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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 1113 by tim, Thu Apr 15 16:18:26 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 38 | Line 35 | double Thermo::getKinetic(){
35    double aVel[3], aJ[3], I[3][3];
36    int j, 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 <      
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        for (j=0; j<3; j++)
57          kinetic += aJ[j]*aJ[j] / I[j][j];
58        
# Line 88 | Line 76 | double Thermo::getPotential(){
76    int el, nSRI;
77    Molecule* molecules;
78  
79 <  molecules = entry_plug->molecules;
80 <  nSRI = entry_plug->n_SRI;
79 >  molecules = info->molecules;
80 >  nSRI = info->n_SRI;
81  
82    potential_local = 0.0;
83    potential = 0.0;
84 <  potential_local += entry_plug->lrPot;
84 >  potential_local += info->lrPot;
85  
86 <  for( el=0; el<entry_plug->n_mol; el++ ){    
86 >  for( el=0; el<info->n_mol; el++ ){    
87      potential_local += molecules[el].getPotential();
88    }
89  
# Line 107 | Line 95 | double Thermo::getPotential(){
95    potential = potential_local;
96   #endif // is_mpi
97  
110 – #ifdef IS_MPI
111 –  /*
112 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
113 –  */
114 – #endif
115 –
98    return potential;
99   }
100  
# Line 126 | Line 108 | double Thermo::getTemperature(){
108  
109   double Thermo::getTemperature(){
110  
111 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
111 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
112    double temperature;
113 <  
114 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
113 >
114 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
115    return temperature;
116   }
117  
118 < double Thermo::getEnthalpy() {
118 > double Thermo::getVolume() {
119  
120 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
121 <  double u, p, v;
120 >  return info->boxVol;
121 > }
122 >
123 > double Thermo::getPressure() {
124 >
125 >  // Relies on the calculation of the full molecular pressure tensor
126 >  
127 >  const double p_convert = 1.63882576e8;
128    double press[3][3];
129 +  double pressure;
130  
131 <  u = this->getTotalE();
131 >  this->getPressureTensor(press);
132  
133 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
134 +
135 +  return pressure;
136 + }
137 +
138 + double Thermo::getPressureX() {
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 pressureX;
145 +
146    this->getPressureTensor(press);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
147  
148 <  v = this->getVolume();
148 >  pressureX = p_convert * press[0][0];
149  
150 <  return (u + (p*v)/e_convert);
150 >  return pressureX;
151   }
152  
153 < double Thermo::getVolume() {
153 > double Thermo::getPressureY() {
154  
155 <  return entry_plug->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 pressureY;
160 >
161 >  this->getPressureTensor(press);
162 >
163 >  pressureY = p_convert * press[1][1];
164 >
165 >  return pressureY;
166   }
167  
168 < double Thermo::getPressure() {
168 > double Thermo::getPressureZ() {
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 pressureZ;
175  
176    this->getPressureTensor(press);
177  
178 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
178 >  pressureZ = p_convert * press[2][2];
179  
180 <  return pressure;
180 >  return pressureZ;
181   }
182  
183  
# Line 180 | Line 191 | void Thermo::getPressureTensor(double press[3][3]){
191    double molmass, volume;
192    double vcom[3];
193    double p_local[9], p_global[9];
194 <  int i, j, k, l, nMols;
194 >  int i, j, k, nMols;
195    Molecule* molecules;
196  
197 <  nMols = entry_plug->n_mol;
198 <  molecules = entry_plug->molecules;
