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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 479 by chuckv, Tue Apr 8 15:20:44 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 16 | Line 16 | using namespace std;
16   #include "mpiSimulation.hpp"
17   #endif // is_mpi
18  
19 <
20 < #define BASE_SEED 123456789
21 <
22 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  int baseSeed = BASE_SEED;
19 > Thermo::Thermo( SimInfo* the_info ) {
20 >  info = the_info;
21 >  int baseSeed = the_info->getSeed();
22    
23    gaussStream = new gaussianSPRNG( baseSeed );
24   }
# Line 33 | Line 30 | double Thermo::getKinetic(){
30   double Thermo::getKinetic(){
31  
32    const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
33 <  double vx2, vy2, vz2;
34 <  double kinetic, v_sqr;
35 <  int kl;
36 <  double jx2, jy2, jz2; // the square of the angular momentums
33 >  double kinetic;
34 >  double amass;
35 >  double aVel[3], aJ[3], I[3][3];
36 >  int j, kl;
37  
38    DirectionalAtom *dAtom;
39  
# Line 45 | Line 42 | double Thermo::getKinetic(){
42    Atom** atoms;
43  
44    
45 <  n_atoms = entry_plug->n_atoms;
46 <  atoms = entry_plug->atoms;
45 >  n_atoms = info->n_atoms;
46 >  atoms = info->atoms;
47  
48    kinetic = 0.0;
49    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];
57  
55 –    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
56 –    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
57 –    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
58 –
59 –    v_sqr = vx2 + vy2 + vz2;
60 –    kinetic += atoms[kl]->getMass() * v_sqr;
61 –
58      if( atoms[kl]->isDirectional() ){
59              
60        dAtom = (DirectionalAtom *)atoms[kl];
61 +
62 +      dAtom->getJ( aJ );
63 +      dAtom->getI( I );
64        
65 <      jx2 = dAtom->getJx() * dAtom->getJx();    
66 <      jy2 = dAtom->getJy() * dAtom->getJy();
68 <      jz2 = dAtom->getJz() * dAtom->getJz();
65 >      for (j=0; j<3; j++)
66 >        kinetic += aJ[j]*aJ[j] / I[j][j];
67        
70 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
71 –        + (jz2 / dAtom->getIzz());
68      }
69    }
70   #ifdef IS_MPI
# Line 89 | Line 85 | double Thermo::getPotential(){
85    int el, nSRI;
86    Molecule* molecules;
87  
88 <  molecules = entry_plug->molecules;
89 <  nSRI = entry_plug->n_SRI;
88 >  molecules = info->molecules;
89 >  nSRI = info->n_SRI;
90  
91    potential_local = 0.0;
92    potential = 0.0;
93 <  potential_local += entry_plug->lrPot;
93 >  potential_local += info->lrPot;
94  
95 <  for( el=0; el<entry_plug->n_mol; el++ ){    
95 >  for( el=0; el<info->n_mol; el++ ){    
96      potential_local += molecules[el].getPotential();
97    }
98  
# Line 127 | Line 123 | double Thermo::getTemperature(){
123  
124   double Thermo::getTemperature(){
125  
126 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
126 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
127    double temperature;
128    
129 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
129 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130    return temperature;
131   }
132  
133 < double Thermo::getPressure(){
134 <  // returns pressure in units amu*fs^-2*Ang^-1
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 >
149 > double Thermo::getVolume() {
150 >
151 >  return info->boxVol;
152 > }
153 >
154 > double Thermo::getPressure() {
155 >
156 >  // Relies on the calculation of the full molecular pressure tensor
157 >  
158 >  const double p_convert = 1.63882576e8;
159 >  double press[3][3];
160 >  double pressure;
161 >
162 >  this->getPressureTensor(press);
163 >
164 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
165 >
166 >  return pressure;
167 > }
168 >
169 > double Thermo::getPressureX() {
170 >
171 >  // Relies on the calculation of the full molecular pressure tensor
172 >  
173 >  const double p_convert = 1.63882576e8;
174 >  double press[3][3];
175 >  double pressureX;
176 >
177 >  this->getPressureTensor(press);
178 >
179 >  pressureX = p_convert * press[0][0];
180 >
181 >  return pressureX;
182 > }
183 >
184 > double Thermo::getPressureY() {
185 >
186 >  // Relies on the calculation of the full molecular pressure tensor
187 >  
188 >  const double p_convert = 1.63882576e8;
189 >  double press[3][3];
190 >  double pressureY;
191 >
192 >  this->getPressureTensor(press);
193 >
194 >  pressureY = p_convert * press[1][1];
195 >
196 >  return pressureY;
197 > }
198 >
199 > double Thermo::getPressureZ() {
200 >
201 >  // Relies on the calculation of the full molecular pressure tensor
