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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 576 by gezelter, Tue Jul 8 21:10:16 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC

# Line 1 | Line 1
1 + #include <cmath>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 8 | 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
16 > // Basic non-isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
18   //
19   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
# Line 19 | Line 23 | NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
23   //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26 < NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 <  Integrator( theInfo, the_ff )
26 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
28   {
29 <  int i;
29 >  int i, j;
30    chi = 0.0;
31 <  for(i = 0; i < 9; i++) eta[i] = 0.0;
31 >  integralOfChidt = 0.0;
32 >
33 >  for(i = 0; i < 3; i++)
34 >    for (j = 0; j < 3; j++)
35 >      eta[i][j] = 0.0;
36 >
37    have_tau_thermostat = 0;
38    have_tau_barostat = 0;
39    have_target_temp = 0;
40    have_target_pressure = 0;
41 +
42 +  have_chi_tolerance = 0;
43 +  have_eta_tolerance = 0;
44 +  have_pos_iter_tolerance = 0;
45 +
46 +  oldPos = new double[3*nAtoms];
47 +  oldVel = new double[3*nAtoms];
48 +  oldJi = new double[3*nAtoms];
49 + #ifdef IS_MPI
50 +  Nparticles = mpiSim->getTotAtoms();
51 + #else
52 +  Nparticles = theInfo->n_atoms;
53 + #endif
54 +
55   }
56  
57 < void NPTi::moveA() {
58 <  
59 <  int i,j,k;
60 <  int atomIndex, aMatIndex;
57 > template<typename T> NPTf<T>::~NPTf() {
58 >  delete[] oldPos;
59 >  delete[] oldVel;
60 >  delete[] oldJi;
61 > }
62 >
63 > template<typename T> void NPTf<T>::moveA() {
64 >
65 >  // new version of NPTf
66 >  int i, j, k;
67    DirectionalAtom* dAtom;
68 <  double Tb[3];
69 <  double ji[3];
68 >  double Tb[3], ji[3];
69 >
70 >  double mass;
71 >  double vel[3], pos[3], frc[3];
72 >
73    double rj[3];
74    double instaTemp, instaPress, instaVol;
75    double tt2, tb2;
76 <  double angle;
76 >  double sc[3];
77 >  double eta2ij;
78 >  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
79 >  double bigScale, smallScale, offDiagMax;
80 >  double COM[3];
81  
82    tt2 = tauThermostat * tauThermostat;
83    tb2 = tauBarostat * tauBarostat;
84  
85    instaTemp = tStats->getTemperature();
86 <  instaPress = tStats->getPressure();
86 >  tStats->getPressureTensor(press);
87    instaVol = tStats->getVolume();
52 –  
53 –  // first evolve chi a half step
88    
89 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
56 <  
57 <  for (i = 0; i < 9; i++) {
58 <    eta[i] += dt2 * ( instaVol * (sigma[i] - targetPressure*identMat[i]))
59 <      / (NkBT*tb2));
60 < }
89 >  tStats->getCOM(COM);
90  
91 +  //calculate scale factor of veloity
92 +  for (i = 0; i < 3; i++ ) {
93 +    for (j = 0; j < 3; j++ ) {
94 +      vScale[i][j] = eta[i][j];
95 +      
96 +      if (i == j) {
97 +        vScale[i][j] += chi;          
98 +      }              
99 +    }
100 +  }
101 +  
102 +  //evolve velocity half step
103    for( i=0; i<nAtoms; i++ ){
63 –    atomIndex = i * 3;
64 –    aMatIndex = i * 9;
65 –    
66 –    // velocity half step
67 –    for( j=atomIndex; j<(atomIndex+3); j++ )
68 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
69 –                       - vel[j]*(chi+eta));
104  
105 <    // position whole step    
105 >    atoms[i]->getVel( vel );
106 >    atoms[i]->getFrc( frc );
107  
108 <    for( j=atomIndex; j<(atomIndex+3); j=j+3 ) {
109 <      rj[0] = pos[j];
110 <      rj[1] = pos[j+1];
76 <      rj[2] = pos[j+2];
108 >    mass = atoms[i]->getMass();
109 >    
110 >    info->matVecMul3( vScale, vel, sc );
111  
112 <      info->wrapVector(rj);
113 <
114 <      pos[j] += dt * (vel[j] + eta*rj[0]);
81 <      pos[j+1] += dt * (vel[j+1] + eta*rj[1]);
82 <      pos[j+2] += dt * (vel[j+2] + eta*rj[2]);
