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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 4 | Line 4 | using namespace std;
4  
5   #ifdef IS_MPI
6   #include <mpi.h>
7 – #include <mpi++.h>
7   #endif //is_mpi
8  
9   #include "Thermo.hpp"
10   #include "SRI.hpp"
11   #include "Integrator.hpp"
12 + #include "simError.h"
13  
14 < #define BASE_SEED 123456789
14 > #ifdef IS_MPI
15 > #define __C
16 > #include "mpiSimulation.hpp"
17 > #endif // is_mpi
18  
19 < Thermo::Thermo( SimInfo* the_entry_plug ) {
20 <  entry_plug = the_entry_plug;
21 <  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 27 | 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 39 | 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  
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();
52 –
53 –    v_sqr = vx2 + vy2 + vz2;
54 –    kinetic += atoms[kl]->getMass() * v_sqr;
55 –
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();
62 <      jz2 = dAtom->getJz() * dAtom->getJz();
65 >      for (j=0; j<3; j++)
66 >        kinetic += aJ[j]*aJ[j] / I[j][j];
67        
64 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
65 –        + (jz2 / dAtom->getIzz());
68      }
69    }
70   #ifdef IS_MPI
71 <  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
71 >  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
72 >                MPI_SUM, MPI_COMM_WORLD);
73    kinetic = kinetic_global;
74   #endif //is_mpi
75  
# Line 77 | Line 80 | double Thermo::getPotential(){
80  
81   double Thermo::getPotential(){
82    
83 +  double potential_local;
84    double potential;
81 –  double potential_global;
85    int el, nSRI;
86 <  SRI** sris;
86 >  Molecule* molecules;
87  
88 <  sris = entry_plug->sr_interactions;
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_global = 0.0;
90 <  potential += entry_plug->lrPot;
93 >  potential_local += info->lrPot;
94  
95 <  for( el=0; el<nSRI; el++ ){
96 <    
94 <    potential += sris[el]->get_potential();
95 >  for( el=0; el<info->n_mol; el++ ){    
96 >    potential_local += molecules[el].getPotential();
97    }
98  
99    // Get total potential for entire system from MPI.
100   #ifdef IS_MPI
101 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
102 <  potential = potential_global;
103 <
101 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
102 >                MPI_SUM, MPI_COMM_WORLD);
103 > #else
104 >  potential = potential_local;
105   #endif // is_mpi
106  
107 + #ifdef IS_MPI
108 +  /*
109 +  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
110 +  */
111 + #endif
112 +
113    return potential;
114   }
115  
# Line 114 | 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 <  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 <    - entry_plug->n_constraints - 3;
122 <
123 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
129 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130    return temperature;
131   }
132  
133 < double Thermo::getPressure(){
133 > double Thermo::getEnthalpy() {
134  
135 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
136 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
137 < //  const double conv_A_m = 1.0E-10; //convert A -> m
135 >  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
136 >  double u, p, v;
137 >  double press[3][3];
138  
139 <  return 0.0;
139 >  u = this->getTotalE();
140 >
141 >  this->getPressureTensor(press);
142 >  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143 >
144 >  v = this->getVolume();
145 >
146 >  return (u + (p*v)/e_convert);
147   }
148  
149 + double Thermo::getVolume() {
150 +
151 +  return info->boxVol;
152 + }
153 +
154 + double Thermo::getPressure() {
155 +
156 +  // Relies on the calculation of the full molecular pressure tensor
157 +  
158 +  const double p_convert = 1.63882576e8;
159 +  double press[3][3];
160 +  double pressure;
161 +
162 +  this->getPressureTensor(press);
163 +
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 +  // 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
219 +
220 +  const double e_convert = 4.184e-4;
221 +
222 +  double molmass, volume;
223 +  double vcom[3];
224 +  double p_local[9], p_global[9];
225 +  int i, j, k, nMols;
226 +  Molecule* molecules;
227 +
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++) {    
234 +    p_local[i] = 0.0;
235 +    p_global[i] = 0.0;
236 +  }
237 +
238 +  for (i=0; i < nMols; i++) {
239 +    molmass = molecules[i].getCOMvel(vcom);
240 +
241 +    p_local[0] += molmass * (vcom[0] * vcom[0]);
242 +    p_local[1] += molmass * (vcom[0] * vcom[1]);
243 +    p_local[2] += molmass * (vcom[0] * vcom[2]);
244 +    p_local[3] += molmass * (vcom[1] * vcom[0]);
245 +    p_local[4] += molmass * (vcom[1] * vcom[1]);
246 +    p_local[5] += molmass * (vcom[1] * vcom[2]);
247 +    p_local[6] += molmass * (vcom[2] * vcom[0]);
248 +    p_local[7] += molmass * (vcom[2] * vcom[1]);
249 +    p_local[8] += molmass * (vcom[2] * vcom[2]);
250 +  }
251 +
252 +  // Get total for entire system from MPI.
253 +
254 + #ifdef IS_MPI
255 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
256 + #else
257 +  for (i=0; i<9; i++) {
258 +    p_global[i] = p_local[i];
259 +  }
260 + #endif // is_mpi
261 +
262 +  volume = this->getVolume();
263 +
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;
140 <  double jx, jy, jz;
141 <  int i, vr, vd; // velocity randomizer loop counters
275 >  double aVel[3], aJ[3], I[3][3];
276 >  int i, j, vr, vd; // velocity randomizer loop counters
277    double vdrift[3];
143 –  double mtot = 0.0;
278    double vbar;
279    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
280    double av2;
281    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
282    int n_atoms;
283    Atom** atoms;
284    DirectionalAtom* dAtom;
# Line 154 | Line 286 | void Thermo::velocitize() {
286    int n_oriented;
287    int n_constraints;
288  
289 <  atoms         = entry_plug->atoms;
290 <  n_atoms       = entry_plug->n_atoms;
291 <  temperature   = entry_plug->target_temp;
292 <  n_oriented    = entry_plug->n_oriented;
293 <  n_constraints = entry_plug->n_constraints;
289 >  atoms         = info->atoms;
290 >  n_atoms       = info->n_atoms;
291 >  temperature   = info->target_temp;
292 >  n_oriented    = info->n_oriented;
293 >  n_constraints = info->n_constraints;
294    
295 <
296 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
295 >  kebar = kb * temperature * (double)info->ndfRaw /
296 >    ( 2.0 * (double)info->ndf );
297    
298    for(vr = 0; vr < n_atoms; vr++){
299      
# Line 171 | Line 301 | void Thermo::velocitize() {
301  
302      av2 = 2.0 * kebar / atoms[vr]->getMass();
303      vbar = sqrt( av2 );
304 <
304 >
305   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
306      
307      // picks random velocities from a gaussian distribution
308      // centered on vbar
309  
310 <    vx = vbar * gaussStream->getGaussian();
311 <    vy = vbar * gaussStream->getGaussian();
312 <    vz = vbar * gaussStream->getGaussian();
310 >    for (j=0; j<3; j++)
311 >      aVel[j] = vbar * gaussStream->getGaussian();
312 >    
313 >    atoms[vr]->setVel( aVel );
314  
184 –    atoms[vr]->set_vx( vx );
185 –    atoms[vr]->set_vy( vy );
186 –    atoms[vr]->set_vz( vz );
315    }
316 +
317 +  // Get the Center of Mass drift velocity.
318 +
319 +  getCOMVel(vdrift);
320    
321    //  Corrects for the center of mass drift.
322    // sums all the momentum and divides by total mass.