202 >  
203 >  const double p_convert = 1.63882576e8;
204 >  double press[3][3];
205 >  double pressureZ;
206 >
207 >  this->getPressureTensor(press);
208 >
209 >  pressureZ = p_convert * press[2][2];
210 >
211 >  return pressureZ;
212 > }
213 >
214 >
215 > void Thermo::getPressureTensor(double press[3][3]){
216 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
217    // routine derived via viral theorem description in:
218    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
219  
220    const double e_convert = 4.184e-4;
221 <  const double p_convert = 1.63882576e8;
222 <  double molmass;
221 >
222 >  double molmass, volume;
223    double vcom[3];
224 <  double p_local, p_sum, p_mol, virial;
225 <  double theBox[3];
148 <  double* tau;
149 <  int i, nMols;
224 >  double p_local[9], p_global[9];
225 >  int i, j, k, nMols;
226    Molecule* molecules;
227  
228 <  nMols = entry_plug->n_mol;
229 <  molecules = entry_plug->molecules;
230 <  tau = entry_plug->tau;
228 >  nMols = info->n_mol;
229 >  molecules = info->molecules;
230 >  //tau = info->tau;
231  
232    // use velocities of molecular centers of mass and molecular masses:
233 <  p_local = 0.0;
233 >  for (i=0; i < 9; i++) {    
234 >    p_local[i] = 0.0;
235 >    p_global[i] = 0.0;
236 >  }
237  
238    for (i=0; i < nMols; i++) {
239      molmass = molecules[i].getCOMvel(vcom);
240 <    p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass;
240 >
241 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
242 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
243 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
244 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
245 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
246 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
247 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
248 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
249 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
250    }
251  
252    // Get total for entire system from MPI.
253  
254   #ifdef IS_MPI
255 <  MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
255 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
256   #else
257 <  p_sum = p_local;
257 >  for (i=0; i<9; i++) {
258 >    p_global[i] = p_local[i];
259 >  }
260   #endif // is_mpi
261  
262 <  virial = tau[0] + tau[4] + tau[8];
173 <  entry_plug->getBox(theBox);
262 >  volume = this->getVolume();
263  
264 <  p_mol = p_convert * (p_sum - virial*e_convert) /
265 <    (3.0 * theBox[0] * theBox[1]* theBox[2]);
264 >  for(i = 0; i < 3; i++) {
265 >    for (j = 0; j < 3; j++) {
266 >      k = 3*i + j;
267 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
268  
269 <  return p_mol;
269 >    }
270 >  }
271   }
272  
273   void Thermo::velocitize() {
274    
275 <  double x,y;
276 <  double vx, vy, vz;
185 <  double jx, jy, jz;
186 <  int i, vr, vd; // velocity randomizer loop counters
275 >  double aVel[3], aJ[3], I[3][3];
276 >  int i, j, vr, vd; // velocity randomizer loop counters
277    double vdrift[3];
278    double vbar;
279    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
# Line 196 | Line 286 | void Thermo::velocitize() {
286    int n_oriented;
287    int n_constraints;
288  
289 <  atoms         = entry_plug->atoms;
290 <  n_atoms       = entry_plug->n_atoms;
291 <  temperature   = entry_plug->target_temp;
292 <  n_oriented    = entry_plug->n_oriented;
293 <  n_constraints = entry_plug->n_constraints;
289 >  atoms         = info->atoms;
290 >  n_atoms       = info->n_atoms;
291 >  temperature   = info->target_temp;
292 >  n_oriented    = info->n_oriented;
293 >  n_constraints = info->n_constraints;
294    
295 <  kebar = kb * temperature * (double)entry_plug->ndf /
296 <    ( 2.0 * (double)entry_plug->ndfRaw );
295 >  kebar = kb * temperature * (double)info->ndfRaw /
296 >    ( 2.0 * (double)info->ndf );
297    
298    for(vr = 0; vr < n_atoms; vr++){
299      
# Line 217 | Line 307 | void Thermo::velocitize() {
307      // picks random velocities from a gaussian distribution
308      // centered on vbar
309  
310 <    vx = vbar * gaussStream->getGaussian();
311 <    vy = vbar * gaussStream->getGaussian();
312 <    vz = vbar * gaussStream->getGaussian();
310 >    for (j=0; j<3; j++)
311 >      aVel[j] = vbar * gaussStream->getGaussian();
312 >    
313 >    atoms[vr]->setVel( aVel );
314  
224 –    atoms[vr]->set_vx( vx );
225 –    atoms[vr]->set_vy( vy );
226 –    atoms[vr]->set_vz( vz );
315    }
316  
317    // Get the Center of Mass drift velocity.
