ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/NPTf.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 772 by gezelter, Fri Sep 19 16:01:07 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 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  
42 <  have_tau_thermostat = 0;
43 <  have_tau_barostat = 0;
44 <  have_target_temp = 0;
45 <  have_target_pressure = 0;
42 >    // retrieve eta array from simInfo if it exists
43 >    data = info->getProperty(ETAVALUE_ID);
44 >    if(data){
45 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
46  
47 <  have_chi_tolerance = 0;
48 <  have_eta_tolerance = 0;
44 <  have_pos_iter_tolerance = 0;
47 >      if(etaValue){
48 >        etaArray = etaValue->getData();
49  
50 <  oldPos = new double[3*nAtoms];
51 <  oldVel = new double[3*nAtoms];
52 <  oldJi = new double[3*nAtoms];
53 < #ifdef IS_MPI
54 <  Nparticles = mpiSim->getTotAtoms();
55 < #else
52 <  Nparticles = theInfo->n_atoms;
53 < #endif
50 >        for(i = 0; i < 3; i++){
51 >          for (j = 0; j < 3; j++){
52 >            eta[i][j] = etaArray[3*i+j];
53 >            oldEta[i][j] = eta[i][j];
54 >          }
55 >        }
56  
57 +      }
58 +    }
59 +
60   }
61  
62   template<typename T> NPTf<T>::~NPTf() {
63 <  delete[] oldPos;
64 <  delete[] oldVel;
60 <  delete[] oldJi;
63 >
64 >  // empty for now
65   }
66  
67 < template<typename T> void NPTf<T>::moveA() {
67 > template<typename T> void NPTf<T>::resetIntegrator() {
68  
69 <  // new version of NPTf
66 <  int i, j, k;
67 <  DirectionalAtom* dAtom;
68 <  double Tb[3], ji[3];
69 <  double A[3][3], I[3][3];
70 <  double angle, mass;
71 <  double vel[3], pos[3], frc[3];
69 >  int i, j;
70  
71 <  double rj[3];
72 <  double instaTemp, instaPress, instaVol;
73 <  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];
71 >  for(i = 0; i < 3; i++)
72 >    for (j = 0; j < 3; j++)
73 >      eta[i][j] = 0.0;
74  
75 <  tt2 = tauThermostat * tauThermostat;
76 <  tb2 = tauBarostat * tauBarostat;
75 >  T::resetIntegrator();
76 > }
77  
78 <  instaTemp = tStats->getTemperature();
86 <  tStats->getPressureTensor(press);
87 <  instaVol = tStats->getVolume();
88 <  
89 <  tStats->getCOM(COM);
78 > template<typename T> void NPTf<T>::evolveEtaA() {
79  
80 <  //calculate scale factor of veloity
81 <  for (i = 0; i < 3; i++ ) {
82 <    for (j = 0; j < 3; j++ ) {
83 <      vScale[i][j] = eta[i][j];
84 <      
85 <      if (i == j) {
86 <        vScale[i][j] += chi;          
87 <      }              
80 >  int i, j;
81 >
82 >  for(i = 0; i < 3; i ++){
83 >    for(j = 0; j < 3; j++){
84 >      if( i == j)
85 >        eta[i][j] += dt2 *  instaVol *
86 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
87 >      else
88 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
89      }
90    }
101 –  
102 –  //evolve velocity half step
103 –  for( i=0; i<nAtoms; i++ ){
91  
92 <    atoms[i]->getVel( vel );
93 <    atoms[i]->getFrc( frc );
92 >  for(i = 0; i < 3; i++)
93 >    for (j = 0; j < 3; j++)
94 >      oldEta[i][j] = eta[i][j];
95 > }
96  
97 <    mass = atoms[i]->getMass();
109 <    
110 <    info->matVecMul3( vScale, vel, sc );
97 > template<typename T> void NPTf<T>::evolveEtaB() {
98  
99 <    for (j=0; j < 3; j++) {
113 <      // velocity half step
114 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
115 <    }
99 >  int i,j;
100  
101 <    atoms[i]->setVel( vel );
102 <  
103 <    if( atoms[i]->isDirectional() ){
101 >  for(i = 0; i < 3; i++)
102 >    for (j = 0; j < 3; j++)
103 >      prevEta[i][j] = eta[i][j];
104  
105 <      dAtom = (DirectionalAtom *)atoms[i];
105 >  for(i = 0; i < 3; i ++){
106 >    for(j = 0; j < 3; j++){
107 >      if( i == j) {
