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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 7 | Line 7
7   #include "Thermo.hpp"
8   #include "ReadWrite.hpp"
9   #include "Integrator.hpp"
10 < #include "simError.h"
10 > #include "simError.h"
11  
12   #ifdef IS_MPI
13   #include "mpiSimulation.hpp"
# Line 17 | Line 17
17   // modification of the Hoover algorithm:
18   //
19   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
20 < //       Molec. Phys., 78, 533.
20 > //       Molec. Phys., 78, 533.
21   //
22   //           and
23 < //
23 > //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26   template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27    T( theInfo, the_ff )
28   {
29 <  int i, j;
30 <  chi = 0.0;
31 <  integralOfChidt = 0.0;
29 >  GenericData* data;
30 >  DoubleArrayData * etaValue;
31 >  vector<double> etaArray;
32 >  int i,j;
33  
34 <  for(i = 0; i < 3; i++)
35 <    for (j = 0; j < 3; j++)
34 >  for(i = 0; i < 3; i++){
35 >    for (j = 0; j < 3; j++){
36 >
37        eta[i][j] = 0.0;
38 +      oldEta[i][j] = 0.0;
39 +    }
40 +  }
41  
37 –  have_tau_thermostat = 0;
38 –  have_tau_barostat = 0;
39 –  have_target_temp = 0;
40 –  have_target_pressure = 0;
42  
43 <  have_chi_tolerance = 0;
44 <  have_eta_tolerance = 0;
45 <  have_pos_iter_tolerance = 0;
43 >  if( theInfo->useInitXSstate ){
44 >    // retrieve eta array from simInfo if it exists
45 >    data = info->getProperty(ETAVALUE_ID);
46 >    if(data){
47 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
48 >      
49 >      if(etaValue){
50 >        etaArray = etaValue->getData();
51 >        
52 >        for(i = 0; i < 3; i++){
53 >          for (j = 0; j < 3; j++){
54 >            eta[i][j] = etaArray[3*i+j];
55 >            oldEta[i][j] = eta[i][j];
56 >          }
57 >        }
58 >      }
59 >    }
60 >  }
61  
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 –
62   }
63  
64   template<typename T> NPTf<T>::~NPTf() {
65 <  delete[] oldPos;
66 <  delete[] oldVel;
60 <  delete[] oldJi;
65 >
66 >  // empty for now
67   }
68  
69 < template<typename T> void NPTf<T>::moveA() {
69 > template<typename T> void NPTf<T>::resetIntegrator() {
70  
71 <  // new version of NPTf
66 <  int i, j, k;
67 <  DirectionalAtom* dAtom;
68 <  double Tb[3], ji[3];
71 >  int i, j;
72  
73 <  double mass;
74 <  double vel[3], pos[3], frc[3];
73 >  for(i = 0; i < 3; i++)
74 >    for (j = 0; j < 3; j++)
75 >      eta[i][j] = 0.0;
76  
77 <  double rj[3];
78 <  double instaTemp, instaPress, instaVol;
75 <  double tt2, tb2;
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];
77 >  T::resetIntegrator();
78 > }
79  
80 <  tt2 = tauThermostat * tauThermostat;
83 <  tb2 = tauBarostat * tauBarostat;
80 > template<typename T> void NPTf<T>::evolveEtaA() {
81  
82 <  instaTemp = tStats->getTemperature();
86 <  tStats->getPressureTensor(press);
87 <  instaVol = tStats->getVolume();
88 <  
89 <  tStats->getCOM(COM);
82 >  int i, j;
83  
84 <  //calculate scale factor of veloity
85 <  for (i = 0; i < 3; i++ ) {
86 <    for (j = 0; j < 3; j++ ) {
87 <      vScale[i][j] = eta[i][j];
88 <      
89 <      if (i == j) {
90 <        vScale[i][j] += chi;          
98 <      }              
84 >  for(i = 0; i < 3; i ++){
85 >    for(j = 0; j < 3; j++){
86 >      if( i == j)
87 >        eta[i][j] += dt2 *  instaVol *
88 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89 >      else
90 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
91      }
92    }
101 –  
102 –  //evolve velocity half step
103 –  for( i=0; i<nAtoms; i++ ){
93  
94 <    atoms[i]->getVel( vel );
95 <    atoms[i]->getFrc( frc );
94 >  for(i = 0; i < 3; i++)
95 >    for (j = 0; j < 3; j++)
96 >      oldEta[i][j] = eta[i][j];
97 > }
98  
99 <    mass = atoms[i]->getMass();
109 <    
110 <    info->matVecMul3( vScale, vel, sc );
99 > template<typename T> void NPTf<T>::evolveEtaB() {
100  
101 <    for (j=0; j < 3; j++) {
113 <      // velocity half step
114 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
115 <    }
101 >  int i,j;
102  
103 <    atoms[i]->setVel( vel );
104 <  
105 <    if( atoms[i]->isDirectional() ){
103 >  for(i = 0; i < 3; i++)
104 >    for (j = 0; j < 3; j++)
105 >      prevEta[i][j] = eta[i][j];
106  
107 <      dAtom = (DirectionalAtom *)atoms[i];
107 >  for(i = 0; i < 3; i ++){
108 >    for(j = 0; j < 3; j++){
109 >      if( i == j) {
110 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
111 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
112 >      } else {
113 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
114 >      }
115 >    }
116 >  }
117 > }
118  
119 <      // get and convert the torque to body frame
120 <      
121 <      dAtom->getTrq( Tb );
126 <      dAtom->lab2Body( Tb );
127 <      
128 <      // get the angular momentum, and propagate a half step
