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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 1127 by tim, Tue Apr 20 16:56:40 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  
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 i, j, k, kl;
37  
35 –  DirectionalAtom *dAtom;
36 –
37 –  int n_atoms;
38    double kinetic_global;
39 <  Atom** atoms;
40 <
39 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
40    
42 –  n_atoms = entry_plug->n_atoms;
43 –  atoms = entry_plug->atoms;
44 –
41    kinetic = 0.0;
42    kinetic_global = 0.0;
47 –  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];
54 <      
55 <      jx2 = dAtom->getJx() * dAtom->getJx();    
56 <      jy2 = dAtom->getJy() * dAtom->getJy();
57 <      jz2 = dAtom->getJz() * dAtom->getJz();
58 <      
59 <      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
60 <        + (jz2 / dAtom->getIzz());
61 <    }
51 >   if (integrableObjects[kl]->isDirectional()){
52 >
53 >      integrableObjects[kl]->getJ( aJ );
54 >      integrableObjects[kl]->getI( I );
55 >
56 >      if (integrableObjects[kl]->isLinear()) {
57 >        i = integrableObjects[kl]->linearAxis();
58 >        j = (i+1)%3;
59 >        k = (i+2)%3;
60 >        kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
61 >      } else {
62 >        for (j=0; j<3; j++)
63 >          kinetic += aJ[j]*aJ[j] / I[j][j];
64 >      }
65 >   }
66    }
67   #ifdef IS_MPI
68 <  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
68 >  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
69 >                MPI_SUM, MPI_COMM_WORLD);
70    kinetic = kinetic_global;
71   #endif //is_mpi
72 <
72 >  
73    kinetic = kinetic * 0.5 / e_convert;
74  
75    return kinetic;
# Line 77 | Line 77 | double Thermo::getPotential(){
77  
78   double Thermo::getPotential(){
79    
80 +  double potential_local;
81    double potential;
81 –  double potential_global;
82    int el, nSRI;
83 <  SRI** sris;
83 >  Molecule* molecules;
84  
85 <  sris = entry_plug->sr_interactions;
86 <  nSRI = entry_plug->n_SRI;
85 >  molecules = info->molecules;
86 >  nSRI = info->n_SRI;
87  
88 +  potential_local = 0.0;
89    potential = 0.0;
90 <  potential_global = 0.0;
90 <  potential += entry_plug->lrPot;
90 >  potential_local += info->lrPot;
91  
92 <  for( el=0; el<nSRI; el++ ){
93 <    
94 <    potential += sris[el]->get_potential();
92 >  for( el=0; el<info->n_mol; el++ ){    
93 >    potential_local += molecules[el].getPotential();
94    }
95  
96    // Get total potential for entire system from MPI.
97   #ifdef IS_MPI
98 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
99 <  potential = potential_global;
100 <
98 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
99 >                MPI_SUM, MPI_COMM_WORLD);
100 > #else
101 >  potential = potential_local;
102   #endif // is_mpi
103  
104    return potential;
# Line 114 | Line 114 | double Thermo::getTemperature(){
114  
115   double Thermo::getTemperature(){
116  
117 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
117 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
118    double temperature;
119 –  
120 –  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 –    - entry_plug->n_constraints - 3;
119  
120 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
120 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
121    return temperature;
122   }
123  
124 < double Thermo::getPressure(){
124 > double Thermo::getVolume() {
125  
126 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
127 < // 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
126 >  return info->boxVol;
127 > }
128  
129 <  return 0.0;
129 > double Thermo::getPressure() {
130 >
131 >  // Relies on the calculation of the full molecular pressure tensor
132 >  
133 >  const double p_convert = 1.63882576e8;
134 >  double press[3][3];
135 >  double pressure;
136 >
137 >  this->getPressureTensor(press);
138 >
139 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
140 >
141 >  return pressure;
142   }
143  
144 + double Thermo::getPressureX() {
145 +
146 +  // Relies on the calculation of the full molecular pressure tensor
147 +  
148 +  const double p_convert = 1.63882576e8;
149 +  double press[3][3];
150 +  double pressureX;
151 +
152 +  this->getPressureTensor(press);
153 +
154 +  pressureX = p_convert * press[0][0];
155 +
156 +  return pressureX;
157 + }
158 +
159 + double Thermo::getPressureY() {
160 +
161 +  // Relies on the calculation of the full molecular pressure tensor
162 +  
163 +  const double p_convert = 1.63882576e8;
164 +  double press[3][3];
165 +  double pressureY;
166 +
167 +  this->getPressureTensor(press);
168 +
169 +  pressureY = p_convert * press[1][1];
170 +
171 +  return pressureY;
172 + }
173 +
174 + double Thermo::getPressureZ() {
175 +
176 +  // Relies on the calculation of the full molecular pressure tensor
177 +  
178 +  const double p_convert = 1.63882576e8;
179 +  double press[3][3];
180 +  double pressureZ;
181 +
182 +  this->getPressureTensor(press);
183 +
184 +  pressureZ = p_convert * press[2][2];
185 +
186 +  return pressureZ;
187 + }
188 +
189 +
190 + void Thermo::getPressureTensor(double press[3][3]){
191 +  // returns pressure tensor in units amu*fs^-2*Ang^-1
192 +  // routine derived via viral theorem description in:
193 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
194 +
195 +  const double e_convert = 4.184e-4;
196 +
197 +  double molmass, volume;
198 +  double vcom[3];
199 +  double p_local[9], p_global[9];
200 +  int i, j, k, nMols;
201 +  Molecule* molecules;
202 +
203 +  nMols = info->n_mol;
204 +  molecules = info->molecules;
205 +  //tau = info->tau;
206 +
207 +  // use velocities of molecular centers of mass and molecular masses:
208 +  for (i=0; i < 9; i++) {    
209 +    p_local[i] = 0.0;
210 +    p_global[i] = 0.0;
211 +  }
212 +
213 +  for (i=0; i < nMols; i++) {
214 +    molmass = molecules[i].getCOMvel(vcom);
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]);
225 +  }
226 +
227 +  // Get total for entire system from MPI.
