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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 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2 >
3 > #include "MatVec3.h"
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "AbstractClasses.hpp"
# Line 7 | Line 9
9   #include "Thermo.hpp"
10   #include "ReadWrite.hpp"
11   #include "Integrator.hpp"
12 < #include "simError.h"
12 > #include "simError.h"
13  
14   #ifdef IS_MPI
15   #include "mpiSimulation.hpp"
# Line 17 | Line 19
19   // modification of the Hoover algorithm:
20   //
21   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22 < //       Molec. Phys., 78, 533.
22 > //       Molec. Phys., 78, 533.
23   //
24   //           and
25 < //
25 > //
26   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27  
28   template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29    T( theInfo, the_ff )
30   {
31 <  int i, j;
32 <  chi = 0.0;
33 <  integralOfChidt = 0.0;
31 >  GenericData* data;
32 >  DoubleArrayData * etaValue;
33 >  vector<double> etaArray;
34 >  int i,j;
35  
36 <  for(i = 0; i < 3; i++)
37 <    for (j = 0; j < 3; j++)
36 >  for(i = 0; i < 3; i++){
37 >    for (j = 0; j < 3; j++){
38 >
39        eta[i][j] = 0.0;
40 +      oldEta[i][j] = 0.0;
41 +    }
42 +  }
43  
37 –  have_tau_thermostat = 0;
38 –  have_tau_barostat = 0;
39 –  have_target_temp = 0;
40 –  have_target_pressure = 0;
44  
45 <  have_chi_tolerance = 0;
46 <  have_eta_tolerance = 0;
47 <  have_pos_iter_tolerance = 0;
45 >  if( theInfo->useInitXSstate ){
46 >    // retrieve eta array from simInfo if it exists
47 >    data = info->getProperty(ETAVALUE_ID);
48 >    if(data){
49 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
50 >      
51 >      if(etaValue){
52 >        etaArray = etaValue->getData();
53 >        
54 >        for(i = 0; i < 3; i++){
55 >          for (j = 0; j < 3; j++){
56 >            eta[i][j] = etaArray[3*i+j];
57 >            oldEta[i][j] = eta[i][j];
58 >          }
59 >        }
60 >      }
61 >    }
62 >  }
63  
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 –
64   }
65  
66   template<typename T> NPTf<T>::~NPTf() {
67 <  delete[] oldPos;
68 <  delete[] oldVel;
60 <  delete[] oldJi;
67 >
68 >  // empty for now
69   }
70  
71 < template<typename T> void NPTf<T>::moveA() {
71 > template<typename T> void NPTf<T>::resetIntegrator() {
72  
73 <  // new version of NPTf
66 <  int i, j, k;
67 <  DirectionalAtom* dAtom;
68 <  double Tb[3], ji[3];
73 >  int i, j;
74  
75 <  double mass;
76 <  double vel[3], pos[3], frc[3];
75 >  for(i = 0; i < 3; i++)
76 >    for (j = 0; j < 3; j++)
77 >      eta[i][j] = 0.0;
78  
79 <  double rj[3];
80 <  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];
79 >  T::resetIntegrator();
80 > }
81  
82 <  tt2 = tauThermostat * tauThermostat;
83 <  tb2 = tauBarostat * tauBarostat;
82 > template<typename T> void NPTf<T>::evolveEtaA() {
83  
84 <  instaTemp = tStats->getTemperature();
86 <  tStats->getPressureTensor(press);
87 <  instaVol = tStats->getVolume();
88 <  
89 <  tStats->getCOM(COM);
84 >  int i, j;
85  
86 <  //calculate scale factor of veloity
87 <  for (i = 0; i < 3; i++ ) {
88 <    for (j = 0; j < 3; j++ ) {
89 <      vScale[i][j] = eta[i][j];
90 <      
91 <      if (i == j) {
92 <        vScale[i][j] += chi;          
98 <      }              
86 >  for(i = 0; i < 3; i ++){
87 >    for(j = 0; j < 3; j++){
88 >      if( i == j)
89 >        eta[i][j] += dt2 *  instaVol *
90 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91 >      else
92 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
93      }
94    }
101 –  
102 –  //evolve velocity half step
103 –  for( i=0; i<nAtoms; i++ ){
95  
96 <    atoms[i]->getVel( vel );
97 <    atoms[i]->getFrc( frc );
96 >  for(i = 0; i < 3; i++)
97 >    for (j = 0; j < 3; j++)
98 >      oldEta[i][j] = eta[i][j];
99 > }
100  
101 <    mass = atoms[i]->getMass();
109 <    
110 <    info->matVecMul3( vScale, vel, sc );
101 > template<typename T> void NPTf<T>::evolveEtaB() {
102  
103 <    for (j=0; j < 3; j++) {
113 <      // velocity half step
114 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
115 <    }
103 >  int i,j;
104  
105 <    atoms[i]->setVel( vel );
106 <  
