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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 799 by mmeineke, Fri Oct 3 22:11:53 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 33 | 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  
38 –  DirectionalAtom *dAtom;
39 –
40 –  int n_atoms;
38    double kinetic_global;
39 <  Atom** atoms;
43 <
39 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
40    
45 –  n_atoms = info->n_atoms;
46 –  atoms = info->atoms;
47 –
41    kinetic = 0.0;
42    kinetic_global = 0.0;
50 –  for( kl=0; kl < n_atoms; kl++ ){
51 –    
52 –    atoms[kl]->getVel(aVel);
53 –    amass = atoms[kl]->getMass();
54 –    
55 –    for (j=0; j < 3; j++)
56 –      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 103 | Line 100 | double Thermo::getPotential(){
100   #else
101    potential = potential_local;
102   #endif // is_mpi
106 –
107 – #ifdef IS_MPI
108 –  /*
109 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
110 –  */
111 – #endif
103  
104    return potential;
105   }
# Line 125 | Line 116 | double Thermo::getTemperature(){
116  
117    const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
118    double temperature;
119 <  
119 >
120    temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
121    return temperature;
122   }
# Line 257 | Line 248 | void Thermo::velocitize() {
248   void Thermo::velocitize() {
249    
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;
266 –  int n_atoms;
267 –  Atom** atoms;
268 –  DirectionalAtom* dAtom;
257    double temperature;
258 <  int n_oriented;
271 <  int n_constraints;
258 >  int nobj;
259  
260 <  atoms         = info->atoms;
261 <  n_atoms       = info->n_atoms;
260 >  nobj = info->integrableObjects.size();
261 >  
262    temperature   = info->target_temp;
276 –  n_oriented    = info->n_oriented;
277 –  n_constraints = info->n_constraints;
263    
264    kebar = kb * temperature * (double)info->ndfRaw /
265      ( 2.0 * (double)info->ndf );
266    
267 <  for(vr = 0; vr < n_atoms; vr++){
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 <
289 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
290 <    
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 305 | 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    }
317 –  if( n_oriented ){
318 –  
319 –    for( i=0; i<n_atoms; i++ ){
320 –      
321 –      if( atoms[i]->isDirectional() ){
322 –        
323 –        dAtom = (DirectionalAtom *)atoms[i];
324 –        dAtom->getI( I );
325 –        
326 –        for (j = 0 ; j < 3; j++) {
327  
328 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
329 –          aJ[j] = vbar * gaussStream->getGaussian();
330 –
331 –        }      
332 –
333 –        dAtom->setJ( aJ );
334 –
335 –      }
336 –    }  
337 –  }
328   }
329  
330   void Thermo::getCOMVel(double vdrift[3]){
# Line 342 | 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
349 <  // We should really fix this before someone pokes an eye out.
338 >  nobj   = info->integrableObjects.size();
339  
351 –  n_atoms = info->n_atoms;  
352 –  atoms   = info->atoms;
353 –
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 388 | Line 374 | void Thermo::getCOM(double COM[3]){
374    double mtot, mtot_local;
375    double aPos[3], amass;
376    double COM_local[3];
377 <  int i, n_atoms, j;
378 <  Atom** atoms;
377 >  int i, j;
378 >  int nobj;
379  
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 –
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 <  for(i = 0; i < n_atoms; i++){
384 >
385 >  nobj = info->integrableObjects.size();
386 >  for(i = 0; i < nobj; i++){
387      
388 <    amass = atoms[i]->getMass();
389 <    atoms[i]->getPos( aPos );
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;
# Line 427 | Line 408 | void Thermo::getCOM(double COM[3]){
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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