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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 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2   #include <iostream>
3   using namespace std;
4  
# 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 );
130    return temperature;
131   }
132  
133 < double Thermo::getEnthalpy() {
133 > double Thermo::getVolume() {
134  
135 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
136 <  double u, p, v;
140 <  double press[3][3];
135 >  return info->boxVol;
136 > }
137  
138 <  u = this->getTotalE();
138 > double Thermo::getPressure() {
139  
140 +  // Relies on the calculation of the full molecular pressure tensor
141 +  
142 +  const double p_convert = 1.63882576e8;
143 +  double press[3][3];
144 +  double pressure;
145 +
146    this->getPressureTensor(press);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
147  
148 <  v = this->getVolume();
148 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
149  
150 <  return (u + (p*v)/e_convert);
150 >  return pressure;
151   }
152  
153 < double Thermo::getVolume() {
153 > double Thermo::getPressureX() {
154  
155 <  return info->boxVol;
155 >  // Relies on the calculation of the full molecular pressure tensor
156 >  
157 >  const double p_convert = 1.63882576e8;
158 >  double press[3][3];
159 >  double pressureX;
160 >
161 >  this->getPressureTensor(press);
162 >
163 >  pressureX = p_convert * press[0][0];
164 >
165 >  return pressureX;
166   }
167  
168 < double Thermo::getPressure() {
168 > double Thermo::getPressureY() {
169  
170    // Relies on the calculation of the full molecular pressure tensor
171    
172    const double p_convert = 1.63882576e8;
173    double press[3][3];
174 <  double pressure;
174 >  double pressureY;
175  
176    this->getPressureTensor(press);
177  
178 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
178 >  pressureY = p_convert * press[1][1];
179  
180 <  return pressure;
180 >  return pressureY;
181   }
182  
183 + double Thermo::getPressureZ() {
184  
185 +  // Relies on the calculation of the full molecular pressure tensor
186 +  
187 +  const double p_convert = 1.63882576e8;
188 +  double press[3][3];
189 +  double pressureZ;
190 +
191 +  this->getPressureTensor(press);
192 +
193 +  pressureZ = p_convert * press[2][2];
194 +
195 +  return pressureZ;
196 + }
197 +
198 +
199   void Thermo::getPressureTensor(double press[3][3]){
200    // returns pressure tensor in units amu*fs^-2*Ang^-1
201    // routine derived via viral theorem description in:
# Line 230 | Line 256 | void Thermo::velocitize() {
256  
257   void Thermo::velocitize() {
258    
233 –  double x,y;
259    double aVel[3], aJ[3], I[3][3];
260    int i, j, vr, vd; // velocity randomizer loop counters
261    double vdrift[3];
# Line 251 | Line 276 | void Thermo::velocitize() {
276    n_oriented    = info->n_oriented;
277    n_constraints = info->n_constraints;
278    
279 <  kebar = kb * temperature * (double)info->ndf /
280 <    ( 2.0 * (double)info->ndfRaw );
279 >  kebar = kb * temperature * (double)info->ndfRaw /
280 >    ( 2.0 * (double)info->ndf );
281    
282    for(vr = 0; vr < n_atoms; vr++){
283      
# Line 358 | Line 383 | void Thermo::getCOMVel(double vdrift[3]){
383    
384   }
385  
386 + void Thermo::getCOM(double COM[3]){
387 +
388 +  double mtot, mtot_local;
389 +  double aPos[3], amass;
390 +  double COM_local[3];
391 +  int i, n_atoms, j;
392 +  Atom** atoms;
393 +
394 +  // We are very careless here with the distinction between n_atoms and n_local
395 +  // We should really fix this before someone pokes an eye out.
396 +
397 +  n_atoms = info->n_atoms;  
398 +  atoms   = info->atoms;
399 +
400 +  mtot_local = 0.0;
401 +  COM_local[0] = 0.0;
402 +  COM_local[1] = 0.0;
403 +  COM_local[2] = 0.0;
404 +  
405 +  for(i = 0; i < n_atoms; i++){
406 +    
407 +    amass = atoms[i]->getMass();
408 +    atoms[i]->getPos( aPos );
409 +
410 +    for(j = 0; j < 3; j++)
411 +      COM_local[j] += aPos[j] * amass;
412 +    
413 +    mtot_local += amass;
414 +  }
415 +
416 + #ifdef IS_MPI
417 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
418 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
419 + #else
420 +  mtot = mtot_local;
421 +  for(i = 0; i < 3; i++) {
422 +    COM[i] = COM_local[i];
423 +  }
424 + #endif
425 +    
426 +  for (i = 0; i < 3; i++) {
427 +    COM[i] = COM[i] / mtot;
428 +  }
429 + }

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