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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 1127 by tim, Tue Apr 20 16:56:40 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;
126 >  return info->boxVol;
127 > }
128 >
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 <  u = this->getTotalE();
137 >  this->getPressureTensor(press);
138  
139 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
140 +
141 +  return pressure;
142 + }
143 +
144 + double Thermo::getPressureX() {
145 +
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);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
153  
154 <  v = this->getVolume();
154 >  pressureX = p_convert * press[0][0];
155  
156 <  return (u + (p*v)/e_convert);
156 >  return pressureX;
157   }
158  
159 < double Thermo::getVolume() {
159 > double Thermo::getPressureY() {
160  
161 <  return entry_plug->boxVol;
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 pressureY;
166 >
167 >  this->getPressureTensor(press);
168 >
169 >  pressureY = p_convert * press[1][1];
170 >
171 >  return pressureY;
172   }
173  
174 < double Thermo::getPressure() {
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 pressure;
180 >  double pressureZ;
181  
182    this->getPressureTensor(press);
183  
184 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
184 >  pressureZ = p_convert * press[2][2];
185  
186 <  return pressure;
186 >  return pressureZ;
187   }
188  
189  
# 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 217 | Line 234 | void Thermo::getPressureTensor(double press[3][3]){
234    }
235   #endif // is_mpi
236  
237 <  volume = entry_plug->boxVol;
237 >  volume = this->getVolume();
238  
239    for(i = 0; i < 3; i++) {
240      for (j = 0; j < 3; j++) {
241        k = 3*i + j;
242 <      l = 3*j + i;
243 <      press[i][j] = (p_global[k] - entry_plug->tau[l]*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    
233 –  double x,y;
250    double aVel[3], aJ[3], I[3][3];
251 <  int i, j, vr, vd; // velocity randomizer loop counters
251 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
252    double vdrift[3];
253    double vbar;
254    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
255    double av2;
256    double kebar;
241 –  int n_atoms;
242 –  Atom** atoms;
243 –  DirectionalAtom* dAtom;
257    double temperature;
258 <  int n_oriented;
246 <  int n_constraints;
258 >  int nobj;
259  
260 <  atoms         = entry_plug->atoms;
249 <  n_atoms       = entry_plug->n_atoms;
250 <  temperature   = entry_plug->target_temp;
251 <  n_oriented    = entry_plug->n_oriented;
252 <  n_constraints = entry_plug->n_constraints;
260 >  nobj = info->integrableObjects.size();
261    
262 <  kebar = kb * temperature * (double)entry_plug->ndf /
255 <    ( 2.0 * (double)entry_plug->ndfRaw );
262 >  temperature   = info->target_temp;
263    
264 <  for(vr = 0; vr < n_atoms; vr++){
264 >  kebar = kb * temperature * (double)info->ndfRaw /
265 >    ( 2.0 * (double)info->ndf );
266 >  
267 >  for(vr = 0; vr < nobj; vr++){
268      
269      // uses equipartition theory to solve for vbar in angstrom/fs
270  
271 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
271 >    av2 = 2.0 * kebar / info->integrableObjects[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  
277      for (j=0; j<3; j++)
278        aVel[j] = vbar * gaussStream->getGaussian();
279      
280 <    atoms[vr]->setVel( aVel );
280 >    info->integrableObjects[vr]->setVel( aVel );
281 >    
282 >    if(info->integrableObjects[vr]->isDirectional()){
283  
284 +      info->integrableObjects[vr]->getI( I );
285 +
286 +      if (info->integrableObjects[vr]->isLinear()) {
287 +
288 +        l= info->integrableObjects[vr]->linearAxis();
289 +        m = (l+1)%3;
290 +        n = (l+2)%3;
291 +
292 +        aJ[l] = 0.0;
293 +        vbar = sqrt( 2.0 * kebar * I[m][m] );
294 +        aJ[m] = vbar * gaussStream->getGaussian();
295 +        vbar = sqrt( 2.0 * kebar * I[n][n] );
296 +        aJ[n] = vbar * gaussStream->getGaussian();
297 +        
298 +      } else {
299 +        for (j = 0 ; j < 3; j++) {
300 +          vbar = sqrt( 2.0 * kebar * I[j][j] );
301 +          aJ[j] = vbar * gaussStream->getGaussian();
302 +        }      
303 +      } // else isLinear
304 +
305 +      info->integrableObjects[vr]->setJ( aJ );
306 +      
307 +    }//isDirectional
308 +
309    }
310  
311    // Get the Center of Mass drift velocity.
# Line 280 | Line 315 | void Thermo::velocitize() {
315    //  Corrects for the center of mass drift.