108 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
109 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
110 >      } else {
111 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
112 >      }
113 >    }
114 >  }
115 > }
116  
117 <      // get and convert the torque to body frame
118 <      
119 <      dAtom->getTrq( Tb );
126 <      dAtom->lab2Body( Tb );
127 <      
128 <      // get the angular momentum, and propagate a half step
117 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
118 >  int i,j;
119 >  double vScale[3][3];
120  
121 <      dAtom->getJ( ji );
121 >  for (i = 0; i < 3; i++ ) {
122 >    for (j = 0; j < 3; j++ ) {
123 >      vScale[i][j] = eta[i][j];
124  
125 <      for (j=0; j < 3; j++)
126 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
127 <      
128 <      // use the angular velocities to propagate the rotation matrix a
136 <      // full time step
137 <
138 <      dAtom->getA(A);
139 <      dAtom->getI(I);
140 <    
141 <      // rotate about the x-axis      
142 <      angle = dt2 * ji[0] / I[0][0];
143 <      this->rotate( 1, 2, angle, ji, A );
144 <
145 <      // rotate about the y-axis
146 <      angle = dt2 * ji[1] / I[1][1];
147 <      this->rotate( 2, 0, angle, ji, A );
148 <      
149 <      // rotate about the z-axis
150 <      angle = dt * ji[2] / I[2][2];
151 <      this->rotate( 0, 1, angle, ji, A);
152 <      
153 <      // rotate about the y-axis
154 <      angle = dt2 * ji[1] / I[1][1];
155 <      this->rotate( 2, 0, angle, ji, A );
156 <      
157 <       // rotate about the x-axis
158 <      angle = dt2 * ji[0] / I[0][0];
159 <      this->rotate( 1, 2, angle, ji, A );
160 <      
161 <      dAtom->setJ( ji );
162 <      dAtom->setA( A  );    
163 <    }    
125 >      if (i == j) {
126 >        vScale[i][j] += chi;
127 >      }
128 >    }
129    }
130  
131 <  // advance chi half step
132 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
131 >  info->matVecMul3( vScale, vel, sc );
132 > }
133  
134 <  // calculate the integral of chidt
135 <  integralOfChidt += dt2*chi;
134 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
135 >  int i,j;
136 >  double myVel[3];
137 >  double vScale[3][3];
138  
139 <  // advance eta half step
139 >  for (i = 0; i < 3; i++ ) {
140 >    for (j = 0; j < 3; j++ ) {
141 >      vScale[i][j] = eta[i][j];
142  
143 <  for(i = 0; i < 3; i ++)
144 <    for(j = 0; j < 3; j++){
145 <      if( i == j)
177 <        eta[i][j] += dt2 *  instaVol *
178 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
179 <      else
180 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
143 >      if (i == j) {
144 >        vScale[i][j] += chi;
145 >      }
146      }
182 –    
183 –  //save the old positions
184 –  for(i = 0; i < nAtoms; i++){
185 –    atoms[i]->getPos(pos);
186 –    for(j = 0; j < 3; j++)
187 –      oldPos[i*3 + j] = pos[j];
147    }
189 –  
190 –  //the first estimation of r(t+dt) is equal to  r(t)
191 –    
192 –  for(k = 0; k < 4; k ++){
148  
149 <    for(i =0 ; i < nAtoms; i++){
149 >  for (j = 0; j < 3; j++)
150 >    myVel[j] = oldVel[3*index + j];
151  
152 <      atoms[i]->getVel(vel);
153 <      atoms[i]->getPos(pos);
152 >  info->matVecMul3( vScale, myVel, sc );
153 > }
154  
155 <      for(j = 0; j < 3; j++)
156 <        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
157 <      
158 <      info->matVecMul3( eta, rj, sc );
203 <      
204 <      for(j = 0; j < 3; j++)
205 <        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
155 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
156 >                                               int index, double sc[3]){
