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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 611 by gezelter, Tue Jul 15 17:10:50 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 <
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  
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;
135 >  return info->boxVol;
136 > }
137 >
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 <  u = this->getTotalE();
146 >  this->getPressureTensor(press);
147  
148 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
149 +
150 +  return pressure;
151 + }
152 +
153 + double Thermo::getPressureX() {
154 +
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);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
162  
163 <  v = this->getVolume();
163 >  pressureX = p_convert * press[0][0];
164  
165 <  return (u + (p*v)/e_convert);
165 >  return pressureX;
166   }
167  
168 < double Thermo::getVolume() {
168 > double Thermo::getPressureY() {
169  
170 <  return entry_plug->boxVol;
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 pressureY;
175 >
176 >  this->getPressureTensor(press);
177 >
178 >  pressureY = p_convert * press[1][1];
179 >
180 >  return pressureY;
181   }
182  
183 < double Thermo::getPressure() {
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 pressure;
189 >  double pressureZ;
190  
191    this->getPressureTensor(press);
192  
193 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
193 >  pressureZ = p_convert * press[2][2];
194  
195 <  return pressure;
195 >  return pressureZ;
196   }
197  
198  
# Line 180 | Line 206 | void Thermo::getPressureTensor(double press[3][3]){
206    double molmass, volume;
207    double vcom[3];
208    double p_local[9], p_global[9];
209 <  int i, j, k, l, nMols;
209 >  int i, j, k, nMols;
210    Molecule* molecules;
211  
212 <  nMols = entry_plug->n_mol;
213 <  molecules = entry_plug->molecules;
214 <  //tau = entry_plug->tau;
212 >  nMols = info->n_mol;
213 >  molecules = info->molecules;
214 >  //tau = info->tau;
215  
216    // use velocities of molecular centers of mass and molecular masses:
217    for (i=0; i < 9; i++) {    
# Line 222 | Line 248 | void Thermo::getPressureTensor(double press[3][3]){
248    for(i = 0; i < 3; i++) {
249      for (j = 0; j < 3; j++) {
250        k = 3*i + j;
251 <      press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume;
251 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
252 >
253      }
254    }
255   }
256  
257   void Thermo::velocitize() {
258    
232 –  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 244 | Line 270 | void Thermo::velocitize() {
270    int n_oriented;
271    int n_constraints;
272  
273 <  atoms         = entry_plug->atoms;
274 <  n_atoms       = entry_plug->n_atoms;
275 <  temperature   = entry_plug->target_temp;
276 <  n_oriented    = entry_plug->n_oriented;
277 <  n_constraints = entry_plug->n_constraints;
273 >  atoms         = info->atoms;
274 >  n_atoms       = info->n_atoms;
275 >  temperature   = info->target_temp;
276 >  n_oriented    = info->n_oriented;
277 >  n_constraints = info->n_constraints;
278    
279 <  kebar = kb * temperature * (double)entry_plug->ndf /
280 <    ( 2.0 * (double)entry_plug->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 322 | Line 348 | void Thermo::getCOMVel(double vdrift[3]){
348    // We are very careless here with the distinction between n_atoms and n_local
349    // We should really fix this before someone pokes an eye out.
350  
351 <  n_atoms = entry_plug->n_atoms;  
352 <  atoms   = entry_plug->atoms;
351 >  n_atoms = info->n_atoms;  
352 >  atoms   = info->atoms;
353  
354    mtot_local = 0.0;
355    vdrift_local[0] = 0.0;
# Line 357 | 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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