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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 1192 by gezelter, Mon May 24 21:03:30 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 + inline double roundMe( double x ){
21 +          return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22 + }
23  
24 < #define BASE_SEED 123456789
25 <
26 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  int baseSeed = BASE_SEED;
24 > Thermo::Thermo( SimInfo* the_info ) {
25 >  info = the_info;
26 >  int baseSeed = the_info->getSeed();
27    
28    gaussStream = new gaussianSPRNG( baseSeed );
29   }
# Line 33 | Line 35 | double Thermo::getKinetic(){
35   double Thermo::getKinetic(){
36  
37    const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
38 <  double vx2, vy2, vz2;
39 <  double kinetic, v_sqr;
40 <  int kl;
41 <  double jx2, jy2, jz2; // the square of the angular momentums
38 >  double kinetic;
39 >  double amass;
40 >  double aVel[3], aJ[3], I[3][3];
41 >  int i, j, k, kl;
42  
41 –  DirectionalAtom *dAtom;
42 –
43 –  int n_atoms;
43    double kinetic_global;
44 <  Atom** atoms;
46 <
44 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
45    
48 –  n_atoms = entry_plug->n_atoms;
49 –  atoms = entry_plug->atoms;
50 –
46    kinetic = 0.0;
47    kinetic_global = 0.0;
53 –  for( kl=0; kl < n_atoms; kl++ ){
48  
49 <    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
50 <    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
51 <    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
49 >  for (kl=0; kl<integrableObjects.size(); kl++) {
50 >    integrableObjects[kl]->getVel(aVel);
51 >    amass = integrableObjects[kl]->getMass();
52  
53 <    v_sqr = vx2 + vy2 + vz2;
54 <    kinetic += atoms[kl]->getMass() * v_sqr;
53 >   for(j=0; j<3; j++)
54 >      kinetic += amass*aVel[j]*aVel[j];
55  
56 <    if( atoms[kl]->isDirectional() ){
57 <            
58 <      dAtom = (DirectionalAtom *)atoms[kl];
59 <      
60 <      jx2 = dAtom->getJx() * dAtom->getJx();    
61 <      jy2 = dAtom->getJy() * dAtom->getJy();
62 <      jz2 = dAtom->getJz() * dAtom->getJz();
63 <      
64 <      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
65 <        + (jz2 / dAtom->getIzz());
66 <    }
56 >   if (integrableObjects[kl]->isDirectional()){
57 >
58 >      integrableObjects[kl]->getJ( aJ );
59 >      integrableObjects[kl]->getI( I );
60 >
61 >      if (integrableObjects[kl]->isLinear()) {
62 >        i = integrableObjects[kl]->linearAxis();
63 >        j = (i+1)%3;
64 >        k = (i+2)%3;
65 >        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
66 >      } else {
67 >        for (j=0; j<3; j++)
68 >          kinetic += aJ[j]*aJ[j] / I[j][j];
69 >      }
70 >   }
71    }
72   #ifdef IS_MPI
73    MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74                  MPI_SUM, MPI_COMM_WORLD);
75    kinetic = kinetic_global;
76   #endif //is_mpi
77 <
77 >  
78    kinetic = kinetic * 0.5 / e_convert;
79  
80    return kinetic;
# Line 89 | Line 87 | double Thermo::getPotential(){
87    int el, nSRI;
88    Molecule* molecules;
89  
90 <  molecules = entry_plug->molecules;
91 <  nSRI = entry_plug->n_SRI;
90 >  molecules = info->molecules;
91 >  nSRI = info->n_SRI;
92  
93    potential_local = 0.0;
94    potential = 0.0;
95 <  potential_local += entry_plug->lrPot;
95 >  potential_local += info->lrPot;
96  
97 <  for( el=0; el<entry_plug->n_mol; el++ ){    
97 >  for( el=0; el<info->n_mol; el++ ){    
98      potential_local += molecules[el].getPotential();
99    }
100  
# Line 108 | Line 106 | double Thermo::getPotential(){
106    potential = potential_local;
107   #endif // is_mpi
108  
111 – #ifdef IS_MPI
112 –  /*
113 –  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
114 –  */
115 – #endif
116 –
109    return potential;
110   }
111  
# Line 127 | Line 119 | double Thermo::getTemperature(){
119  
120   double Thermo::getTemperature(){
121  
122 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
122 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123    double temperature;
124 <  
125 <  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
124 >
125 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126    return temperature;
127   }
128  
129 < double Thermo::getEnthalpy() {
129 > double Thermo::getVolume() {
130  
131 <  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
132 <  double u, p, v;
141 <  double press[9];
131 >  return info->boxVol;
132 > }
133  
134 <  u = this->getTotalE();
134 > double Thermo::getPressure() {
135  
136 <  this->getPressureTensor(press);
137 <  p = (press[0] + press[4] + press[8]) / 3.0;
136 >  // Relies on the calculation of the full molecular pressure tensor
137 >  
138 >  const double p_convert = 1.63882576e8;
139 >  double press[3][3];
140 >  double pressure;
141  
142 <  v = this->getVolume();
142 >  this->getPressureTensor(press);
143  
144 <  return (u + (p*v)/e_convert);
144 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
145 >
146 >  return pressure;
147   }
148  
149 < double Thermo::getVolume() {
149 > double Thermo::getPressureX() {
150  
151 <  return entry_plug->boxVol;
151 >  // Relies on the calculation of the full molecular pressure tensor
152 >  
153 >  const double p_convert = 1.63882576e8;
154 >  double press[3][3];
155 >  double pressureX;
156 >
157 >  this->getPressureTensor(press);
158 >
159 >  pressureX = p_convert * press[0][0];
160 >
161 >  return pressureX;
162   }
163  
164 < double Thermo::getPressure() {
164 > double Thermo::getPressureY() {
165  
166    // Relies on the calculation of the full molecular pressure tensor
167    
168    const double p_convert = 1.63882576e8;
169 <  double press[9];
170 <  double pressure;
169 >  double press[3][3];
170 >  double pressureY;
171  
172    this->getPressureTensor(press);
173  
174 <  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
174 >  pressureY = p_convert * press[1][1];
175  
176 <  return pressure;
176 >  return pressureY;
177   }
178  
179 + double Thermo::getPressureZ() {
180  
181 < void Thermo::getPressureTensor(double press[9]){
181 >  // Relies on the calculation of the full molecular pressure tensor
182 >  
183 >  const double p_convert = 1.63882576e8;
184 >  double press[3][3];
185 >  double pressureZ;
186 >
187 >  this->getPressureTensor(press);
188 >
189 >  pressureZ = p_convert * press[2][2];
190 >
191 >  return pressureZ;
192 > }
193 >
194 >
195 > void Thermo::getPressureTensor(double press[3][3]){
196    // returns pressure tensor in units amu*fs^-2*Ang^-1
197    // routine derived via viral theorem description in:
198    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
# Line 179 | Line 200 | void Thermo::getPressureTensor(double press[9]){
200    const double e_convert = 4.184e-4;
201  
202    double molmass, volume;
203 <  double vcom[3];
203 >  double vcom[3], pcom[3], fcom[3], scaled[3];
204    double p_local[9], p_global[9];
205 <  double theBox[3];
185 <  //double* tau;
186 <  int i, nMols;
205 >  int i, j, k, nMols;
206    Molecule* molecules;
207  
208 <  nMols = entry_plug->n_mol;
209 <  molecules = entry_plug->molecules;
210 <  //tau = entry_plug->tau;
208 >  nMols = info->n_mol;
209 >  molecules = info->molecules;
210 >  //tau = info->tau;
211  
212    // use velocities of molecular centers of mass and molecular masses:
213    for (i=0; i < 9; i++) {    
# Line 196 | Line 215 | void Thermo::getPressureTensor(double press[9]){
215      p_global[i] = 0.0;
216    }
217  
218 <  for (i=0; i < nMols; i++) {
200 <    molmass = molecules[i].getCOMvel(vcom);
218 >  for (i=0; i < info->integrableObjects.size(); i++) {
219  
220 +    molmass = info->integrableObjects[i]->getMass();
221 +    
222 +    info->integrableObjects[i]->getVel(vcom);
223 +    info->integrableObjects[i]->getPos(pcom);
224 +    info->integrableObjects[i]->getFrc(fcom);
225 +
226 +    matVecMul3(info->HmatInv, pcom, scaled);
227 +  
228 +    for(j=0; j<3; j++)
229 +      scaled[j] -= roundMe(scaled[j]);
230 +
231 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
232 +  
233 +    matVecMul3(info->Hmat, scaled, pcom);
234 +    
235      p_local[0] += molmass * (vcom[0] * vcom[0]);
236      p_local[1] += molmass * (vcom[0] * vcom[1]);
237      p_local[2] += molmass * (vcom[0] * vcom[2]);
# Line 208 | Line 241 | void Thermo::getPressureTensor(double press[9]){
241      p_local[6] += molmass * (vcom[2] * vcom[0]);
242      p_local[7] += molmass * (vcom[2] * vcom[1]);
243      p_local[8] += molmass * (vcom[2] * vcom[2]);
244 +    
245    }
246  
247    // Get total for entire system from MPI.
# Line 220 | Line 254 | void Thermo::getPressureTensor(double press[9]){
254    }
255   #endif // is_mpi
256  
257 <  volume = entry_plug->boxVol;
257 >  volume = this->getVolume();
258  
259 <  for(i=0; i<9; i++) {
260 <    press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume;
259 >  for(i = 0; i < 3; i++) {
260 >    for (j = 0; j < 3; j++) {
261 >      k = 3*i + j;
262 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
263 >    }
264    }
265   }
266  
267   void Thermo::velocitize() {
268    
269 <  double x,y;
270 <  double vx, vy, vz;
234 <  double jx, jy, jz;
235 <  int i, vr, vd; // velocity randomizer loop counters
269 >  double aVel[3], aJ[3], I[3][3];
270 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
271    double vdrift[3];
272    double vbar;
273    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
274    double av2;
275    double kebar;
241 –  int n_atoms;
242 –  Atom** atoms;
243 –  DirectionalAtom* dAtom;
276    double temperature;
277 <  int n_oriented;
246 <  int n_constraints;
277 >  int nobj;
278  
279 <  atoms         = entry_plug->atoms;
249 <  n_atoms       = entry_plug->n_atoms;
250 <  temperature   = entry_plug->target_temp;
251 <  n_oriented    = entry_plug->n_oriented;
252 <  n_constraints = entry_plug->n_constraints;
279 >  nobj = info->integrableObjects.size();
280    
281 <  kebar = kb * temperature * (double)entry_plug->ndf /
255 <    ( 2.0 * (double)entry_plug->ndfRaw );
281 >  temperature   = info->target_temp;
282    
283 <  for(vr = 0; vr < n_atoms; vr++){
283 >  kebar = kb * temperature * (double)info->ndfRaw /
284 >    ( 2.0 * (double)info->ndf );
285 >  
286 >  for(vr = 0; vr < nobj; vr++){
287      
288      // uses equipartition theory to solve for vbar in angstrom/fs
289  
290 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
290 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
291      vbar = sqrt( av2 );
292 <
264 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
265 <    
292 >
293      // picks random velocities from a gaussian distribution
294      // centered on vbar
295  
296 <    vx = vbar * gaussStream->getGaussian();
297 <    vy = vbar * gaussStream->getGaussian();
298 <    vz = vbar * gaussStream->getGaussian();
296 >    for (j=0; j<3; j++)
297 >      aVel[j] = vbar * gaussStream->getGaussian();
298 >    
299 >    info->integrableObjects[vr]->setVel( aVel );
300 >    
301 >    if(info->integrableObjects[vr]->isDirectional()){
302  
303 <    atoms[vr]->set_vx( vx );
304 <    atoms[vr]->set_vy( vy );
305 <    atoms[vr]->set_vz( vz );
303 >      info->integrableObjects[vr]->getI( I );
304 >
305 >      if (info->integrableObjects[vr]->isLinear()) {
306 >
307 >        l= info->integrableObjects[vr]->linearAxis();
308 >        m = (l+1)%3;
309 >        n = (l+2)%3;
310 >
311 >        aJ[l] = 0.0;
312 >        vbar = sqrt( 2.0 * kebar * I[m][m] );
313 >        aJ[m] = vbar * gaussStream->getGaussian();
314 >        vbar = sqrt( 2.0 * kebar * I[n][n] );
315 >        aJ[n] = vbar * gaussStream->getGaussian();
316 >        
317 >      } else {
318 >        for (j = 0 ; j < 3; j++) {
319 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
320 >          aJ[j] = vbar * gaussStream->getGaussian();
321 >        }      
322 >      } // else isLinear
323 >
324 >      info->integrableObjects[vr]->setJ( aJ );
325 >      
326 >    }//isDirectional
327 >
328    }
329  
330    // Get the Center of Mass drift velocity.
# Line 282 | Line 334 | void Thermo::velocitize() {
334    //  Corrects for the center of mass drift.
335    // sums all the momentum and divides by total mass.
336  
337 <  for(vd = 0; vd < n_atoms; vd++){
337 >  for(vd = 0; vd < nobj; vd++){
338      
339 <    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];
339 >    info->integrableObjects[vd]->getVel(aVel);
340      
341 <    atoms[vd]->set_vx(vx);
342 <    atoms[vd]->set_vy(vy);
297 <    atoms[vd]->set_vz(vz);
298 <  }
299 <  if( n_oriented ){
300 <  
301 <    for( i=0; i<n_atoms; i++ ){
302 <      
303 <      if( atoms[i]->isDirectional() ){
304 <        
305 <        dAtom = (DirectionalAtom *)atoms[i];
306 <
307 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
308 <        jx = vbar * gaussStream->getGaussian();
309 <
310 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
311 <        jy = vbar * gaussStream->getGaussian();
341 >    for (j=0; j < 3; j++)
342 >      aVel[j] -= vdrift[j];
343          
344 <        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 );
319 <      }
320 <    }  
344 >    info->integrableObjects[vd]->setVel( aVel );
345    }
346 +
347   }
348  
349   void Thermo::getCOMVel(double vdrift[3]){
350  
351    double mtot, mtot_local;
352 +  double aVel[3], amass;
353    double vdrift_local[3];
354 <  int vd, n_atoms;
355 <  Atom** atoms;
354 >  int vd, j;
355 >  int nobj;
356  
357 <  // 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.
357 >  nobj   = info->integrableObjects.size();
358  
334 –  n_atoms = entry_plug->n_atoms;  
335 –  atoms   = entry_plug->atoms;
336 –
359    mtot_local = 0.0;
360    vdrift_local[0] = 0.0;
361    vdrift_local[1] = 0.0;
362    vdrift_local[2] = 0.0;
363    
364 <  for(vd = 0; vd < n_atoms; vd++){
364 >  for(vd = 0; vd < nobj; vd++){
365      
366 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
367 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
368 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
366 >    amass = info->integrableObjects[vd]->getMass();
367 >    info->integrableObjects[vd]->getVel( aVel );
368 >
369 >    for(j = 0; j < 3; j++)
370 >      vdrift_local[j] += aVel[j] * amass;
371      
372 <    mtot_local += atoms[vd]->getMass();
372 >    mtot_local += amass;
373    }
374  
375   #ifdef IS_MPI
# Line 364 | Line 388 | void Thermo::getCOMVel(double vdrift[3]){
388    
389   }
390  
391 + void Thermo::getCOM(double COM[3]){
392 +
393 +  double mtot, mtot_local;
394 +  double aPos[3], amass;
395 +  double COM_local[3];
396 +  int i, j;
397 +  int nobj;
398 +
399 +  mtot_local = 0.0;
400 +  COM_local[0] = 0.0;
401 +  COM_local[1] = 0.0;
402 +  COM_local[2] = 0.0;
403 +
404 +  nobj = info->integrableObjects.size();
405 +  for(i = 0; i < nobj; i++){
406 +    
407 +    amass = info->integrableObjects[i]->getMass();
408 +    info->integrableObjects[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 + }
430 +
431 + void Thermo::removeCOMdrift() {
432 +  double vdrift[3], aVel[3];
433 +  int vd, j, nobj;
434 +
435 +  nobj = info->integrableObjects.size();
436 +
437 +  // Get the Center of Mass drift velocity.
438 +
439 +  getCOMVel(vdrift);
440 +  
441 +  //  Corrects for the center of mass drift.
442 +  // sums all the momentum and divides by total mass.
443 +
444 +  for(vd = 0; vd < nobj; vd++){
445 +    
446 +    info->integrableObjects[vd]->getVel(aVel);
447 +    
448 +    for (j=0; j < 3; j++)
449 +      aVel[j] -= vdrift[j];
450 +        
451 +    info->integrableObjects[vd]->setVel( aVel );
452 +  }
453 + }

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