119 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
120 >  int i,j;
121 >  double vScale[3][3];
122  
123 <      dAtom->getJ( ji );
123 >  for (i = 0; i < 3; i++ ) {
124 >    for (j = 0; j < 3; j++ ) {
125 >      vScale[i][j] = eta[i][j];
126  
127 <      for (j=0; j < 3; j++)
128 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
129 <      
130 <      this->rotationPropagation( dAtom, ji );
136 <  
137 <      dAtom->setJ( ji );
138 <    }    
127 >      if (i == j) {
128 >        vScale[i][j] += chi;
129 >      }
130 >    }
131    }
132  
133 <  // advance chi half step
134 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
133 >  info->matVecMul3( vScale, vel, sc );
134 > }
135  
136 <  // calculate the integral of chidt
137 <  integralOfChidt += dt2*chi;
136 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
137 >  int i,j;
138 >  double myVel[3];
139 >  double vScale[3][3];
140  
141 <  // advance eta half step
141 >  for (i = 0; i < 3; i++ ) {
142 >    for (j = 0; j < 3; j++ ) {
143 >      vScale[i][j] = eta[i][j];
144  
145 <  for(i = 0; i < 3; i ++)
146 <    for(j = 0; j < 3; j++){
147 <      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);
145 >      if (i == j) {
146 >        vScale[i][j] += chi;
147 >      }
148      }
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];
149    }
164 –  
165 –  //the first estimation of r(t+dt) is equal to  r(t)
166 –    
167 –  for(k = 0; k < 4; k ++){
150  
151 <    for(i =0 ; i < nAtoms; i++){
151 >  for (j = 0; j < 3; j++)
152 >    myVel[j] = oldVel[3*index + j];
153  
154 <      atoms[i]->getVel(vel);
155 <      atoms[i]->getPos(pos);
154 >  info->matVecMul3( vScale, myVel, sc );
155 > }
156  
157 <      for(j = 0; j < 3; j++)
158 <        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
159 <      
160 <      info->matVecMul3( eta, rj, sc );
178 <      
179 <      for(j = 0; j < 3; j++)
180 <        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
157 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
158 >                                               int index, double sc[3]){
159 >  int j;
160 >  double rj[3];
161  
162 <      atoms[i]->setPos( pos );
162 >  for(j=0; j<3; j++)
163 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164  
165 <    }
165 >  info->matVecMul3( eta, rj, sc );
166 > }
167  
168 <    if (nConstrained) {
187 <      constrainA();
188 <    }
189 <  }  
168 > template<typename T> void NPTf<T>::scaleSimBox( void ){
169  
170 <
170 >  int i,j,k;
171 >  double scaleMat[3][3];
172 >  double eta2ij;
173 >  double bigScale, smallScale, offDiagMax;
174 >  double hm[3][3], hmnew[3][3];
175 >
176 >
177 >
178    // Scale the box after all the positions have been moved:
179 <  
179 >
180    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
181    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
182 <  
182 >
183    bigScale = 1.0;
184    smallScale = 1.0;
185    offDiagMax = 0.0;
186 <  
186 >
187    for(i=0; i<3; i++){
188      for(j=0; j<3; j++){
189 <      
189 >
190        // Calculate the matrix Product of the eta array (we only need
191        // the ij element right now):
192 <      
192 >
193        eta2ij = 0.0;
194        for(k=0; k<3; k++){
195          eta2ij += eta[i][k] * eta[k][j];
196        }
197 <      
197 >
198        scaleMat[i][j] = 0.0;
199        // identity matrix (see above):
200        if (i == j) scaleMat[i][j] = 1.0;
# Line 216 | Line 202 | template<typename T> void NPTf<T>::moveA() {
202        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
203  
204        if (i != j)
205 <        if (fabs(scaleMat[i][j]) > offDiagMax)
205 >        if (fabs(scaleMat[i][j]) > offDiagMax)
206            offDiagMax = fabs(scaleMat[i][j]);
207      }
208  
209      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
210      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
211    }
212 <  
213 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
212 >
213 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
214      sprintf( painCave.errMsg,
215 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
215 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
216               " Check your tauBarostat, as it is probably too small!\n\n"
217               " scaleMat = [%lf\t%lf\t%lf]\n"
218               "            [%lf\t%lf\t%lf]\n"
# Line 236 | Line 222 | template<typename T> void NPTf<T>::moveA() {
222               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
223      painCave.isFatal = 1;
224      simError();
225 <  } else if (offDiagMax > 0.1) {
225 >  } else if (offDiagMax > 0.01) {
226      sprintf( painCave.errMsg,
227 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
227 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
228               " Check your tauBarostat, as it is probably too small!\n\n"
229               " scaleMat = [%lf\t%lf\t%lf]\n"
