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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 772 by gezelter, Fri Sep 19 16:01:07 2003 UTC vs.
Revision 857 by mmeineke, Fri Nov 7 17:09:48 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> 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;
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;
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;
53 <  delete[] oldVel;
54 <  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;
61 <  DirectionalAtom* dAtom;
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];
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;
73 <  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 <  
79 <  tStats->getCOM(COM);
80 <  
81 <  //evolve velocity half step
82 <  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>::calcVelScale(void) {
74 >  vScale = chi + eta;
75 > }
76  
77 <    mass = atoms[i]->getMass();
77 > template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
78 >  int i;
79  
80 <    for (j=0; j < 3; j++) {
81 <      // velocity half step
91 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
92 <    }
80 >  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
81 > }
82  
83 <    atoms[i]->setVel( vel );
84 <  
96 <    if( atoms[i]->isDirectional() ){
83 > template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
84 >  int i;
85  
86 <      dAtom = (DirectionalAtom *)atoms[i];
86 >  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale;
87 > }
88  
100 –      // get and convert the torque to body frame
101 –      
102 –      dAtom->getTrq( Tb );
103 –      dAtom->lab2Body( Tb );
104 –      
105 –      // get the angular momentum, and propagate a half step
89  
90 <      dAtom->getJ( ji );
90 > template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
91 >                                               int index, double sc[3]){
92 >  int j;
93  
94 <      for (j=0; j < 3; j++)
95 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
111 <      
112 <      // use the angular velocities to propagate the rotation matrix a
113 <      // full time step
94 >  for(j=0; j<3; j++)
95 >    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
96  
97 <      dAtom->getA(A);
98 <      dAtom->getI(I);
99 <    
118 <      // rotate about the x-axis      
119 <      angle = dt2 * ji[0] / I[0][0];
120 <      this->rotate( 1, 2, angle, ji, A );
97 >  for(j=0; j<3; j++)
98 >    sc[j] *= eta;
99 > }
100  
101 <      // rotate about the y-axis
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] / I[2][2];
128 <      this->rotate( 0, 1, angle, ji, A);
129 <      
130 <      // rotate about the y-axis
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] / I[0][0];
136 <      this->rotate( 1, 2, angle, ji, A );
137 <      
138 <      dAtom->setJ( ji );
139 <      dAtom->setA( A  );    
140 <    }    
141 <  }
101 > template<typename T> void NPTi<T>::scaleSimBox( void ){
102  
103 <  // advance chi half step
144 <  
145 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
103 >  double scaleFactor;
104  
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 –  
105    scaleFactor = exp(dt*eta);
106  
107    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
# Line 195 | Line 112 | template<typename T> void NPTi<T>::moveA() {
112               );
113      painCave.isFatal = 1;
114      simError();
115 <  } else {        
116 <    info->scaleBox(scaleFactor);      
200 <  }  
201 <
202 < }
203 <
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], 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 <  // Set things up for the iteration:
222 <
223 <  oldChi = chi;
224 <  oldEta = eta;
225 <
226 <  for( i=0; i<nAtoms; i++ ){
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 <
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 <    }
115 >  } else {
116 >    info->scaleBox(scaleFactor);
117    }
118  
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 –      mass = atoms[i]->getMass();
273 –      
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 –      atoms[i]->setVel( vel );
279 –      
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 –          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 –
119   }
120  
121 < template<typename T> void NPTi<T>::resetIntegrator() {
311 <  chi = 0.0;
312 <  eta = 0.0;
313 < }
121 > template<typename T> bool NPTi<T>::etaConverged() {
122  
123 < 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.
323 <  
324 <  if (!have_target_temp) {
325 <    sprintf( painCave.errMsg,
326 <             "NPTi error: You can't use the NPTi integrator\n"
327 <             "   without a targetTemp!\n"
328 <             );
329 <    painCave.isFatal = 1;
330 <    simError();
331 <    return -1;
332 <  }
333 <
334 <  if (!have_target_pressure) {
335 <    sprintf( painCave.errMsg,
336 <             "NPTi error: You can't use the NPTi integrator\n"
337 <             "   without a targetPressure!\n"
338 <             );
339 <    painCave.isFatal = 1;
340 <    simError();
341 <    return -1;
342 <  }
343 <  
344 <  // We must set tauThermostat.
345 <  
346 <  if (!have_tau_thermostat) {
347 <    sprintf( painCave.errMsg,
348 <             "NPTi error: If you use the NPTi\n"
349 <             "   integrator, you must set tauThermostat.\n");
350 <    painCave.isFatal = 1;
351 <    simError();
352 <    return -1;
353 <  }    
354 <
355 <  // We must set tauBarostat.
356 <  
357 <  if (!have_tau_barostat) {
358 <    sprintf( painCave.errMsg,
359 <             "NPTi error: If you use the NPTi\n"
360 <             "   integrator, you must set tauBarostat.\n");
361 <    painCave.isFatal = 1;
362 <    simError();
363 <    return -1;
364 <  }    
365 <
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 <  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;
123 >  return ( fabs(prevEta - eta) <= etaTolerance );
124   }
125  
126   template<typename T> double NPTi<T>::getConservedQuantity(void){
127  
128    double conservedQuantity;
403 –  double Three_NkBT;
129    double Energy;
130    double thermostat_kinetic;
131    double thermostat_potential;
132    double barostat_kinetic;
133    double barostat_potential;
409 –  double tb2;
410 –  double eta2;
134  
135    Energy = tStats->getTotalE();
136  
137 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
137 >  thermostat_kinetic = fkBT* tt2 * chi * chi /
138      (2.0 * eConvert);
139  
140    thermostat_potential = fkBT* integralOfChidt / eConvert;
141  
142  
143 <  barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta /
143 >  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
144      (2.0 * eConvert);
145 <  
146 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
145 >
146 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
147      eConvert;
148  
149    conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
150      barostat_kinetic + barostat_potential;
428 –  
429 –  cout.width(8);
430 –  cout.precision(8);
151  
152 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
153 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
434 <      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
152 > //   cout.width(8);
153 > //   cout.precision(8);
154  
155 <  return conservedQuantity;
155 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
156 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
157 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
158 >  return conservedQuantity;
159   }
160 +
161 + template<typename T> string NPTi<T>::getAdditionalParameters(void){
162 +  string parameters;
163 +  const int BUFFERSIZE = 2000; // size of the read buffer
164 +  char buffer[BUFFERSIZE];
165 +
166 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
167 +  parameters += buffer;
168 +
169 +  sprintf(buffer,"\t%G\t0\t0;", eta);
170 +  parameters += buffer;
171 +
172 +  sprintf(buffer,"\t0\t%G\t0;", eta);
173 +  parameters += buffer;
174 +
175 +  sprintf(buffer,"\t0\t0\t%G;", eta);
176 +  parameters += buffer;
177 +
178 +  return parameters;
179 +
180 + }

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