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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 575 by gezelter, Tue Jul 8 21:06:14 2003 UTC vs.
Revision 772 by gezelter, Fri Sep 19 16:01:07 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
17   // modification of the Hoover algorithm:
# Line 19 | Line 23
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> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
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 < void NPTi::moveA() {
52 <  
53 <  int i,j,k;
54 <  int atomIndex, aMatIndex;
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 >  //new version of NPTi
60 >  int i, j, k;
61    DirectionalAtom* dAtom;
62 <  double Tb[3];
63 <  double ji[3];
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];
66 >
67    double rj[3];
68    double instaTemp, instaPress, instaVol;
69 <  double tt2, tb2;
70 <  double angle;
69 >  double tt2, tb2, scaleFactor;
70 >  double COM[3];
71  
72    tt2 = tauThermostat * tauThermostat;
73    tb2 = tauBarostat * tauBarostat;
# Line 48 | Line 75 | void NPTi::moveA() {
75    instaTemp = tStats->getTemperature();
76    instaPress = tStats->getPressure();
77    instaVol = tStats->getVolume();
51 –  
52 –  // first evolve chi a half step
78    
79 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
80 <  eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2));
81 <
79 >  tStats->getCOM(COM);
80 >  
81 >  //evolve velocity half step
82    for( i=0; i<nAtoms; i++ ){
58 –    atomIndex = i * 3;
59 –    aMatIndex = i * 9;
60 –    
61 –    // velocity half step
62 –    for( j=atomIndex; j<(atomIndex+3); j++ )
63 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
64 –                       - vel[j]*(chi+eta));
83  
84 <    // position whole step    
84 >    atoms[i]->getVel( vel );
85 >    atoms[i]->getFrc( frc );
86  
87 <    for( j=atomIndex; j<(atomIndex+3); j=j+3 ) {
69 <      rj[0] = pos[j];
70 <      rj[1] = pos[j+1];
71 <      rj[2] = pos[j+2];
87 >    mass = atoms[i]->getMass();
88  
89 <      info->wrapVector(rj);
90 <
91 <      pos[j] += dt * (vel[j] + eta*rj[0]);
76 <      pos[j+1] += dt * (vel[j+1] + eta*rj[1]);
77 <      pos[j+2] += dt * (vel[j+2] + eta*rj[2]);
89 >    for (j=0; j < 3; j++) {
90 >      // velocity half step
91 >      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
92      }
93  
94 <    // Scale the box after all the positions have been moved:
81 <
82 <    info->scaleBox(exp(dt*eta));
94 >    atoms[i]->setVel( vel );
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 <      Tb[0] = dAtom->getTx();
91 <      Tb[1] = dAtom->getTy();
92 <      Tb[2] = dAtom->getTz();
93 <      
102 >      dAtom->getTrq( Tb );
103        dAtom->lab2Body( Tb );
104        
105        // get the angular momentum, and propagate a half step
106  
107 <      ji[0] = dAtom->getJx();
108 <      ji[1] = dAtom->getJy();
109 <      ji[2] = dAtom->getJz();
107 >      dAtom->getJ( ji );
108 >
109 >      for (j=0; j < 3; j++)
110 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
111        
102 –      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
103 –      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
104 –      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
105 –      
112        // use the angular velocities to propagate the rotation matrix a
113        // full time step
114 <      
114 >
115 >      dAtom->getA(A);
116 >      dAtom->getI(I);
117 >    
118        // rotate about the x-axis      
119 <      angle = dt2 * ji[0] / dAtom->getIxx();
120 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
121 <      
119 >      angle = dt2 * ji[0] / I[0][0];
120 >      this->rotate( 1, 2, angle, ji, A );
121 >
122        // rotate about the y-axis
123 <      angle = dt2 * ji[1] / dAtom->getIyy();
124 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
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] / dAtom->getIzz();
128 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
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] / dAtom->getIyy();
132 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
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] / dAtom->getIxx();
136 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
135 >      angle = dt2 * ji[0] / I[0][0];
136 >      this->rotate( 1, 2, angle, ji, A );
137        
138 <      dAtom->setJx( ji[0] );
139 <      dAtom->setJy( ji[1] );
140 <      dAtom->setJz( ji[2] );
138 >      dAtom->setJ( ji );
139 >      dAtom->setA( A  );    
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);
189 +
190 +  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
191 +    sprintf( painCave.errMsg,
192 +             "NPTi error: Attempting a Box scaling of more than 10 percent"
193 +             " check your tauBarostat, as it is probably too small!\n"
194 +             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
195 +             );
196 +    painCave.isFatal = 1;
197 +    simError();
198 +  } else {        
199 +    info->scaleBox(scaleFactor);      
200 +  }  
201 +
202   }
203  
204 < void NPTi::moveB( void ){
205 <  int i,j,k;
206 <  int atomIndex;
204 > 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];
210 <  double ji[3];
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 <  instaTemp = tStats->getTemperature();
150 <  instaPress = tStats->getPressure();
151 <  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) / (NkBT*tb2));
225 <  
223 >  oldChi = chi;
224 >  oldEta = eta;
225 >
226    for( i=0; i<nAtoms; i++ ){
227 <    atomIndex = i * 3;
228 <    
229 <    // velocity half step
230 <    for( j=atomIndex; j<(atomIndex+3); j++ )
231 <    for( j=atomIndex; j<(atomIndex+3); j++ )
232 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert
163 <                       - vel[j]*(chi+eta));
164 <    
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 <      
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 <      // get and convert the torque to body frame
272 >      mass = atoms[i]->getMass();
273        
274 <      Tb[0] = dAtom->getTx();
275 <      Tb[1] = dAtom->getTy();
276 <      Tb[2] = dAtom->getTz();
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 <      dAtom->lab2Body( Tb );
278 >      atoms[i]->setVel( vel );
279        
280 <      // get the angular momentum, and complete the angular momentum
281 <      // half step
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 <      ji[0] = dAtom->getJx();
293 <      ji[1] = dAtom->getJy();
182 <      ji[2] = dAtom->getJz();
183 <      
184 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
185 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
186 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
187 <      
188 <      dAtom->setJx( ji[0] );
189 <      dAtom->setJy( ji[1] );
190 <      dAtom->setJz( ji[2] );
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 < int NPTi::readyCheck() {
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.
# Line 239 | Line 363 | int NPTi::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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