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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 1192 by gezelter, Mon May 24 21:03:30 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 220 | Line 200 | void Thermo::getPressureTensor(double press[3][3]){
200    const double e_convert = 4.184e-4;
201  
202    double molmass, volume;
203 <  double vcom[3];
203 >  double vcom[3], pcom[3], fcom[3], scaled[3];
204    double p_local[9], p_global[9];
205    int i, j, k, nMols;
206    Molecule* molecules;
# Line 235 | Line 215 | void Thermo::getPressureTensor(double press[3][3]){
215      p_global[i] = 0.0;
216    }
217  
218 <  for (i=0; i < nMols; i++) {
239 <    molmass = molecules[i].getCOMvel(vcom);
218 >  for (i=0; i < info->integrableObjects.size(); i++) {
219  
220 +    molmass = info->integrableObjects[i]->getMass();
221 +    
222 +    info->integrableObjects[i]->getVel(vcom);
223 +    info->integrableObjects[i]->getPos(pcom);
224 +    info->integrableObjects[i]->getFrc(fcom);
225 +
226 +    matVecMul3(info->HmatInv, pcom, scaled);
227 +  
228 +    for(j=0; j<3; j++)
229 +      scaled[j] -= roundMe(scaled[j]);
230 +
231 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
232 +  
233 +    matVecMul3(info->Hmat, scaled, pcom);
234 +    
235      p_local[0] += molmass * (vcom[0] * vcom[0]);
236      p_local[1] += molmass * (vcom[0] * vcom[1]);
237      p_local[2] += molmass * (vcom[0] * vcom[2]);
# Line 247 | Line 241 | void Thermo::getPressureTensor(double press[3][3]){
241      p_local[6] += molmass * (vcom[2] * vcom[0]);
242      p_local[7] += molmass * (vcom[2] * vcom[1]);
243      p_local[8] += molmass * (vcom[2] * vcom[2]);
244 +    
245    }
246  
247    // Get total for entire system from MPI.
# Line 265 | Line 260 | void Thermo::getPressureTensor(double press[3][3]){
260      for (j = 0; j < 3; j++) {
261        k = 3*i + j;
262        press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
268 –
263      }
264    }
265   }
# Line 273 | Line 267 | void Thermo::velocitize() {
267   void Thermo::velocitize() {
268    
269    double aVel[3], aJ[3], I[3][3];
270 <  int i, j, vr, vd; // velocity randomizer loop counters
270 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
271    double vdrift[3];
272    double vbar;
273    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
274    double av2;
275    double kebar;
282 –  int n_atoms;
283 –  Atom** atoms;
284 –  DirectionalAtom* dAtom;
276    double temperature;
277 <  int n_oriented;
287 <  int n_constraints;
277 >  int nobj;
278  
279 <  atoms         = info->atoms;
280 <  n_atoms       = info->n_atoms;
279 >  nobj = info->integrableObjects.size();
280 >  
281    temperature   = info->target_temp;
292 –  n_oriented    = info->n_oriented;
293 –  n_constraints = info->n_constraints;
282    
283    kebar = kb * temperature * (double)info->ndfRaw /
284      ( 2.0 * (double)info->ndf );
285    
286 <  for(vr = 0; vr < n_atoms; vr++){
286 >  for(vr = 0; vr < nobj; vr++){
287      
288      // uses equipartition theory to solve for vbar in angstrom/fs
289  
290 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
290 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
291      vbar = sqrt( av2 );
292 <
305 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
306 <    
292 >
293      // picks random velocities from a gaussian distribution
294      // centered on vbar
295  
296      for (j=0; j<3; j++)
297        aVel[j] = vbar * gaussStream->getGaussian();
298      
299 <    atoms[vr]->setVel( aVel );
299 >    info->integrableObjects[vr]->setVel( aVel );
300 >    
301 >    if(info->integrableObjects[vr]->isDirectional()){
302  
303 +      info->integrableObjects[vr]->getI( I );
304 +
305 +      if (info->integrableObjects[vr]->isLinear()) {
306 +
307 +        l= info->integrableObjects[vr]->linearAxis();
308 +        m = (l+1)%3;
309 +        n = (l+2)%3;
310 +
311 +        aJ[l] = 0.0;
312 +        vbar = sqrt( 2.0 * kebar * I[m][m] );
313 +        aJ[m] = vbar * gaussStream->getGaussian();
314 +        vbar = sqrt( 2.0 * kebar * I[n][n] );
315 +        aJ[n] = vbar * gaussStream->getGaussian();
316 +        
317 +      } else {
318 +        for (j = 0 ; j < 3; j++) {
319 +          vbar = sqrt( 2.0 * kebar * I[j][j] );
320 +          aJ[j] = vbar * gaussStream->getGaussian();
321 +        }      
322 +      } // else isLinear
323 +
324 +      info->integrableObjects[vr]->setJ( aJ );
325 +      
326 +    }//isDirectional
327 +
328    }
329  
330    // Get the Center of Mass drift velocity.
