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 767 by tim, Tue Sep 16 20:02:11 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   // Basic non-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> 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  
34 –  have_tau_thermostat = 0;
35 –  have_tau_barostat = 0;
36 –  have_target_temp = 0;
37 –  have_target_pressure = 0;
42  
43 <  have_chi_tolerance = 0;
44 <  have_eta_tolerance = 0;
45 <  have_pos_iter_tolerance = 0;
43 >  if( theInfo->useInitXSstate ){
44 >    // retrieve eta array from simInfo if it exists
45 >    data = info->getProperty(ETAVALUE_ID);
46 >    if(data){
47 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
48 >      
49 >      if(etaValue){
50 >        etaArray = etaValue->getData();
51 >        
52 >        for(i = 0; i < 3; i++){
53 >          for (j = 0; j < 3; j++){
54 >            eta[i][j] = etaArray[3*i+j];
55 >            oldEta[i][j] = eta[i][j];
56 >          }
57 >        }
58 >      }
59 >    }
60 >  }
61  
43 –  oldPos = new double[3*nAtoms];
44 –  oldVel = new double[3*nAtoms];
45 –  oldJi = new double[3*nAtoms];
46 – #ifdef IS_MPI
47 –  Nparticles = mpiSim->getTotAtoms();
48 – #else
49 –  Nparticles = theInfo->n_atoms;
50 – #endif
62   }
63  
64   template<typename T> NPTf<T>::~NPTf() {
65 <  delete[] oldPos;
66 <  delete[] oldVel;
56 <  delete[] oldJi;
65 >
66 >  // empty for now
67   }
68  
69 < template<typename T> void NPTf<T>::moveA() {
60 <  
61 <  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];
69 > template<typename T> void NPTf<T>::resetIntegrator() {
70  
71 <  double rj[3];
69 <  double instaTemp, instaPress, instaVol;
70 <  double tt2, tb2;
71 <  double sc[3];
72 <  double eta2ij;
73 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
74 <  double bigScale, smallScale, offDiagMax;
75 <  double COM[3];
71 >  int i, j;
72  
73 <  tt2 = tauThermostat * tauThermostat;
74 <  tb2 = tauBarostat * tauBarostat;
73 >  for(i = 0; i < 3; i++)
74 >    for (j = 0; j < 3; j++)
75 >      eta[i][j] = 0.0;
76  
77 <  instaTemp = tStats->getTemperature();
78 <  tStats->getPressureTensor(press);
82 <  instaVol = tStats->getVolume();
83 <  
84 <  tStats->getCOM(COM);
77 >  T::resetIntegrator();
78 > }
79  
80 <  //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;          
93 <      }              
94 <    }
95 <  }
96 <  
97 <  //evolve velocity half step
98 <  for( i=0; i<nAtoms; i++ ){
80 > template<typename T> void NPTf<T>::evolveEtaA() {
81  
82 <    atoms[i]->getVel( vel );
101 <    atoms[i]->getFrc( frc );
82 >  int i, j;
83  
84 <    mass = atoms[i]->getMass();
85 <    
86 <    info->matVecMul3( vScale, vel, sc );
87 <
88 <    for (j=0; j < 3; j++) {
89 <      // velocity half step  (use chi from previous step here):
90 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
110 <  
84 >  for(i = 0; i < 3; i ++){
85 >    for(j = 0; j < 3; j++){
86 >      if( i == j)
87 >        eta[i][j] += dt2 *  instaVol *
88 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89 >      else
90 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
91      }
92 +  }
93  
94 <    atoms[i]->setVel( vel );
95 <  
96 <    if( atoms[i]->isDirectional() ){
94 >  for(i = 0; i < 3; i++)
95 >    for (j = 0; j < 3; j++)
96 >      oldEta[i][j] = eta[i][j];
97 > }
98  
99 <      dAtom = (DirectionalAtom *)atoms[i];
99 > template<typename T> void NPTf<T>::evolveEtaB() {
100  
101 <      // get and convert the torque to body frame
120 <      
121 <      dAtom->getTrq( Tb );
122 <      dAtom->lab2Body( Tb );
123 <      
124 <      // get the angular momentum, and propagate a half step
101 >  int i,j;
102  
103 <      dAtom->getJ( ji );
103 >  for(i = 0; i < 3; i++)
104 >    for (j = 0; j < 3; j++)
105 >      prevEta[i][j] = eta[i][j];
106  
107 <      for (j=0; j < 3; j++)
108 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
109 <      