112 >    for (j=0; j < 3; j++) {
113 >      // velocity half step
114 >      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
115      }
116  
117 <    // Scale the box after all the positions have been moved:
86 <
87 <    info->scaleBox(exp(dt*eta));
117 >    atoms[i]->setVel( vel );
118    
119      if( atoms[i]->isDirectional() ){
120  
121        dAtom = (DirectionalAtom *)atoms[i];
122 <          
122 >
123        // get and convert the torque to body frame
124        
125 <      Tb[0] = dAtom->getTx();
96 <      Tb[1] = dAtom->getTy();
97 <      Tb[2] = dAtom->getTz();
98 <      
125 >      dAtom->getTrq( Tb );
126        dAtom->lab2Body( Tb );
127        
128        // get the angular momentum, and propagate a half step
129  
130 <      ji[0] = dAtom->getJx();
131 <      ji[1] = dAtom->getJy();
132 <      ji[2] = dAtom->getJz();
130 >      dAtom->getJ( ji );
131 >
132 >      for (j=0; j < 3; j++)
133 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
134        
135 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
136 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
137 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
135 >      this->rotationPropagation( dAtom, ji );
136 >  
137 >      dAtom->setJ( ji );
138 >    }    
139 >  }
140 >
141 >  // advance chi half step
142 >  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
143 >
144 >  // calculate the integral of chidt
145 >  integralOfChidt += dt2*chi;
146 >
147 >  // advance eta half step
148 >
149 >  for(i = 0; i < 3; i ++)
150 >    for(j = 0; j < 3; j++){
151 >      if( i == j)
152 >        eta[i][j] += dt2 *  instaVol *
153 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
154 >      else
155 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
156 >    }
157 >    
158 >  //save the old positions
159 >  for(i = 0; i < nAtoms; i++){
160 >    atoms[i]->getPos(pos);
161 >    for(j = 0; j < 3; j++)
162 >      oldPos[i*3 + j] = pos[j];
163 >  }
164 >  
165 >  //the first estimation of r(t+dt) is equal to  r(t)
166 >    
167 >  for(k = 0; k < 4; k ++){
168 >
169 >    for(i =0 ; i < nAtoms; i++){
170 >
171 >      atoms[i]->getVel(vel);
172 >      atoms[i]->getPos(pos);
173 >
174 >      for(j = 0; j < 3; j++)
175 >        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
176        
177 <      // use the angular velocities to propagate the rotation matrix a
112 <      // full time step
177 >      info->matVecMul3( eta, rj, sc );
178        
179 <      // rotate about the x-axis      
180 <      angle = dt2 * ji[0] / dAtom->getIxx();
181 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
179 >      for(j = 0; j < 3; j++)
180 >        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
181 >
182 >      atoms[i]->setPos( pos );
183 >
184 >    }
185 >
186 >    if (nConstrained) {
187 >      constrainA();
188 >    }
189 >  }  
190 >
191 >
192 >  // Scale the box after all the positions have been moved:
193 >  
194 >  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
195 >  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
196 >  
197 >  bigScale = 1.0;
198 >  smallScale = 1.0;
199 >  offDiagMax = 0.0;
200 >  
201 >  for(i=0; i<3; i++){
202 >    for(j=0; j<3; j++){
203        
204 <      // rotate about the y-axis
205 <      angle = dt2 * ji[1] / dAtom->getIyy();
120 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
204 >      // Calculate the matrix Product of the eta array (we only need
205 >      // the ij element right now):
206        
207 <      // rotate about the z-axis
208 <      angle = dt * ji[2] / dAtom->getIzz();
209 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
207 >      eta2ij = 0.0;
208 >      for(k=0; k<3; k++){
209 >        eta2ij += eta[i][k] * eta[k][j];
210 >      }
211        
212 <      // rotate about the y-axis
213 <      angle = dt2 * ji[1] / dAtom->getIyy();
214 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
