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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 1125 by gezelter, Mon Apr 19 22:13:01 2004 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 36 | Line 33 | double Thermo::getKinetic(){
33    double kinetic;
34    double amass;
35    double aVel[3], aJ[3], I[3][3];
36 <  int j, kl;
36 >  int i, j, k, kl;
37  
41 –  DirectionalAtom *dAtom;
42 –
43 –  int n_atoms;
38    double kinetic_global;
39 <  Atom** atoms;
46 <
39 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
40    
48 –  n_atoms = entry_plug->n_atoms;
49 –  atoms = entry_plug->atoms;
50 –
41    kinetic = 0.0;
42    kinetic_global = 0.0;
53 –  for( kl=0; kl < n_atoms; kl++ ){
54 –    
55 –    atoms[kl]->getVel(aVel);
56 –    amass = atoms[kl]->getMass();
57 –    
58 –    for (j=0; j < 3; j++)
59 –      kinetic += amass * aVel[j] * aVel[j];
43  
44 <    if( atoms[kl]->isDirectional() ){
45 <            
46 <      dAtom = (DirectionalAtom *)atoms[kl];
44 >  for (kl=0; kl<integrableObjects.size(); kl++) {
45 >    integrableObjects[kl]->getVel(aVel);
46 >    amass = integrableObjects[kl]->getMass();
47  
48 <      dAtom->getJ( aJ );
49 <      dAtom->getI( I );
50 <      
51 <      for (j=0; j<3; j++)
52 <        kinetic += aJ[j]*aJ[j] / I[j][j];
53 <      
54 <    }
48 >   for(j=0; j<3; j++)
49 >      kinetic += amass*aVel[j]*aVel[j];
50 >
51 >   if (integrableObjects[kl]->isDirectional()){
52 >
53 >      integrableObjects[kl]->getJ( aJ );
54 >      integrableObjects[kl]->getI( I );
55 >
56 >      if (integrableObjects[kl]->isLinear()) {
57 >        i = integrableObjects[kl]->linearAxis();
58 >        j = (i+1)%3;
59 >        k = (i+2)%3;
60 >        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
61 >      } else {
62 >        for (j=0; j<3; j++)
63 >          kinetic += aJ[j]*aJ[j] / I[j][j];
64 >      }
65 >   }
66    }
67   #ifdef IS_MPI
68    MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
69                  MPI_SUM, MPI_COMM_WORLD);
70    kinetic = kinetic_global;
71   #endif //is_mpi
72 <
72 >  
73    kinetic = kinetic * 0.5 / e_convert;
74  
75    return kinetic;
# Line 88 | Line 82 | double Thermo::getPotential(){
82    int el, nSRI;
83    Molecule* molecules;
84  
85 <  molecules = entry_plug->molecules;
86 <  nSRI = entry_plug->n_SRI;
85 >  molecules = info->molecules;
86 >  nSRI = info->n_SRI;
87  
88    potential_local = 0.0;
89    potential = 0.0;
90 <  potential_local += entry_plug->lrPot;
90 >  potential_local += info->lrPot;
91  
92 <  for( el=0; el<entry_plug->n_mol; el++ ){    
92 >  for( el=0; el<info->n_mol; el++ ){    
93      potential_local += molecules[el].getPotential();
94    }
95  
# Line 107 | Line 101 | double Thermo::getPotential(){
101    potential = potential_local;
102   #endif // is_mpi
103  
110 – #ifdef IS_MPI
111 –  /*
112 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
113 –  */
114 – #endif
115 –
104    return potential;
105   }
106  
# Line 126 | Line 114 | double Thermo::getTemperature(){
114  
115   double Thermo::getTemperature(){
116  
117 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
117 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
118    double temperature;
119 <  
120 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
119 >
120 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
121    return temperature;
122   }
123  
124 < double Thermo::getEnthalpy() {
124 > double Thermo::getVolume() {
125  
126 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
127 <  double u, p, v;
140 <  double press[3][3];
126 >  return info->boxVol;
127 > }
128  
129 <  u = this->getTotalE();
129 > double Thermo::getPressure() {
130  
131 +  // Relies on the calculation of the full molecular pressure tensor
132 +  
133 +  const double p_convert = 1.63882576e8;
134 +  double press[3][3];
135 +  double pressure;
136 +
137    this->getPressureTensor(press);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
138  
139 <  v = this->getVolume();
139 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
140  
141 <  return (u + (p*v)/e_convert);
141 >  return pressure;
142   }
143  
144 < double Thermo::getVolume() {
144 > double Thermo::getPressureX() {
145  
146 <  return entry_plug->boxVol;
146 >  // Relies on the calculation of the full molecular pressure tensor
147 >  
148 >  const double p_convert = 1.63882576e8;
149 >  double press[3][3];
150 >  double pressureX;
151 >
152 >  this->getPressureTensor(press);
153 >
154 >  pressureX = p_convert * press[0][0];
155 >
156 >  return pressureX;
157   }
158  
159 < double Thermo::getPressure() {
159 > double Thermo::getPressureY() {
160  
161    // Relies on the calculation of the full molecular pressure tensor
162    
163    const double p_convert = 1.63882576e8;