316    // sums all the momentum and divides by total mass.
317  
318 <  for(vd = 0; vd < n_atoms; vd++){
318 >  for(vd = 0; vd < nobj; vd++){
319      
320 <    atoms[vd]->getVel(aVel);
320 >    info->integrableObjects[vd]->getVel(aVel);
321      
322      for (j=0; j < 3; j++)
323        aVel[j] -= vdrift[j];
324          
325 <    atoms[vd]->setVel( aVel );
325 >    info->integrableObjects[vd]->setVel( aVel );
326    }
292 –  if( n_oriented ){
293 –  
294 –    for( i=0; i<n_atoms; i++ ){
295 –      
296 –      if( atoms[i]->isDirectional() ){
297 –        
298 –        dAtom = (DirectionalAtom *)atoms[i];
299 –        dAtom->getI( I );
300 –        
301 –        for (j = 0 ; j < 3; j++) {
327  
303 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
304 –          aJ[j] = vbar * gaussStream->getGaussian();
305 –
306 –        }      
307 –
308 –        dAtom->setJ( aJ );
309 –
310 –      }
311 –    }  
312 –  }
328   }
329  
330   void Thermo::getCOMVel(double vdrift[3]){
# Line 317 | Line 332 | void Thermo::getCOMVel(double vdrift[3]){
332    double mtot, mtot_local;
333    double aVel[3], amass;
334    double vdrift_local[3];
335 <  int vd, n_atoms, j;
336 <  Atom** atoms;
335 >  int vd, j;
336 >  int nobj;
337  
338 <  // We are very careless here with the distinction between n_atoms and n_local
324 <  // We should really fix this before someone pokes an eye out.
338 >  nobj   = info->integrableObjects.size();
339  
326 –  n_atoms = entry_plug->n_atoms;  
327 –  atoms   = entry_plug->atoms;
328 –
340    mtot_local = 0.0;
341    vdrift_local[0] = 0.0;
342    vdrift_local[1] = 0.0;
343    vdrift_local[2] = 0.0;
344    
345 <  for(vd = 0; vd < n_atoms; vd++){
345 >  for(vd = 0; vd < nobj; vd++){
346      
347 <    amass = atoms[vd]->getMass();
348 <    atoms[vd]->getVel( aVel );
347 >    amass = info->integrableObjects[vd]->getMass();
348 >    info->integrableObjects[vd]->getVel( aVel );
349  
350      for(j = 0; j < 3; j++)
351        vdrift_local[j] += aVel[j] * amass;
# Line 358 | Line 369 | void Thermo::getCOMVel(double vdrift[3]){
369    
370   }
371  
372 + void Thermo::getCOM(double COM[3]){
373 +
374 +  double mtot, mtot_local;
375 +  double aPos[3], amass;
376 +  double COM_local[3];
377 +  int i, j;
378 +  int nobj;
379 +
380 +  mtot_local = 0.0;
381 +  COM_local[0] = 0.0;
382 +  COM_local[1] = 0.0;
383 +  COM_local[2] = 0.0;
384 +
385 +  nobj = info->integrableObjects.size();
386 +  for(i = 0; i < nobj; i++){
387 +    
388 +    amass = info->integrableObjects[i]->getMass();
389 +    info->integrableObjects[i]->getPos( aPos );
390 +
391 +    for(j = 0; j < 3; j++)
392 +      COM_local[j] += aPos[j] * amass;
393 +    
394 +    mtot_local += amass;
395 +  }
396 +
397 + #ifdef IS_MPI
398 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
399 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
400 + #else
401 +  mtot = mtot_local;
402 +  for(i = 0; i < 3; i++) {
403 +    COM[i] = COM_local[i];
404 +  }
405 + #endif
406 +    
407 +  for (i = 0; i < 3; i++) {
408 +    COM[i] = COM[i] / mtot;
409 +  }
410 + }
411 +
412 + void Thermo::removeCOMdrift() {
413 +  double vdrift[3], aVel[3];
414 +  int vd, j, nobj;
415 +
416 +  nobj = info->integrableObjects.size();
417 +
418 +  // Get the Center of Mass drift velocity.
419 +
420 +  getCOMVel(vdrift);
421 +  
422 +  //  Corrects for the center of mass drift.
423 +  // sums all the momentum and divides by total mass.
424 +
425 +  for(vd = 0; vd < nobj; vd++){
426 +    
427 +    info->integrableObjects[vd]->getVel(aVel);
428 +    
429 +    for (j=0; j < 3; j++)
430 +      aVel[j] -= vdrift[j];
431 +        
432 +    info->integrableObjects[vd]->setVel( aVel );
433 +  }
434 + }

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