocity half step
177 –    for (j=0; j < 3; j++)
178 –      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta));
179 –    
180 –    atoms[i]->setVel( vel );
181 –
233      if( atoms[i]->isDirectional() ){
234  
235        dAtom = (DirectionalAtom *)atoms[i];
236  
237 <      // get and convert the torque to body frame      
237 >      dAtom->getJ( ji );
238  
239 <      dAtom->getTrq( Tb );
240 <      dAtom->lab2Body( Tb );
239 >      for (j=0; j < 3; j++)
240 >        oldJi[3*i + j] = ji[j];
241  
242 <      // get the angular momentum, and propagate a half step
242 >    }
243 >  }
244  
245 <      dAtom->getJ( ji );
245 >  // do the iteration:
246  
247 +  instaVol = tStats->getVolume();
248 +  
249 +  for (k=0; k < 4; k++) {
250 +    
251 +    instaTemp = tStats->getTemperature();
252 +    instaPress = tStats->getPressure();
253 +
254 +    // evolve chi another half step using the temperature at t + dt/2
255 +
256 +    prevChi = chi;
257 +    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
258 +
259 +    prevEta = eta;
260 +
261 +    // advance eta half step and calculate scale factor for velocity
262 +
263 +    eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
264 +       (p_convert*NkBT*tb2));
265 +
266 +  
267 +    for( i=0; i<nAtoms; i++ ){
268 +
269 +      atoms[i]->getFrc( frc );
270 +      atoms[i]->getVel(vel);
271 +      
272 +      mass = atoms[i]->getMass();
273 +      
274 +      // velocity half step
275        for (j=0; j < 3; j++)
276 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);    
276 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta));
277 >      
278 >      atoms[i]->setVel( vel );
279 >      
280 >      if( atoms[i]->isDirectional() ){
281  
282 <      dAtom->setJ( ji );
282 >        dAtom = (DirectionalAtom *)atoms[i];
283 >  
284 >        // get and convert the torque to body frame      
285 >  
286 >        dAtom->getTrq( Tb );
287 >        dAtom->lab2Body( Tb );      
288 >            
289 >        for (j=0; j < 3; j++)
290 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
291 >      
292 >          dAtom->setJ( ji );
293 >      }
294      }
295 +    
296 +    if (nConstrained){
297 +      constrainB();
298 +    }    
299 +    
300 +    if (fabs(prevChi - chi) <=
301 +        chiTolerance && fabs(prevEta -eta) <= etaTolerance)
302 +      break;
303    }
304 +
305 +  //calculate integral of chidt
306 +  integralOfChidt += dt2*chi;
307 +
308   }
309  
310   template<typename T> void NPTi<T>::resetIntegrator() {
# Line 256 | Line 363 | template<typename T> int NPTi<T>::readyCheck() {
363      return -1;
364    }    
365  
366 <  // We need NkBT a lot, so just set it here:
366 >  if (!have_chi_tolerance) {
367 >    sprintf( painCave.errMsg,
368 >             "NPTi warning: setting chi tolerance to 1e-6\n");
369 >    chiTolerance = 1e-6;
370 >    have_chi_tolerance = 1;
371 >    painCave.isFatal = 0;
372 >    simError();
373 >  }
374  
375 <  NkBT = (double)info->ndf * kB * targetTemp;
375 >  if (!have_eta_tolerance) {
376 >    sprintf( painCave.errMsg,
377 >             "NPTi warning: setting eta tolerance to 1e-6\n");
378 >    etaTolerance = 1e-6;
379 >    have_eta_tolerance = 1;
380 >    painCave.isFatal = 0;
381 >    simError();
382 >  }
383 >  
384 >  
385 >  // We need NkBT a lot, so just set it here: This is the RAW number
386 >  // of particles, so no subtraction or addition of constraints or
387 >  // orientational degrees of freedom:
388 >  
389 >  NkBT = (double)Nparticles * kB * targetTemp;
390 >  
391 >  // fkBT is used because the thermostat operates on more degrees of freedom
392 >  // than the barostat (when there are particles with orientational degrees
393 >  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
394 >  
395 >  fkBT = (double)info->ndf * kB * targetTemp;
396  
397    return 1;
398   }
399 +
400 + template<typename T> double NPTi<T>::getConservedQuantity(void){
401 +
402 +  double conservedQuantity;
403 +  double Three_NkBT;
404 +  double Energy;
405 +  double thermostat_kinetic;
406 +  double thermostat_potential;
407 +  double barostat_kinetic;
408 +  double barostat_potential;
409 +  double tb2;
410 +  double eta2;
411 +
412 +  Energy = tStats->getTotalE();
413 +
414 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
415 +    (2.0 * eConvert);
416 +
417 +  thermostat_potential = fkBT* integralOfChidt / eConvert;
418 +
419 +
420 +  barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta /
421 +    (2.0 * eConvert);
422 +  
423 +  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
424 +    eConvert;
425 +
426 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
427 +    barostat_kinetic + barostat_potential;
428 +  
429 +  cout.width(8);
430 +  cout.precision(8);
431 +
432 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
433 +      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
434 +      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
435 +
436 +  return conservedQuantity;
437 + }

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