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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 1131 by tim, Thu Apr 22 21:33:55 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
# Line 33 | Line 34 | double Thermo::getKinetic(){
34    double kinetic;
35    double amass;
36    double aVel[3], aJ[3], I[3][3];
37 <  int j, kl;
37 >  int i, j, k, kl;
38  
38 –  DirectionalAtom *dAtom;
39 –
40 –  int n_atoms;
39    double kinetic_global;
40 <  Atom** atoms;
43 <
40 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
41    
45 –  n_atoms = info->n_atoms;
46 –  atoms = info->atoms;
47 –
42    kinetic = 0.0;
43    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];
44  
45 <    if( atoms[kl]->isDirectional() ){
46 <            
47 <      dAtom = (DirectionalAtom *)atoms[kl];
45 >  for (kl=0; kl<integrableObjects.size(); kl++) {
46 >    integrableObjects[kl]->getVel(aVel);
47 >    amass = integrableObjects[kl]->getMass();
48  
49 <      dAtom->getJ( aJ );
50 <      dAtom->getI( I );
51 <      
52 <      for (j=0; j<3; j++)
53 <        kinetic += aJ[j]*aJ[j] / I[j][j];
54 <      
55 <    }
49 >   for(j=0; j<3; j++)
50 >      kinetic += amass*aVel[j]*aVel[j];
51 >
52 >   if (integrableObjects[kl]->isDirectional()){
53 >
54 >      integrableObjects[kl]->getJ( aJ );
55 >      integrableObjects[kl]->getI( I );
56 >
57 >      if (integrableObjects[kl]->isLinear()) {
58 >        i = integrableObjects[kl]->linearAxis();
59 >        j = (i+1)%3;
60 >        k = (i+2)%3;
61 >        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
62 >      } else {
63 >        for (j=0; j<3; j++)
64 >          kinetic += aJ[j]*aJ[j] / I[j][j];
65 >      }
66 >   }
67    }
68   #ifdef IS_MPI
69    MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
70                  MPI_SUM, MPI_COMM_WORLD);
71    kinetic = kinetic_global;
72   #endif //is_mpi
73 <
73 >  
74    kinetic = kinetic * 0.5 / e_convert;
75  
76    return kinetic;
# Line 104 | Line 102 | double Thermo::getPotential(){
102    potential = potential_local;
103   #endif // is_mpi
104  
107 – #ifdef IS_MPI
108 –  /*
109 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
110 –  */
111 – #endif
112 –
105    return potential;
106   }
107  
# Line 123 | Line 115 | double Thermo::getTemperature(){
115  
116   double Thermo::getTemperature(){
117  
118 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
118 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
119    double temperature;
120 <  
120 >
121    temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
122    return temperature;
123   }
124  
125 < double Thermo::getEnthalpy() {
125 > double Thermo::getVolume() {
126  
127 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
128 <  double u, p, v;
137 <  double press[3][3];
127 >  return info->boxVol;
128 > }
129  
130 <  u = this->getTotalE();
130 > double Thermo::getPressure() {
131  
132 +  // Relies on the calculation of the full molecular pressure tensor
133 +  
134 +  const double p_convert = 1.63882576e8;
135 +  double press[3][3];
136 +  double pressure;
137 +
138    this->getPressureTensor(press);
142 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
139  
140 <  v = this->getVolume();
140 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
141  
142 <  return (u + (p*v)/e_convert);
142 >  return pressure;
143   }
144  
145 < double Thermo::getVolume() {
145 > double Thermo::getPressureX() {
146  
147 <  return info->boxVol;
147 >  // Relies on the calculation of the full molecular pressure tensor
148 >  
149 >  const double p_convert = 1.63882576e8;
150 >  double press[3][3];
151 >  double pressureX;
152 >
153 >  this->getPressureTensor(press);
154 >
155 >  pressureX = p_convert * press[0][0];
156 >
157 >  return pressureX;
158   }
159  
160 < double Thermo::getPressure() {
160 > double Thermo::getPressureY() {
161  
162    // Relies on the calculation of the full molecular pressure tensor
163    
164    const double p_convert = 1.63882576e8;
165    double press[3][3];
166 <  double pressure;
166 >  double pressureY;
167  
168    this->getPressureTensor(press);
169  
170 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
170 >  pressureY = p_convert * press[1][1];
171  
172 <  return pressure;
172 >  return pressureY;
173   }
174  
175 + double Thermo::getPressureZ() {
176  
177 +  // Relies on the calculation of the full molecular pressure tensor
178 +  
179 +  const double p_convert = 1.63882576e8;
180 +  double press[3][3];
181 +  double pressureZ;
182 +
183 +  this->getPressureTensor(press);
184 +
185 +  pressureZ = p_convert * press[2][2];
186 +
187 +  return pressureZ;
188 + }
189 +
190 +
191   void Thermo::getPressureTensor(double press[3][3]){
192    // returns pressure tensor in units amu*fs^-2*Ang^-1
193    // routine derived via viral theorem description in:
# Line 175 | Line 196 | void Thermo::getPressureTensor(double press[3][3]){
196    const double e_convert = 4.184e-4;
197  
198    double molmass, volume;
199 <  double vcom[3];
199 >  double vcom[3], pcom[3], fcom[3], scaled[3];