110 <      // use the angular velocities to propagate the rotation matrix a
111 <      // full time step
112 <
113 <      dAtom->getA(A);
114 <      dAtom->getI(I);
115 <    
116 <      // rotate about the x-axis      
117 <      angle = dt2 * ji[0] / I[0][0];
139 <      this->rotate( 1, 2, angle, ji, A );
107 >  for(i = 0; i < 3; i ++){
108 >    for(j = 0; j < 3; j++){
109 >      if( i == j) {
110 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
111 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
112 >      } else {
113 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
114 >      }
115 >    }
116 >  }
117 > }
118  
119 <      // rotate about the y-axis
120 <      angle = dt2 * ji[1] / I[1][1];
121 <      this->rotate( 2, 0, angle, ji, A );
122 <      
123 <      // rotate about the z-axis
124 <      angle = dt * ji[2] / I[2][2];
125 <      this->rotate( 0, 1, angle, ji, A);
126 <      
127 <      // rotate about the y-axis
128 <      angle = dt2 * ji[1] / I[1][1];
129 <      this->rotate( 2, 0, angle, ji, A );
130 <      
153 <       // rotate about the x-axis
154 <      angle = dt2 * ji[0] / I[0][0];
155 <      this->rotate( 1, 2, angle, ji, A );
156 <      
157 <      dAtom->setJ( ji );
158 <      dAtom->setA( A  );    
159 <    }    
119 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
120 >  int i,j;
121 >  double vScale[3][3];
122 >
123 >  for (i = 0; i < 3; i++ ) {
124 >    for (j = 0; j < 3; j++ ) {
125 >      vScale[i][j] = eta[i][j];
126 >
127 >      if (i == j) {
128 >        vScale[i][j] += chi;
129 >      }
130 >    }
131    }
132  
133 <  // advance chi half step
134 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
133 >  info->matVecMul3( vScale, vel, sc );
134 > }
135  
136 <  //calculate the integral of chidt
137 <  integralOfChidt += dt2*chi;
136 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
137 >  int i,j;
138 >  double myVel[3];
139 >  double vScale[3][3];
140  
141 <  //advance eta half step
142 <  for(i = 0; i < 3; i ++)
143 <    for(j = 0; j < 3; j++){
144 <      if( i == j)
145 <        eta[i][j] += dt2 *  instaVol *
146 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
147 <      else
175 <        eta[i][j] += dt2 * instaVol * press[i][j] / ( NkBT*tb2);
141 >  for (i = 0; i < 3; i++ ) {
142 >    for (j = 0; j < 3; j++ ) {
143 >      vScale[i][j] = eta[i][j];
144 >
145 >      if (i == j) {
146 >        vScale[i][j] += chi;
147 >      }
148      }
177 –    
178 –  //save the old positions
179 –  for(i = 0; i < nAtoms; i++){
180 –    atoms[i]->getPos(pos);
181 –    for(j = 0; j < 3; j++)
182 –      oldPos[i*3 + j] = pos[j];
149    }
184 –  
185 –  //the first estimation of r(t+dt) is equal to  r(t)
186 –    
187 –  for(k = 0; k < 4; k ++){
150  
151 <    for(i =0 ; i < nAtoms; i++){
151 >  for (j = 0; j < 3; j++)
152 >    myVel[j] = oldVel[3*index + j];
153  
154 <      atoms[i]->getVel(vel);
155 <      atoms[i]->getPos(pos);
154 >  info->matVecMul3( vScale, myVel, sc );
155 > }
156  
157 <      for(j = 0; j < 3; j++)
158 <        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
159 <      
160 <      info->matVecMul3( eta, rj, sc );
198 <      
199 <      for(j = 0; j < 3; j++)
200 <        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
157 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
158 >                                               int index, double sc[3]){
159 >  int j;
160 >  double rj[3];
161  
162 <      atoms[i]->setPos( pos );
162 >  for(j=0; j<3; j++)
163 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164  
165 <    }
165 >  info->matVecMul3( eta, rj, sc );
166 > }
167  
168 <  }  
168 > template<typename T> void NPTf<T>::scaleSimBox( void ){
169  
170 <
170 >  int i,j,k;
171 >  double scaleMat[3][3];
172 >  double eta2ij;
173 >  double bigScale, smallScale, offDiagMax;
174 >  double hm[3][3], hmnew[3][3];
175 >
176 >
177 >
