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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 590 by mmeineke, Thu Jul 10 22:15:53 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2   #include <iostream>
3   using namespace std;
4  
# 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::getEnthalpy() {
133 > double Thermo::getVolume() {
134  
135 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
136 <  double u, p, v;
135 >  return info->boxVol;
136 > }
137 >
138 > double Thermo::getPressure() {
139 >
140 >  // Relies on the calculation of the full molecular pressure tensor
141 >  
142 >  const double p_convert = 1.63882576e8;
143    double press[3][3];
144 +  double pressure;
145  
146 <  u = this->getTotalE();
146 >  this->getPressureTensor(press);
147  
148 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
149 +
150 +  return pressure;
151 + }
152 +
153 + double Thermo::getPressureX() {
154 +
155 +  // Relies on the calculation of the full molecular pressure tensor
156 +  
157 +  const double p_convert = 1.63882576e8;
158 +  double press[3][3];
159 +  double pressureX;
160 +
161    this->getPressureTensor(press);
146 –  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
162  
163 <  v = this->getVolume();
163 >  pressureX = p_convert * press[0][0];
164  
165 <  return (u + (p*v)/e_convert);
165 >  return pressureX;
166   }
167  
168 < double Thermo::getVolume() {
168 > double Thermo::getPressureY() {
169  
170 <  return entry_plug->boxVol;
170 >  // Relies on the calculation of the full molecular pressure tensor
171 >  
172 >  const double p_convert = 1.63882576e8;
173 >  double press[3][3];
174 >  double pressureY;
175 >
176 >  this->getPressureTensor(press);
177 >
178 >  pressureY = p_convert * press[1][1];
179 >
180 >  return pressureY;
181   }
182  
183 < double Thermo::getPressure() {
183 > double Thermo::getPressureZ() {
184  
185    // Relies on the calculation of the full molecular pressure tensor
186    
187    const double p_convert = 1.63882576e8;
188    double press[3][3];
189 <  double pressure;
189 >  double pressureZ;
190  
191    this->getPressureTensor(press);
192  
193 <  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
193 >  pressureZ = p_convert * press[2][2];
194  
195 <  return pressure;
195 >  return pressureZ;
196   }
197  
198  
# Line 181 | Line 206 | void Thermo::getPressureTensor(double press[3][3]){
206    double molmass, volume;
207    double vcom[3];
208    double p_local[9], p_global[9];
209 <  int i, j, k, l, nMols;
209 >  int i, j, k, nMols;
210    Molecule* molecules;
211  
212 <  nMols = entry_plug->n_mol;
213 <  molecules = entry_plug->molecules;
214 <  //tau = entry_plug->tau;
212 >  nMols = info->n_mol;
213 >  molecules = info->molecules;
214 >  //tau = info->tau;
215  
216    // use velocities of molecular centers of mass and molecular masses:
217    for (i=0; i < 9; i++) {    
# Line 218 | Line 243 | void Thermo::getPressureTensor(double press[3][3]){
243    }
244   #endif // is_mpi
245  
246 <  volume = entry_plug->boxVol;
246 >  volume = this->getVolume();
247  
248    for(i = 0; i < 3; i++) {
249      for (j = 0; j < 3; j++) {
250        k = 3*i + j;
251 <      l = 3*j + i;
252 <      press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume;
251 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
252 >
253      }
254    }
255   }
256  
257   void Thermo::velocitize() {
258    
259 <  double x,y;
260 <  double vx, vy, vz;
236 <  double jx, jy, jz;
237 <  int i, vr, vd; // velocity randomizer loop counters
259 >  double aVel[3], aJ[3], I[3][3];
260 >  int i, j, vr, vd; // velocity randomizer loop counters
261    double vdrift[3];
262    double vbar;
263    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
# Line 247 | Line 270 | void Thermo::velocitize() {
270    int n_oriented;
271    int n_constraints;
272  
273 <  atoms         = entry_plug->atoms;
274 <  n_atoms       = entry_plug->n_atoms;
275 <  temperature   = entry_plug->target_temp;
276 <  n_oriented    = entry_plug->n_oriented;
277 <  n_constraints = entry_plug->n_constraints;
273 >  atoms         = info->atoms;
274 >  n_atoms       = info->n_atoms;
275 >  temperature   = info->target_temp;
276 >  n_oriented    = info->n_oriented;
277 >  n_constraints = info->n_constraints;
278    
279 <  kebar = kb * temperature * (double)entry_plug->ndf /
280 <    ( 2.0 * (double)entry_plug->ndfRaw );
279 >  kebar = kb * temperature * (double)info->ndfRaw /
280 >    ( 2.0 * (double)info->ndf );
281    
282    for(vr = 0; vr < n_atoms; vr++){
283      
# Line 268 | Line 291 | void Thermo::velocitize() {
291      // picks random velocities from a gaussian distribution
292      // centered on vbar
293  
294 <    vx = vbar * gaussStream->getGaussian();
295 <    vy = vbar * gaussStream->getGaussian();
296 <    vz = vbar * gaussStream->getGaussian();
294 >    for (j=0; j<3; j++)
295 >      aVel[j] = vbar * gaussStream->getGaussian();
296 >    
297 >    atoms[vr]->setVel( aVel );
298  
275 –    atoms[vr]->set_vx( vx );
276 –    atoms[vr]->set_vy( vy );
277 –    atoms[vr]->set_vz( vz );
299    }
300  
301    // Get the Center of Mass drift velocity.
