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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 608 by gezelter, Tue Jul 15 14:45:09 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 < #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;
131 –  
132 –  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
133 –  return temperature;
134 – }
135 –
136 – double Thermo::getEnthalpy() {
137 –
138 –  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
139 –  double u, p, v;
140 –  double press[3][3];
141 –
142 –  u = this->getTotalE();
143 –
144 –  this->getPressureTensor(press);
145 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
124  
125 <  v = this->getVolume();
126 <
149 <  return (u + (p*v)/e_convert);
125 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126 >  return temperature;
127   }
128  
129   double Thermo::getVolume() {
130  
131 <  return entry_plug->boxVol;
131 >  return info->boxVol;
132   }
133  
134   double Thermo::getPressure() {
# Line 169 | Line 146 | double Thermo::getPressure() {
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);
158 +
159 +  pressureX = p_convert * press[0][0];
160 +
161 +  return pressureX;
162 + }
163 +
164 + double Thermo::getPressureY() {
165 +
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::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 pressureZ;
186 +
187 +  this->getPressureTensor(press);
188 +
189 +  pressureZ = p_convert * press[2][2];
190 +
191 +  return pressureZ;
192 + }
193 +
194 +
195   void Thermo::getPressureTensor(double press[3][3]){
196    // returns pressure tensor in units amu*fs^-2*Ang^-1
197    // routine derived via viral theorem description in:
# Line 178 | 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, l, nMols;
205 >  int i, j, k, nMols;
206    Molecule* molecules;
207  
208 <  nMols = entry_plug->n_mol;
209 <  molecules = entry_plug->molecules;
210 <  //tau = entry_plug->tau;
208 >  nMols = info->n_mol;
209 >  molecules = info->molecules;
210 >  //tau = info->tau;
211  
212    // use velocities of molecular centers of mass and molecular masses:
213    for (i=0; i < 9; i++) {    
# Line 193 | Line 215 | void Thermo::getPressureTensor(double press[3][3]){
215      p_global[i] = 0.0;
216    }
217  
218 <  for (i=0; i < nMols; i++) {
197 <    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 205 | 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 217 | Line 254 | void Thermo::getPressureTensor(double press[3][3]){
254    }
255   #endif // is_mpi
256  
257 <  volume = entry_plug->boxVol;
257 >  volume = this->getVolume();
258  
259    for(i = 0; i < 3; i++) {
260      for (j = 0; j < 3; j++) {
261        k = 3*i + j;
262 <      l = 3*j + i;
226 <      press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume;
262 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
263      }
264    }
265   }
266  
267   void Thermo::velocitize() {
268    
233 –  double x,y;
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;
241 –  int n_atoms;
242 –  Atom** atoms;
243 –  DirectionalAtom* dAtom;
276    double temperature;
277 <  int n_oriented;
246 <  int n_constraints;
277 >  int nobj;
278  
279 <  atoms         = entry_plug->atoms;
249 <  n_atoms       = entry_plug->n_atoms;
250 <  temperature   = entry_plug->target_temp;
251 <  n_oriented    = entry_plug->n_oriented;
252 <  n_constraints = entry_plug->n_constraints;
279 >  nobj = info->integrableObjects.size();
280    
281 <  kebar = kb * temperature * (double)entry_plug->ndf /
255 <    ( 2.0 * (double)entry_plug->ndfRaw );
281 >  temperature   = info->target_temp;
282    
283 <  for(vr = 0; vr < n_atoms; vr++){
283 >  kebar = kb * temperature * (double)info->ndfRaw /
284 >    ( 2.0 * (double)info->ndf );
285 >  
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 <
264 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
265 <    
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 280 | 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    }
292 –  if( n_oriented ){
293 –  
294 –    for( i=0; i<n_atoms; i++ ){
295 –      
296 –      if( atoms[i]->isDirectional() ){
297 –        
298 –        dAtom = (DirectionalAtom *)atoms[i];
299 –        dAtom->getI( I );
300 –        
301 –        for (j = 0 ; j < 3; j++) {
346  
303 –          vbar = sqrt( 2.0 * kebar * I[j][j] );
304 –          aJ[j] = vbar * gaussStream->getGaussian();
305 –
306 –        }      
307 –
308 –        dAtom->setJ( aJ );
309 –
310 –      }
311 –    }  
312 –  }
347   }
348  
349   void Thermo::getCOMVel(double vdrift[3]){
# Line 317 | 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
324 <  // We should really fix this before someone pokes an eye out.
357 >  nobj   = info->integrableObjects.size();
358  
326 –  n_atoms = entry_plug->n_atoms;  
327 –  atoms   = entry_plug->atoms;
328 –
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 358 | Line 388 | void Thermo::getCOMVel(double vdrift[3]){
388    
389   }
390  
391 + void Thermo::getCOM(double COM[3]){
392 +
393 +  double mtot, mtot_local;
394 +  double aPos[3], amass;
395 +  double COM_local[3];
396 +  int i, j;
397 +  int nobj;
398 +
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 +  nobj = info->integrableObjects.size();
405 +  for(i = 0; i < nobj; i++){
406 +    
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;
412 +    
413 +    mtot_local += amass;
414 +  }
415 +
416 + #ifdef IS_MPI
417 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
418 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
419 + #else
420 +  mtot = mtot_local;
421 +  for(i = 0; i < 3; i++) {
422 +    COM[i] = COM_local[i];
423 +  }
424 + #endif
425 +    
426 +  for (i = 0; i < 3; i++) {
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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