107 <    if( atoms[i]->isDirectional() ){
105 >  for(i = 0; i < 3; i++)
106 >    for (j = 0; j < 3; j++)
107 >      prevEta[i][j] = eta[i][j];
108  
109 <      dAtom = (DirectionalAtom *)atoms[i];
109 >  for(i = 0; i < 3; i ++){
110 >    for(j = 0; j < 3; j++){
111 >      if( i == j) {
112 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
113 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114 >      } else {
115 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
116 >      }
117 >    }
118 >  }
119 > }
120  
121 <      // get and convert the torque to body frame
122 <      
125 <      dAtom->getTrq( Tb );
126 <      dAtom->lab2Body( Tb );
127 <      
128 <      // get the angular momentum, and propagate a half step
121 > template<typename T> void NPTf<T>::calcVelScale(void){
122 >  int i,j;
123  
124 <      dAtom->getJ( ji );
124 >  for (i = 0; i < 3; i++ ) {
125 >    for (j = 0; j < 3; j++ ) {
126 >      vScale[i][j] = eta[i][j];
127  
128 <      for (j=0; j < 3; j++)
129 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
130 <      
131 <      this->rotationPropagation( dAtom, ji );
136 <  
137 <      dAtom->setJ( ji );
138 <    }    
128 >      if (i == j) {
129 >        vScale[i][j] += chi;
130 >      }
131 >    }
132    }
133 + }
134  
135 <  // advance chi half step
136 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
135 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
136 >
137 >  matVecMul3( vScale, vel, sc );
138 > }
139  
140 <  // calculate the integral of chidt
141 <  integralOfChidt += dt2*chi;
140 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
141 >  int j;
142 >  double myVel[3];
143 >  double vScale[3][3];
144  
145 <  // advance eta half step
145 >  for (j = 0; j < 3; j++)
146 >    myVel[j] = oldVel[3*index + j];
147  
148 <  for(i = 0; i < 3; i ++)
149 <    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 ++){
148 >  matVecMul3( vScale, myVel, sc );
149 > }
150  
151 <    for(i =0 ; i < nAtoms; i++){
151 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
152 >                                               int index, double sc[3]){
153 >  int j;
154 >  double rj[3];
155  
156 <      atoms[i]->getVel(vel);
157 <      atoms[i]->getPos(pos);
156 >  for(j=0; j<3; j++)
157 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
158  
159 <      for(j = 0; j < 3; j++)
160 <        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
176 <      
177 <      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]);
159 >  matVecMul3( eta, rj, sc );
160 > }
161  
162 <      atoms[i]->setPos( pos );
162 > template<typename T> void NPTf<T>::scaleSimBox( void ){
163  
164 <    }
164 >  int i,j,k;
165 >  double scaleMat[3][3];
166 >  double eta2ij;
167 >  double bigScale, smallScale, offDiagMax;
168 >  double hm[3][3], hmnew[3][3];
169  
186 –    if (nConstrained) {
187 –      constrainA();
188 –    }
189 –  }  
170  
171 <
171 >
172    // Scale the box after all the positions have been moved:
173 <  
173 >
174    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
175    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
176 <  
176 >
177    bigScale = 1.0;
178    smallScale = 1.0;
179    offDiagMax = 0.0;
180 <  
180 >
181    for(i=0; i<3; i++){
182      for(j=0; j<3; j++){
183 <      
183 >
184        // Calculate the matrix Product of the eta array (we only need
185        // the ij element right now):
186 <      
186 >
187        eta2ij = 0.0;
188        for(k=0; k<3; k++){
189          eta2ij += eta[i][k] * eta[k][j];
190        }
191 <      
191 >
192        scaleMat[i][j] = 0.0;
193        // identity matrix (see above):
194        if (i == j) scaleMat[i][j] = 1.0;
# Line 216 | Line 196 | template<typename T> void NPTf<T>::moveA() {
196        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
197  
198        if (i != j)
199 <        if (fabs(scaleMat[i][j]) > offDiagMax)
199 >        if (fabs(scaleMat[i][j]) > offDiagMax)
200            offDiagMax = fabs(scaleMat[i][j]);
201      }
202  
203      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
204      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
205    }
206 <  
207 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
