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root/group/branches/no-template-branch/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 123 | Line 123 | double Thermo::getTemperature(){
123  
124   double Thermo::getTemperature(){
125  
126 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
126 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
127    double temperature;
128    
129    temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
# Line 166 | Line 166 | double Thermo::getPressure() {
166    return pressure;
167   }
168  
169 + double Thermo::getPressureX() {
170  
171 +  // Relies on the calculation of the full molecular pressure tensor
172 +  
173 +  const double p_convert = 1.63882576e8;
174 +  double press[3][3];
175 +  double pressureX;
176 +
177 +  this->getPressureTensor(press);
178 +
179 +  pressureX = p_convert * press[0][0];
180 +
181 +  return pressureX;
182 + }
183 +
184 + double Thermo::getPressureY() {
185 +
186 +  // Relies on the calculation of the full molecular pressure tensor
187 +  
188 +  const double p_convert = 1.63882576e8;
189 +  double press[3][3];
190 +  double pressureY;
191 +
192 +  this->getPressureTensor(press);
193 +
194 +  pressureY = p_convert * press[1][1];
195 +
196 +  return pressureY;
197 + }
198 +
199 + double Thermo::getPressureZ() {
200 +
201 +  // Relies on the calculation of the full molecular pressure tensor
202 +  
203 +  const double p_convert = 1.63882576e8;
204 +  double press[3][3];
205 +  double pressureZ;
206 +
207 +  this->getPressureTensor(press);
208 +
209 +  pressureZ = p_convert * press[2][2];
210 +
211 +  return pressureZ;
212 + }
213 +
214 +
215   void Thermo::getPressureTensor(double press[3][3]){
216    // returns pressure tensor in units amu*fs^-2*Ang^-1
217    // routine derived via viral theorem description in:
# Line 227 | Line 272 | void Thermo::velocitize() {
272  
273   void Thermo::velocitize() {
274    
230 –  double x,y;
275    double aVel[3], aJ[3], I[3][3];
276    int i, j, vr, vd; // velocity randomizer loop counters
277    double vdrift[3];
# Line 248 | Line 292 | void Thermo::velocitize() {
292    n_oriented    = info->n_oriented;
293    n_constraints = info->n_constraints;
294    
295 <  kebar = kb * temperature * (double)info->ndf /
296 <    ( 2.0 * (double)info->ndfRaw );
295 >  kebar = kb * temperature * (double)info->ndfRaw /
296 >    ( 2.0 * (double)info->ndf );
297    
298    for(vr = 0; vr < n_atoms; vr++){
299      
# Line 355 | Line 399 | void Thermo::getCOMVel(double vdrift[3]){
399    
400   }
401  
402 + void Thermo::getCOM(double COM[3]){
403 +
404 +  double mtot, mtot_local;
405 +  double aPos[3], amass;
406 +  double COM_local[3];
407 +  int i, n_atoms, j;
408 +  Atom** atoms;
409 +
410 +  // We are very careless here with the distinction between n_atoms and n_local
411 +  // We should really fix this before someone pokes an eye out.
412 +
413 +  n_atoms = info->n_atoms;  
414 +  atoms   = info->atoms;
415 +
416 +  mtot_local = 0.0;
417 +  COM_local[0] = 0.0;
418 +  COM_local[1] = 0.0;
419 +  COM_local[2] = 0.0;
420 +  
421 +  for(i = 0; i < n_atoms; i++){
422 +    
423 +    amass = atoms[i]->getMass();
424 +    atoms[i]->getPos( aPos );
425 +
426 +    for(j = 0; j < 3; j++)
427 +      COM_local[j] += aPos[j] * amass;
428 +    
429 +    mtot_local += amass;
430 +  }
431 +
432 + #ifdef IS_MPI
433 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
434 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
435 + #else
436 +  mtot = mtot_local;
437 +  for(i = 0; i < 3; i++) {
438 +    COM[i] = COM_local[i];
439 +  }
440 + #endif
441 +    
442 +  for (i = 0; i < 3; i++) {
443 +    COM[i] = COM[i] / mtot;
444 +  }
445 + }

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