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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 484 by gezelter, Wed Apr 9 13:59:35 2003 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 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  
41 –  DirectionalAtom *dAtom;
42 –
43 –  int n_atoms;
38    double kinetic_global;
39 <  Atom** atoms;
46 <
39 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
40    
48 –  n_atoms = entry_plug->n_atoms;
49 –  atoms = entry_plug->atoms;
50 –
41    kinetic = 0.0;
42    kinetic_global = 0.0;
53 –  for( kl=0; kl < n_atoms; kl++ ){
43  
44 <    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
45 <    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
46 <    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
44 >  for (kl=0; kl<integrableObjects.size(); kl++) {
45 >    integrableObjects[kl]->getVel(aVel);
46 >    amass = integrableObjects[kl]->getMass();
47  
48 <    v_sqr = vx2 + vy2 + vz2;
49 <    kinetic += atoms[kl]->getMass() * v_sqr;
48 >   for(j=0; j<3; j++)
49 >      kinetic += amass*aVel[j]*aVel[j];
50  
51 <    if( atoms[kl]->isDirectional() ){
52 <            
53 <      dAtom = (DirectionalAtom *)atoms[kl];
51 >   if (integrableObjects[kl]->isDirectional()){
52 >
53 >      integrableObjects[kl]->getJ( aJ );
54 >      integrableObjects[kl]->getI( I );
55 >
56 >      for (j=0; j<3; j++)
57 >        kinetic += aJ[j]*aJ[j] / I[j][j];
58        
66 –      jx2 = dAtom->getJx() * dAtom->getJx();    
67 –      jy2 = dAtom->getJy() * dAtom->getJy();
68 –      jz2 = dAtom->getJz() * dAtom->getJz();
69 –      
70 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
71 –        + (jz2 / dAtom->getIzz());
59      }
60    }
61   #ifdef IS_MPI
# Line 89 | Line 76 | double Thermo::getPotential(){
76    int el, nSRI;
77    Molecule* molecules;
78  
79 <  molecules = entry_plug->molecules;
80 <  nSRI = entry_plug->n_SRI;
79 >  molecules = info->molecules;
80 >  nSRI = info->n_SRI;
81  
82    potential_local = 0.0;
83    potential = 0.0;
84 <  potential_local += entry_plug->lrPot;
84 >  potential_local += info->lrPot;
85  
86 <  for( el=0; el<entry_plug->n_mol; el++ ){    
86 >  for( el=0; el<info->n_mol; el++ ){    
87      potential_local += molecules[el].getPotential();
88    }
89  
# Line 108 | Line 95 | double Thermo::getPotential(){
95    potential = potential_local;
96   #endif // is_mpi
97  
111 – #ifdef IS_MPI
112 –  /*
113 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
114 –  */
115 – #endif
116 –
98    return potential;
99   }
100  
# Line 127 | Line 108 | double Thermo::getTemperature(){
108  
109   double Thermo::getTemperature(){
110  
111 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
111 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
112    double temperature;
113 <  
114 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
113 >
114 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
115    return temperature;
116   }
117  
118 < double Thermo::getEnthalpy() {
118 > double Thermo::getVolume() {
119  
120 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
121 <  double u, p, v;
141 <  double press[9];
120 >  return info->boxVol;
121 > }
122  
123 <  u = this->getTotalE();
123 > double Thermo::getPressure() {
124  
125 +  // Relies on the calculation of the full molecular pressure tensor
126 +  
127 +  const double p_convert = 1.63882576e8;
128 +  double press[3][3];
129 +  double pressure;
130 +
131    this->getPressureTensor(press);
146 –  p = (press[0] + press[4] + press[8]) / 3.0;
132  
133 <  v = this->getVolume();
133 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
134  
135 <  return (u + (p*v)/e_convert);
135 >  return pressure;
136   }
137  
138 < double Thermo::getVolume() {
154 <  double theBox[3];
138 > double Thermo::getPressureX() {
139  
140 <  entry_plug->getBox(theBox);
141 <  return (theBox[0] * theBox[1] * theBox[2]);
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 pressureX;
145 >
146 >  this->getPressureTensor(press);
147 >
148 >  pressureX = p_convert * press[0][0];
149 >
150 >  return pressureX;
151   }
152  
153 < double Thermo::getPressure() {