# Line 286 | Line 307 | void Thermo::velocitize() {
307  
308    for(vd = 0; vd < n_atoms; vd++){
309      
310 <    vx = atoms[vd]->get_vx();
290 <    vy = atoms[vd]->get_vy();
291 <    vz = atoms[vd]->get_vz();
292 <        
293 <    vx -= vdrift[0];
294 <    vy -= vdrift[1];
295 <    vz -= vdrift[2];
310 >    atoms[vd]->getVel(aVel);
311      
312 <    atoms[vd]->set_vx(vx);
313 <    atoms[vd]->set_vy(vy);
314 <    atoms[vd]->set_vz(vz);
312 >    for (j=0; j < 3; j++)
313 >      aVel[j] -= vdrift[j];
314 >        
315 >    atoms[vd]->setVel( aVel );
316    }
317    if( n_oriented ){
318    
# Line 305 | Line 321 | void Thermo::velocitize() {
321        if( atoms[i]->isDirectional() ){
322          
323          dAtom = (DirectionalAtom *)atoms[i];
324 +        dAtom->getI( I );
325 +        
326 +        for (j = 0 ; j < 3; j++) {
327  
328 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
329 <        jx = vbar * gaussStream->getGaussian();
328 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
329 >          aJ[j] = vbar * gaussStream->getGaussian();
330  
331 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
332 <        jy = vbar * gaussStream->getGaussian();
333 <        
334 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
316 <        jz = vbar * gaussStream->getGaussian();
317 <        
318 <        dAtom->setJx( jx );
319 <        dAtom->setJy( jy );
320 <        dAtom->setJz( jz );
331 >        }      
332 >
333 >        dAtom->setJ( aJ );
334 >
335        }
336      }  
337    }
# Line 326 | Line 340 | void Thermo::getCOMVel(double vdrift[3]){
340   void Thermo::getCOMVel(double vdrift[3]){
341  
342    double mtot, mtot_local;
343 +  double aVel[3], amass;
344    double vdrift_local[3];
345 <  int vd, n_atoms;
345 >  int vd, n_atoms, j;
346    Atom** atoms;
347  
348    // We are very careless here with the distinction between n_atoms and n_local
349    // We should really fix this before someone pokes an eye out.
350  
351 <  n_atoms = entry_plug->n_atoms;  
352 <  atoms   = entry_plug->atoms;
351 >  n_atoms = info->n_atoms;  
352 >  atoms   = info->atoms;
353  
354    mtot_local = 0.0;
355    vdrift_local[0] = 0.0;
# Line 343 | Line 358 | void Thermo::getCOMVel(double vdrift[3]){
358    
359    for(vd = 0; vd < n_atoms; vd++){
360      
361 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
362 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
363 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
361 >    amass = atoms[vd]->getMass();
362 >    atoms[vd]->getVel( aVel );
363 >
364 >    for(j = 0; j < 3; j++)
365 >      vdrift_local[j] += aVel[j] * amass;
366      
367 <    mtot_local += atoms[vd]->getMass();
367 >    mtot_local += amass;
368    }
369  
370   #ifdef IS_MPI
# Line 366 | Line 383 | void Thermo::getCOMVel(double vdrift[3]){
383    
384   }
385  
386 + void Thermo::getCOM(double COM[3]){
387 +
388 +  double mtot, mtot_local;
389 +  double aPos[3], amass;
390 +  double COM_local[3];
391 +  int i, n_atoms, j;
392 +  Atom** atoms;
393 +
394 +  // We are very careless here with the distinction between n_atoms and n_local
395 +  // We should really fix this before someone pokes an eye out.
396 +
397 +  n_atoms = info->n_atoms;  
398 +  atoms   = info->atoms;
399 +
400 +  mtot_local = 0.0;
401 +  COM_local[0] = 0.0;
402 +  COM_local[1] = 0.0;
403 +  COM_local[2] = 0.0;
404 +  
405 +  for(i = 0; i < n_atoms; i++){
406 +    
407 +    amass = atoms[i]->getMass();
408 +    atoms[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 + }

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