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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 1251 by chrisfen, Mon Jun 7 14:09:02 2004 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2   #include <iostream>
3   using namespace std;
4  
# 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 33 | Line 38 | double Thermo::getKinetic(){
38    double kinetic;
39    double amass;
40    double aVel[3], aJ[3], I[3][3];
41 <  int j, kl;
41 >  int i, j, k, kl;
42  
38 –  DirectionalAtom *dAtom;
39 –
40 –  int n_atoms;
43    double kinetic_global;
44 <  Atom** atoms;
43 <
44 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
45    
45 –  n_atoms = info->n_atoms;
46 –  atoms = info->atoms;
47 –
46    kinetic = 0.0;
47    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];
48  
49 <    if( atoms[kl]->isDirectional() ){
50 <            
51 <      dAtom = (DirectionalAtom *)atoms[kl];
49 >  for (kl=0; kl<integrableObjects.size(); kl++) {
50 >    integrableObjects[kl]->getVel(aVel);
51 >    amass = integrableObjects[kl]->getMass();
52  
53 <      dAtom->getJ( aJ );
54 <      dAtom->getI( I );
55 <      
56 <      for (j=0; j<3; j++)
57 <        kinetic += aJ[j]*aJ[j] / I[j][j];
58 <      
59 <    }
53 >   for(j=0; j<3; j++)
54 >      kinetic += amass*aVel[j]*aVel[j];
55 >
56 >   if (integrableObjects[kl]->isDirectional()){
57 >
58 >      integrableObjects[kl]->getJ( aJ );
59 >      integrableObjects[kl]->getI( I );
60 >
61 >      if (integrableObjects[kl]->isLinear()) {
62 >        i = integrableObjects[kl]->linearAxis();
63 >        j = (i+1)%3;
64 >        k = (i+2)%3;
65 >        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
66 >      } else {
67 >        for (j=0; j<3; j++)
68 >          kinetic += aJ[j]*aJ[j] / I[j][j];
69 >      }
70 >   }
71    }
72   #ifdef IS_MPI
73    MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74                  MPI_SUM, MPI_COMM_WORLD);
75    kinetic = kinetic_global;
76   #endif //is_mpi
77 <
77 >  
78    kinetic = kinetic * 0.5 / e_convert;
79  
80    return kinetic;
# Line 104 | Line 106 | double Thermo::getPotential(){
106    potential = potential_local;
107   #endif // is_mpi
108  
107 – #ifdef IS_MPI
108 –  /*
109 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
110 –  */
111 – #endif
112 –
109    return potential;
110   }
111  
# Line 125 | Line 121 | double Thermo::getTemperature(){
121  
122    const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123    double temperature;
124 <  
124 >
125    temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126    return temperature;
127   }
128  
133 – double Thermo::getEnthalpy() {
134 –
135 –  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
136 –  double u, p, v;
137 –  double press[3][3];
138 –
139 –  u = this->getTotalE();
140 –
141 –  this->getPressureTensor(press);
142 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143 –
144 –  v = this->getVolume();
145 –
146 –  return (u + (p*v)/e_convert);
147 – }
148 –
129   double Thermo::getVolume() {
130  
131    return info->boxVol;
# Line 222 | 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;
226 <  Molecule* molecules;
205 >  int i, j, k;
206  
228 –  nMols = info->n_mol;
229 –  molecules = info->molecules;
230 –  //tau = info->tau;
207  
208 <  // use velocities of molecular centers of mass and molecular masses:
208 >
209    for (i=0; i < 9; i++) {    
210      p_local[i] = 0.0;
211      p_global[i] = 0.0;
212    }
213  
214 <  for (i=0; i < nMols; i++) {
239 <    molmass = molecules[i].getCOMvel(vcom);
214 >  // use velocities of integrableObjects and their masses:  
215  
216 +  for (i=0; i < info->integrableObjects.size(); i++) {
217 +
218 +    molmass = info->integrableObjects[i]->getMass();
219 +    
220 +    info->integrableObjects[i]->getVel(vcom);
221 +    
222      p_local[0] += molmass * (vcom[0] * vcom[0]);
223      p_local[1] += molmass * (vcom[0] * vcom[1]);
224      p_local[2] += molmass * (vcom[0] * vcom[2]);
# Line 247 | Line 228 | void Thermo::getPressureTensor(double press[3][3]){
228      p_local[6] += molmass * (vcom[2] * vcom[0]);
229      p_local[7] += molmass * (vcom[2] * vcom[1]);
230      p_local[8] += molmass * (vcom[2] * vcom[2]);
231 +    
232    }
233  
234    // Get total for entire system from MPI.
235 <
235 >  
236   #ifdef IS_MPI
237    MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
238   #else
# Line 265 | Line 247 | void Thermo::getPressureTensor(double press[3][3]){
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;
268 –
250      }
251    }
252   }
# Line 273 | 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;
282 –  int n_atoms;
283 –  Atom** atoms;
284 –  DirectionalAtom* dAtom;
263    double temperature;
264 <  int n_oriented;
287 <  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;
292 –  n_oriented    = info->n_oriented;
293 –  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 <
305 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
306 <    
279 >
280      // picks random velocities from a gaussian distribution
281      // centered on vbar
282  
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 321 | 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    }
333 –  if( n_oriented ){
334 –  
335 –    for( i=0; i<n_atoms; i++ ){
336 –      
337 –      if( atoms[i]->isDirectional() ){
338 –        
339 –        dAtom = (DirectionalAtom *)atoms[i];
340 –        dAtom->getI( I );
341 –        
342 –        for (j = 0 ; j < 3; j++) {
333  
344 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
345 –          aJ[j] = vbar * gaussStream->getGaussian();
346 –
347 –        }      
348 –
349 –        dAtom->setJ( aJ );
350 –
351 –      }
352 –    }  
353 –  }
334   }
335  
336   void Thermo::getCOMVel(double vdrift[3]){
# Line 358 | 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
365 <  // We should really fix this before someone pokes an eye out.
344 >  nobj   = info->integrableObjects.size();
345  
367 –  n_atoms = info->n_atoms;  
368 –  atoms   = info->atoms;
369 –
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 404 | 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  
410 –  // We are very careless here with the distinction between n_atoms and n_local
411 –  // We should really fix this before someone pokes an eye out.
412 –
413 –  n_atoms = info->n_atoms;  
414 –  atoms   = info->atoms;
415 –
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 443 | 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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