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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 768 by mmeineke, Wed Sep 17 14:22:15 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"
14   #endif
15  
16 –
16   // Basic isotropic thermostating and barostating via the Melchionna
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> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
27    T( theInfo, the_ff )
28   {
29 <  chi = 0.0;
29 >  GenericData* data;
30 >  DoubleArrayData * etaValue;
31 >  vector<double> etaArray;
32 >
33    eta = 0.0;
34 <  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;
34 >  oldEta = 0.0;
35  
36 <  oldPos = new double[3*nAtoms];
37 <  oldVel = new double[3*nAtoms];
38 <  oldJi = new double[3*nAtoms];
39 < #ifdef IS_MPI
40 <  Nparticles = mpiSim->getTotAtoms();
41 < #else
42 <  Nparticles = theInfo->n_atoms;
43 < #endif
44 <
36 >  if( theInfo->useInitXSstate ){
37 >    // retrieve eta from simInfo if
38 >    data = info->getProperty(ETAVALUE_ID);
39 >    if(data){
40 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
41 >      
42 >      if(etaValue){
43 >        etaArray = etaValue->getData();
44 >        eta = etaArray[0];
45 >        oldEta = eta;
46 >      }
47 >    }
48 >  }
49   }
50  
51   template<typename T> NPTi<T>::~NPTi() {
52 <  delete[] oldPos;
54 <  delete[] oldVel;
55 <  delete[] oldJi;
52 >  //nothing for now
53   }
54  
55 < template<typename T> void NPTi<T>::moveA() {
56 <
57 <  //new version of NPTi
58 <  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];
55 > template<typename T> void NPTi<T>::resetIntegrator() {
56 >  eta = 0.0;
57 >  T::resetIntegrator();
58 > }
59  
60 <  double rj[3];
61 <  double instaTemp, instaPress, instaVol;
62 <  double tt2, tb2, scaleFactor;
63 <  double COM[3];
60 > template<typename T> void NPTi<T>::evolveEtaA() {
61 >  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
62 >                 (p_convert*NkBT*tb2));
63 >  oldEta = eta;
64 > }
65  
66 <  tt2 = tauThermostat * tauThermostat;
74 <  tb2 = tauBarostat * tauBarostat;
66 > template<typename T> void NPTi<T>::evolveEtaB() {
67  
68 <  instaTemp = tStats->getTemperature();
69 <  instaPress = tStats->getPressure();
70 <  instaVol = tStats->getVolume();
71 <  
80 <  tStats->getCOM(COM);
81 <  
82 <  //evolve velocity half step
83 <  for( i=0; i<nAtoms; i++ ){
68 >  prevEta = eta;
69 >  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
70 >                 (p_convert*NkBT*tb2));
71 > }
72  
73 <    atoms[i]->getVel( vel );
74 <    atoms[i]->getFrc( frc );
73 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
74 >  int i;
75  
76 <    mass = atoms[i]->getMass();
76 >  for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
77 > }
78  
79 <    for (j=0; j < 3; j++) {
80 <      // velocity half step  (use chi from previous step here):
92 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
93 <  
94 <    }
79 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
80 >  int i;
81  
82 <    atoms[i]->setVel( vel );
83 <  
98 <    if( atoms[i]->isDirectional() ){
82 >  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta );
83 > }
84  
100 –      dAtom = (DirectionalAtom *)atoms[i];
85  
86 <      // get and convert the torque to body frame
87 <      
88 <      dAtom->getTrq( Tb );
105 <      dAtom->lab2Body( Tb );
106 <      
107 <      // get the angular momentum, and propagate a half step
86 > template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
87 >                                               int index, double sc[3]){
88 >  int j;
89  
90 <      dAtom->getJ( ji );
90 >  for(j=0; j<3; j++)
91 >    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
92  
93 <      for (j=0; j < 3; j++)
94 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
95 <      
114 <      // use the angular velocities to propagate the rotation matrix a
115 <      // full time step
93 >  for(j=0; j<3; j++)
94 >    sc[j] *= eta;
95 > }
96  
97 <      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 );
97 > template<typename T> void NPTi<T>::scaleSimBox( void ){
98  
99 <      // 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 <  }
99 >  double scaleFactor;
100  
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 –  
101    scaleFactor = exp(dt*eta);
102  
103    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
# Line 193 | Line 108 | template<typename T> void NPTi<T>::moveA() {
108               );