215 <      
216 <       // rotate about the x-axis
217 <      angle = dt2 * ji[0] / dAtom->getIxx();
218 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
219 <      
220 <      dAtom->setJx( ji[0] );
135 <      dAtom->setJy( ji[1] );
136 <      dAtom->setJz( ji[2] );
212 >      scaleMat[i][j] = 0.0;
213 >      // identity matrix (see above):
214 >      if (i == j) scaleMat[i][j] = 1.0;
215 >      // Taylor expansion for the exponential truncated at second order:
216 >      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
217 >
218 >      if (i != j)
219 >        if (fabs(scaleMat[i][j]) > offDiagMax)
220 >          offDiagMax = fabs(scaleMat[i][j]);
221      }
222 <    
222 >
223 >    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
224 >    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
225    }
226 +  
227 +  if ((bigScale > 1.1) || (smallScale < 0.9)) {
228 +    sprintf( painCave.errMsg,
229 +             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
230 +             " Check your tauBarostat, as it is probably too small!\n\n"
231 +             " scaleMat = [%lf\t%lf\t%lf]\n"
232 +             "            [%lf\t%lf\t%lf]\n"
233 +             "            [%lf\t%lf\t%lf]\n",
234 +             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
235 +             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
236 +             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
237 +    painCave.isFatal = 1;
238 +    simError();
239 +  } else if (offDiagMax > 0.1) {
240 +    sprintf( painCave.errMsg,
241 +             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
242 +             " Check your tauBarostat, as it is probably too small!\n\n"
243 +             " scaleMat = [%lf\t%lf\t%lf]\n"
244 +             "            [%lf\t%lf\t%lf]\n"
245 +             "            [%lf\t%lf\t%lf]\n",
246 +             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
247 +             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
248 +             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
249 +    painCave.isFatal = 1;
250 +    simError();
251 +  } else {
252 +    info->getBoxM(hm);
253 +    info->matMul3(hm, scaleMat, hmnew);
254 +    info->setBoxM(hmnew);
255 +  }
256 +  
257   }
258  
259 < void NPTi::moveB( void ){
260 <  int i,j,k;
261 <  int atomIndex;
259 > template<typename T> void NPTf<T>::moveB( void ){
260 >
261 >  //new version of NPTf
262 >  int i, j, k;
263    DirectionalAtom* dAtom;
264 <  double Tb[3];
265 <  double ji[3];
264 >  double Tb[3], ji[3];
265 >  double vel[3], myVel[3], frc[3];
266 >  double mass;
267 >
268    double instaTemp, instaPress, instaVol;
269    double tt2, tb2;
270 +  double sc[3];
271 +  double press[3][3], vScale[3][3];
272 +  double oldChi, prevChi;
273 +  double oldEta[3][3], prevEta[3][3], diffEta;
274    
275    tt2 = tauThermostat * tauThermostat;
276    tb2 = tauBarostat * tauBarostat;
277  
278 <  instaTemp = tStats->getTemperature();
155 <  instaPress = tStats->getPressure();
156 <  instaVol = tStats->getVolume();
278 >  // Set things up for the iteration:
279  
280 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
159 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
280 >  oldChi = chi;
281    
282 +  for(i = 0; i < 3; i++)
283 +    for(j = 0; j < 3; j++)
284 +      oldEta[i][j] = eta[i][j];
285 +
286    for( i=0; i<nAtoms; i++ ){
287 <    atomIndex = i * 3;
287 >
288 >    atoms[i]->getVel( vel );
289 >
290 >    for (j=0; j < 3; j++)
291 >      oldVel[3*i + j]  = vel[j];
292 >
293 >    if( atoms[i]->isDirectional() ){
294 >
295 >      dAtom = (DirectionalAtom *)atoms[i];
296 >
297 >      dAtom->getJ( ji );
298 >
299 >      for (j=0; j < 3; j++)
300 >        oldJi[3*i + j] = ji[j];
301 >
302 >    }
303 >  }
304 >
305 >  // do the iteration:
306 >
307 >  instaVol = tStats->getVolume();