164    double press[3][3];
165 <  double pressure;
165 >  double pressureY;
166  
167    this->getPressureTensor(press);
168  
169 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
169 >  pressureY = p_convert * press[1][1];
170  
171 <  return pressure;
171 >  return pressureY;
172   }
173  
174 + double Thermo::getPressureZ() {
175  
176 +  // Relies on the calculation of the full molecular pressure tensor
177 +  
178 +  const double p_convert = 1.63882576e8;
179 +  double press[3][3];
180 +  double pressureZ;
181 +
182 +  this->getPressureTensor(press);
183 +
184 +  pressureZ = p_convert * press[2][2];
185 +
186 +  return pressureZ;
187 + }
188 +
189 +
190   void Thermo::getPressureTensor(double press[3][3]){
191    // returns pressure tensor in units amu*fs^-2*Ang^-1
192    // routine derived via viral theorem description in:
# Line 180 | Line 197 | void Thermo::getPressureTensor(double press[3][3]){
197    double molmass, volume;
198    double vcom[3];
199    double p_local[9], p_global[9];
200 <  int i, j, k, l, nMols;
200 >  int i, j, k, nMols;
201    Molecule* molecules;
202  
203 <  nMols = entry_plug->n_mol;
204 <  molecules = entry_plug->molecules;
205 <  //tau = entry_plug->tau;
203 >  nMols = info->n_mol;
204 >  molecules = info->molecules;
205 >  //tau = info->tau;
206  
207    // use velocities of molecular centers of mass and molecular masses:
208    for (i=0; i < 9; i++) {    
# Line 222 | Line 239 | void Thermo::getPressureTensor(double press[3][3]){
239    for(i = 0; i < 3; i++) {
240      for (j = 0; j < 3; j++) {
241        k = 3*i + j;
242 <      press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume;
242 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
243 >
244      }
245    }
246   }
247  
248   void Thermo::velocitize() {
249    
232 –  double x,y;
250    double aVel[3], aJ[3], I[3][3];
251    int i, j, vr, vd; // velocity randomizer loop counters
252    double vdrift[3];
# Line 244 | Line 261 | void Thermo::velocitize() {
261    int n_oriented;
262    int n_constraints;
263  
264 <  atoms         = entry_plug->atoms;
265 <  n_atoms       = entry_plug->n_atoms;
266 <  temperature   = entry_plug->target_temp;
267 <  n_oriented    = entry_plug->n_oriented;
268 <  n_constraints = entry_plug->n_constraints;
264 >  atoms         = info->atoms;
265 >  n_atoms       = info->n_atoms;
266 >  temperature   = info->target_temp;
267 >  n_oriented    = info->n_oriented;
268 >  n_constraints = info->n_constraints;
269    
270 <  kebar = kb * temperature * (double)entry_plug->ndf /
271 <    ( 2.0 * (double)entry_plug->ndfRaw );
270 >  kebar = kb * temperature * (double)info->ndfRaw /
271 >    ( 2.0 * (double)info->ndf );
272    
273    for(vr = 0; vr < n_atoms; vr++){
274      
# Line 259 | Line 276 | void Thermo::velocitize() {
276  
277      av2 = 2.0 * kebar / atoms[vr]->getMass();
278      vbar = sqrt( av2 );
279 <
263 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
264 <    
279 >
280      // picks random velocities from a gaussian distribution
281      // centered on vbar
282  
# Line 322 | Line 337 | void Thermo::getCOMVel(double vdrift[3]){
337    // We are very careless here with the distinction between n_atoms and n_local
338    // We should really fix this before someone pokes an eye out.
339  
340 <  n_atoms = entry_plug->n_atoms;  
341 <  atoms   = entry_plug->atoms;
340 >  n_atoms = info->n_atoms;  
341 >  atoms   = info->atoms;
342  
343    mtot_local = 0.0;
344    vdrift_local[0] = 0.0;
# Line 357 | Line 372 | void Thermo::getCOMVel(double vdrift[3]){
372    
373   }
374  
375 + void Thermo::getCOM(double COM[3]){
376 +
377 +  double mtot, mtot_local;
378 +  double aPos[3], amass;
379 +  double COM_local[3];
380 +  int i, n_atoms, j;
381 +  Atom** atoms;
382 +
383 +  // We are very careless here with the distinction between n_atoms and n_local
384 +  // We should really fix this before someone pokes an eye out.
385 +
386 +  n_atoms = info->n_atoms;  
387 +  atoms   = info->atoms;
388 +
389 +  mtot_local = 0.0;
390 +  COM_local[0] = 0.0;
391 +  COM_local[1] = 0.0;
392 +  COM_local[2] = 0.0;
393 +  
394 +  for(i = 0; i < n_atoms; i++){
395 +    
396 +    amass = atoms[i]->getMass();
397 +    atoms[i]->getPos( aPos );
398 +
399 +    for(j = 0; j < 3; j++)
400 +      COM_local[j] += aPos[j] * amass;
401 +    
402 +    mtot_local += amass;
403 +  }
404 +
405 + #ifdef IS_MPI
406 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
407 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
408 + #else
409 +  mtot = mtot_local;
410 +  for(i = 0; i < 3; i++) {
411 +    COM[i] = COM_local[i];
412 +  }
413 + #endif
414 +    
415 +  for (i = 0; i < 3; i++) {
416 +    COM[i] = COM[i] / mtot;
417 +  }
418 + }

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