178    // Scale the box after all the positions have been moved:
179 <  
179 >
180    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
181    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
182 <  
182 >
183    bigScale = 1.0;
184    smallScale = 1.0;
185    offDiagMax = 0.0;
186 <  
186 >
187    for(i=0; i<3; i++){
188      for(j=0; j<3; j++){
189 <      
189 >
190        // Calculate the matrix Product of the eta array (we only need
191        // the ij element right now):
192 <      
192 >
193        eta2ij = 0.0;
194        for(k=0; k<3; k++){
195          eta2ij += eta[i][k] * eta[k][j];
196        }
197 <      
197 >
198        scaleMat[i][j] = 0.0;
199        // identity matrix (see above):
200        if (i == j) scaleMat[i][j] = 1.0;
# Line 233 | Line 202 | template<typename T> void NPTf<T>::moveA() {
202        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
203  
204        if (i != j)
205 <        if (fabs(scaleMat[i][j]) > offDiagMax)
205 >        if (fabs(scaleMat[i][j]) > offDiagMax)
206            offDiagMax = fabs(scaleMat[i][j]);
207      }
208  
209      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
210      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
211    }
212 <  
213 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
212 >
213 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
214      sprintf( painCave.errMsg,
215 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
215 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
216               " Check your tauBarostat, as it is probably too small!\n\n"
217               " scaleMat = [%lf\t%lf\t%lf]\n"
218               "            [%lf\t%lf\t%lf]\n"
# Line 253 | Line 222 | template<typename T> void NPTf<T>::moveA() {
222               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
223      painCave.isFatal = 1;
224      simError();
225 <  } else if (offDiagMax > 0.1) {
225 >  } else if (offDiagMax > 0.01) {
226      sprintf( painCave.errMsg,
227 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
227 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
228               " Check your tauBarostat, as it is probably too small!\n\n"
229               " scaleMat = [%lf\t%lf\t%lf]\n"
230               "            [%lf\t%lf\t%lf]\n"
# Line 270 | Line 239 | template<typename T> void NPTf<T>::moveA() {
239      info->matMul3(hm, scaleMat, hmnew);
240      info->setBoxM(hmnew);
241    }
273 –  
242   }
243  
244 < template<typename T> void NPTf<T>::moveB( void ){
244 > template<typename T> bool NPTf<T>::etaConverged() {
245 >  int i;
246 >  double diffEta, sumEta;
247  
248 <  int i, j, k;
279 <  DirectionalAtom* dAtom;
280 <  double Tb[3], ji[3];
281 <  double vel[3], frc[3];
282 <  double mass;
283 <
284 <  double instaTemp, instaPress, instaVol;
285 <  double tt2, tb2;
286 <  double sc[3];
287 <  double press[3][3], vScale[3][3];
288 <  double oldChi, prevChi;
289 <  double oldEta[3][3], preEta[3][3], diffEta;
290 <  
291 <  tt2 = tauThermostat * tauThermostat;
292 <  tb2 = tauBarostat * tauBarostat;
293 <
294 <
295 <  // Set things up for the iteration:
296 <
297 <  oldChi = chi;
298 <  
248 >  sumEta = 0;
249    for(i = 0; i < 3; i++)
250 <    for(j = 0; j < 3; j++)
301 <      oldEta[i][j] = eta[i][j];
250 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
251  
252 <  for( i=0; i<nAtoms; i++ ){
252 >  diffEta = sqrt( sumEta / 3.0 );
253  
254 <    atoms[i]->getVel( vel );
254 >  return ( diffEta <= etaTolerance );
255 > }
256  
257 <    for (j=0; j < 3; j++)
308 <      oldVel[3*i + j]  = vel[j];
257 > template<typename T> double NPTf<T>::getConservedQuantity(void){
258  
259 <    if( atoms[i]->isDirectional() ){
259 >  double conservedQuantity;
260 >  double totalEnergy;
261 >  double thermostat_kinetic;
262 >  double thermostat_potential;
263 >  double barostat_kinetic;
264 >  double barostat_potential;
265 >  double trEta;