# Line 321 | Line 334 | void Thermo::velocitize() {
334    //  Corrects for the center of mass drift.
335    // sums all the momentum and divides by total mass.
336  
337 <  for(vd = 0; vd < n_atoms; vd++){
337 >  for(vd = 0; vd < nobj; vd++){
338      
339 <    atoms[vd]->getVel(aVel);
339 >    info->integrableObjects[vd]->getVel(aVel);
340      
341      for (j=0; j < 3; j++)
342        aVel[j] -= vdrift[j];
343          
344 <    atoms[vd]->setVel( aVel );
344 >    info->integrableObjects[vd]->setVel( aVel );
345    }
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++) {
346  
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 –  }
347   }
348  
349   void Thermo::getCOMVel(double vdrift[3]){
# Line 358 | Line 351 | void Thermo::getCOMVel(double vdrift[3]){
351    double mtot, mtot_local;
352    double aVel[3], amass;
353    double vdrift_local[3];
354 <  int vd, n_atoms, j;
355 <  Atom** atoms;
354 >  int vd, j;
355 >  int nobj;
356  
357 <  // 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.
357 >  nobj   = info->integrableObjects.size();
358  
367 –  n_atoms = info->n_atoms;  
368 –  atoms   = info->atoms;
369 –
359    mtot_local = 0.0;
360    vdrift_local[0] = 0.0;
361    vdrift_local[1] = 0.0;
362    vdrift_local[2] = 0.0;
363    
364 <  for(vd = 0; vd < n_atoms; vd++){
364 >  for(vd = 0; vd < nobj; vd++){
365      
366 <    amass = atoms[vd]->getMass();
367 <    atoms[vd]->getVel( aVel );
366 >    amass = info->integrableObjects[vd]->getMass();
367 >    info->integrableObjects[vd]->getVel( aVel );
368  
369      for(j = 0; j < 3; j++)
370        vdrift_local[j] += aVel[j] * amass;
# Line 404 | Line 393 | void Thermo::getCOM(double COM[3]){
393    double mtot, mtot_local;
394    double aPos[3], amass;
395    double COM_local[3];
396 <  int i, n_atoms, j;
397 <  Atom** atoms;
396 >  int i, j;
397 >  int nobj;
398  
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 –
399    mtot_local = 0.0;
400    COM_local[0] = 0.0;
401    COM_local[1] = 0.0;
402    COM_local[2] = 0.0;
403 <  
404 <  for(i = 0; i < n_atoms; i++){
403 >
404 >  nobj = info->integrableObjects.size();
405 >  for(i = 0; i < nobj; i++){
406      
407 <    amass = atoms[i]->getMass();
408 <    atoms[i]->getPos( aPos );
407 >    amass = info->integrableObjects[i]->getMass();
408 >    info->integrableObjects[i]->getPos( aPos );
409  
410      for(j = 0; j < 3; j++)
411        COM_local[j] += aPos[j] * amass;
# Line 443 | Line 427 | void Thermo::getCOM(double COM[3]){
427      COM[i] = COM[i] / mtot;
428    }
429   }
430 +
431 + void Thermo::removeCOMdrift() {
432 +  double vdrift[3], aVel[3];
433 +  int vd, j, nobj;
434 +
435 +  nobj = info->integrableObjects.size();
436 +
437 +  // Get the Center of Mass drift velocity.
438 +
439 +  getCOMVel(vdrift);
440 +  
441 +  //  Corrects for the center of mass drift.
442 +  // sums all the momentum and divides by total mass.
443 +
444 +  for(vd = 0; vd < nobj; vd++){
445 +    
446 +    info->integrableObjects[vd]->getVel(aVel);
447 +    
448 +    for (j=0; j < 3; j++)
449 +      aVel[j] -= vdrift[j];
450 +        
451 +    info->integrableObjects[vd]->setVel( aVel );
452 +  }
453 + }

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