109      painCave.isFatal = 1;
110      simError();
111 <  } else {        
112 <    info->scaleBox(scaleFactor);      
113 <  }  
111 >  } else {
112 >    info->scaleBox(scaleFactor);
113 >  }
114  
115   }
116  
117 < 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;
117 > template<typename T> bool NPTi<T>::etaConverged() {
118  
119 <  double instTemp, instPress, instVol;
120 <  double tt2, tb2;
213 <  double oldChi, prevChi;
214 <  double oldEta, preEta;
215 <  
216 <  tt2 = tauThermostat * tauThermostat;
217 <  tb2 = tauBarostat * tauBarostat;
119 >  return ( fabs(prevEta - eta) <= etaTolerance );
120 > }
121  
122 + template<typename T> double NPTi<T>::getConservedQuantity(void){
123  
124 <  // Set things up for the iteration:
124 >  double conservedQuantity;
125 >  double Energy;
126 >  double thermostat_kinetic;
127 >  double thermostat_potential;
128 >  double barostat_kinetic;
129 >  double barostat_potential;
130  
131 <  oldChi = chi;
223 <  oldEta = eta;
131 >  Energy = tStats->getTotalE();
132  
133 <  for( i=0; i<nAtoms; i++ ){
133 >  thermostat_kinetic = fkBT* tt2 * chi * chi /
134 >    (2.0 * eConvert);
135  
136 <    atoms[i]->getVel( vel );
136 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
137  
229 –    for (j=0; j < 3; j++)
230 –      oldVel[3*i + j]  = vel[j];
138  
139 <    if( atoms[i]->isDirectional() ){
139 >  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
140 >    (2.0 * eConvert);
141  
142 <      dAtom = (DirectionalAtom *)atoms[i];
142 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
143 >    eConvert;
144  
145 <      dAtom->getJ( ji );
145 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
146 >    barostat_kinetic + barostat_potential;
147  
148 <      for (j=0; j < 3; j++)
149 <        oldJi[3*i + j] = ji[j];
148 > //   cout.width(8);
149 > //   cout.precision(8);
150  
151 <    }
152 <  }
153 <
154 <  // 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 <
151 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
152 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
153 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
154 >  return conservedQuantity;
155   }
156  
157 < template<typename T> void NPTi<T>::resetIntegrator() {
158 <  chi = 0.0;
159 <  eta = 0.0;
160 < }
157 > template<typename T> string NPTi<T>::getAdditionalParameters(void){
158 >  string parameters;
159 >  const int BUFFERSIZE = 2000; // size of the read buffer
160 >  char buffer[BUFFERSIZE];
161  
162 < template<typename T> int NPTi<T>::readyCheck() {
162 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
163 >  parameters += buffer;
164  
165 <  //check parent's readyCheck() first
166 <  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 <  }
165 >  sprintf(buffer,"\t%G\t0\t0;", eta);
166 >  parameters += buffer;
167  
168 <  if (!have_target_pressure) {
169 <    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 <  }    
168 >  sprintf(buffer,"\t0\t%G\t0;", eta);
169 >  parameters += buffer;
170  
171 <  // We must set tauBarostat.
172 <  
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 <  }    
171 >  sprintf(buffer,"\t0\t0\t%G;", eta);
172 >  parameters += buffer;
173  
174 <  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 <  }
174 >  return parameters;
175  
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;
176   }
388 –
389 – template<typename T> double NPTi<T>::getConservedQuantity(void){
390 –
391 –  double conservedQuantity;
392 –  double tb2;
393 –  double eta2;  
394 –  double E_NPT;
395 –  double U;
396 –  double TS;
397 –  double PV;
398 –  double extra;
399 –
400 –  U = tStats->getTotalE();
401 –
402 –  TS = fkBT *
403 –    (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert;
404 –
405 –  PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert;
406 –
407 –  tb2 = tauBarostat * tauBarostat;
408 –  eta2 = eta * eta;
409 –
410 –
411 –  extra = ((double)info->ndfTrans * kB * targetTemp * tb2 * eta2 / 2.0) / eConvert;
412 –
413 –  cout.width(8);
414 –  cout.precision(8);
415 –
416 –  
417 – //   cout << info->getTime() << "\t"
418 – //        << chi << "\t"
419 – //        << eta << "\t"
420 – //        << U << "\t"
421 – //        << TS << "\t"
422 – //        << PV << "\t"
423 – //        << extra << "\t"
424 – //        << U+TS+PV+extra << endl;
425 –
426 –  conservedQuantity = U+TS+PV+extra;
427 –  return conservedQuantity;
428 – }

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