228 +
229 + #ifdef IS_MPI
230 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
231 + #else
232 +  for (i=0; i<9; i++) {
233 +    p_global[i] = p_local[i];
234 +  }
235 + #endif // is_mpi
236 +
237 +  volume = this->getVolume();
238 +
239 +  for(i = 0; i < 3; i++) {
240 +    for (j = 0; j < 3; j++) {
241 +      k = 3*i + j;
242 +      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
243 +
244 +    }
245 +  }
246 + }
247 +
248   void Thermo::velocitize() {
249    
250 <  double x,y;
251 <  double vx, vy, vz;
140 <  double jx, jy, jz;
141 <  int i, vr, vd; // velocity randomizer loop counters
250 >  double aVel[3], aJ[3], I[3][3];
251 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
252    double vdrift[3];
143 –  double mtot = 0.0;
253    double vbar;
254    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
255    double av2;
256    double kebar;
257 <  int ndf; // number of degrees of freedom
258 <  int ndfRaw; // the raw number of degrees of freedom
150 <  int n_atoms;
151 <  Atom** atoms;
152 <  DirectionalAtom* dAtom;
153 <  double temperature;
154 <  int n_oriented;
155 <  int n_constraints;
257 >  double temperature;
258 >  int nobj;
259  
260 <  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;
260 >  nobj = info->integrableObjects.size();
261    
262 <
164 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
262 >  temperature   = info->target_temp;
263    
264 <  for(vr = 0; vr < n_atoms; vr++){
264 >  kebar = kb * temperature * (double)info->ndfRaw /
265 >    ( 2.0 * (double)info->ndf );
266 >  
267 >  for(vr = 0; vr < nobj; vr++){
268      
269      // uses equipartition theory to solve for vbar in angstrom/fs
270  
271 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
271 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
272      vbar = sqrt( av2 );
273  
175 – //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
176 –    
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 >    info->integrableObjects[vr]->setVel( aVel );
281 >    
282 >    if(info->integrableObjects[vr]->isDirectional()){
283  
284 <    atoms[vr]->set_vx( vx );
285 <    atoms[vr]->set_vy( vy );
286 <    atoms[vr]->set_vz( vz );
284 >      info->integrableObjects[vr]->getI( I );
285 >
286 >      if (info->integrableObjects[vr]->isLinear()) {
287 >
288 >        l= info->integrableObjects[vr]->linearAxis();
289 >        m = (l+1)%3;
290 >        n = (l+2)%3;
291 >
292 >        aJ[l] = 0.0;
293 >        vbar = sqrt( 2.0 * kebar * I[m][m] );
294 >        aJ[m] = vbar * gaussStream->getGaussian();
295 >        vbar = sqrt( 2.0 * kebar * I[n][n] );
296 >        aJ[n] = vbar * gaussStream->getGaussian();
297 >        
298 >      } else {
299 >        for (j = 0 ; j < 3; j++) {
300 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
301 >          aJ[j] = vbar * gaussStream->getGaussian();
302 >        }      
303 >      } // else isLinear
304 >
305 >      info->integrableObjects[vr]->setJ( aJ );
306 >      
307 >    }//isDirectional
308 >
309    }
310 +
311 +  // Get the Center of Mass drift velocity.
312 +
313 +  getCOMVel(vdrift);
314    
315    //  Corrects for the center of mass drift.
316    // sums all the momentum and divides by total mass.
317 <  
318 <  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++){
317 >
318 >  for(vd = 0; vd < nobj; vd++){
319      
320 <    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();
320 >    info->integrableObjects[vd]->getVel(aVel);
321      
322 <    mtot += atoms[vd]->getMass();
322 >    for (j=0; j < 3; j++)
323 >      aVel[j] -= vdrift[j];
324 >        
325 >    info->integrableObjects[vd]->setVel( aVel );
326    }
327 +
328 + }
329 +
330 + void Thermo::getCOMVel(double vdrift[3]){
331 +
332 +  double mtot, mtot_local;
333 +  double aVel[3], amass;
334 +  double vdrift_local[3];
335 +  int vd, j;
336 +  int nobj;
337 +
338 +  nobj   = info->integrableObjects.size();
339 +
340 +  mtot_local = 0.0;
341 +  vdrift_local[0] = 0.0;
342 +  vdrift_local[1] = 0.0;
343 +  vdrift_local[2] = 0.0;
344    
345 +  for(vd = 0; vd < nobj; vd++){
346 +    
347 +    amass = info->integrableObjects[vd]->getMass();
348 +    info->integrableObjects[vd]->getVel( aVel );
349 +
350 +    for(j = 0; j < 3; j++)
351 +      vdrift_local[j] += aVel[j] * amass;
352 +    
353 +    mtot_local += amass;
354 +  }
355 +
356 + #ifdef IS_MPI
357 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
358 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
359 + #else
360 +  mtot = mtot_local;
361 +  for(vd = 0; vd < 3; vd++) {
362 +    vdrift[vd] = vdrift_local[vd];
363 +  }
364 + #endif
365 +    
366    for (vd = 0; vd < 3; vd++) {
367      vdrift[vd] = vdrift[vd] / mtot;
368    }
369    
370 + }
371  
372 <  for(vd = 0; vd < n_atoms; vd++){
372 > void Thermo::getCOM(double COM[3]){
373 >
374 >  double mtot, mtot_local;
375 >  double aPos[3], amass;
376 >  double COM_local[3];
377 >  int i, j;
378 >  int nobj;
379 >
380 >  mtot_local = 0.0;
381 >  COM_local[0] = 0.0;
382 >  COM_local[1] = 0.0;
383 >  COM_local[2] = 0.0;
384 >
385 >  nobj = info->integrableObjects.size();
386 >  for(i = 0; i < nobj; i++){
387      
388 <    vx = atoms[vd]->get_vx();
389 <    vy = atoms[vd]->get_vy();
390 <    vz = atoms[vd]->get_vz();
388 >    amass = info->integrableObjects[i]->getMass();
389 >    info->integrableObjects[i]->getPos( aPos );
390 >
391 >    for(j = 0; j < 3; j++)
392 >      COM_local[j] += aPos[j] * amass;
393      
394 +    mtot_local += amass;
395 +  }
396 +
397 + #ifdef IS_MPI
398 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
399 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
400 + #else
401 +  mtot = mtot_local;
402 +  for(i = 0; i < 3; i++) {
403 +    COM[i] = COM_local[i];
404 +  }
405 + #endif
406      
407 <    vx -= vdrift[0];
408 <    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);
407 >  for (i = 0; i < 3; i++) {
408 >    COM[i] = COM[i] / mtot;
409    }
410 <  if( n_oriented ){
226 <  
227 <    for( i=0; i<n_atoms; i++ ){
228 <      
229 <      if( atoms[i]->isDirectional() ){
230 <        
231 <        dAtom = (DirectionalAtom *)atoms[i];
410 > }
411  
412 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
413 <        jx = vbar * gaussStream->getGaussian();
412 > void Thermo::removeCOMdrift() {
413 >  double vdrift[3], aVel[3];
414 >  int vd, j, nobj;
415  
416 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
237 <        jy = vbar * gaussStream->getGaussian();
416 >  nobj = info->integrableObjects.size();
417  
418 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
419 <        jz = vbar * gaussStream->getGaussian();
420 <        
421 <        dAtom->setJx( jx );
422 <        dAtom->setJy( jy );
423 <        dAtom->setJz( jz );
424 <      }
425 <    }  
418 >  // Get the Center of Mass drift velocity.
419 >
420 >  getCOMVel(vdrift);
421 >  
422 >  //  Corrects for the center of mass drift.
423 >  // sums all the momentum and divides by total mass.
424 >
425 >  for(vd = 0; vd < nobj; vd++){
426 >    
427 >    info->integrableObjects[vd]->getVel(aVel);
428 >    
429 >    for (j=0; j < 3; j++)
430 >      aVel[j] -= vdrift[j];
431 >        
432 >    info->integrableObjects[vd]->setVel( aVel );
433    }
434 < }
434 > }

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