266 >  double a[3][3], b[3][3];
267  
268 <      dAtom = (DirectionalAtom *)atoms[i];
268 >  totalEnergy = tStats->getTotalE();
269  
270 <      dAtom->getJ( ji );
270 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
271 >    (2.0 * eConvert);
272  
273 <      for (j=0; j < 3; j++)
317 <        oldJi[3*i + j] = ji[j];
273 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
274  
275 <    }
276 <  }
275 >  info->transposeMat3(eta, a);
276 >  info->matMul3(a, eta, b);
277 >  trEta = info->matTrace3(b);
278  
279 <  // do the iteration:
279 >  barostat_kinetic = NkBT * tb2 * trEta /
280 >    (2.0 * eConvert);
281  
282 <  instaVol = tStats->getVolume();
283 <  
326 <  for (k=0; k < 4; k++) {
327 <    
328 <    instaTemp = tStats->getTemperature();
329 <    tStats->getPressureTensor(press);
282 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283 >    eConvert;
284  
285 <    // evolve chi another half step using the temperature at t + dt/2
285 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
286 >    barostat_kinetic + barostat_potential;
287  
288 <    prevChi = chi;
334 <    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
335 <    
336 <    for(i = 0; i < 3; i++)
337 <      for(j = 0; j < 3; j++)
338 <        preEta[i][j] = eta[i][j];
288 >  return conservedQuantity;
289  
340 –    //advance eta half step and calculate scale factor for velocity
341 –    for(i = 0; i < 3; i ++)
342 –      for(j = 0; j < 3; j++){
343 –        if( i == j){
344 –          eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
345 –            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
346 –          vScale[i][j] = eta[i][j] + chi;
347 –        }
348 –        else
349 –        {
350 –          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
351 –          vScale[i][j] = eta[i][j];
352 –        }
353 –    }      
354 –
355 –    //advance velocity half step
356 –    for( i=0; i<nAtoms; i++ ){
357 –
358 –      atoms[i]->getFrc( frc );
359 –      atoms[i]->getVel(vel);
360 –      
361 –      mass = atoms[i]->getMass();
362 –      
363 –      info->matVecMul3( vScale, vel, sc );
364 –
365 –      for (j=0; j < 3; j++) {
366 –        // velocity half step  (use chi from previous step here):
367 –        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
368 –      }
369 –      
370 –      atoms[i]->setVel( vel );
371 –      
372 –      if( atoms[i]->isDirectional() ){
373 –
374 –        dAtom = (DirectionalAtom *)atoms[i];
375 –  
376 –        // get and convert the torque to body frame      
377 –  
378 –        dAtom->getTrq( Tb );
379 –        dAtom->lab2Body( Tb );      
380 –            
381 –        for (j=0; j < 3; j++)
382 –          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
383 –      
384 –          dAtom->setJ( ji );
385 –      }
386 –    }
387 –
388 –    
389 –    diffEta = 0;
390 –    for(i = 0; i < 3; i++)
391 –      diffEta += pow(preEta[i][i] - eta[i][i], 2);    
392 –    
393 –    if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance)
394 –      break;
395 –  }
396 –
397 –  //calculate integral of chida
398 –  integralOfChidt += dt2*chi;
399 –
400 –  
290   }
291  
292 < template<typename T> void NPTf<T>::resetIntegrator() {
293 <  int i,j;
294 <  
295 <  chi = 0.0;
292 > template<typename T> string NPTf<T>::getAdditionalParameters(void){
293 >  string parameters;
294 >  const int BUFFERSIZE = 2000; // size of the read buffer
295 >  char buffer[BUFFERSIZE];
296  
297 <  for(i = 0; i < 3; i++)
298 <    for (j = 0; j < 3; j++)
410 <      eta[i][j] = 0.0;
297 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
298 >  parameters += buffer;
299  
300 < }
301 <
302 < template<typename T> int NPTf<T>::readyCheck() {
415 <
416 <  //check parent's readyCheck() first
417 <  if (T::readyCheck() == -1)
418 <    return -1;
419 <
420 <  // First check to see if we have a target temperature.