# Line 235 | Line 323 | void Thermo::velocitize() {
323  
324    for(vd = 0; vd < n_atoms; vd++){
325      
326 <    vx = atoms[vd]->get_vx();
239 <    vy = atoms[vd]->get_vy();
240 <    vz = atoms[vd]->get_vz();
241 <        
242 <    vx -= vdrift[0];
243 <    vy -= vdrift[1];
244 <    vz -= vdrift[2];
326 >    atoms[vd]->getVel(aVel);
327      
328 <    atoms[vd]->set_vx(vx);
329 <    atoms[vd]->set_vy(vy);
330 <    atoms[vd]->set_vz(vz);
328 >    for (j=0; j < 3; j++)
329 >      aVel[j] -= vdrift[j];
330 >        
331 >    atoms[vd]->setVel( aVel );
332    }
333    if( n_oriented ){
334    
# Line 254 | Line 337 | void Thermo::velocitize() {
337        if( atoms[i]->isDirectional() ){
338          
339          dAtom = (DirectionalAtom *)atoms[i];
340 +        dAtom->getI( I );
341 +        
342 +        for (j = 0 ; j < 3; j++) {
343  
344 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
345 <        jx = vbar * gaussStream->getGaussian();
344 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
345 >          aJ[j] = vbar * gaussStream->getGaussian();
346  
347 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
348 <        jy = vbar * gaussStream->getGaussian();
349 <        
350 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
265 <        jz = vbar * gaussStream->getGaussian();
266 <        
267 <        dAtom->setJx( jx );
268 <        dAtom->setJy( jy );
269 <        dAtom->setJz( jz );
347 >        }      
348 >
349 >        dAtom->setJ( aJ );
350 >
351        }
352      }  
353    }
# Line 275 | Line 356 | void Thermo::getCOMVel(double vdrift[3]){
356   void Thermo::getCOMVel(double vdrift[3]){
357  
358    double mtot, mtot_local;
359 +  double aVel[3], amass;
360    double vdrift_local[3];
361 <  int vd, n_atoms;
361 >  int vd, n_atoms, j;
362    Atom** atoms;
363  
364    // 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.
366  
367 <  n_atoms = entry_plug->n_atoms;  
368 <  atoms   = entry_plug->atoms;
367 >  n_atoms = info->n_atoms;  
368 >  atoms   = info->atoms;
369  
370    mtot_local = 0.0;
371    vdrift_local[0] = 0.0;
# Line 292 | Line 374 | void Thermo::getCOMVel(double vdrift[3]){
374    
375    for(vd = 0; vd < n_atoms; vd++){
376      
377 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
378 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
379 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
377 >    amass = atoms[vd]->getMass();
378 >    atoms[vd]->getVel( aVel );
379 >
380 >    for(j = 0; j < 3; j++)
381 >      vdrift_local[j] += aVel[j] * amass;
382      
383 <    mtot_local += atoms[vd]->getMass();
383 >    mtot_local += amass;
384    }
385  
386   #ifdef IS_MPI
# Line 315 | Line 399 | void Thermo::getCOMVel(double vdrift[3]){
399    
400   }
401  
402 + void Thermo::getCOM(double COM[3]){
403 +
404 +  double mtot, mtot_local;
405 +  double aPos[3], amass;
406 +  double COM_local[3];
407 +  int i, n_atoms, j;
408 +  Atom** atoms;
409 +
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 +
416 +  mtot_local = 0.0;
417 +  COM_local[0] = 0.0;
418 +  COM_local[1] = 0.0;
419 +  COM_local[2] = 0.0;
420 +  
421 +  for(i = 0; i < n_atoms; i++){
422 +    
423 +    amass = atoms[i]->getMass();
424 +    atoms[i]->getPos( aPos );
425 +
426 +    for(j = 0; j < 3; j++)
427 +      COM_local[j] += aPos[j] * amass;
428 +    
429 +    mtot_local += amass;
430 +  }
431 +
432 + #ifdef IS_MPI
433 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
434 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
435 + #else
436 +  mtot = mtot_local;
437 +  for(i = 0; i < 3; i++) {
438 +    COM[i] = COM_local[i];
439 +  }
440 + #endif
441 +    
442 +  for (i = 0; i < 3; i++) {
443 +    COM[i] = COM[i] / mtot;
444 +  }
445 + }

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