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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 769 by tim, Fri Sep 19 14:22:29 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC

# Line 13 | Line 13
13   #include "mpiSimulation.hpp"
14   #endif
15  
16 –
16   // Basic isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
18   //
# Line 27 | 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   {
30 –  chi = 0.0;
29    eta = 0.0;
30 <  integralOfChidt = 0.0;
33 <  have_tau_thermostat = 0;
34 <  have_tau_barostat = 0;
35 <  have_target_temp = 0;
36 <  have_target_pressure = 0;
37 <  have_chi_tolerance = 0;
38 <  have_eta_tolerance = 0;
39 <  have_pos_iter_tolerance = 0;
40 <
41 <  oldPos = new double[3*nAtoms];
42 <  oldVel = new double[3*nAtoms];
43 <  oldJi = new double[3*nAtoms];
44 < #ifdef IS_MPI
45 <  Nparticles = mpiSim->getTotAtoms();
46 < #else
47 <  Nparticles = theInfo->n_atoms;
48 < #endif
49 <
30 >  oldEta = 0.0;
31   }
32  
33   template<typename T> NPTi<T>::~NPTi() {
34 <  delete[] oldPos;
54 <  delete[] oldVel;
55 <  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;
62 <  DirectionalAtom* dAtom;
63 <  double Tb[3], ji[3];
64 <  double A[3][3], I[3][3];
65 <  double angle, mass;
66 <  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;
74 <  tb2 = tauBarostat * tauBarostat;
75 <
76 <  instaTemp = tStats->getTemperature();
77 <  instaPress = tStats->getPressure();
78 <  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  (use chi from previous step here):
92 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
93 <  
94 <    }
61 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
62 >  int i;
63  
64 <    atoms[i]->setVel( vel );
65 <  
98 <    if( atoms[i]->isDirectional() ){
64 >  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
65 > }
66  
100 –      dAtom = (DirectionalAtom *)atoms[i];
67  
68 <      // get and convert the torque to body frame
69 <      
70 <      dAtom->getTrq( Tb );
105 <      dAtom->lab2Body( Tb );
106 <      
107 <      // 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 <      
114 <      // use the angular velocities to propagate the rotation matrix a
115 <      // full time step
75 >  for(j=0; j<3; j++)
76 >    sc[j] *= eta;
77 > }
78  
79 <      dAtom->getA(A);
118 <      dAtom->getI(I);
119 <    
120 <      // rotate about the x-axis      
121 <      angle = dt2 * ji[0] / I[0][0];
122 <      this->rotate( 1, 2, angle, ji, A );
79 > template<typename T> void NPTi<T>::scaleSimBox( void ){
80  
81 <      // rotate about the y-axis
125 <      angle = dt2 * ji[1] / I[1][1];
126 <      this->rotate( 2, 0, angle, ji, A );
127 <      
128 <      // rotate about the z-axis
129 <      angle = dt * ji[2] / I[2][2];
130 <      this->rotate( 0, 1, angle, ji, A);
131 <      
132 <      // rotate about the y-axis
133 <      angle = dt2 * ji[1] / I[1][1];
134 <      this->rotate( 2, 0, angle, ji, A );
135 <      
136 <       // rotate about the x-axis
137 <      angle = dt2 * ji[0] / I[0][0];
138 <      this->rotate( 1, 2, angle, ji, A );
139 <      
140 <      dAtom->setJ( ji );
141 <      dAtom->setA( A  );    
142 <    }    
143 <  }
81 >  double scaleFactor;
82  
145 –  // evolve chi and eta  half step
146 –  
147 –  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
148 –  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2));
149 –
150 –  //calculate the integral of chidt
151 –  integralOfChidt += dt2*chi;
152 –
153 –  //save the old positions
154 –  for(i = 0; i < nAtoms; i++){
155 –    atoms[i]->getPos(pos);
156 –    for(j = 0; j < 3; j++)
157 –      oldPos[i*3 + j] = pos[j];
158 –  }
159 –  
160 –  //the first estimation of r(t+dt) is equal to  r(t)
161 –    
162 –  for(k = 0; k < 4; k ++){
163 –
164 –    for(i =0 ; i < nAtoms; i++){
165 –
