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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 574 by gezelter, Tue Jul 8 20:56:10 2003 UTC vs.
Revision 1131 by tim, Thu Apr 22 21:33:55 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 <
21 < #define BASE_SEED 123456789
22 <
22 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  int baseSeed = BASE_SEED;
20 > Thermo::Thermo( SimInfo* the_info ) {
21 >  info = the_info;
22 >  int baseSeed = the_info->getSeed();
23    
24    gaussStream = new gaussianSPRNG( baseSeed );
25   }
# Line 33 | Line 31 | double Thermo::getKinetic(){
31   double Thermo::getKinetic(){
32  
33    const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
34 <  double vx2, vy2, vz2;
35 <  double kinetic, v_sqr;
36 <  int kl;
37 <  double jx2, jy2, jz2; // the square of the angular momentums
34 >  double kinetic;
35 >  double amass;
36 >  double aVel[3], aJ[3], I[3][3];
37 >  int i, j, k, kl;
38  
41 –  DirectionalAtom *dAtom;
42 –
43 –  int n_atoms;
39    double kinetic_global;
40 <  Atom** atoms;
46 <
40 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
41    
48 –  n_atoms = entry_plug->n_atoms;
49 –  atoms = entry_plug->atoms;
50 –
42    kinetic = 0.0;
43    kinetic_global = 0.0;
53 –  for( kl=0; kl < n_atoms; kl++ ){
44  
45 <    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
46 <    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
47 <    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
45 >  for (kl=0; kl<integrableObjects.size(); kl++) {
46 >    integrableObjects[kl]->getVel(aVel);
47 >    amass = integrableObjects[kl]->getMass();
48  
49 <    v_sqr = vx2 + vy2 + vz2;
50 <    kinetic += atoms[kl]->getMass() * v_sqr;
49 >   for(j=0; j<3; j++)
50 >      kinetic += amass*aVel[j]*aVel[j];
51  
52 <    if( atoms[kl]->isDirectional() ){
53 <            
54 <      dAtom = (DirectionalAtom *)atoms[kl];
55 <      
56 <      jx2 = dAtom->getJx() * dAtom->getJx();    
57 <      jy2 = dAtom->getJy() * dAtom->getJy();
58 <      jz2 = dAtom->getJz() * dAtom->getJz();
59 <      
60 <      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
61 <        + (jz2 / dAtom->getIzz());
62 <    }
52 >   if (integrableObjects[kl]->isDirectional()){
53 >
54 >      integrableObjects[kl]->getJ( aJ );
55 >      integrableObjects[kl]->getI( I );
56 >
57 >      if (integrableObjects[kl]->isLinear()) {
58 >        i = integrableObjects[kl]->linearAxis();
59 >        j = (i+1)%3;
60 >        k = (i+2)%3;
61 >        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
62 >      } else {
63 >        for (j=0; j<3; j++)
64 >          kinetic += aJ[j]*aJ[j] / I[j][j];
65 >      }
66 >   }
67    }
68   #ifdef IS_MPI
69    MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
70                  MPI_SUM, MPI_COMM_WORLD);
71    kinetic = kinetic_global;
72   #endif //is_mpi
73 <
73 >  
74    kinetic = kinetic * 0.5 / e_convert;
75  
76    return kinetic;
# Line 89 | Line 83 | double Thermo::getPotential(){
83    int el, nSRI;
84    Molecule* molecules;
85  
86 <  molecules = entry_plug->molecules;
87 <  nSRI = entry_plug->n_SRI;
86 >  molecules = info->molecules;
87 >  nSRI = info->n_SRI;
88  
89    potential_local = 0.0;
90    potential = 0.0;
91 <  potential_local += entry_plug->lrPot;
91 >  potential_local += info->lrPot;
92  
93 <  for( el=0; el<entry_plug->n_mol; el++ ){    
93 >  for( el=0; el<info->n_mol; el++ ){    
94      potential_local += molecules[el].getPotential();
95    }
96  
# Line 108 | Line 102 | double Thermo::getPotential(){
102    potential = potential_local;
103   #endif // is_mpi
104  
111 – #ifdef IS_MPI
112 –  /*
113 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
114 –  */
115 – #endif
116 –
105    return potential;
106   }
107  
# Line 127 | Line 115 | double Thermo::getTemperature(){
115  
116   double Thermo::getTemperature(){
117  
118 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
118 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
119    double temperature;
120 <  
121 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
120 >
121 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
122    return temperature;
123   }
124  
125 < double Thermo::getEnthalpy() {
125 > double Thermo::getVolume() {
126  
127 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
128 <  double u, p, v;
141 <  double press[9];
127 >  return info->boxVol;
128 > }
129  
130 <  u = this->getTotalE();
130 > double Thermo::getPressure() {
131  
132 +  // Relies on the calculation of the full molecular pressure tensor
133 +  
134 +  const double p_convert = 1.63882576e8;
135 +  double press[3][3];
136 +  double pressure;
137 +
138    this->getPressureTensor(press);
146 –  p = (press[0] + press[4] + press[8]) / 3.0;
139  
140 <  v = this->getVolume();
140 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
141  
142 <  return (u + (p*v)/e_convert);
142 >  return pressure;
143   }
144  
145 < double Thermo::getVolume() {
145 > double Thermo::getPressureX() {
146  
147 <  double volume;
148 <  double Hmat[9];
147 >  // Relies on the calculation of the full molecular pressure tensor
148 >  
149 >  const double p_convert = 1.63882576e8;
150 >  double press[3][3];
151 >  double pressureX;
152  
153 <  entry_plug->getBoxM(Hmat);
153 >  this->getPressureTensor(press);
154  
155 <  // volume = h1 (dot) h2 (cross) h3
155 >  pressureX = p_convert * press[0][0];
156  
157 <  volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
158 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
164 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
157 >  return pressureX;
158 > }
159  
160 <  return volume;
160 > double Thermo::getPressureY() {
161 >
162 >  // Relies on the calculation of the full molecular pressure tensor
163 >  
164 >  const double p_convert = 1.63882576e8;
165 >  double press[3][3];
166 >  double pressureY;
167 >
168 >  this->getPressureTensor(press);
169 >
170 >  pressureY = p_convert * press[1][1];
171 >
172 >  return pressureY;
173   }
174  
175 < double Thermo::getPressure() {
175 > double Thermo::getPressureZ() {
176  
177    // Relies on the calculation of the full molecular pressure tensor
178    
179    const double p_convert = 1.63882576e8;
180 <  double press[9];
181 <  double pressure;
180 >  double press[3][3];
181 >  double pressureZ;
182  
183    this->getPressureTensor(press);
184  
185 <  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
185 >  pressureZ = p_convert * press[2][2];
186  
187 <  return pressure;
187 >  return pressureZ;
188   }
189  
190  
191 < void Thermo::getPressureTensor(double press[9]){
191 > void Thermo::getPressureTensor(double press[3][3]){
192    // returns pressure tensor in units amu*fs^-2*Ang^-1
193    // routine derived via viral theorem description in:
194    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
# Line 190 | Line 196 | void Thermo::getPressureTensor(double press[9]){
196    const double e_convert = 4.184e-4;
197  
198    double molmass, volume;
199 <  double vcom[3];
199 >  double vcom[3], pcom[3], fcom[3], scaled[3];
200    double p_local[9], p_global[9];
201 <  double theBox[3];
196 <  //double* tau;
197 <  int i, nMols;
201 >  int i, j, k, nMols;
202    Molecule* molecules;
203  
204 <  nMols = entry_plug->n_mol;
205 <  molecules = entry_plug->molecules;
206 <  //tau = entry_plug->tau;
204 >  nMols = info->n_mol;
205 >  molecules = info->molecules;
206 >  //tau = info->tau;
207  
208    // use velocities of molecular centers of mass and molecular masses:
209    for (i=0; i < 9; i++) {    
# Line 207 | Line 211 | void Thermo::getPressureTensor(double press[9]){
211      p_global[i] = 0.0;
212    }
213  
214 <  for (i=0; i < nMols; i++) {
211 <    molmass = molecules[i].getCOMvel(vcom);
214 >  for (i=0; i < info->integrableObjects.size(); i++) {
215  
216 <    p_local[0] += molmass * (vcom[0] * vcom[0]);
217 <    p_local[1] += molmass * (vcom[0] * vcom[1]);
218 <    p_local[2] += molmass * (vcom[0] * vcom[2]);
219 <    p_local[3] += molmass * (vcom[1] * vcom[0]);
220 <    p_local[4] += molmass * (vcom[1] * vcom[1]);
221 <    p_local[5] += molmass * (vcom[1] * vcom[2]);
222 <    p_local[6] += molmass * (vcom[2] * vcom[0]);
223 <    p_local[7] += molmass * (vcom[2] * vcom[1]);
224 <    p_local[8] += molmass * (vcom[2] * vcom[2]);
216 >    molmass = info->integrableObjects[i]->getMass();
217 >    
218 >    info->integrableObjects[i]->getVel(vcom);
219 >    info->integrableObjects[i]->getPos(pcom);
220 >    info->integrableObjects[i]->getFrc(fcom);
221 >
222 >    matVecMul3(info->HmatInv, pcom, scaled);
223 >  
224 >    for(j=0; j<3; j++)
225 >      scaled[j] -= roundMe(scaled[j]);
226 >
227 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
228 >  
229 >    matVecMul3(info->Hmat, scaled, pcom);
230 >    
231 >    p_local[0] += molmass * (vcom[0] * vcom[0]) + fcom[0]*pcom[0]*eConvert;
232 >    p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert;
233 >    p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert;
234 >    p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert;
235 >    p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert;
236 >    p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert;
237 >    p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert;
238 >    p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert;
239 >    p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert;
240 >    
241    }
242  
243    // Get total for entire system from MPI.
# Line 231 | Line 250 | void Thermo::getPressureTensor(double press[9]){
250    }
251   #endif // is_mpi
252  
253 <  volume = entry_plug->boxVol;
253 >  volume = this->getVolume();
254  
255 <  for(i=0; i<9; i++) {
256 <    press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume;
255 >  for(i = 0; i < 3; i++) {
256 >    for (j = 0; j < 3; j++) {
257 >      k = 3*i + j;
258 >      press[i][j] = p_global[k] /  volume;
259 >
260 >    }
261    }
262   }
263  
264   void Thermo::velocitize() {
265    
266 <  double x,y;
267 <  double vx, vy, vz;
245 <  double jx, jy, jz;
246 <  int i, vr, vd; // velocity randomizer loop counters
266 >  double aVel[3], aJ[3], I[3][3];
267 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
268    double vdrift[3];
269    double vbar;
270    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
271    double av2;
272    double kebar;
252 –  int n_atoms;
253 –  Atom** atoms;
254 –  DirectionalAtom* dAtom;
273    double temperature;
274 <  int n_oriented;
257 <  int n_constraints;
274 >  int nobj;
275  
276 <  atoms         = entry_plug->atoms;
260 <  n_atoms       = entry_plug->n_atoms;
261 <  temperature   = entry_plug->target_temp;
262 <  n_oriented    = entry_plug->n_oriented;
263 <  n_constraints = entry_plug->n_constraints;
276 >  nobj = info->integrableObjects.size();
277    
278 <  kebar = kb * temperature * (double)entry_plug->ndf /
266 <    ( 2.0 * (double)entry_plug->ndfRaw );
278 >  temperature   = info->target_temp;
279    
280 <  for(vr = 0; vr < n_atoms; vr++){
280 >  kebar = kb * temperature * (double)info->ndfRaw /
281 >    ( 2.0 * (double)info->ndf );
282 >  
283 >  for(vr = 0; vr < nobj; vr++){
284      
285      // uses equipartition theory to solve for vbar in angstrom/fs
286  
287 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
287 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
288      vbar = sqrt( av2 );
289 <
275 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
276 <    
289 >
290      // picks random velocities from a gaussian distribution
291      // centered on vbar
292  
293 <    vx = vbar * gaussStream->getGaussian();
294 <    vy = vbar * gaussStream->getGaussian();
295 <    vz = vbar * gaussStream->getGaussian();
293 >    for (j=0; j<3; j++)
294 >      aVel[j] = vbar * gaussStream->getGaussian();
295 >    
296 >    info->integrableObjects[vr]->setVel( aVel );
297 >    
298 >    if(info->integrableObjects[vr]->isDirectional()){
299  
300 <    atoms[vr]->set_vx( vx );
301 <    atoms[vr]->set_vy( vy );
302 <    atoms[vr]->set_vz( vz );
300 >      info->integrableObjects[vr]->getI( I );
301 >
302 >      if (info->integrableObjects[vr]->isLinear()) {
303 >
304 >        l= info->integrableObjects[vr]->linearAxis();
305 >        m = (l+1)%3;
306 >        n = (l+2)%3;
307 >
308 >        aJ[l] = 0.0;
309 >        vbar = sqrt( 2.0 * kebar * I[m][m] );
310 >        aJ[m] = vbar * gaussStream->getGaussian();
311 >        vbar = sqrt( 2.0 * kebar * I[n][n] );
312 >        aJ[n] = vbar * gaussStream->getGaussian();
313 >        
314 >      } else {
315 >        for (j = 0 ; j < 3; j++) {
316 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
317 >          aJ[j] = vbar * gaussStream->getGaussian();
318 >        }      
319 >      } // else isLinear
320 >
321 >      info->integrableObjects[vr]->setJ( aJ );
322 >      
323 >    }//isDirectional
324 >
325    }
326  
327    // Get the Center of Mass drift velocity.
# Line 293 | Line 331 | void Thermo::velocitize() {
331    //  Corrects for the center of mass drift.
332    // sums all the momentum and divides by total mass.
333  
334 <  for(vd = 0; vd < n_atoms; vd++){
334 >  for(vd = 0; vd < nobj; vd++){
335      
336 <    vx = atoms[vd]->get_vx();
299 <    vy = atoms[vd]->get_vy();
300 <    vz = atoms[vd]->get_vz();
301 <        
302 <    vx -= vdrift[0];
303 <    vy -= vdrift[1];
304 <    vz -= vdrift[2];
336 >    info->integrableObjects[vd]->getVel(aVel);
337      
338 <    atoms[vd]->set_vx(vx);
339 <    atoms[vd]->set_vy(vy);
308 <    atoms[vd]->set_vz(vz);
309 <  }
310 <  if( n_oriented ){
311 <  
312 <    for( i=0; i<n_atoms; i++ ){
313 <      
314 <      if( atoms[i]->isDirectional() ){
315 <        
316 <        dAtom = (DirectionalAtom *)atoms[i];
317 <
318 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
319 <        jx = vbar * gaussStream->getGaussian();
320 <
321 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
322 <        jy = vbar * gaussStream->getGaussian();
338 >    for (j=0; j < 3; j++)
339 >      aVel[j] -= vdrift[j];
340          
341 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
325 <        jz = vbar * gaussStream->getGaussian();
326 <        
327 <        dAtom->setJx( jx );
328 <        dAtom->setJy( jy );
329 <        dAtom->setJz( jz );
330 <      }
331 <    }  
341 >    info->integrableObjects[vd]->setVel( aVel );
342    }
343 +
344   }
345  
346   void Thermo::getCOMVel(double vdrift[3]){
347  
348    double mtot, mtot_local;
349 +  double aVel[3], amass;
350    double vdrift_local[3];
351 <  int vd, n_atoms;
352 <  Atom** atoms;
351 >  int vd, j;
352 >  int nobj;
353  
354 <  // We are very careless here with the distinction between n_atoms and n_local
343 <  // We should really fix this before someone pokes an eye out.
354 >  nobj   = info->integrableObjects.size();
355  
345 –  n_atoms = entry_plug->n_atoms;  
346 –  atoms   = entry_plug->atoms;
347 –
356    mtot_local = 0.0;
357    vdrift_local[0] = 0.0;
358    vdrift_local[1] = 0.0;
359    vdrift_local[2] = 0.0;
360    
361 <  for(vd = 0; vd < n_atoms; vd++){
361 >  for(vd = 0; vd < nobj; vd++){
362      
363 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
364 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
365 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
363 >    amass = info->integrableObjects[vd]->getMass();
364 >    info->integrableObjects[vd]->getVel( aVel );
365 >
366 >    for(j = 0; j < 3; j++)
367 >      vdrift_local[j] += aVel[j] * amass;
368      
369 <    mtot_local += atoms[vd]->getMass();
369 >    mtot_local += amass;
370    }
371  
372   #ifdef IS_MPI
# Line 375 | Line 385 | void Thermo::getCOMVel(double vdrift[3]){
385    
386   }
387  
388 + void Thermo::getCOM(double COM[3]){
389 +
390 +  double mtot, mtot_local;
391 +  double aPos[3], amass;
392 +  double COM_local[3];
393 +  int i, j;
394 +  int nobj;
395 +
396 +  mtot_local = 0.0;
397 +  COM_local[0] = 0.0;
398 +  COM_local[1] = 0.0;
399 +  COM_local[2] = 0.0;
400 +
401 +  nobj = info->integrableObjects.size();
402 +  for(i = 0; i < nobj; i++){
403 +    
404 +    amass = info->integrableObjects[i]->getMass();
405 +    info->integrableObjects[i]->getPos( aPos );
406 +
407 +    for(j = 0; j < 3; j++)
408 +      COM_local[j] += aPos[j] * amass;
409 +    
410 +    mtot_local += amass;
411 +  }
412 +
413 + #ifdef IS_MPI
414 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
415 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
416 + #else
417 +  mtot = mtot_local;
418 +  for(i = 0; i < 3; i++) {
419 +    COM[i] = COM_local[i];
420 +  }
421 + #endif
422 +    
423 +  for (i = 0; i < 3; i++) {
424 +    COM[i] = COM[i] / mtot;
425 +  }
426 + }
427 +
428 + void Thermo::removeCOMdrift() {
429 +  double vdrift[3], aVel[3];
430 +  int vd, j, nobj;
431 +
432 +  nobj = info->integrableObjects.size();
433 +
434 +  // Get the Center of Mass drift velocity.
435 +
436 +  getCOMVel(vdrift);
437 +  
438 +  //  Corrects for the center of mass drift.
439 +  // sums all the momentum and divides by total mass.
440 +
441 +  for(vd = 0; vd < nobj; vd++){
442 +    
443 +    info->integrableObjects[vd]->getVel(aVel);
444 +    
445 +    for (j=0; j < 3; j++)
446 +      aVel[j] -= vdrift[j];
447 +        
448 +    info->integrableObjects[vd]->setVel( aVel );
449 +  }
450 + }

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