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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 582 by mmeineke, Wed Jul 9 15:33:46 2003 UTC vs.
Revision 763 by tim, Mon Sep 15 16:52:02 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  
# Line 138 | Line 134 | 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[9];
137 >  double press[3][3];
138  
139    u = this->getTotalE();
140  
141    this->getPressureTensor(press);
142 <  p = (press[0] + press[4] + press[8]) / 3.0;
142 >  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143  
144    v = this->getVolume();
145  
# Line 152 | Line 148 | double Thermo::getVolume() {
148  
149   double Thermo::getVolume() {
150  
151 <  return entry_plug->boxVol;
151 >  return info->boxVol;
152   }
153  
154   double Thermo::getPressure() {
# Line 160 | Line 156 | double Thermo::getPressure() {
156    // Relies on the calculation of the full molecular pressure tensor
157    
158    const double p_convert = 1.63882576e8;
159 <  double press[9];
159 >  double press[3][3];
160    double pressure;
161  
162    this->getPressureTensor(press);
163  
164 <  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
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 < void Thermo::getPressureTensor(double press[9]){
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
# Line 181 | Line 222 | void Thermo::getPressureTensor(double press[9]){
222    double molmass, volume;
223    double vcom[3];
224    double p_local[9], p_global[9];
225 <  double theBox[3];
185 <  //double* tau;
186 <  int i, nMols;
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    for (i=0; i < 9; i++) {    
# Line 220 | Line 259 | void Thermo::getPressureTensor(double press[9]){
259    }
260   #endif // is_mpi
261  
262 <  volume = entry_plug->boxVol;
262 >  volume = this->getVolume();
263  
264 <  for(i=0; i<9; i++) {
265 <    press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume;
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 >    }
270    }
271   }
272  
273   void Thermo::velocitize() {
274    
275    double x,y;
276 <  double vx, vy, vz;
277 <  double jx, jy, jz;
235 <  int i, vr, vd; // velocity randomizer loop counters
276 >  double aVel[3], aJ[3], I[3][3];
277 >  int i, j, vr, vd; // velocity randomizer loop counters
278    double vdrift[3];
279    double vbar;
280    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
# Line 245 | Line 287 | void Thermo::velocitize() {
287    int n_oriented;
288    int n_constraints;
289  
290 <  atoms         = entry_plug->atoms;
291 <  n_atoms       = entry_plug->n_atoms;
292 <  temperature   = entry_plug->target_temp;
293 <  n_oriented    = entry_plug->n_oriented;
294 <  n_constraints = entry_plug->n_constraints;
290 >  atoms         = info->atoms;
291 >  n_atoms       = info->n_atoms;
292 >  temperature   = info->target_temp;
293 >  n_oriented    = info->n_oriented;
294 >  n_constraints = info->n_constraints;
295    
296 <  kebar = kb * temperature * (double)entry_plug->ndf /
297 <    ( 2.0 * (double)entry_plug->ndfRaw );
296 >  kebar = kb * temperature * (double)info->ndfRaw /
297 >    ( 2.0 * (double)info->ndf );
298    
299    for(vr = 0; vr < n_atoms; vr++){
300      
# Line 266 | Line 308 | void Thermo::velocitize() {
308      // picks random velocities from a gaussian distribution
309      // centered on vbar
310  
311 <    vx = vbar * gaussStream->getGaussian();
312 <    vy = vbar * gaussStream->getGaussian();
313 <    vz = vbar * gaussStream->getGaussian();
311 >    for (j=0; j<3; j++)
312 >      aVel[j] = vbar * gaussStream->getGaussian();
313 >    
314 >    atoms[vr]->setVel( aVel );
315  
273 –    atoms[vr]->set_vx( vx );
274 –    atoms[vr]->set_vy( vy );
275 –    atoms[vr]->set_vz( vz );
316    }
317  
318    // Get the Center of Mass drift velocity.