308 >  
309 >  for (k=0; k < 4; k++) {
310      
311 <    // velocity half step
312 <    for( j=atomIndex; j<(atomIndex+3); j++ )
313 <    for( j=atomIndex; j<(atomIndex+3); j++ )
314 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
315 <                       - vel[j]*(chi+eta));
311 >    instaTemp = tStats->getTemperature();
312 >    tStats->getPressureTensor(press);
313 >
314 >    // evolve chi another half step using the temperature at t + dt/2
315 >
316 >    prevChi = chi;
317 >    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
318      
319 <    if( atoms[i]->isDirectional() ){
319 >    for(i = 0; i < 3; i++)
320 >      for(j = 0; j < 3; j++)
321 >        prevEta[i][j] = eta[i][j];
322 >
323 >    //advance eta half step and calculate scale factor for velocity
324 >
325 >    for(i = 0; i < 3; i ++)
326 >      for(j = 0; j < 3; j++){
327 >        if( i == j) {
328 >          eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
329 >            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
330 >          vScale[i][j] = eta[i][j] + chi;
331 >        } else {
332 >          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
333 >          vScale[i][j] = eta[i][j];
334 >        }
335 >      }  
336 >    
337 >    for( i=0; i<nAtoms; i++ ){
338 >
339 >      atoms[i]->getFrc( frc );
340 >      atoms[i]->getVel(vel);
341        
342 <      dAtom = (DirectionalAtom *)atoms[i];
342 >      mass = atoms[i]->getMass();
343 >    
344 >      for (j = 0; j < 3; j++)
345 >        myVel[j] = oldVel[3*i + j];
346        
347 <      // get and convert the torque to body frame
347 >      info->matVecMul3( vScale, myVel, sc );
348        
349 <      Tb[0] = dAtom->getTx();
350 <      Tb[1] = dAtom->getTy();
351 <      Tb[2] = dAtom->getTz();
349 >      // velocity half step
350 >      for (j=0; j < 3; j++) {
351 >        // velocity half step  (use chi from previous step here):
352 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
353 >      }
354        
355 <      dAtom->lab2Body( Tb );
355 >      atoms[i]->setVel( vel );
356        
357 <      // get the angular momentum, and complete the angular momentum
358 <      // half step
357 >      if( atoms[i]->isDirectional() ){
358 >
359 >        dAtom = (DirectionalAtom *)atoms[i];
360 >  
361 >        // get and convert the torque to body frame      
362 >  
363 >        dAtom->getTrq( Tb );
364 >        dAtom->lab2Body( Tb );      
365 >            
366 >        for (j=0; j < 3; j++)
367 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
368        
369 <      ji[0] = dAtom->getJx();
370 <      ji[1] = dAtom->getJy();
187 <      ji[2] = dAtom->getJz();
188 <      
189 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
190 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
191 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
192 <      
193 <      dAtom->setJx( ji[0] );
194 <      dAtom->setJy( ji[1] );
195 <      dAtom->setJz( ji[2] );
369 >          dAtom->setJ( ji );
370 >      }
371      }
372 +
373 +    if (nConstrained) {
374 +      constrainB();
375 +    }
376 +    
377 +    diffEta = 0;
378 +    for(i = 0; i < 3; i++)
379 +      diffEta += pow(prevEta[i][i] - eta[i][i], 2);    
380 +    
381 +    if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance)
382 +      break;
383    }
384 +
385 +  //calculate integral of chidt
386 +  integralOfChidt += dt2*chi;
387 +  
388   }
389  
390 < int NPTi::readyCheck() {
390 > template<typename T> void NPTf<T>::resetIntegrator() {
391 >  int i,j;
392 >  
393 >  chi = 0.0;
394 >
395 >  for(i = 0; i < 3; i++)
396 >    for (j = 0; j < 3; j++)
397 >      eta[i][j] = 0.0;
398 >
399 > }
400 >
401 > template<typename T> int NPTf<T>::readyCheck() {
402 >
403 >  //check parent's readyCheck() first
404 >  if (T::readyCheck() == -1)
405 >    return -1;
406  
407    // First check to see if we have a target temperature.