166 –      atoms[i]->getVel(vel);
167 –      atoms[i]->getPos(pos);
168 –
169 –      for(j = 0; j < 3; j++)
170 –        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];    
171 –      
172 –      for(j = 0; j < 3; j++)
173 –        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]);
174 –
175 –      atoms[i]->setPos( pos );
176 –    }
177 –    
178 –    if (nConstrained){
179 –      constrainA();
180 –    }
181 –  }
182 –    
183 –
184 –  // Scale the box after all the positions have been moved:
185 –  
83    scaleFactor = exp(dt*eta);
84  
85    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
# Line 199 | Line 96 | template<typename T> void NPTi<T>::moveB( void ){
96  
97   }
98  
99 < template<typename T> void NPTi<T>::moveB( void ){
203 <  
204 <  //new version of NPTi
205 <  int i, j, k;
206 <  DirectionalAtom* dAtom;
207 <  double Tb[3], ji[3];
208 <  double vel[3], frc[3];
209 <  double mass;
210 <
211 <  double instTemp, instPress, instVol;
212 <  double tt2, tb2;
213 <  double oldChi, prevChi;
214 <  double oldEta, preEta;
215 <  
216 <  tt2 = tauThermostat * tauThermostat;
217 <  tb2 = tauBarostat * tauBarostat;
218 <
219 <
220 <  // Set things up for the iteration:
221 <
222 <  oldChi = chi;
223 <  oldEta = eta;
99 > template<typename T> bool NPTi<T>::etaConverged() {
100  
101 <  for( i=0; i<nAtoms; i++ ){
226 <
227 <    atoms[i]->getVel( vel );
228 <
229 <    for (j=0; j < 3; j++)
230 <      oldVel[3*i + j]  = vel[j];
231 <
232 <    if( atoms[i]->isDirectional() ){
233 <
234 <      dAtom = (DirectionalAtom *)atoms[i];
235 <
236 <      dAtom->getJ( ji );
237 <
238 <      for (j=0; j < 3; j++)
239 <        oldJi[3*i + j] = ji[j];
240 <
241 <    }
242 <  }
243 <
244 <  // do the iteration:
245 <
246 <  instVol = tStats->getVolume();
247 <  
248 <  for (k=0; k < 4; k++) {
249 <    
250 <    instTemp = tStats->getTemperature();
251 <    instPress = tStats->getPressure();
252 <
253 <    // evolve chi another half step using the temperature at t + dt/2
254 <
255 <    prevChi = chi;
256 <    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
257 <      (tauThermostat*tauThermostat);
258 <
259 <    preEta = eta;
260 <    eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) /
261 <       (p_convert*NkBT*tb2));
262 <
263 <  
264 <    for( i=0; i<nAtoms; i++ ){
265 <
266 <      atoms[i]->getFrc( frc );
267 <      atoms[i]->getVel(vel);
268 <      
269 <      mass = atoms[i]->getMass();
270 <      
271 <      // velocity half step
272 <      for (j=0; j < 3; j++)
273 <        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta));
274 <      
275 <      atoms[i]->setVel( vel );
276 <      
277 <      if( atoms[i]->isDirectional() ){
278 <
279 <        dAtom = (DirectionalAtom *)atoms[i];
280 <  
281 <        // get and convert the torque to body frame      
282 <  
283 <        dAtom->getTrq( Tb );
284 <        dAtom->lab2Body( Tb );      
285 <            
286 <        for (j=0; j < 3; j++)
287 <          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
288 <      
289 <          dAtom->setJ( ji );
290 <      }
291 <    }
292 <    
293 <    if (nConstrained){
294 <      constrainB();
295 <    }    
296 <    
297 <    if (fabs(prevChi - chi) <=
298 <        chiTolerance && fabs(preEta -eta) <= etaTolerance)
299 <      break;
300 <  }
301 <
302 <  //calculate integral of chida
303 <  integralOfChidt += dt2*chi;
304 <
305 <
101 >  return ( fabs(prevEta - eta) <= etaTolerance );
102   }
103  
308 – template<typename T> void NPTi<T>::resetIntegrator() {
309 –  chi = 0.0;
310 –  eta = 0.0;
311 – }
312 –
313 – template<typename T> int NPTi<T>::readyCheck() {
314 –
315 –  //check parent's readyCheck() first
316 –  if (T::readyCheck() == -1)
317 –    return -1;
318 –
319 –  // First check to see if we have a target temperature.