# Line 284 | Line 324 | void Thermo::velocitize() {
324  
325    for(vd = 0; vd < n_atoms; vd++){
326      
327 <    vx = atoms[vd]->get_vx();
288 <    vy = atoms[vd]->get_vy();
289 <    vz = atoms[vd]->get_vz();
290 <        
291 <    vx -= vdrift[0];
292 <    vy -= vdrift[1];
293 <    vz -= vdrift[2];
327 >    atoms[vd]->getVel(aVel);
328      
329 <    atoms[vd]->set_vx(vx);
330 <    atoms[vd]->set_vy(vy);
331 <    atoms[vd]->set_vz(vz);
329 >    for (j=0; j < 3; j++)
330 >      aVel[j] -= vdrift[j];
331 >        
332 >    atoms[vd]->setVel( aVel );
333    }
334    if( n_oriented ){
335    
# Line 303 | Line 338 | void Thermo::velocitize() {
338        if( atoms[i]->isDirectional() ){
339          
340          dAtom = (DirectionalAtom *)atoms[i];
341 +        dAtom->getI( I );
342 +        
343 +        for (j = 0 ; j < 3; j++) {
344  
345 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
346 <        jx = vbar * gaussStream->getGaussian();
345 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
346 >          aJ[j] = vbar * gaussStream->getGaussian();
347  
348 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
349 <        jy = vbar * gaussStream->getGaussian();
350 <        
351 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
314 <        jz = vbar * gaussStream->getGaussian();
315 <        
316 <        dAtom->setJx( jx );
317 <        dAtom->setJy( jy );
318 <        dAtom->setJz( jz );
348 >        }      
349 >
350 >        dAtom->setJ( aJ );
351 >
352        }
353      }  
354    }
# Line 324 | Line 357 | void Thermo::getCOMVel(double vdrift[3]){
357   void Thermo::getCOMVel(double vdrift[3]){
358  
359    double mtot, mtot_local;
360 +  double aVel[3], amass;
361    double vdrift_local[3];
362 <  int vd, n_atoms;
362 >  int vd, n_atoms, j;
363    Atom** atoms;
364  
365    // We are very careless here with the distinction between n_atoms and n_local
366    // We should really fix this before someone pokes an eye out.
367  
368 <  n_atoms = entry_plug->n_atoms;  
369 <  atoms   = entry_plug->atoms;
368 >  n_atoms = info->n_atoms;  
369 >  atoms   = info->atoms;
370  
371    mtot_local = 0.0;
372    vdrift_local[0] = 0.0;
# Line 341 | Line 375 | void Thermo::getCOMVel(double vdrift[3]){
375    
376    for(vd = 0; vd < n_atoms; vd++){
377      
378 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
379 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
380 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
378 >    amass = atoms[vd]->getMass();
379 >    atoms[vd]->getVel( aVel );
380 >
381 >    for(j = 0; j < 3; j++)
382 >      vdrift_local[j] += aVel[j] * amass;
383      
384 <    mtot_local += atoms[vd]->getMass();
384 >    mtot_local += amass;
385    }
386  
387   #ifdef IS_MPI
# Line 364 | Line 400 | void Thermo::getCOMVel(double vdrift[3]){
400    
401   }
402  
403 + void Thermo::getCOM(double COM[3]){
404 +
405 +  double mtot, mtot_local;
406 +  double aPos[3], amass;
407 +  double COM_local[3];
408 +  int i, n_atoms, j;
409 +  Atom** atoms;
410 +
411 +  // We are very careless here with the distinction between n_atoms and n_local
412 +  // We should really fix this before someone pokes an eye out.
413 +
414 +  n_atoms = info->n_atoms;  
415 +  atoms   = info->atoms;
416 +
417 +  mtot_local = 0.0;
418 +  COM_local[0] = 0.0;
419 +  COM_local[1] = 0.0;
420 +  COM_local[2] = 0.0;
421 +  
422 +  for(i = 0; i < n_atoms; i++){
423 +    
424 +    amass = atoms[i]->getMass();
425 +    atoms[i]->getPos( aPos );
426 +
427 +    for(j = 0; j < 3; j++)
428 +      COM_local[j] += aPos[j] * amass;
429 +    
430 +    mtot_local += amass;
431 +  }
432 +
433 + #ifdef IS_MPI
434 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
435 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
436 + #else
437 +  mtot = mtot_local;
438 +  for(i = 0; i < 3; i++) {
439 +    COM[i] = COM_local[i];
440 +  }
441 + #endif
442 +    
443 +  for (i = 0; i < 3; i++) {
444 +    COM[i] = COM[i] / mtot;
445 +  }
446 + }

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