157 >  int j;
158 >  double rj[3];
159  
160 <      atoms[i]->setPos( pos );
160 >  for(j=0; j<3; j++)
161 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
162  
163 <    }
163 >  info->matVecMul3( eta, rj, sc );
164 > }
165  
166 <    if (nConstrained) {
212 <      constrainA();
213 <    }
214 <  }  
166 > template<typename T> void NPTf<T>::scaleSimBox( void ){
167  
168 <
168 >  int i,j,k;
169 >  double scaleMat[3][3];
170 >  double eta2ij;
171 >  double bigScale, smallScale, offDiagMax;
172 >  double hm[3][3], hmnew[3][3];
173 >
174 >
175 >
176    // Scale the box after all the positions have been moved:
177 <  
177 >
178    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
179    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
180 <  
180 >
181    bigScale = 1.0;
182    smallScale = 1.0;
183    offDiagMax = 0.0;
184 <  
184 >
185    for(i=0; i<3; i++){
186      for(j=0; j<3; j++){
187 <      
187 >
188        // Calculate the matrix Product of the eta array (we only need
189        // the ij element right now):
190 <      
190 >
191        eta2ij = 0.0;
192        for(k=0; k<3; k++){
193          eta2ij += eta[i][k] * eta[k][j];
194        }
195 <      
195 >
196        scaleMat[i][j] = 0.0;
197        // identity matrix (see above):
198        if (i == j) scaleMat[i][j] = 1.0;
# Line 241 | Line 200 | template<typename T> void NPTf<T>::moveA() {
200        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
201  
202        if (i != j)
203 <        if (fabs(scaleMat[i][j]) > offDiagMax)
203 >        if (fabs(scaleMat[i][j]) > offDiagMax)
204            offDiagMax = fabs(scaleMat[i][j]);
205      }
206  
207      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
208      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
209    }
210 <  
211 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
210 >
211 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
212      sprintf( painCave.errMsg,
213 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
213 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
214               " Check your tauBarostat, as it is probably too small!\n\n"
215               " scaleMat = [%lf\t%lf\t%lf]\n"
216               "            [%lf\t%lf\t%lf]\n"
# Line 261 | Line 220 | template<typename T> void NPTf<T>::moveA() {
220               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
221      painCave.isFatal = 1;
222      simError();
223 <  } else if (offDiagMax > 0.1) {
223 >  } else if (offDiagMax > 0.01) {
224      sprintf( painCave.errMsg,
225 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
225 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
226               " Check your tauBarostat, as it is probably too small!\n\n"
227               " scaleMat = [%lf\t%lf\t%lf]\n"
228               "            [%lf\t%lf\t%lf]\n"
# Line 278 | Line 237 | template<typename T> void NPTf<T>::moveA() {
237      info->matMul3(hm, scaleMat, hmnew);
238      info->setBoxM(hmnew);
239    }
281 –  
240   }
241  
242 < template<typename T> void NPTf<T>::moveB( void ){
242 > template<typename T> bool NPTf<T>::etaConverged() {
243 >  int i;
244 >  double diffEta, sumEta;
245  
246 <  //new version of NPTf
287 <  int i, j, k;
288 <  DirectionalAtom* dAtom;
289 <  double Tb[3], ji[3];
290 <  double vel[3], myVel[3], frc[3];
291 <  double mass;
292 <
293 <  double instaTemp, instaPress, instaVol;
294 <  double tt2, tb2;
295 <  double sc[3];
296 <  double press[3][3], vScale[3][3];
297 <  double oldChi, prevChi;
298 <  double oldEta[3][3], prevEta[3][3], diffEta;
299 <  
300 <  tt2 = tauThermostat * tauThermostat;
301 <  tb2 = tauBarostat * tauBarostat;
302 <
