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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 1125 by gezelter, Mon Apr 19 22:13:01 2004 UTC vs.
Revision 1253 by gezelter, Tue Jun 8 16:49:46 2004 UTC

# Line 10 | Line 10 | using namespace std;
10   #include "SRI.hpp"
11   #include "Integrator.hpp"
12   #include "simError.h"
13 + #include "MatVec3.h"
14  
15   #ifdef IS_MPI
16   #define __C
17   #include "mpiSimulation.hpp"
18   #endif // is_mpi
19  
20 + inline double roundMe( double x ){
21 +          return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22 + }
23 +
24   Thermo::Thermo( SimInfo* the_info ) {
25    info = the_info;
26    int baseSeed = the_info->getSeed();
# Line 197 | Line 202 | void Thermo::getPressureTensor(double press[3][3]){
202    double molmass, volume;
203    double vcom[3];
204    double p_local[9], p_global[9];
205 <  int i, j, k, nMols;
201 <  Molecule* molecules;
205 >  int i, j, k;
206  
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:
207    for (i=0; i < 9; i++) {    
208      p_local[i] = 0.0;
209      p_global[i] = 0.0;
210    }
211  
212 <  for (i=0; i < nMols; i++) {
214 <    molmass = molecules[i].getCOMvel(vcom);
212 >  // use velocities of integrableObjects and their masses:  
213  
214 +  for (i=0; i < info->integrableObjects.size(); i++) {
215 +
216 +    molmass = info->integrableObjects[i]->getMass();
217 +    
218 +    info->integrableObjects[i]->getVel(vcom);
219 +    
220      p_local[0] += molmass * (vcom[0] * vcom[0]);
221      p_local[1] += molmass * (vcom[0] * vcom[1]);
222      p_local[2] += molmass * (vcom[0] * vcom[2]);
# Line 222 | Line 226 | void Thermo::getPressureTensor(double press[3][3]){
226      p_local[6] += molmass * (vcom[2] * vcom[0]);
227      p_local[7] += molmass * (vcom[2] * vcom[1]);
228      p_local[8] += molmass * (vcom[2] * vcom[2]);
229 +
230    }
231  
232    // Get total for entire system from MPI.
233 <
233 >  
234   #ifdef IS_MPI
235    MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
236   #else
# Line 236 | Line 241 | void Thermo::getPressureTensor(double press[3][3]){
241  
242    volume = this->getVolume();
243  
244 +
245 +
246    for(i = 0; i < 3; i++) {
247      for (j = 0; j < 3; j++) {
248        k = 3*i + j;
249        press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
243 –
250      }
251    }
252   }
# Line 248 | Line 254 | void Thermo::velocitize() {
254   void Thermo::velocitize() {
255    
256    double aVel[3], aJ[3], I[3][3];
257 <  int i, j, vr, vd; // velocity randomizer loop counters
257 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
258    double vdrift[3];
259    double vbar;
260    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
261    double av2;
262    double kebar;
257 –  int n_atoms;
258 –  Atom** atoms;
259 –  DirectionalAtom* dAtom;
263    double temperature;
264 <  int n_oriented;
262 <  int n_constraints;
264 >  int nobj;
265  
266 <  atoms         = info->atoms;
267 <  n_atoms       = info->n_atoms;
266 >  nobj = info->integrableObjects.size();
267 >  
268    temperature   = info->target_temp;
267 –  n_oriented    = info->n_oriented;
268 –  n_constraints = info->n_constraints;
269    
270    kebar = kb * temperature * (double)info->ndfRaw /
271      ( 2.0 * (double)info->ndf );
272    
273 <  for(vr = 0; vr < n_atoms; vr++){
273 >  for(vr = 0; vr < nobj; vr++){
274      
275      // uses equipartition theory to solve for vbar in angstrom/fs
276  
277 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
277 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
278      vbar = sqrt( av2 );
279  
280      // picks random velocities from a gaussian distribution
# Line 283 | Line 283 | void Thermo::velocitize() {
283      for (j=0; j<3; j++)
284        aVel[j] = vbar * gaussStream->getGaussian();
285      
286 <    atoms[vr]->setVel( aVel );
286 >    info->integrableObjects[vr]->setVel( aVel );
287 >    
288 >    if(info->integrableObjects[vr]->isDirectional()){
289  
290 +      info->integrableObjects[vr]->getI( I );
291 +
292 +      if (info->integrableObjects[vr]->isLinear()) {
293 +
294 +        l= info->integrableObjects[vr]->linearAxis();
295 +        m = (l+1)%3;
296 +        n = (l+2)%3;
297 +
298 +        aJ[l] = 0.0;
299 +        vbar = sqrt( 2.0 * kebar * I[m][m] );
300 +        aJ[m] = vbar * gaussStream->getGaussian();
301 +        vbar = sqrt( 2.0 * kebar * I[n][n] );
302 +        aJ[n] = vbar * gaussStream->getGaussian();
303 +        
304 +      } else {
305 +        for (j = 0 ; j < 3; j++) {
306 +          vbar = sqrt( 2.0 * kebar * I[j][j] );
307 +          aJ[j] = vbar * gaussStream->getGaussian();
308 +        }      
309 +      } // else isLinear
310 +
311 +      info->integrableObjects[vr]->setJ( aJ );
312 +      
313 +    }//isDirectional
314 +
315    }
316  
317    // Get the Center of Mass drift velocity.