154 <  // returns the pressure in units of atm
153 > double Thermo::getPressureY() {
154 >
155    // Relies on the calculation of the full molecular pressure tensor
156    
157    const double p_convert = 1.63882576e8;
158 <  double press[9];
159 <  double pressure;
158 >  double press[3][3];
159 >  double pressureY;
160  
161    this->getPressureTensor(press);
162  
163 <  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
163 >  pressureY = p_convert * press[1][1];
164  
165 <  return pressure;
165 >  return pressureY;
166   }
167  
168 + double Thermo::getPressureZ() {
169  
170 < void Thermo::getPressureTensor(double press[9]){
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 pressureZ;
175 >
176 >  this->getPressureTensor(press);
177 >
178 >  pressureZ = p_convert * press[2][2];
179 >
180 >  return pressureZ;
181 > }
182 >
183 >
184 > void Thermo::getPressureTensor(double press[3][3]){
185    // returns pressure tensor in units amu*fs^-2*Ang^-1
186    // routine derived via viral theorem description in:
187    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
# Line 183 | Line 191 | void Thermo::getPressureTensor(double press[9]){
191    double molmass, volume;
192    double vcom[3];
193    double p_local[9], p_global[9];
194 <  double theBox[3];
187 <  double* tau;
188 <  int i, nMols;
194 >  int i, j, k, nMols;
195    Molecule* molecules;
196  
197 <  nMols = entry_plug->n_mol;
198 <  molecules = entry_plug->molecules;
199 <  tau = entry_plug->tau;
197 >  nMols = info->n_mol;
198 >  molecules = info->molecules;
199 >  //tau = info->tau;
200  
201    // use velocities of molecular centers of mass and molecular masses:
202    for (i=0; i < 9; i++) {    
# Line 222 | Line 228 | void Thermo::getPressureTensor(double press[9]){
228    }
229   #endif // is_mpi
230  
231 <  entry_plug->getBox(theBox);
231 >  volume = this->getVolume();
232  
233 <  volume = theBox[0] * theBox[1] * theBox[2];
233 >  for(i = 0; i < 3; i++) {
234 >    for (j = 0; j < 3; j++) {
235 >      k = 3*i + j;
236 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
237  
238 <  for(i=0; i<9; i++) {
230 <    press[i] = (p_global[i] - tau[i]*e_convert) / volume;
238 >    }
239    }
240   }
241  
242   void Thermo::velocitize() {
243    
244 <  double x,y;
245 <  double vx, vy, vz;
238 <  double jx, jy, jz;
239 <  int i, vr, vd; // velocity randomizer loop counters
244 >  double aVel[3], aJ[3], I[3][3];
245 >  int i, j, vr, vd; // velocity randomizer loop counters
246    double vdrift[3];
247    double vbar;
248    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
# Line 249 | Line 255 | void Thermo::velocitize() {
255    int n_oriented;
256    int n_constraints;
257  
258 <  atoms         = entry_plug->atoms;
259 <  n_atoms       = entry_plug->n_atoms;
260 <  temperature   = entry_plug->target_temp;
261 <  n_oriented    = entry_plug->n_oriented;
262 <  n_constraints = entry_plug->n_constraints;
258 >  atoms         = info->atoms;
259 >  n_atoms       = info->n_atoms;
260 >  temperature   = info->target_temp;
261 >  n_oriented    = info->n_oriented;
262 >  n_constraints = info->n_constraints;
263    
264 <  kebar = kb * temperature * (double)entry_plug->ndf /
265 <    ( 2.0 * (double)entry_plug->ndfRaw );
264 >  kebar = kb * temperature * (double)info->ndfRaw /
265 >    ( 2.0 * (double)info->ndf );
266    
267    for(vr = 0; vr < n_atoms; vr++){
268      
# Line 264 | Line 270 | void Thermo::velocitize() {
270  
271      av2 = 2.0 * kebar / atoms[vr]->getMass();
272      vbar = sqrt( av2 );
273 <
268 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
269 <    
273 >
274      // picks random velocities from a gaussian distribution
275      // centered on vbar
276  
277 <    vx = vbar * gaussStream->getGaussian();
278 <    vy = vbar * gaussStream->getGaussian();
279 <    vz = vbar * gaussStream->getGaussian();
277 >    for (j=0; j<3; j++)
278 >      aVel[j] = vbar * gaussStream->getGaussian();
279 >    
280 >    atoms[vr]->setVel( aVel );
281  
277 –    atoms[vr]->set_vx( vx );
278 –    atoms[vr]->set_vy( vy );
279 –    atoms[vr]->set_vz( vz );
282    }
283  
284    // Get the Center of Mass drift velocity.
