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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 608 by gezelter, Tue Jul 15 14:45:09 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 <
22 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  int baseSeed = BASE_SEED;
19 > Thermo::Thermo( SimInfo* the_info ) {
20 >  info = the_info;
21 >  int baseSeed = the_info->getSeed();
22    
23    gaussStream = new gaussianSPRNG( baseSeed );
24   }
# Line 45 | Line 42 | double Thermo::getKinetic(){
42    Atom** atoms;
43  
44    
45 <  n_atoms = entry_plug->n_atoms;
46 <  atoms = entry_plug->atoms;
45 >  n_atoms = info->n_atoms;
46 >  atoms = info->atoms;
47  
48    kinetic = 0.0;
49    kinetic_global = 0.0;
# Line 88 | Line 85 | double Thermo::getPotential(){
85    int el, nSRI;
86    Molecule* molecules;
87  
88 <  molecules = entry_plug->molecules;
89 <  nSRI = entry_plug->n_SRI;
88 >  molecules = info->molecules;
89 >  nSRI = info->n_SRI;
90  
91    potential_local = 0.0;
92    potential = 0.0;
93 <  potential_local += entry_plug->lrPot;
93 >  potential_local += info->lrPot;
94  
95 <  for( el=0; el<entry_plug->n_mol; el++ ){    
95 >  for( el=0; el<info->n_mol; el++ ){    
96      potential_local += molecules[el].getPotential();
97    }
98  
# 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)entry_plug->ndf * kb );
129 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130    return temperature;
131   }
132  
# Line 151 | Line 148 | double Thermo::getVolume() {
148  
149   double Thermo::getVolume() {
150  
151 <  return entry_plug->boxVol;
151 >  return info->boxVol;
152   }
153  
154   double Thermo::getPressure() {
# Line 169 | 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 180 | Line 222 | void Thermo::getPressureTensor(double press[3][3]){
222    double molmass, volume;
223    double vcom[3];
224    double p_local[9], p_global[9];
225 <  int i, j, k, l, nMols;
225 >  int i, j, k, nMols;
226    Molecule* molecules;
227  
228 <  nMols = entry_plug->n_mol;
229 <  molecules = entry_plug->molecules;
230 <  //tau = entry_plug->tau;
228 >  nMols = info->n_mol;
229 >  molecules = info->molecules;
230 >  //tau = info->tau;
231  
232    // use velocities of molecular centers of mass and molecular masses:
233    for (i=0; i < 9; i++) {    
# Line 217 | Line 259 | void Thermo::getPressureTensor(double press[3][3]){
259    }
260   #endif // is_mpi
261  
262 <  volume = entry_plug->boxVol;
262 >  volume = this->getVolume();
263  
264    for(i = 0; i < 3; i++) {
265      for (j = 0; j < 3; j++) {
266        k = 3*i + j;
267 <      l = 3*j + i;
268 <      press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume;
267 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
268 >
269      }
270    }
271   }
# Line 245 | Line 287 | void Thermo::velocitize() {
287    int n_oriented;
288    int n_constraints;
289  
290 <  atoms         = entry_plug->atoms;
291 <  n_atoms       = entry_plug->n_atoms;
292 <  temperature   = entry_plug->target_temp;
293 <  n_oriented    = entry_plug->n_oriented;
294 <  n_constraints = entry_plug->n_constraints;
290 >  atoms         = info->atoms;
291 >  n_atoms       = info->n_atoms;
292 >  temperature   = info->target_temp;
293 >  n_oriented    = info->n_oriented;
294 >  n_constraints = info->n_constraints;
295    
296 <  kebar = kb * temperature * (double)entry_plug->ndf /
297 <    ( 2.0 * (double)entry_plug->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 323 | Line 365 | void Thermo::getCOMVel(double vdrift[3]){
365    // We are very careless here with the distinction between n_atoms and n_local
366    // We should really fix this before someone pokes an eye out.
367  
368 <  n_atoms = entry_plug->n_atoms;  
369 <  atoms   = entry_plug->atoms;
368 >  n_atoms = info->n_atoms;  
369 >  atoms   = info->atoms;
370  
371    mtot_local = 0.0;
372    vdrift_local[0] = 0.0;
# 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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