303 <  // Set things up for the iteration:
304 <
305 <  oldChi = chi;
306 <  
246 >  sumEta = 0;
247    for(i = 0; i < 3; i++)
248 <    for(j = 0; j < 3; j++)
309 <      oldEta[i][j] = eta[i][j];
248 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
249  
250 <  for( i=0; i<nAtoms; i++ ){
250 >  diffEta = sqrt( sumEta / 3.0 );
251  
252 <    atoms[i]->getVel( vel );
314 <
315 <    for (j=0; j < 3; j++)
316 <      oldVel[3*i + j]  = vel[j];
317 <
318 <    if( atoms[i]->isDirectional() ){
319 <
320 <      dAtom = (DirectionalAtom *)atoms[i];
321 <
322 <      dAtom->getJ( ji );
323 <
324 <      for (j=0; j < 3; j++)
325 <        oldJi[3*i + j] = ji[j];
326 <
327 <    }
328 <  }
329 <
330 <  // do the iteration:
331 <
332 <  instaVol = tStats->getVolume();
333 <  
334 <  for (k=0; k < 4; k++) {
335 <    
336 <    instaTemp = tStats->getTemperature();
337 <    tStats->getPressureTensor(press);
338 <
339 <    // evolve chi another half step using the temperature at t + dt/2
340 <
341 <    prevChi = chi;
342 <    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
343 <    
344 <    for(i = 0; i < 3; i++)
345 <      for(j = 0; j < 3; j++)
346 <        prevEta[i][j] = eta[i][j];
347 <
348 <    //advance eta half step and calculate scale factor for velocity
349 <
350 <    for(i = 0; i < 3; i ++)
351 <      for(j = 0; j < 3; j++){
352 <        if( i == j) {
353 <          eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
354 <            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
355 <          vScale[i][j] = eta[i][j] + chi;
356 <        } else {
357 <          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
358 <          vScale[i][j] = eta[i][j];
359 <        }
360 <      }  
361 <    
362 <    for( i=0; i<nAtoms; i++ ){
363 <
364 <      atoms[i]->getFrc( frc );
365 <      atoms[i]->getVel(vel);
366 <      
367 <      mass = atoms[i]->getMass();
368 <    
369 <      for (j = 0; j < 3; j++)
370 <        myVel[j] = oldVel[3*i + j];
371 <      
372 <      info->matVecMul3( vScale, myVel, sc );
373 <      
374 <      // velocity half step
375 <      for (j=0; j < 3; j++) {
376 <        // velocity half step  (use chi from previous step here):
377 <        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
378 <      }
379 <      
380 <      atoms[i]->setVel( vel );
381 <      
382 <      if( atoms[i]->isDirectional() ){
383 <
384 <        dAtom = (DirectionalAtom *)atoms[i];
385 <  
386 <        // get and convert the torque to body frame      
387 <  
388 <        dAtom->getTrq( Tb );
389 <        dAtom->lab2Body( Tb );      
390 <            
391 <        for (j=0; j < 3; j++)
392 <          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
393 <      
394 <          dAtom->setJ( ji );
395 <      }
396 <    }
397 <
398 <    if (nConstrained) {
399 <      constrainB();
400 <    }
401 <    
402 <    diffEta = 0;
403 <    for(i = 0; i < 3; i++)
404 <      diffEta += pow(prevEta[i][i] - eta[i][i], 2);    
405 <    
406 <    if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance)
407 <      break;
408 <  }
409 <
410 <  //calculate integral of chidt
411 <  integralOfChidt += dt2*chi;
412 <  
252 >  return ( diffEta <= etaTolerance );
253   }
254  
415 – template<typename T> void NPTf<T>::resetIntegrator() {
416 –  int i,j;
417 –  
418 –  chi = 0.0;
419 –
420 –  for(i = 0; i < 3; i++)
421 –    for (j = 0; j < 3; j++)
422 –      eta[i][j] = 0.0;
423 –
424 – }
425 –
426 – template<typename T> int NPTf<T>::readyCheck() {
427 –
428 –  //check parent's readyCheck() first
429 –  if (T::readyCheck() == -1)
430 –    return -1;
431 –
432 –  // First check to see if we have a target temperature.