200    double p_local[9], p_global[9];
201    int i, j, k, nMols;
202    Molecule* molecules;
# Line 190 | Line 211 | void Thermo::getPressureTensor(double press[3][3]){
211      p_global[i] = 0.0;
212    }
213  
214 <  for (i=0; i < nMols; i++) {
194 <    molmass = molecules[i].getCOMvel(vcom);
214 >  for (i=0; i < info->integrableObjects.size(); i++) {
215  
216 <    p_local[0] += molmass * (vcom[0] * vcom[0]);
217 <    p_local[1] += molmass * (vcom[0] * vcom[1]);
218 <    p_local[2] += molmass * (vcom[0] * vcom[2]);
219 <    p_local[3] += molmass * (vcom[1] * vcom[0]);
220 <    p_local[4] += molmass * (vcom[1] * vcom[1]);
221 <    p_local[5] += molmass * (vcom[1] * vcom[2]);
222 <    p_local[6] += molmass * (vcom[2] * vcom[0]);
223 <    p_local[7] += molmass * (vcom[2] * vcom[1]);
224 <    p_local[8] += molmass * (vcom[2] * vcom[2]);
216 >    molmass = info->integrableObjects[i]->getMass();
217 >    
218 >    info->integrableObjects[i]->getVel(vcom);
219 >    info->integrableObjects[i]->getPos(pcom);
220 >    info->integrableObjects[i]->getFrc(fcom);
221 >
222 >    matVecMul3(info->HmatInv, pcom, scaled);
223 >  
224 >    for(j=0; j<3; j++)
225 >      scaled[j] -= roundMe(scaled[j]);
226 >
227 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
228 >  
229 >    matVecMul3(info->Hmat, scaled, pcom);
230 >    
231 >    p_local[0] += molmass * (vcom[0] * vcom[0]) + fcom[0]*pcom[0]*eConvert;
232 >    p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert;
233 >    p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert;
234 >    p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert;
235 >    p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert;
236 >    p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert;
237 >    p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert;
238 >    p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert;
239 >    p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert;
240 >    
241    }
242  
243    // Get total for entire system from MPI.
# Line 219 | Line 255 | void Thermo::getPressureTensor(double press[3][3]){
255    for(i = 0; i < 3; i++) {
256      for (j = 0; j < 3; j++) {
257        k = 3*i + j;
258 <      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
258 >      press[i][j] = p_global[k] /  volume;
259  
260      }
261    }
# Line 227 | Line 263 | void Thermo::velocitize() {
263  
264   void Thermo::velocitize() {
265    
230 –  double x,y;
266    double aVel[3], aJ[3], I[3][3];
267 <  int i, j, vr, vd; // velocity randomizer loop counters
267 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
268    double vdrift[3];
269    double vbar;
270    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
271    double av2;
272    double kebar;
238 –  int n_atoms;
239 –  Atom** atoms;
240 –  DirectionalAtom* dAtom;
273    double temperature;
274 <  int n_oriented;
243 <  int n_constraints;
274 >  int nobj;
275  
276 <  atoms         = info->atoms;
277 <  n_atoms       = info->n_atoms;
276 >  nobj = info->integrableObjects.size();
277 >  
278    temperature   = info->target_temp;
248 –  n_oriented    = info->n_oriented;
249 –  n_constraints = info->n_constraints;
279    
280 <  kebar = kb * temperature * (double)info->ndf /
281 <    ( 2.0 * (double)info->ndfRaw );
280 >  kebar = kb * temperature * (double)info->ndfRaw /
281 >    ( 2.0 * (double)info->ndf );
282    
283 <  for(vr = 0; vr < n_atoms; vr++){
283 >  for(vr = 0; vr < nobj; vr++){
284      
285      // uses equipartition theory to solve for vbar in angstrom/fs
286  
287 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
287 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
288      vbar = sqrt( av2 );
289 <
261 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
262 <    
289 >
290      // picks random velocities from a gaussian distribution
291      // centered on vbar
292  
293      for (j=0; j<3; j++)
294        aVel[j] = vbar * gaussStream->getGaussian();
295      
296 <    atoms[vr]->setVel( aVel );
296 >    info->integrableObjects[vr]->setVel( aVel );
297 >    
298 >    if(info->integrableObjects[vr]->isDirectional()){
299  
300 +      info->integrableObjects[vr]->getI( I );
301 +
302 +      if (info->integrableObjects[vr]->isLinear()) {
303 +
304 +        l= info->integrableObjects[vr]->linearAxis();
305 +        m = (l+1)%3;
306 +        n = (l+2)%3;
307 +
308 +        aJ[l] = 0.0;
309 +        vbar = sqrt( 2.0 * kebar * I[m][m] );
310 +        aJ[m] = vbar * gaussStream->getGaussian();
311 +        vbar = sqrt( 2.0 * kebar * I[n][n] );
312 +        aJ[n] = vbar * gaussStream->getGaussian();
313 +        
314 +      } else {
315 +        for (j = 0 ; j < 3; j++) {
316 +          vbar = sqrt( 2.0 * kebar * I[j][j] );
317 +          aJ[j] = vbar * gaussStream->getGaussian();
318 +        }      
319 +      } // else isLinear
320 +
321 +      info->integrableObjects[vr]->setJ( aJ );
322 +      
323 +    }//isDirectional
324 +
325    }
326  
327    // Get the Center of Mass drift velocity.