199 <  //tau = entry_plug->tau;
197 >  nMols = info->n_mol;
198 >  molecules = info->molecules;
199 >  //tau = info->tau;
200  
201    // use velocities of molecular centers of mass and molecular masses:
202    for (i=0; i < 9; i++) {    
# Line 217 | Line 228 | void Thermo::getPressureTensor(double press[3][3]){
228    }
229   #endif // is_mpi
230  
231 <  volume = entry_plug->boxVol;
231 >  volume = this->getVolume();
232  
233    for(i = 0; i < 3; i++) {
234      for (j = 0; j < 3; j++) {
235        k = 3*i + j;
236 <      l = 3*j + i;
237 <      press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume;
236 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
237 >
238      }
239    }
240   }
241  
242   void Thermo::velocitize() {
243    
233 –  double x,y;
244    double aVel[3], aJ[3], I[3][3];
245    int i, j, vr, vd; // velocity randomizer loop counters
246    double vdrift[3];
# Line 245 | Line 255 | void Thermo::velocitize() {
255    int n_oriented;
256    int n_constraints;
257  
258 <  atoms         = entry_plug->atoms;
259 <  n_atoms       = entry_plug->n_atoms;
260 <  temperature   = entry_plug->target_temp;
261 <  n_oriented    = entry_plug->n_oriented;
262 <  n_constraints = entry_plug->n_constraints;
258 >  atoms         = info->atoms;
259 >  n_atoms       = info->n_atoms;
260 >  temperature   = info->target_temp;
261 >  n_oriented    = info->n_oriented;
262 >  n_constraints = info->n_constraints;
263    
264 <  kebar = kb * temperature * (double)entry_plug->ndf /
265 <    ( 2.0 * (double)entry_plug->ndfRaw );
264 >  kebar = kb * temperature * (double)info->ndfRaw /
265 >    ( 2.0 * (double)info->ndf );
266    
267    for(vr = 0; vr < n_atoms; vr++){
268      
# Line 260 | Line 270 | void Thermo::velocitize() {
270  
271      av2 = 2.0 * kebar / atoms[vr]->getMass();
272      vbar = sqrt( av2 );
273 <
264 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
265 <    
273 >
274      // picks random velocities from a gaussian distribution
275      // centered on vbar
276  
# Line 323 | Line 331 | void Thermo::getCOMVel(double vdrift[3]){
331    // We are very careless here with the distinction between n_atoms and n_local
332    // We should really fix this before someone pokes an eye out.
333  
334 <  n_atoms = entry_plug->n_atoms;  
335 <  atoms   = entry_plug->atoms;
334 >  n_atoms = info->n_atoms;  
335 >  atoms   = info->atoms;
336  
337    mtot_local = 0.0;
338    vdrift_local[0] = 0.0;
# Line 358 | Line 366 | void Thermo::getCOMVel(double vdrift[3]){
366    
367   }
368  
369 + void Thermo::getCOM(double COM[3]){
370 +
371 +  double mtot, mtot_local;
372 +  double aPos[3], amass;
373 +  double COM_local[3];
374 +  int i, n_atoms, j;
375 +  Atom** atoms;
376 +
377 +  // We are very careless here with the distinction between n_atoms and n_local
378 +  // We should really fix this before someone pokes an eye out.
379 +
380 +  n_atoms = info->n_atoms;  
381 +  atoms   = info->atoms;
382 +
383 +  mtot_local = 0.0;
384 +  COM_local[0] = 0.0;
385 +  COM_local[1] = 0.0;
386 +  COM_local[2] = 0.0;
387 +  
388 +  for(i = 0; i < n_atoms; i++){
389 +    
390 +    amass = atoms[i]->getMass();
391 +    atoms[i]->getPos( aPos );
392 +
393 +    for(j = 0; j < 3; j++)
394 +      COM_local[j] += aPos[j] * amass;
395 +    
396 +    mtot_local += amass;
397 +  }
398 +
399 + #ifdef IS_MPI
400 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
401 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
402 + #else
403 +  mtot = mtot_local;
404 +  for(i = 0; i < 3; i++) {
405 +    COM[i] = COM_local[i];
406 +  }
407 + #endif
408 +    
409 +  for (i = 0; i < 3; i++) {
410 +    COM[i] = COM[i] / mtot;
411 +  }
412 + }

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