206 >
207 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
208      sprintf( painCave.errMsg,
209 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
209 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
210               " Check your tauBarostat, as it is probably too small!\n\n"
211               " scaleMat = [%lf\t%lf\t%lf]\n"
212               "            [%lf\t%lf\t%lf]\n"
# Line 236 | Line 216 | template<typename T> void NPTf<T>::moveA() {
216               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
217      painCave.isFatal = 1;
218      simError();
219 <  } else if (offDiagMax > 0.1) {
219 >  } else if (offDiagMax > 0.01) {
220      sprintf( painCave.errMsg,
221 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
221 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
222               " Check your tauBarostat, as it is probably too small!\n\n"
223               " scaleMat = [%lf\t%lf\t%lf]\n"
224               "            [%lf\t%lf\t%lf]\n"
# Line 250 | Line 230 | template<typename T> void NPTf<T>::moveA() {
230      simError();
231    } else {
232      info->getBoxM(hm);
233 <    info->matMul3(hm, scaleMat, hmnew);
233 >    matMul3(hm, scaleMat, hmnew);
234      info->setBoxM(hmnew);
235    }
256 –  
236   }
237  
238 < template<typename T> void NPTf<T>::moveB( void ){
239 <
240 <  //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;
238 > template<typename T> bool NPTf<T>::etaConverged() {
239 >  int i;
240 >  double diffEta, sumEta;
241  
242 <  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 <  
242 >  sumEta = 0;
243    for(i = 0; i < 3; i++)
244 <    for(j = 0; j < 3; j++)
284 <      oldEta[i][j] = eta[i][j];
244 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
245  
246 <  for( i=0; i<nAtoms; i++ ){
246 >  diffEta = sqrt( sumEta / 3.0 );
247  
248 <    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 <  
248 >  return ( diffEta <= etaTolerance );
249   }
250  
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 –
251   template<typename T> double NPTf<T>::getConservedQuantity(void){
252  
253    double conservedQuantity;
254 <  double Energy;
254 >  double totalEnergy;
255    double thermostat_kinetic;
256    double thermostat_potential;
257    double barostat_kinetic;
# Line 476 | Line 259 | template<typename T> double NPTf<T>::getConservedQuant
259    double trEta;
260    double a[3][3], b[3][3];
261  
262 <  Energy = tStats->getTotalE();
262 >  totalEnergy = tStats->getTotalE();
263  
264 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
264 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
265      (2.0 * eConvert);
266  
267    thermostat_potential = fkBT* integralOfChidt / eConvert;
268  
269 <  info->transposeMat3(eta, a);
270 <  info->matMul3(a, eta, b);
271 <  trEta = info->matTrace3(b);
269 >  transposeMat3(eta, a);
270 >  matMul3(a, eta, b);
271 >  trEta = matTrace3(b);
272  
273 <  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta /
273 >  barostat_kinetic = NkBT * tb2 * trEta /
274      (2.0 * eConvert);
275 <  
276 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
275 >
276 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
277      eConvert;
278  
279 <  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
279 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
280      barostat_kinetic + barostat_potential;
498 –  
499 –  cout.width(8);
500 –  cout.precision(8);
281  
282 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
503 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
504 <      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
282 >  return conservedQuantity;
283  
506 –  return conservedQuantity;
284   }
285 +
286 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
287 +  string parameters;
288 +  const int BUFFERSIZE = 2000; // size of the read buffer
289 +  char buffer[BUFFERSIZE];
290 +
291 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
292 +  parameters += buffer;
293 +
294 +  for(int i = 0; i < 3; i++){
295 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
296 +    parameters += buffer;
297 +  }
298 +
299 +  return parameters;
300 +
301 + }

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