# Line 277 | Line 331 | void Thermo::velocitize() {
331    //  Corrects for the center of mass drift.
332    // sums all the momentum and divides by total mass.
333  
334 <  for(vd = 0; vd < n_atoms; vd++){
334 >  for(vd = 0; vd < nobj; vd++){
335      
336 <    atoms[vd]->getVel(aVel);
336 >    info->integrableObjects[vd]->getVel(aVel);
337      
338      for (j=0; j < 3; j++)
339        aVel[j] -= vdrift[j];
340          
341 <    atoms[vd]->setVel( aVel );
341 >    info->integrableObjects[vd]->setVel( aVel );
342    }
289 –  if( n_oriented ){
290 –  
291 –    for( i=0; i<n_atoms; i++ ){
292 –      
293 –      if( atoms[i]->isDirectional() ){
294 –        
295 –        dAtom = (DirectionalAtom *)atoms[i];
296 –        dAtom->getI( I );
297 –        
298 –        for (j = 0 ; j < 3; j++) {
343  
300 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
301 –          aJ[j] = vbar * gaussStream->getGaussian();
302 –
303 –        }      
304 –
305 –        dAtom->setJ( aJ );
306 –
307 –      }
308 –    }  
309 –  }
344   }
345  
346   void Thermo::getCOMVel(double vdrift[3]){
# Line 314 | Line 348 | void Thermo::getCOMVel(double vdrift[3]){
348    double mtot, mtot_local;
349    double aVel[3], amass;
350    double vdrift_local[3];
351 <  int vd, n_atoms, j;
352 <  Atom** atoms;
351 >  int vd, j;
352 >  int nobj;
353  
354 <  // We are very careless here with the distinction between n_atoms and n_local
321 <  // We should really fix this before someone pokes an eye out.
354 >  nobj   = info->integrableObjects.size();
355  
323 –  n_atoms = info->n_atoms;  
324 –  atoms   = info->atoms;
325 –
356    mtot_local = 0.0;
357    vdrift_local[0] = 0.0;
358    vdrift_local[1] = 0.0;
359    vdrift_local[2] = 0.0;
360    
361 <  for(vd = 0; vd < n_atoms; vd++){
361 >  for(vd = 0; vd < nobj; vd++){
362      
363 <    amass = atoms[vd]->getMass();
364 <    atoms[vd]->getVel( aVel );
363 >    amass = info->integrableObjects[vd]->getMass();
364 >    info->integrableObjects[vd]->getVel( aVel );
365  
366      for(j = 0; j < 3; j++)
367        vdrift_local[j] += aVel[j] * amass;
# Line 355 | Line 385 | void Thermo::getCOMVel(double vdrift[3]){
385    
386   }
387  
388 + void Thermo::getCOM(double COM[3]){
389 +
390 +  double mtot, mtot_local;
391 +  double aPos[3], amass;
392 +  double COM_local[3];
393 +  int i, j;
394 +  int nobj;
395 +
396 +  mtot_local = 0.0;
397 +  COM_local[0] = 0.0;
398 +  COM_local[1] = 0.0;
399 +  COM_local[2] = 0.0;
400 +
401 +  nobj = info->integrableObjects.size();
402 +  for(i = 0; i < nobj; i++){
403 +    
404 +    amass = info->integrableObjects[i]->getMass();
405 +    info->integrableObjects[i]->getPos( aPos );
406 +
407 +    for(j = 0; j < 3; j++)
408 +      COM_local[j] += aPos[j] * amass;
409 +    
410 +    mtot_local += amass;
411 +  }
412 +
413 + #ifdef IS_MPI
414 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
415 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
416 + #else
417 +  mtot = mtot_local;
418 +  for(i = 0; i < 3; i++) {
419 +    COM[i] = COM_local[i];
420 +  }
421 + #endif
422 +    
423 +  for (i = 0; i < 3; i++) {
424 +    COM[i] = COM[i] / mtot;
425 +  }
426 + }
427 +
428 + void Thermo::removeCOMdrift() {
429 +  double vdrift[3], aVel[3];
430 +  int vd, j, nobj;
431 +
432 +  nobj = info->integrableObjects.size();
433 +
434 +  // Get the Center of Mass drift velocity.
435 +
436 +  getCOMVel(vdrift);
437 +  
438 +  //  Corrects for the center of mass drift.
439 +  // sums all the momentum and divides by total mass.
440 +
441 +  for(vd = 0; vd < nobj; vd++){
442 +    
443 +    info->integrableObjects[vd]->getVel(aVel);
444 +    
445 +    for (j=0; j < 3; j++)
446 +      aVel[j] -= vdrift[j];
447 +        
448 +    info->integrableObjects[vd]->setVel( aVel );
449 +  }
450 + }

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