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root/group/trunk/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 853 by mmeineke, Thu Nov 6 19:11:38 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 107 | Line 104 | double Thermo::getPotential(){
104    potential = potential_local;
105   #endif // is_mpi
106  
110 – #ifdef IS_MPI
111 –  /*
112 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
113 –  */
114 – #endif
115 –
107    return potential;
108   }
109  
# Line 126 | Line 117 | double Thermo::getTemperature(){
117  
118   double Thermo::getTemperature(){
119  
120 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
120 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
121    double temperature;
122    
123 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
123 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
124    return temperature;
125   }
126  
127 < double Thermo::getEnthalpy() {
127 > double Thermo::getVolume() {
128  
129 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
130 <  double u, p, v;
129 >  return info->boxVol;
130 > }
131 >
132 > double Thermo::getPressure() {
133 >
134 >  // Relies on the calculation of the full molecular pressure tensor
135 >  
136 >  const double p_convert = 1.63882576e8;
137    double press[3][3];
138 +  double pressure;
139  
140 <  u = this->getTotalE();
140 >  this->getPressureTensor(press);
141  
142 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143 +
144 +  return pressure;
145 + }
146 +
147 + double Thermo::getPressureX() {
148 +
149 +  // Relies on the calculation of the full molecular pressure tensor
150 +  
151 +  const double p_convert = 1.63882576e8;
152 +  double press[3][3];
153 +  double pressureX;
154 +
155    this->getPressureTensor(press);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
156  
157 <  v = this->getVolume();
157 >  pressureX = p_convert * press[0][0];
158  
159 <  return (u + (p*v)/e_convert);
159 >  return pressureX;
160   }
161  
162 < double Thermo::getVolume() {
162 > double Thermo::getPressureY() {
163  
164 <  return entry_plug->boxVol;
164 >  // Relies on the calculation of the full molecular pressure tensor
165 >  
166 >  const double p_convert = 1.63882576e8;
167 >  double press[3][3];
168 >  double pressureY;
169 >
170 >  this->getPressureTensor(press);
171 >
172 >  pressureY = p_convert * press[1][1];
173 >
174 >  return pressureY;
175   }
176  
177 < double Thermo::getPressure() {
177 > double Thermo::getPressureZ() {
178  
179    // Relies on the calculation of the full molecular pressure tensor
180    
181    const double p_convert = 1.63882576e8;
182    double press[3][3];
183 <  double pressure;
183 >  double pressureZ;
184  
185    this->getPressureTensor(press);
186  
187 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
187 >  pressureZ = p_convert * press[2][2];
188  
189 <  return pressure;
189 >  return pressureZ;
190   }
191  
192  
# Line 180 | Line 200 | void Thermo::getPressureTensor(double press[3][3]){
200    double molmass, volume;
201    double vcom[3];
202    double p_local[9], p_global[9];
203 <  int i, j, k, l, nMols;
203 >  int i, j, k, nMols;
204    Molecule* molecules;
205  
206 <  nMols = entry_plug->n_mol;
207 <  molecules = entry_plug->molecules;
208 <  //tau = entry_plug->tau;
206 >  nMols = info->n_mol;
207 >  molecules = info->molecules;
208 >  //tau = info->tau;
209  
210    // use velocities of molecular centers of mass and molecular masses:
211    for (i=0; i < 9; i++) {    
# Line 217 | Line 237 | void Thermo::getPressureTensor(double press[3][3]){
237    }
238   #endif // is_mpi
239  
240 <  volume = entry_plug->boxVol;
240 >  volume = this->getVolume();
241  
242    for(i = 0; i < 3; i++) {
243      for (j = 0; j < 3; j++) {
244        k = 3*i + j;
245 <      l = 3*j + i;
246 <      press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume;
245 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
246 >
247      }
248    }
249   }
250  
251   void Thermo::velocitize() {
252    
233 –  double x,y;
253    double aVel[3], aJ[3], I[3][3];
254    int i, j, vr, vd; // velocity randomizer loop counters
255    double vdrift[3];
# Line 245 | Line 264 | void Thermo::velocitize() {
264    int n_oriented;
265    int n_constraints;
266  
267 <  atoms         = entry_plug->atoms;
268 <  n_atoms       = entry_plug->n_atoms;
269 <  temperature   = entry_plug->target_temp;
270 <  n_oriented    = entry_plug->n_oriented;
271 <  n_constraints = entry_plug->n_constraints;
267 >  atoms         = info->atoms;
268 >  n_atoms       = info->n_atoms;
269 >  temperature   = info->target_temp;
270 >  n_oriented    = info->n_oriented;
271 >  n_constraints = info->n_constraints;
272    
273 <  kebar = kb * temperature * (double)entry_plug->ndf /
274 <    ( 2.0 * (double)entry_plug->ndfRaw );
273 >  kebar = kb * temperature * (double)info->ndfRaw /
274 >    ( 2.0 * (double)info->ndf );
275    
276    for(vr = 0; vr < n_atoms; vr++){
277      
# Line 260 | Line 279 | void Thermo::velocitize() {
279  
280      av2 = 2.0 * kebar / atoms[vr]->getMass();
281      vbar = sqrt( av2 );
282 <
264 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
265 <    
282 >
283      // picks random velocities from a gaussian distribution
284      // centered on vbar
285  
# Line 323 | Line 340 | void Thermo::getCOMVel(double vdrift[3]){
340    // We are very careless here with the distinction between n_atoms and n_local
341    // We should really fix this before someone pokes an eye out.
342  
343 <  n_atoms = entry_plug->n_atoms;  
344 <  atoms   = entry_plug->atoms;
343 >  n_atoms = info->n_atoms;  
344 >  atoms   = info->atoms;
345  
346    mtot_local = 0.0;
347    vdrift_local[0] = 0.0;
# Line 358 | Line 375 | void Thermo::getCOMVel(double vdrift[3]){
375    
376   }
377  
378 + void Thermo::getCOM(double COM[3]){
379 +
380 +  double mtot, mtot_local;
381 +  double aPos[3], amass;
382 +  double COM_local[3];
383 +  int i, n_atoms, j;
384 +  Atom** atoms;
385 +
386 +  // We are very careless here with the distinction between n_atoms and n_local
387 +  // We should really fix this before someone pokes an eye out.
388 +
389 +  n_atoms = info->n_atoms;  
390 +  atoms   = info->atoms;
391 +
392 +  mtot_local = 0.0;
393 +  COM_local[0] = 0.0;
394 +  COM_local[1] = 0.0;
395 +  COM_local[2] = 0.0;
396 +  
397 +  for(i = 0; i < n_atoms; i++){
398 +    
399 +    amass = atoms[i]->getMass();
400 +    atoms[i]->getPos( aPos );
401 +
402 +    for(j = 0; j < 3; j++)
403 +      COM_local[j] += aPos[j] * amass;
404 +    
405 +    mtot_local += amass;
406 +  }
407 +
408 + #ifdef IS_MPI
409 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
410 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
411 + #else
412 +  mtot = mtot_local;
413 +  for(i = 0; i < 3; i++) {
414 +    COM[i] = COM_local[i];
415 +  }
416 + #endif
417 +    
418 +  for (i = 0; i < 3; i++) {
419 +    COM[i] = COM[i] / mtot;
420 +  }
421 + }

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