# Line 288 | Line 290 | void Thermo::velocitize() {
290  
291    for(vd = 0; vd < n_atoms; vd++){
292      
293 <    vx = atoms[vd]->get_vx();
292 <    vy = atoms[vd]->get_vy();
293 <    vz = atoms[vd]->get_vz();
294 <        
295 <    vx -= vdrift[0];
296 <    vy -= vdrift[1];
297 <    vz -= vdrift[2];
293 >    atoms[vd]->getVel(aVel);
294      
295 <    atoms[vd]->set_vx(vx);
296 <    atoms[vd]->set_vy(vy);
297 <    atoms[vd]->set_vz(vz);
295 >    for (j=0; j < 3; j++)
296 >      aVel[j] -= vdrift[j];
297 >        
298 >    atoms[vd]->setVel( aVel );
299    }
300    if( n_oriented ){
301    
# Line 307 | Line 304 | void Thermo::velocitize() {
304        if( atoms[i]->isDirectional() ){
305          
306          dAtom = (DirectionalAtom *)atoms[i];
307 +        dAtom->getI( I );
308 +        
309 +        for (j = 0 ; j < 3; j++) {
310  
311 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
312 <        jx = vbar * gaussStream->getGaussian();
311 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
312 >          aJ[j] = vbar * gaussStream->getGaussian();
313  
314 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
315 <        jy = vbar * gaussStream->getGaussian();
316 <        
317 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
318 <        jz = vbar * gaussStream->getGaussian();
319 <        
320 <        dAtom->setJx( jx );
321 <        dAtom->setJy( jy );
322 <        dAtom->setJz( jz );
314 >        }      
315 >
316 >        dAtom->setJ( aJ );
317 >
318        }
319      }  
320    }
# Line 328 | Line 323 | void Thermo::getCOMVel(double vdrift[3]){
323   void Thermo::getCOMVel(double vdrift[3]){
324  
325    double mtot, mtot_local;
326 +  double aVel[3], amass;
327    double vdrift_local[3];
328 <  int vd, n_atoms;
328 >  int vd, n_atoms, j;
329    Atom** atoms;
330  
331    // We are very careless here with the distinction between n_atoms and n_local
332    // We should really fix this before someone pokes an eye out.
333  
334 <  n_atoms = entry_plug->n_atoms;  
335 <  atoms   = entry_plug->atoms;
334 >  n_atoms = info->n_atoms;  
335 >  atoms   = info->atoms;
336  
337    mtot_local = 0.0;
338    vdrift_local[0] = 0.0;
# Line 345 | Line 341 | void Thermo::getCOMVel(double vdrift[3]){
341    
342    for(vd = 0; vd < n_atoms; vd++){
343      
344 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
345 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
346 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
344 >    amass = atoms[vd]->getMass();
345 >    atoms[vd]->getVel( aVel );
346 >
347 >    for(j = 0; j < 3; j++)
348 >      vdrift_local[j] += aVel[j] * amass;
349      
350 <    mtot_local += atoms[vd]->getMass();
350 >    mtot_local += amass;
351    }
352  
353   #ifdef IS_MPI
# Line 368 | Line 366 | void Thermo::getCOMVel(double vdrift[3]){
366    
367   }
368  
369 + void Thermo::getCOM(double COM[3]){
370 +
371 +  double mtot, mtot_local;
372 +  double aPos[3], amass;
373 +  double COM_local[3];
374 +  int i, n_atoms, j;
375 +  Atom** atoms;
376 +
377 +  // We are very careless here with the distinction between n_atoms and n_local
378 +  // We should really fix this before someone pokes an eye out.
379 +
380 +  n_atoms = info->n_atoms;  
381 +  atoms   = info->atoms;
382 +
383 +  mtot_local = 0.0;
384 +  COM_local[0] = 0.0;
385 +  COM_local[1] = 0.0;
386 +  COM_local[2] = 0.0;
387 +  
388 +  for(i = 0; i < n_atoms; i++){
389 +    
390 +    amass = atoms[i]->getMass();
391 +    atoms[i]->getPos( aPos );
392 +
393 +    for(j = 0; j < 3; j++)
394 +      COM_local[j] += aPos[j] * amass;
395 +    
396 +    mtot_local += amass;
397 +  }
398 +
399 + #ifdef IS_MPI
400 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
401 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
402 + #else
403 +  mtot = mtot_local;
404 +  for(i = 0; i < 3; i++) {
405 +    COM[i] = COM_local[i];
406 +  }
407 + #endif
408 +    
409 +  for (i = 0; i < 3; i++) {
410 +    COM[i] = COM[i] / mtot;
411 +  }
412 + }

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