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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC

# Line 16 | Line 16 | using namespace std;
16   #include "mpiSimulation.hpp"
17   #endif // is_mpi
18  
19 –
20 – #define BASE_SEED 123456789
21 –
19   Thermo::Thermo( SimInfo* the_info ) {
20    info = the_info;
21 <  int baseSeed = BASE_SEED;
21 >  int baseSeed = the_info->getSeed();
22    
23    gaussStream = new gaussianSPRNG( baseSeed );
24   }
# Line 126 | 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 167 | Line 164 | double Thermo::getPressure() {
164    pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
165  
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  
# Line 251 | Line 293 | void Thermo::velocitize() {
293    n_oriented    = info->n_oriented;
294    n_constraints = info->n_constraints;
295    
296 <  kebar = kb * temperature * (double)info->ndf /
297 <    ( 2.0 * (double)info->ndfRaw );
296 >  kebar = kb * temperature * (double)info->ndfRaw /
297 >    ( 2.0 * (double)info->ndf );
298    
299    for(vr = 0; vr < n_atoms; vr++){
300      
# Line 358 | Line 400 | void Thermo::getCOMVel(double vdrift[3]){
400    
401   }
402  
403 + void Thermo::getCOM(double COM[3]){
404 +
405 +  double mtot, mtot_local;
406 +  double aPos[3], amass;
407 +  double COM_local[3];
408 +  int i, n_atoms, j;
409 +  Atom** atoms;
410 +
411 +  // We are very careless here with the distinction between n_atoms and n_local
412 +  // We should really fix this before someone pokes an eye out.
413 +
414 +  n_atoms = info->n_atoms;  
415 +  atoms   = info->atoms;
416 +
417 +  mtot_local = 0.0;
418 +  COM_local[0] = 0.0;
419 +  COM_local[1] = 0.0;
420 +  COM_local[2] = 0.0;
421 +  
422 +  for(i = 0; i < n_atoms; i++){
423 +    
424 +    amass = atoms[i]->getMass();
425 +    atoms[i]->getPos( aPos );
426 +
427 +    for(j = 0; j < 3; j++)
428 +      COM_local[j] += aPos[j] * amass;
429 +    
430 +    mtot_local += amass;
431 +  }
432 +
433 + #ifdef IS_MPI
434 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
435 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
436 + #else
437 +  mtot = mtot_local;
438 +  for(i = 0; i < 3; i++) {
439 +    COM[i] = COM_local[i];
440 +  }
441 + #endif
442 +    
443 +  for (i = 0; i < 3; i++) {
444 +    COM[i] = COM[i] / mtot;
445 +  }
446 + }

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