433 –  // Not having one is fatal.
434 –  
435 –  if (!have_target_temp) {
436 –    sprintf( painCave.errMsg,
437 –             "NPTf error: You can't use the NPTf integrator\n"
438 –             "   without a targetTemp!\n"
439 –             );
440 –    painCave.isFatal = 1;
441 –    simError();
442 –    return -1;
443 –  }
444 –
445 –  if (!have_target_pressure) {
446 –    sprintf( painCave.errMsg,
447 –             "NPTf error: You can't use the NPTf integrator\n"
448 –             "   without a targetPressure!\n"
449 –             );
450 –    painCave.isFatal = 1;
451 –    simError();
452 –    return -1;
453 –  }
454 –  
455 –  // We must set tauThermostat.
456 –  
457 –  if (!have_tau_thermostat) {
458 –    sprintf( painCave.errMsg,
459 –             "NPTf error: If you use the NPTf\n"
460 –             "   integrator, you must set tauThermostat.\n");
461 –    painCave.isFatal = 1;
462 –    simError();
463 –    return -1;
464 –  }    
465 –
466 –  // We must set tauBarostat.
467 –  
468 –  if (!have_tau_barostat) {
469 –    sprintf( painCave.errMsg,
470 –             "NPTf error: If you use the NPTf\n"
471 –             "   integrator, you must set tauBarostat.\n");
472 –    painCave.isFatal = 1;
473 –    simError();
474 –    return -1;
475 –  }    
476 –
477 –  
478 –  // We need NkBT a lot, so just set it here: This is the RAW number
479 –  // of particles, so no subtraction or addition of constraints or
480 –  // orientational degrees of freedom:
481 –  
482 –  NkBT = (double)Nparticles * kB * targetTemp;
483 –  
484 –  // fkBT is used because the thermostat operates on more degrees of freedom
485 –  // than the barostat (when there are particles with orientational degrees
486 –  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
487 –  
488 –  fkBT = (double)info->ndf * kB * targetTemp;
489 –
490 –  return 1;
491 – }
492 –
255   template<typename T> double NPTf<T>::getConservedQuantity(void){
256  
257    double conservedQuantity;
258 <  double Energy;
258 >  double totalEnergy;
259    double thermostat_kinetic;
260    double thermostat_potential;
261    double barostat_kinetic;
# Line 501 | Line 263 | template<typename T> double NPTf<T>::getConservedQuant
263    double trEta;
264    double a[3][3], b[3][3];
265  
266 <  Energy = tStats->getTotalE();
266 >  totalEnergy = tStats->getTotalE();
267  
268 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
268 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
269      (2.0 * eConvert);
270  
271    thermostat_potential = fkBT* integralOfChidt / eConvert;
# Line 512 | Line 274 | template<typename T> double NPTf<T>::getConservedQuant
274    info->matMul3(a, eta, b);
275    trEta = info->matTrace3(b);
276  
277 <  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta /
277 >  barostat_kinetic = NkBT * tb2 * trEta /
278      (2.0 * eConvert);
279 <  
280 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
279 >
280 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
281      eConvert;
282  
283 <  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
283 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
284      barostat_kinetic + barostat_potential;
523 –  
524 –  cout.width(8);
525 –  cout.precision(8);
285  
286 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
528 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
529 <      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
286 >  return conservedQuantity;
287  
531 –  return conservedQuantity;
288   }
289 +
290 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
291 +  string parameters;
292 +  const int BUFFERSIZE = 2000; // size of the read buffer
293 +  char buffer[BUFFERSIZE];
294 +
295 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
296 +  parameters += buffer;
297 +
298 +  for(int i = 0; i < 3; i++){
299 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
300 +    parameters += buffer;
301 +  }
302 +
303 +  return parameters;
304 +
305 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines