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Comparing trunk/OOPSE/libmdtools/NPTi.cpp (file contents):
Revision 770 by gezelter, Fri Sep 19 14:55:41 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"
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>::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  (use chi from previous step here):
92 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta));
93 <  
94 <    }
80 >  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
81 > }
82  
83 <    atoms[i]->setVel( vel );
84 <  
98 <    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  
102 –      // get and convert the torque to body frame
103 –      
104 –      dAtom->getTrq( Tb );
105 –      dAtom->lab2Body( Tb );
106 –      
107 –      // 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);
113 <      
114 <      // use the angular velocities to propagate the rotation matrix a
115 <      // 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 <    
120 <      // rotate about the x-axis      
121 <      angle = dt2 * ji[0] / I[0][0];
122 <      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
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 <  }
101 > template<typename T> void NPTi<T>::scaleSimBox( void ){
102  
103 <  // 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));
103 >  double scaleFactor;
104  
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 –  
105    scaleFactor = exp(dt*eta);
106  
107    if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
# Line 193 | Line 112 | template<typename T> void NPTi<T>::moveA() {
112               );
113      painCave.isFatal = 1;
114      simError();
115 <  } else {        
116 <    info->scaleBox(scaleFactor);      
117 <  }  
115 >  } else {
116 >    info->scaleBox(scaleFactor);
117 >  }
118  
119   }
120  
121 < 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;
121 > template<typename T> bool NPTi<T>::etaConverged() {
122  
123 <  double instTemp, instPress, instVol;
212 <  double tt2, tb2;
213 <  double oldChi, prevChi;
214 <  double oldEta, preEta;
215 <  
216 <  tt2 = tauThermostat * tauThermostat;
217 <  tb2 = tauBarostat * tauBarostat;
218 <
219 <  // Set things up for the iteration:
220 <
221 <  oldChi = chi;
222 <  oldEta = eta;
223 <
224 <  for( i=0; i<nAtoms; i++ ){
225 <
226 <    atoms[i]->getVel( vel );
227 <
228 <    for (j=0; j < 3; j++)
229 <      oldVel[3*i + j]  = vel[j];
230 <
231 <    if( atoms[i]->isDirectional() ){
232 <
233 <      dAtom = (DirectionalAtom *)atoms[i];
234 <
235 <      dAtom->getJ( ji );
236 <
237 <      for (j=0; j < 3; j++)
238 <        oldJi[3*i + j] = ji[j];
239 <
240 <    }
241 <  }
242 <
243 <  // do the iteration:
244 <
245 <  instVol = tStats->getVolume();
246 <  
247 <  for (k=0; k < 4; k++) {
248 <    
249 <    instTemp = tStats->getTemperature();
250 <    instPress = tStats->getPressure();
251 <
252 <    // evolve chi another half step using the temperature at t + dt/2
253 <
254 <    prevChi = chi;
255 <    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
256 <      (tauThermostat*tauThermostat);
257 <
258 <    preEta = eta;
259 <    eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) /
260 <       (p_convert*NkBT*tb2));
261 <
262 <  
263 <    for( i=0; i<nAtoms; i++ ){
264 <
265 <      atoms[i]->getFrc( frc );
266 <      atoms[i]->getVel(vel);
267 <      
268 <      mass = atoms[i]->getMass();
269 <      
270 <      // velocity half step
271 <      for (j=0; j < 3; j++)
272 <        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta));
273 <      
274 <      atoms[i]->setVel( vel );
275 <      
276 <      if( atoms[i]->isDirectional() ){
277 <
278 <        dAtom = (DirectionalAtom *)atoms[i];
279 <  
280 <        // get and convert the torque to body frame      
281 <  
282 <        dAtom->getTrq( Tb );
283 <        dAtom->lab2Body( Tb );      
284 <            
285 <        for (j=0; j < 3; j++)
286 <          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
287 <      
288 <          dAtom->setJ( ji );
289 <      }
290 <    }
291 <    
292 <    if (nConstrained){
293 <      constrainB();
294 <    }    
295 <    
296 <    if (fabs(prevChi - chi) <=
297 <        chiTolerance && fabs(preEta -eta) <= etaTolerance)
298 <      break;
299 <  }
300 <
301 <  //calculate integral of chida
302 <  integralOfChidt += dt2*chi;
303 <
304 <
123 >  return ( fabs(prevEta - eta) <= etaTolerance );
124   }
125  
307 – template<typename T> void NPTi<T>::resetIntegrator() {
308 –  chi = 0.0;
309 –  eta = 0.0;
310 – }
311 –
312 – template<typename T> int NPTi<T>::readyCheck() {
313 –
314 –  //check parent's readyCheck() first
315 –  if (T::readyCheck() == -1)
316 –    return -1;
317 –
318 –  // First check to see if we have a target temperature.