421 <  // Not having one is fatal.
422 <  
423 <  if (!have_target_temp) {
424 <    sprintf( painCave.errMsg,
425 <             "NPTf error: You can't use the NPTf integrator\n"
426 <             "   without a targetTemp!\n"
427 <             );
428 <    painCave.isFatal = 1;
429 <    simError();
430 <    return -1;
300 >  for(int i = 0; i < 3; i++){
301 >    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
302 >    parameters += buffer;
303    }
304  
305 <  if (!have_target_pressure) {
434 <    sprintf( painCave.errMsg,
435 <             "NPTf error: You can't use the NPTf integrator\n"
436 <             "   without a targetPressure!\n"
437 <             );
438 <    painCave.isFatal = 1;
439 <    simError();
440 <    return -1;
441 <  }
442 <  
443 <  // We must set tauThermostat.
444 <  
445 <  if (!have_tau_thermostat) {
446 <    sprintf( painCave.errMsg,
447 <             "NPTf error: If you use the NPTf\n"
448 <             "   integrator, you must set tauThermostat.\n");
449 <    painCave.isFatal = 1;
450 <    simError();
451 <    return -1;
452 <  }    
305 >  return parameters;
306  
454 –  // We must set tauBarostat.
455 –  
456 –  if (!have_tau_barostat) {
457 –    sprintf( painCave.errMsg,
458 –             "NPTf error: If you use the NPTf\n"
459 –             "   integrator, you must set tauBarostat.\n");
460 –    painCave.isFatal = 1;
461 –    simError();
462 –    return -1;
463 –  }    
464 –
465 –  // We need NkBT a lot, so just set it here:
466 –
467 –  NkBT = (double)Nparticles * kB * targetTemp;
468 –  fkBT = (double)info->ndf * kB * targetTemp;
469 –
470 –  return 1;
307   }
472 –
473 – template<typename T> double NPTf<T>::getConservedQuantity(void){
474 –
475 –  double conservedQuantity;
476 –  double tb2;
477 –  double trEta;  
478 –  double U;
479 –  double thermo;
480 –  double integral;
481 –  double baro;
482 –  double PV;
483 –
484 –  U = tStats->getTotalE();
485 –  thermo = (fkBT * tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert;
486 –
487 –  tb2 = tauBarostat * tauBarostat;
488 –  trEta = info->matTrace3(eta);
489 –  baro = ((double)info->ndfTrans * kB * targetTemp * tb2 * trEta * trEta / 2.0) / eConvert;
490 –
491 –  integral = ((double)(info->ndf + 1) * kB * targetTemp * integralOfChidt) /eConvert;
492 –
493 –  PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert;
494 –
495 –
496 –  cout.width(8);
497 –  cout.precision(8);
498 –  
499 –  cout << info->getTime() << "\t"
500 –       << chi << "\t"
501 –       << trEta << "\t"
502 –       << U << "\t"
503 –       << thermo << "\t"
504 –       << baro << "\t"
505 –       << integral << "\t"
506 –       << PV << "\t"
507 –       << U+thermo+integral+PV+baro << endl;
508 –
509 –  conservedQuantity = U+thermo+integral+PV+baro;
510 –  return conservedQuantity;
511 –  
512 – }

Diff Legend

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