191 –  
192 –  mtot = 0.0;
193 –  vdrift[0] = 0.0;
194 –  vdrift[1] = 0.0;
195 –  vdrift[2] = 0.0;
196 –  for(vd = 0; vd < n_atoms; vd++){
197 –    
198 –    vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
199 –    vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
200 –    vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
201 –    
202 –    mtot += atoms[vd]->getMass();
203 –  }
204 –  
205 –  for (vd = 0; vd < 3; vd++) {
206 –    vdrift[vd] = vdrift[vd] / mtot;
207 –  }
208 –  
323  
324    for(vd = 0; vd < n_atoms; vd++){
325      
326 <    vx = atoms[vd]->get_vx();
213 <    vy = atoms[vd]->get_vy();
214 <    vz = atoms[vd]->get_vz();
326 >    atoms[vd]->getVel(aVel);
327      
328 <    
329 <    vx -= vdrift[0];
330 <    vy -= vdrift[1];
331 <    vz -= vdrift[2];
220 <    
221 <    atoms[vd]->set_vx(vx);
222 <    atoms[vd]->set_vy(vy);
223 <    atoms[vd]->set_vz(vz);
328 >    for (j=0; j < 3; j++)
329 >      aVel[j] -= vdrift[j];
330 >        
331 >    atoms[vd]->setVel( aVel );
332    }
333    if( n_oriented ){
334    
# Line 229 | Line 337 | void Thermo::velocitize() {
337        if( atoms[i]->isDirectional() ){
338          
339          dAtom = (DirectionalAtom *)atoms[i];
340 +        dAtom->getI( I );
341 +        
342 +        for (j = 0 ; j < 3; j++) {
343  
344 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
345 <        jx = vbar * gaussStream->getGaussian();
344 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
345 >          aJ[j] = vbar * gaussStream->getGaussian();
346  
347 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
237 <        jy = vbar * gaussStream->getGaussian();
347 >        }      
348  
349 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
350 <        jz = vbar * gaussStream->getGaussian();
241 <        
242 <        dAtom->setJx( jx );
243 <        dAtom->setJy( jy );
244 <        dAtom->setJz( jz );
349 >        dAtom->setJ( aJ );
350 >
351        }
352      }  
353    }
354   }
355 +
356 + void Thermo::getCOMVel(double vdrift[3]){
357 +
358 +  double mtot, mtot_local;
359 +  double aVel[3], amass;
360 +  double vdrift_local[3];
361 +  int vd, n_atoms, j;
362 +  Atom** atoms;
363 +
364 +  // We are very careless here with the distinction between n_atoms and n_local
365 +  // We should really fix this before someone pokes an eye out.
366 +
367 +  n_atoms = info->n_atoms;  
368 +  atoms   = info->atoms;
369 +
370 +  mtot_local = 0.0;
371 +  vdrift_local[0] = 0.0;
372 +  vdrift_local[1] = 0.0;
373 +  vdrift_local[2] = 0.0;
374 +  
375 +  for(vd = 0; vd < n_atoms; vd++){
376 +    
377 +    amass = atoms[vd]->getMass();
378 +    atoms[vd]->getVel( aVel );
379 +
380 +    for(j = 0; j < 3; j++)
381 +      vdrift_local[j] += aVel[j] * amass;
382 +    
383 +    mtot_local += amass;
384 +  }
385 +
386 + #ifdef IS_MPI
387 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
388 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
389 + #else
390 +  mtot = mtot_local;
391 +  for(vd = 0; vd < 3; vd++) {
392 +    vdrift[vd] = vdrift_local[vd];
393 +  }
394 + #endif
395 +    
396 +  for (vd = 0; vd < 3; vd++) {
397 +    vdrift[vd] = vdrift[vd] / mtot;
398 +  }
399 +  
400 + }
401 +
402 + void Thermo::getCOM(double COM[3]){
403 +
404 +  double mtot, mtot_local;
405 +  double aPos[3], amass;
406 +  double COM_local[3];
407 +  int i, n_atoms, j;
408 +  Atom** atoms;
409 +
410 +  // We are very careless here with the distinction between n_atoms and n_local
411 +  // We should really fix this before someone pokes an eye out.
412 +
413 +  n_atoms = info->n_atoms;  
414 +  atoms   = info->atoms;
415 +
416 +  mtot_local = 0.0;
417 +  COM_local[0] = 0.0;
418 +  COM_local[1] = 0.0;
419 +  COM_local[2] = 0.0;
420 +  
421 +  for(i = 0; i < n_atoms; i++){
422 +    
423 +    amass = atoms[i]->getMass();
424 +    atoms[i]->getPos( aPos );
425 +
426 +    for(j = 0; j < 3; j++)
427 +      COM_local[j] += aPos[j] * amass;
428 +    
429 +    mtot_local += amass;
430 +  }
431 +
432 + #ifdef IS_MPI
433 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
434 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
435 + #else
436 +  mtot = mtot_local;
437 +  for(i = 0; i < 3; i++) {
438 +    COM[i] = COM_local[i];
439 +  }
440 + #endif
441 +    
442 +  for (i = 0; i < 3; i++) {
443 +    COM[i] = COM[i] / mtot;
444 +  }
445 + }

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