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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 772 by gezelter, Fri Sep 19 16:01:07 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC

# Line 26 | Line 26 | template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo,
26   template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27    T( theInfo, the_ff )
28   {
29 –  chi = 0.0;
29    eta = 0.0;
30 <  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 <
30 >  oldEta = 0.0;
31   }
32  
33   template<typename T> NPTi<T>::~NPTi() {
34 <  delete[] oldPos;
53 <  delete[] oldVel;
54 <  delete[] oldJi;
34 >  //nothing for now
35   }
36  
37 < template<typename T> void NPTi<T>::moveA() {
38 <
39 <  //new version of NPTi
40 <  int i, j, k;
61 <  DirectionalAtom* dAtom;
62 <  double Tb[3], ji[3];
63 <  double A[3][3], I[3][3];
64 <  double angle, mass;
65 <  double vel[3], pos[3], frc[3];
37 > template<typename T> void NPTi<T>::resetIntegrator() {
38 >  eta = 0.0;
39 >  T::resetIntegrator();
40 > }
41  
42 <  double rj[3];
43 <  double instaTemp, instaPress, instaVol;
44 <  double tt2, tb2, scaleFactor;
45 <  double COM[3];
42 > template<typename T> void NPTi<T>::evolveEtaA() {
43 >  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
44 >                 (p_convert*NkBT*tb2));
45 >  oldEta = eta;
46 > }
47  
48 <  tt2 = tauThermostat * tauThermostat;
73 <  tb2 = tauBarostat * tauBarostat;
74 <
75 <  instaTemp = tStats->getTemperature();
76 <  instaPress = tStats->getPressure();
77 <  instaVol = tStats->getVolume();
48 > template<typename T> void NPTi<T>::evolveEtaB() {
49    
50 <  tStats->getCOM(COM);
51 <  
52 <  //evolve velocity half step
53 <  for( i=0; i<nAtoms; i++ ){
50 >  prevEta = eta;
51 >  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
52 >                 (p_convert*NkBT*tb2));
53 > }
54  
55 <    atoms[i]->getVel( vel );
56 <    atoms[i]->getFrc( frc );
55 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
56 >  int i;
57  
58 <    mass = atoms[i]->getMass();
58 >  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
59 > }
60  
61 <    for (j=0; j < 3; j++) {
62 <      // velocity half step
91 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
92 <    }
61 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
62 >  int i;
63  
64 <    atoms[i]->setVel( vel );
65 <  
96 <    if( atoms[i]->isDirectional() ){
64 >  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
65 > }
66  
98 –      dAtom = (DirectionalAtom *)atoms[i];
67  
68 <      // get and convert the torque to body frame
69 <      
70 <      dAtom->getTrq( Tb );
103 <      dAtom->lab2Body( Tb );
104 <      
105 <      // get the angular momentum, and propagate a half step
68 > template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
69 >                                               int index, double sc[3]){
70 >  int j;
71  
72 <      dAtom->getJ( ji );
72 >  for(j=0; j<3; j++)
73 >    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
74  
75 <      for (j=0; j < 3; j++)
76 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
77 <      
112 <      // use the angular velocities to propagate the rotation matrix a
113 <      // full time step
75 >  for(j=0; j<3; j++)
76 >    sc[j] *= eta;
77 > }
78  
79 <      dAtom->getA(A);
116 <      dAtom->getI(I);
117 <    
118 <      // rotate about the x-axis      
119 <      angle = dt2 * ji[0] / I[0][0];
120 <      this->rotate( 1, 2, angle, ji, A );
79 > template<typename T> void NPTi<T>::scaleSimBox( void ){
80  
81 <      // rotate about the y-axis
123 <      angle = dt2 * ji[1] / I[1][1];
124 <      this->rotate( 2, 0, angle, ji, A );
125 <      
126 <      // rotate about the z-axis
127 <      angle = dt * ji[2] / I[2][2];
128 <      this->rotate( 0, 1, angle, ji, A);
129 <      
130 <      // rotate about the y-axis
131 <      angle = dt2 * ji[1] / I[1][1];
132 <      this->rotate( 2, 0, angle, ji, A );
133 <      
134 <       // rotate about the x-axis
135 <      angle = dt2 * ji[0] / I[0][0];
136 <      this->rotate( 1, 2, angle, ji, A );
137 <      
138 <      dAtom->setJ( ji );
139 <      dAtom->setA( A  );    
140 <    }    
141 <  }
81 >  double scaleFactor;
82  
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 –  
83    scaleFactor = exp(dt*eta);
84  
85    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
# Line 201 | Line 96 | template<typename T> void NPTi<T>::moveB( void ){
96  
97   }
98  
99 < template<typename T> void NPTi<T>::moveB( void ){
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];
211 <  double mass;
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 <  // Set things up for the iteration:
99 > template<typename T> bool NPTi<T>::etaConverged() {
100  
101 <  oldChi = chi;
224 <  oldEta = eta;
225 <
226 <  for( i=0; i<nAtoms; i++ ){
227 <
228 <    atoms[i]->getVel( vel );
229 <
230 <    for (j=0; j < 3; j++)
231 <      oldVel[3*i + j]  = vel[j];
232 <
233 <    if( atoms[i]->isDirectional() ){
234 <
235 <      dAtom = (DirectionalAtom *)atoms[i];
236 <
237 <      dAtom->getJ( ji );
238 <
239 <      for (j=0; j < 3; j++)
240 <        oldJi[3*i + j] = ji[j];
241 <
242 <    }
243 <  }
244 <
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 <        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 = (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 <
101 >  return ( fabs(prevEta - eta) <= etaTolerance );
102   }
103  
310 – template<typename T> void NPTi<T>::resetIntegrator() {
311 –  chi = 0.0;
312 –  eta = 0.0;
313 – }
314 –
315 – template<typename T> int NPTi<T>::readyCheck() {
316 –
317 –  //check parent's readyCheck() first
318 –  if (T::readyCheck() == -1)
319 –    return -1;
320 –
321 –  // First check to see if we have a target temperature.
322 –  // Not having one is fatal.
323 –  
324 –  if (!have_target_temp) {
325 –    sprintf( painCave.errMsg,
326 –             "NPTi error: You can't use the NPTi integrator\n"
327 –             "   without a targetTemp!\n"
328 –             );
329 –    painCave.isFatal = 1;
330 –    simError();
331 –    return -1;
332 –  }
333 –
334 –  if (!have_target_pressure) {
335 –    sprintf( painCave.errMsg,
336 –             "NPTi error: You can't use the NPTi integrator\n"
337 –             "   without a targetPressure!\n"
338 –             );
339 –    painCave.isFatal = 1;
340 –    simError();
341 –    return -1;
342 –  }
343 –  
344 –  // We must set tauThermostat.
345 –  
346 –  if (!have_tau_thermostat) {
347 –    sprintf( painCave.errMsg,
348 –             "NPTi error: If you use the NPTi\n"
349 –             "   integrator, you must set tauThermostat.\n");
350 –    painCave.isFatal = 1;
351 –    simError();
352 –    return -1;
353 –  }    
354 –
355 –  // We must set tauBarostat.
356 –  
357 –  if (!have_tau_barostat) {
358 –    sprintf( painCave.errMsg,
359 –             "NPTi error: If you use the NPTi\n"
360 –             "   integrator, you must set tauBarostat.\n");
361 –    painCave.isFatal = 1;
362 –    simError();
363 –    return -1;
364 –  }    
365 –
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 –  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 –
104   template<typename T> double NPTi<T>::getConservedQuantity(void){
105  
106    double conservedQuantity;
# Line 426 | Line 130 | template<typename T> double NPTi<T>::getConservedQuant
130    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
131      barostat_kinetic + barostat_potential;
132    
133 <  cout.width(8);
134 <  cout.precision(8);
133 > //   cout.width(8);
134 > //   cout.precision(8);
135  
136 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
137 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
138 <      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
435 <
136 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
137 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
138 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
139    return conservedQuantity;
140   }

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