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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 611 by gezelter, Tue Jul 15 17:10:50 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 < #define BASE_SEED 123456789
25 <
26 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  int baseSeed = BASE_SEED;
24 > Thermo::Thermo( SimInfo* the_info ) {
25 >  info = the_info;
26 >  int baseSeed = the_info->getSeed();
27    
28    gaussStream = new gaussianSPRNG( baseSeed );
29   }
# Line 36 | 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  
41 –  DirectionalAtom *dAtom;
42 –
43 –  int n_atoms;
43    double kinetic_global;
44 <  Atom** atoms;
46 <
44 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
45    
48 –  n_atoms = entry_plug->n_atoms;
49 –  atoms = entry_plug->atoms;
50 –
46    kinetic = 0.0;
47    kinetic_global = 0.0;
53 –  for( kl=0; kl < n_atoms; kl++ ){
54 –    
55 –    atoms[kl]->getVel(aVel);
56 –    amass = atoms[kl]->getMass();
57 –    
58 –    for (j=0; j < 3; j++)
59 –      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 88 | Line 87 | double Thermo::getPotential(){
87    int el, nSRI;
88    Molecule* molecules;
89  
90 <  molecules = entry_plug->molecules;
91 <  nSRI = entry_plug->n_SRI;
90 >  molecules = info->molecules;
91 >  nSRI = info->n_SRI;
92  
93    potential_local = 0.0;
94    potential = 0.0;
95 <  potential_local += entry_plug->lrPot;
95 >  potential_local += info->lrPot;
96  
97 <  for( el=0; el<entry_plug->n_mol; el++ ){    
97 >  for( el=0; el<info->n_mol; el++ ){    
98      potential_local += molecules[el].getPotential();
99    }
100  
# Line 107 | Line 106 | double Thermo::getPotential(){
106    potential = potential_local;
107   #endif // is_mpi
108  
110 – #ifdef IS_MPI
111 –  /*
112 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
113 –  */
114 – #endif
115 –
109    return potential;
110   }
111  
# Line 126 | Line 119 | double Thermo::getTemperature(){
119  
120   double Thermo::getTemperature(){
121  
122 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
122 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123    double temperature;
124 <  
125 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
124 >
125 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126    return temperature;
127   }
128  
129 < double Thermo::getEnthalpy() {
129 > double Thermo::getVolume() {
130  
131 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
132 <  double u, p, v;
131 >  return info->boxVol;
132 > }
133 >
134 > double Thermo::getPressure() {
135 >
136 >  // Relies on the calculation of the full molecular pressure tensor
137 >  
138 >  const double p_convert = 1.63882576e8;
139    double press[3][3];
140 +  double pressure;
141  
142 <  u = this->getTotalE();
142 >  this->getPressureTensor(press);
143  
144 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
145 +
146 +  return pressure;
147 + }
148 +
149 + double Thermo::getPressureX() {
150 +
151 +  // Relies on the calculation of the full molecular pressure tensor
152 +  
153 +  const double p_convert = 1.63882576e8;
154 +  double press[3][3];
155 +  double pressureX;
156 +
157    this->getPressureTensor(press);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
158  
159 <  v = this->getVolume();
159 >  pressureX = p_convert * press[0][0];
160  
161 <  return (u + (p*v)/e_convert);
161 >  return pressureX;
162   }
163  
164 < double Thermo::getVolume() {
164 > double Thermo::getPressureY() {
165  
166 <  return entry_plug->boxVol;
166 >  // Relies on the calculation of the full molecular pressure tensor
167 >  
168 >  const double p_convert = 1.63882576e8;
169 >  double press[3][3];
170 >  double pressureY;
171 >
172 >  this->getPressureTensor(press);
173 >
174 >  pressureY = p_convert * press[1][1];
175 >
176 >  return pressureY;
177   }
178  
179 < double Thermo::getPressure() {
179 > double Thermo::getPressureZ() {
180  
181    // Relies on the calculation of the full molecular pressure tensor
182    
183    const double p_convert = 1.63882576e8;
184    double press[3][3];
185 <  double pressure;
185 >  double pressureZ;
186  
187    this->getPressureTensor(press);
188  
189 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
189 >  pressureZ = p_convert * press[2][2];
190  
191 <  return pressure;
191 >  return pressureZ;
192   }
193  
194  
# Line 180 | 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, l, nMols;
184 <  Molecule* molecules;
205 >  int i, j, k;
206  
186 –  nMols = entry_plug->n_mol;
187 –  molecules = entry_plug->molecules;
188 –  //tau = entry_plug->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++) {
197 <    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 205 | 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 222 | Line 246 | void Thermo::getPressureTensor(double press[3][3]){
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] + entry_plug->tau[k]*e_convert) / volume;
249 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
250      }
251    }
252   }
253  
254   void Thermo::velocitize() {
255    
232 –  double x,y;
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;
240 –  int n_atoms;
241 –  Atom** atoms;
242 –  DirectionalAtom* dAtom;
263    double temperature;
264 <  int n_oriented;
245 <  int n_constraints;
264 >  int nobj;
265  
266 <  atoms         = entry_plug->atoms;
248 <  n_atoms       = entry_plug->n_atoms;
249 <  temperature   = entry_plug->target_temp;
250 <  n_oriented    = entry_plug->n_oriented;
251 <  n_constraints = entry_plug->n_constraints;
266 >  nobj = info->integrableObjects.size();
267    
268 <  kebar = kb * temperature * (double)entry_plug->ndf /
254 <    ( 2.0 * (double)entry_plug->ndfRaw );
268 >  temperature   = info->target_temp;
269    
270 <  for(vr = 0; vr < n_atoms; vr++){
270 >  kebar = kb * temperature * (double)info->ndfRaw /
271 >    ( 2.0 * (double)info->ndf );
272 >  
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 <
263 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
264 <    
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 279 | 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    }
291 –  if( n_oriented ){
292 –  
293 –    for( i=0; i<n_atoms; i++ ){
294 –      
295 –      if( atoms[i]->isDirectional() ){
296 –        
297 –        dAtom = (DirectionalAtom *)atoms[i];
298 –        dAtom->getI( I );
299 –        
300 –        for (j = 0 ; j < 3; j++) {
333  
302 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
303 –          aJ[j] = vbar * gaussStream->getGaussian();
304 –
305 –        }      
306 –
307 –        dAtom->setJ( aJ );
308 –
309 –      }
310 –    }  
311 –  }
334   }
335  
336   void Thermo::getCOMVel(double vdrift[3]){
# Line 316 | 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
323 <  // We should really fix this before someone pokes an eye out.
344 >  nobj   = info->integrableObjects.size();
345  
325 –  n_atoms = entry_plug->n_atoms;  
326 –  atoms   = entry_plug->atoms;
327 –
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 357 | Line 375 | void Thermo::getCOMVel(double vdrift[3]){
375    
376   }
377  
378 + void Thermo::getCOM(double COM[3]){
379 +
380 +  double mtot, mtot_local;
381 +  double aPos[3], amass;
382 +  double COM_local[3];
383 +  int i, j;
384 +  int nobj;
385 +
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 +  nobj = info->integrableObjects.size();
392 +  for(i = 0; i < nobj; i++){
393 +    
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;
399 +    
400 +    mtot_local += amass;
401 +  }
402 +
403 + #ifdef IS_MPI
404 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
405 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
406 + #else
407 +  mtot = mtot_local;
408 +  for(i = 0; i < 3; i++) {
409 +    COM[i] = COM_local[i];
410 +  }
411 + #endif
412 +    
413 +  for (i = 0; i < 3; i++) {
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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