319 –  // Not having one is fatal.
320 –  
321 –  if (!have_target_temp) {
322 –    sprintf( painCave.errMsg,
323 –             "NPTi error: You can't use the NPTi integrator\n"
324 –             "   without a targetTemp!\n"
325 –             );
326 –    painCave.isFatal = 1;
327 –    simError();
328 –    return -1;
329 –  }
330 –
331 –  if (!have_target_pressure) {
332 –    sprintf( painCave.errMsg,
333 –             "NPTi error: You can't use the NPTi integrator\n"
334 –             "   without a targetPressure!\n"
335 –             );
336 –    painCave.isFatal = 1;
337 –    simError();
338 –    return -1;
339 –  }
340 –  
341 –  // We must set tauThermostat.
342 –  
343 –  if (!have_tau_thermostat) {
344 –    sprintf( painCave.errMsg,
345 –             "NPTi error: If you use the NPTi\n"
346 –             "   integrator, you must set tauThermostat.\n");
347 –    painCave.isFatal = 1;
348 –    simError();
349 –    return -1;
350 –  }    
351 –
352 –  // We must set tauBarostat.
353 –  
354 –  if (!have_tau_barostat) {
355 –    sprintf( painCave.errMsg,
356 –             "NPTi error: If you use the NPTi\n"
357 –             "   integrator, you must set tauBarostat.\n");
358 –    painCave.isFatal = 1;
359 –    simError();
360 –    return -1;
361 –  }    
362 –
363 –  if (!have_chi_tolerance) {
364 –    sprintf( painCave.errMsg,
365 –             "NPTi warning: setting chi tolerance to 1e-6\n");
366 –    chiTolerance = 1e-6;
367 –    have_chi_tolerance = 1;
368 –    painCave.isFatal = 0;
369 –    simError();
370 –  }
371 –
372 –  if (!have_eta_tolerance) {
373 –    sprintf( painCave.errMsg,
374 –             "NPTi warning: setting eta tolerance to 1e-6\n");
375 –    etaTolerance = 1e-6;
376 –    have_eta_tolerance = 1;
377 –    painCave.isFatal = 0;
378 –    simError();
379 –  }
380 –  
381 –  
382 –  // We need NkBT a lot, so just set it here: This is the RAW number
383 –  // of particles, so no subtraction or addition of constraints or
384 –  // orientational degrees of freedom:
385 –  
386 –  NkBT = (double)Nparticles * kB * targetTemp;
387 –  
388 –  // fkBT is used because the thermostat operates on more degrees of freedom
389 –  // than the barostat (when there are particles with orientational degrees
390 –  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
391 –  
392 –  fkBT = (double)info->ndf * kB * targetTemp;
393 –
394 –  return 1;
395 – }
396 –
126   template<typename T> double NPTi<T>::getConservedQuantity(void){
127  
128    double conservedQuantity;
400 –  double Three_NkBT;
129    double Energy;
130    double thermostat_kinetic;
131    double thermostat_potential;
132    double barostat_kinetic;
133    double barostat_potential;
406 –  double tb2;
407 –  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;
425 –  
426 –  cout.width(8);
427 –  cout.precision(8);
151  
152 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
153 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
431 <      "\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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