320 –  // Not having one is fatal.
321 –  
322 –  if (!have_target_temp) {
323 –    sprintf( painCave.errMsg,
324 –             "NPTi error: You can't use the NPTi integrator\n"
325 –             "   without a targetTemp!\n"
326 –             );
327 –    painCave.isFatal = 1;
328 –    simError();
329 –    return -1;
330 –  }
331 –
332 –  if (!have_target_pressure) {
333 –    sprintf( painCave.errMsg,
334 –             "NPTi error: You can't use the NPTi integrator\n"
335 –             "   without a targetPressure!\n"
336 –             );
337 –    painCave.isFatal = 1;
338 –    simError();
339 –    return -1;
340 –  }
341 –  
342 –  // We must set tauThermostat.
343 –  
344 –  if (!have_tau_thermostat) {
345 –    sprintf( painCave.errMsg,
346 –             "NPTi error: If you use the NPTi\n"
347 –             "   integrator, you must set tauThermostat.\n");
348 –    painCave.isFatal = 1;
349 –    simError();
350 –    return -1;
351 –  }    
352 –
353 –  // We must set tauBarostat.
354 –  
355 –  if (!have_tau_barostat) {
356 –    sprintf( painCave.errMsg,
357 –             "NPTi error: If you use the NPTi\n"
358 –             "   integrator, you must set tauBarostat.\n");
359 –    painCave.isFatal = 1;
360 –    simError();
361 –    return -1;
362 –  }    
363 –
364 –  if (!have_chi_tolerance) {
365 –    sprintf( painCave.errMsg,
366 –             "NPTi warning: setting chi tolerance to 1e-6\n");
367 –    chiTolerance = 1e-6;
368 –    have_chi_tolerance = 1;
369 –    painCave.isFatal = 0;
370 –    simError();
371 –  }
372 –
373 –    if (!have_eta_tolerance) {
374 –    sprintf( painCave.errMsg,
375 –             "NPTi warning: setting eta tolerance to 1e-6\n");
376 –    etaTolerance = 1e-6;
377 –    have_eta_tolerance = 1;
378 –    painCave.isFatal = 0;
379 –    simError();
380 –  }
381 –  // We need NkBT a lot, so just set it here:
382 –
383 –  NkBT = (double)Nparticles * kB * targetTemp;
384 –  fkBT = (double)info->ndf * kB * targetTemp;
385 –
386 –  return 1;
387 – }
388 –
104   template<typename T> double NPTi<T>::getConservedQuantity(void){
105  
106    double conservedQuantity;
107 <  double LkBT;
393 <  double fkBT;
394 <  double f1kBT;
395 <  double f2kBT;
396 <  double NkBT;
107 >  double Three_NkBT;
108    double Energy;
109    double thermostat_kinetic;
110    double thermostat_potential;
111    double barostat_kinetic;
112    double barostat_potential;
113    double tb2;
114 <  double eta2;  
114 >  double eta2;
115  
405 –  LkBT = (double)(info->getNDF() + 4) * kB * targetTemp;  // 3N + 1
406 –  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;  // 3N - 3
407 –  f1kBT = (double)(info->getNDF()+ 1) * kB * targetTemp;  // 3N - 3 + 1
408 –  NkBT = (double)(info->getNDF() + 3) * kB * targetTemp;  // 3N
409 –  f2kBT = (double)(info->getNDF()+ 2) * kB * targetTemp;  // 3N - 3 + 1
410 –
116    Energy = tStats->getTotalE();
117  
118    thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
# Line 416 | Line 121 | template<typename T> double NPTi<T>::getConservedQuant
121    thermostat_potential = fkBT* integralOfChidt / eConvert;
122  
123  
124 <  barostat_kinetic = fkBT * tauBarostat * tauBarostat * eta * eta /
124 >  barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta /
125      (2.0 * eConvert);
126    
127    barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
# Line 425 | 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;
434 <
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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