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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Thermo.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Thermo.cpp (file contents), 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  
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 + #include "MatVec3.h"
14  
15 < #define BASE_SEED 123456789
15 > #ifdef IS_MPI
16 > #define __C
17 > #include "mpiSimulation.hpp"
18 > #endif // is_mpi
19  
20 < Thermo::Thermo( SimInfo* the_entry_plug ) {
21 <  entry_plug = the_entry_plug;
22 <  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 27 | 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  
35 –  DirectionalAtom *dAtom;
36 –
37 –  int n_atoms;
39    double kinetic_global;
40 <  Atom** atoms;
40 <
40 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
41    
42 –  n_atoms = entry_plug->n_atoms;
43 –  atoms = entry_plug->atoms;
44 –
42    kinetic = 0.0;
43    kinetic_global = 0.0;
47 –  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::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
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 77 | Line 78 | double Thermo::getPotential(){
78  
79   double Thermo::getPotential(){
80    
81 +  double potential_local;
82    double potential;
81 –  double potential_global;
83    int el, nSRI;
84 <  SRI** sris;
84 >  Molecule* molecules;
85  
86 <  sris = entry_plug->sr_interactions;
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_global = 0.0;
90 <  potential += entry_plug->lrPot;
91 >  potential_local += info->lrPot;
92  
93 <  for( el=0; el<nSRI; el++ ){
94 <    
94 <    potential += sris[el]->get_potential();
93 >  for( el=0; el<info->n_mol; el++ ){    
94 >    potential_local += molecules[el].getPotential();
95    }
96  
97    // Get total potential for entire system from MPI.
98   #ifdef IS_MPI
99 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
100 <  potential = potential_global;
101 <
99 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
100 >                MPI_SUM, MPI_COMM_WORLD);
101 > #else
102 >  potential = potential_local;
103   #endif // is_mpi
104  
105    return potential;
# Line 114 | 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;
119 –  
120 –  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 –    - entry_plug->n_constraints - 3;
120  
121 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
121 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
122    return temperature;
123   }
124  
125 < double Thermo::getPressure(){
125 > double Thermo::getVolume() {
126  
127 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
128 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
131 < //  const double conv_A_m = 1.0E-10; //convert A -> m
127 >  return info->boxVol;
128 > }
129  
130 <  return 0.0;
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);
139 >
140 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
141 >
142 >  return pressure;
143   }
144  
145 + double Thermo::getPressureX() {
146 +
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 +  this->getPressureTensor(press);
154 +
155 +  pressureX = p_convert * press[0][0];
156 +
157 +  return pressureX;
158 + }
159 +
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::getPressureZ() {
176 +
177 +  // Relies on the calculation of the full molecular pressure tensor
178 +  
179 +  const double p_convert = 1.63882576e8;
180 +  double press[3][3];
181 +  double pressureZ;
182 +
183 +  this->getPressureTensor(press);
184 +
185 +  pressureZ = p_convert * press[2][2];
186 +
187 +  return pressureZ;
188 + }
189 +
190 +
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
195 +
196 +  const double e_convert = 4.184e-4;
197 +
198 +  double molmass, volume;
199 +  double vcom[3], pcom[3], fcom[3], scaled[3];
200 +  double p_local[9], p_global[9];
201 +  int i, j, k, nMols;
202 +  Molecule* molecules;
203 +
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++) {    
210 +    p_local[i] = 0.0;
211 +    p_global[i] = 0.0;
212 +  }
213 +
214 +  for (i=0; i < info->integrableObjects.size(); i++) {
215 +
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.
244 +
245 + #ifdef IS_MPI
246 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
247 + #else
248 +  for (i=0; i<9; i++) {
249 +    p_global[i] = p_local[i];
250 +  }
251 + #endif // is_mpi
252 +
253 +  volume = this->getVolume();
254 +
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;
140 <  double jx, jy, jz;
141 <  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];
143 –  double mtot = 0.0;
269    double vbar;
270    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
271    double av2;
272    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
150 –  int n_atoms;
151 –  Atom** atoms;
152 –  DirectionalAtom* dAtom;
273    double temperature;
274 <  int n_oriented;
155 <  int n_constraints;
274 >  int nobj;
275  
276 <  atoms         = entry_plug->atoms;
158 <  n_atoms       = entry_plug->n_atoms;
159 <  temperature   = entry_plug->target_temp;
160 <  n_oriented    = entry_plug->n_oriented;
161 <  n_constraints = entry_plug->n_constraints;
276 >  nobj = info->integrableObjects.size();
277    
278 <
164 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)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  
175 – //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
176 –    
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.
328 +
329 +  getCOMVel(vdrift);
330    
331    //  Corrects for the center of mass drift.
332    // sums all the momentum and divides by total mass.
333 <  
334 <  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++){
333 >
334 >  for(vd = 0; vd < nobj; vd++){
335      
336 <    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();
336 >    info->integrableObjects[vd]->getVel(aVel);
337      
338 <    mtot += atoms[vd]->getMass();
338 >    for (j=0; j < 3; j++)
339 >      aVel[j] -= vdrift[j];
340 >        
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, j;
352 +  int nobj;
353 +
354 +  nobj   = info->integrableObjects.size();
355 +
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 < nobj; vd++){
362 +    
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 += amass;
370 +  }
371 +
372 + #ifdef IS_MPI
373 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
374 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
375 + #else
376 +  mtot = mtot_local;
377 +  for(vd = 0; vd < 3; vd++) {
378 +    vdrift[vd] = vdrift_local[vd];
379 +  }
380 + #endif
381 +    
382    for (vd = 0; vd < 3; vd++) {
383      vdrift[vd] = vdrift[vd] / mtot;
384    }
385    
386 + }
387  
388 <  for(vd = 0; vd < n_atoms; vd++){
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 <    vx = atoms[vd]->get_vx();
405 <    vy = atoms[vd]->get_vy();
406 <    vz = atoms[vd]->get_vz();
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 <    vx -= vdrift[0];
424 <    vy -= vdrift[1];
219 <    vz -= vdrift[2];
220 <    
221 <    atoms[vd]->set_vx(vx);
222 <    atoms[vd]->set_vy(vy);
223 <    atoms[vd]->set_vz(vz);
423 >  for (i = 0; i < 3; i++) {
424 >    COM[i] = COM[i] / mtot;
425    }
426 <  if( n_oriented ){
226 <  
227 <    for( i=0; i<n_atoms; i++ ){
228 <      
229 <      if( atoms[i]->isDirectional() ){
230 <        
231 <        dAtom = (DirectionalAtom *)atoms[i];
426 > }
427  
428 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
429 <        jx = vbar * gaussStream->getGaussian();
428 > void Thermo::removeCOMdrift() {
429 >  double vdrift[3], aVel[3];
430 >  int vd, j, nobj;
431  
432 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
237 <        jy = vbar * gaussStream->getGaussian();
432 >  nobj = info->integrableObjects.size();
433  
434 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
435 <        jz = vbar * gaussStream->getGaussian();
436 <        
437 <        dAtom->setJx( jx );
438 <        dAtom->setJy( jy );
439 <        dAtom->setJz( jz );
440 <      }
441 <    }  
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 < }
450 > }

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