# Line 294 | Line 321 | void Thermo::velocitize() {
321    //  Corrects for the center of mass drift.
322    // sums all the momentum and divides by total mass.
323  
324 <  for(vd = 0; vd < n_atoms; vd++){
324 >  for(vd = 0; vd < nobj; vd++){
325      
326 <    atoms[vd]->getVel(aVel);
326 >    info->integrableObjects[vd]->getVel(aVel);
327      
328      for (j=0; j < 3; j++)
329        aVel[j] -= vdrift[j];
330          
331 <    atoms[vd]->setVel( aVel );
331 >    info->integrableObjects[vd]->setVel( aVel );
332    }
306 –  if( n_oriented ){
307 –  
308 –    for( i=0; i<n_atoms; i++ ){
309 –      
310 –      if( atoms[i]->isDirectional() ){
311 –        
312 –        dAtom = (DirectionalAtom *)atoms[i];
313 –        dAtom->getI( I );
314 –        
315 –        for (j = 0 ; j < 3; j++) {
333  
317 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
318 –          aJ[j] = vbar * gaussStream->getGaussian();
319 –
320 –        }      
321 –
322 –        dAtom->setJ( aJ );
323 –
324 –      }
325 –    }  
326 –  }
334   }
335  
336   void Thermo::getCOMVel(double vdrift[3]){
# Line 331 | Line 338 | void Thermo::getCOMVel(double vdrift[3]){
338    double mtot, mtot_local;
339    double aVel[3], amass;
340    double vdrift_local[3];
341 <  int vd, n_atoms, j;
342 <  Atom** atoms;
341 >  int vd, j;
342 >  int nobj;
343  
344 <  // 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.
344 >  nobj   = info->integrableObjects.size();
345  
340 –  n_atoms = info->n_atoms;  
341 –  atoms   = info->atoms;
342 –
346    mtot_local = 0.0;
347    vdrift_local[0] = 0.0;
348    vdrift_local[1] = 0.0;
349    vdrift_local[2] = 0.0;
350    
351 <  for(vd = 0; vd < n_atoms; vd++){
351 >  for(vd = 0; vd < nobj; vd++){
352      
353 <    amass = atoms[vd]->getMass();
354 <    atoms[vd]->getVel( aVel );
353 >    amass = info->integrableObjects[vd]->getMass();
354 >    info->integrableObjects[vd]->getVel( aVel );
355  
356      for(j = 0; j < 3; j++)
357        vdrift_local[j] += aVel[j] * amass;
# Line 377 | Line 380 | void Thermo::getCOM(double COM[3]){
380    double mtot, mtot_local;
381    double aPos[3], amass;
382    double COM_local[3];
383 <  int i, n_atoms, j;
384 <  Atom** atoms;
383 >  int i, j;
384 >  int nobj;
385  
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 –
386    mtot_local = 0.0;
387    COM_local[0] = 0.0;
388    COM_local[1] = 0.0;
389    COM_local[2] = 0.0;
390 <  
391 <  for(i = 0; i < n_atoms; i++){
390 >
391 >  nobj = info->integrableObjects.size();
392 >  for(i = 0; i < nobj; i++){
393      
394 <    amass = atoms[i]->getMass();
395 <    atoms[i]->getPos( aPos );
394 >    amass = info->integrableObjects[i]->getMass();
395 >    info->integrableObjects[i]->getPos( aPos );
396  
397      for(j = 0; j < 3; j++)
398        COM_local[j] += aPos[j] * amass;
# Line 416 | Line 414 | void Thermo::getCOM(double COM[3]){
414      COM[i] = COM[i] / mtot;
415    }
416   }
417 +
418 + void Thermo::removeCOMdrift() {
419 +  double vdrift[3], aVel[3];
420 +  int vd, j, nobj;
421 +
422 +  nobj = info->integrableObjects.size();
423 +
424 +  // Get the Center of Mass drift velocity.
425 +
426 +  getCOMVel(vdrift);
427 +  
428 +  //  Corrects for the center of mass drift.
429 +  // sums all the momentum and divides by total mass.
430 +
431 +  for(vd = 0; vd < nobj; vd++){
432 +    
433 +    info->integrableObjects[vd]->getVel(aVel);
434 +    
435 +    for (j=0; j < 3; j++)
436 +      aVel[j] -= vdrift[j];
437 +        
438 +    info->integrableObjects[vd]->setVel( aVel );
439 +  }
440 + }

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