230               "            [%lf\t%lf\t%lf]\n"
# Line 252 | Line 238 | template<typename T> void NPTf<T>::moveA() {
238      info->getBoxM(hm);
239      info->matMul3(hm, scaleMat, hmnew);
240      info->setBoxM(hmnew);
241 <  }
256 <  
241 >  }
242   }
243  
244 < template<typename T> void NPTf<T>::moveB( void ){
244 > template<typename T> bool NPTf<T>::etaConverged() {
245 >  int i;
246 >  double diffEta, sumEta;
247  
248 <  //new version of NPTf
262 <  int i, j, k;
263 <  DirectionalAtom* dAtom;
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 <  // Set things up for the iteration:
279 <
280 <  oldChi = chi;
281 <  
248 >  sumEta = 0;
249    for(i = 0; i < 3; i++)
250 <    for(j = 0; j < 3; j++)
284 <      oldEta[i][j] = eta[i][j];
250 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
251  
252 <  for( i=0; i<nAtoms; i++ ){
252 >  diffEta = sqrt( sumEta / 3.0 );
253  
254 <    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 <    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 <    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 <      mass = atoms[i]->getMass();
343 <    
344 <      for (j = 0; j < 3; j++)
345 <        myVel[j] = oldVel[3*i + j];
346 <      
347 <      info->matVecMul3( vScale, myVel, sc );
348 <      
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 <      atoms[i]->setVel( vel );
356 <      
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 <          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 <  
254 >  return ( diffEta <= etaTolerance );
255   }
256  
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 –             "NPTf error: You can't use the NPTf integrator\n"
413 –             "   without a targetTemp!\n"
414 –             );
415 –    painCave.isFatal = 1;
416 –    simError();
417 –    return -1;
418 –  }
419 –
420 –  if (!have_target_pressure) {
421 –    sprintf( painCave.errMsg,
422 –             "NPTf error: You can't use the NPTf integrator\n"
423 –             "   without a targetPressure!\n"
424 –             );
425 –    painCave.isFatal = 1;
426 –    simError();
427 –    return -1;
428 –  }
429 –  
430 –  // We must set tauThermostat.
431 –  
432 –  if (!have_tau_thermostat) {
433 –    sprintf( painCave.errMsg,
434 –             "NPTf error: If you use the NPTf\n"
435 –             "   integrator, you must set tauThermostat.\n");
436 –    painCave.isFatal = 1;
437 –    simError();
438 –    return -1;
439 –  }    
440 –
441 –  // We must set tauBarostat.
442 –  
443 –  if (!have_tau_barostat) {
444 –    sprintf( painCave.errMsg,
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 –  
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 –
465 –  return 1;
466 – }
467 –
257   template<typename T> double NPTf<T>::getConservedQuantity(void){
258  
259    double conservedQuantity;
260 <  double Energy;
260 >  double totalEnergy;
261    double thermostat_kinetic;
262    double thermostat_potential;
263    double barostat_kinetic;
# Line 476 | Line 265 | template<typename T> double NPTf<T>::getConservedQuant
265    double trEta;
266    double a[3][3], b[3][3];
267  
268 <  Energy = tStats->getTotalE();
268 >  totalEnergy = tStats->getTotalE();
269  
270 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
270 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
271      (2.0 * eConvert);
272  
273    thermostat_potential = fkBT* integralOfChidt / eConvert;
# Line 487 | Line 276 | template<typename T> double NPTf<T>::getConservedQuant
276    info->matMul3(a, eta, b);
277    trEta = info->matTrace3(b);
278  
279 <  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta /
279 >  barostat_kinetic = NkBT * tb2 * trEta /
280      (2.0 * eConvert);
281 <  
282 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
281 >
282 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283      eConvert;
284  
285 <  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
285 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
286      barostat_kinetic + barostat_potential;
498 –  
499 –  cout.width(8);
500 –  cout.precision(8);
287  
288 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
503 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
504 <      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
288 >  return conservedQuantity;
289  
506 –  return conservedQuantity;
290   }
291 +
292 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
293 +  string parameters;
294 +  const int BUFFERSIZE = 2000; // size of the read buffer
295 +  char buffer[BUFFERSIZE];
296 +
297 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
298 +  parameters += buffer;
299 +
300 +  for(int i = 0; i < 3; i++){
301 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
302 +    parameters += buffer;
303 +  }
304 +
305 +  return parameters;
306 +
307 + }

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