408    // Not having one is fatal.
409    
410    if (!have_target_temp) {
411      sprintf( painCave.errMsg,
412 <             "NPTi error: You can't use the NPTi integrator\n"
412 >             "NPTf error: You can't use the NPTf integrator\n"
413               "   without a targetTemp!\n"
414               );
415      painCave.isFatal = 1;
# Line 214 | Line 419 | int NPTi::readyCheck() {
419  
420    if (!have_target_pressure) {
421      sprintf( painCave.errMsg,
422 <             "NPTi error: You can't use the NPTi integrator\n"
422 >             "NPTf error: You can't use the NPTf integrator\n"
423               "   without a targetPressure!\n"
424               );
425      painCave.isFatal = 1;
# Line 226 | Line 431 | int NPTi::readyCheck() {
431    
432    if (!have_tau_thermostat) {
433      sprintf( painCave.errMsg,
434 <             "NPTi error: If you use the NPTi\n"
434 >             "NPTf error: If you use the NPTf\n"
435               "   integrator, you must set tauThermostat.\n");
436      painCave.isFatal = 1;
437      simError();
# Line 237 | Line 442 | int NPTi::readyCheck() {
442    
443    if (!have_tau_barostat) {
444      sprintf( painCave.errMsg,
445 <             "NPTi error: If you use the NPTi\n"
445 >             "NPTf error: If you use the NPTf\n"
446               "   integrator, you must set tauBarostat.\n");
447      painCave.isFatal = 1;
448      simError();
449      return -1;
450    }    
451  
452 <  // We need NkBT a lot, so just set it here:
452 >  
453 >  // We need NkBT a lot, so just set it here: This is the RAW number
454 >  // of particles, so no subtraction or addition of constraints or
455 >  // orientational degrees of freedom:
456 >  
457 >  NkBT = (double)Nparticles * kB * targetTemp;
458 >  
459 >  // fkBT is used because the thermostat operates on more degrees of freedom
460 >  // than the barostat (when there are particles with orientational degrees
461 >  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
462 >  
463 >  fkBT = (double)info->ndf * kB * targetTemp;
464  
249 –  NkBT = (double)info->ndf * kB * targetTemp;
250 –
465    return 1;
466   }
467 +
468 + template<typename T> double NPTf<T>::getConservedQuantity(void){
469 +
470 +  double conservedQuantity;
471 +  double Energy;
472 +  double thermostat_kinetic;
473 +  double thermostat_potential;
474 +  double barostat_kinetic;
475 +  double barostat_potential;
476 +  double trEta;
477 +  double a[3][3], b[3][3];
478 +
479 +  Energy = tStats->getTotalE();
480 +
481 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
482 +    (2.0 * eConvert);
483 +
484 +  thermostat_potential = fkBT* integralOfChidt / eConvert;
485 +
486 +  info->transposeMat3(eta, a);
487 +  info->matMul3(a, eta, b);
488 +  trEta = info->matTrace3(b);
489 +
490 +  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta /
491 +    (2.0 * eConvert);
492 +  
493 +  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
494 +    eConvert;
495 +
496 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
497 +    barostat_kinetic + barostat_potential;
498 +  
499 +  cout.width(8);
500 +  cout.precision(8);
501 +
502 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
503 +      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
504 +      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
505 +
506 +  return conservedQuantity;
507 + }

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