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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 853 by mmeineke, Thu Nov 6 19:11:38 2003 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 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    return potential;
# Line 114 | Line 117 | double Thermo::getTemperature(){
117  
118   double Thermo::getTemperature(){
119  
120 <  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
120 >  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
121    double temperature;
122    
123 <  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 );
123 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
124    return temperature;
125   }
126  
127 < double Thermo::getPressure(){
127 > double Thermo::getVolume() {
128  
129 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
130 < // 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
129 >  return info->boxVol;
130 > }
131  
132 <  return 0.0;
132 > double Thermo::getPressure() {
133 >
134 >  // Relies on the calculation of the full molecular pressure tensor
135 >  
136 >  const double p_convert = 1.63882576e8;
137 >  double press[3][3];
138 >  double pressure;
139 >
140 >  this->getPressureTensor(press);
141 >
142 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143 >
144 >  return pressure;
145   }
146  
147 + double Thermo::getPressureX() {
148 +
149 +  // Relies on the calculation of the full molecular pressure tensor
150 +  
151 +  const double p_convert = 1.63882576e8;
152 +  double press[3][3];
153 +  double pressureX;
154 +
155 +  this->getPressureTensor(press);
156 +
157 +  pressureX = p_convert * press[0][0];
158 +
159 +  return pressureX;
160 + }
161 +
162 + double Thermo::getPressureY() {
163 +
164 +  // Relies on the calculation of the full molecular pressure tensor
165 +  
166 +  const double p_convert = 1.63882576e8;
167 +  double press[3][3];
168 +  double pressureY;
169 +
170 +  this->getPressureTensor(press);
171 +
172 +  pressureY = p_convert * press[1][1];
173 +
174 +  return pressureY;
175 + }
176 +
177 + double Thermo::getPressureZ() {
178 +
179 +  // Relies on the calculation of the full molecular pressure tensor
180 +  
181 +  const double p_convert = 1.63882576e8;
182 +  double press[3][3];
183 +  double pressureZ;
184 +
185 +  this->getPressureTensor(press);
186 +
187 +  pressureZ = p_convert * press[2][2];
188 +
189 +  return pressureZ;
190 + }
191 +
192 +
193 + void Thermo::getPressureTensor(double press[3][3]){
194 +  // returns pressure tensor in units amu*fs^-2*Ang^-1
195 +  // routine derived via viral theorem description in:
196 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
197 +
198 +  const double e_convert = 4.184e-4;
199 +
200 +  double molmass, volume;
201 +  double vcom[3];
202 +  double p_local[9], p_global[9];
203 +  int i, j, k, nMols;
204 +  Molecule* molecules;
205 +
206 +  nMols = info->n_mol;
207 +  molecules = info->molecules;
208 +  //tau = info->tau;
209 +
210 +  // use velocities of molecular centers of mass and molecular masses:
211 +  for (i=0; i < 9; i++) {    
212 +    p_local[i] = 0.0;
213 +    p_global[i] = 0.0;
214 +  }
215 +
216 +  for (i=0; i < nMols; i++) {
217 +    molmass = molecules[i].getCOMvel(vcom);
218 +
219 +    p_local[0] += molmass * (vcom[0] * vcom[0]);
220 +    p_local[1] += molmass * (vcom[0] * vcom[1]);
221 +    p_local[2] += molmass * (vcom[0] * vcom[2]);
222 +    p_local[3] += molmass * (vcom[1] * vcom[0]);
223 +    p_local[4] += molmass * (vcom[1] * vcom[1]);
224 +    p_local[5] += molmass * (vcom[1] * vcom[2]);
225 +    p_local[6] += molmass * (vcom[2] * vcom[0]);
226 +    p_local[7] += molmass * (vcom[2] * vcom[1]);
227 +    p_local[8] += molmass * (vcom[2] * vcom[2]);
228 +  }
229 +
230 +  // Get total for entire system from MPI.
231 +
232 + #ifdef IS_MPI
233 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
234 + #else
235 +  for (i=0; i<9; i++) {
236 +    p_global[i] = p_local[i];
237 +  }
238 + #endif // is_mpi
239 +
240 +  volume = this->getVolume();
241 +
242 +  for(i = 0; i < 3; i++) {
243 +    for (j = 0; j < 3; j++) {
244 +      k = 3*i + j;
245 +      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
246 +
247 +    }
248 +  }
249 + }
250 +
251   void Thermo::velocitize() {
252    
253 <  double x,y;
254 <  double vx, vy, vz;
140 <  double jx, jy, jz;
141 <  int i, vr, vd; // velocity randomizer loop counters
253 >  double aVel[3], aJ[3], I[3][3];
254 >  int i, j, vr, vd; // velocity randomizer loop counters
255    double vdrift[3];
143 –  double mtot = 0.0;
256    double vbar;
257    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
258    double av2;
259    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
260    int n_atoms;
261    Atom** atoms;
262    DirectionalAtom* dAtom;
# Line 154 | Line 264 | void Thermo::velocitize() {
264    int n_oriented;
265    int n_constraints;
266  
267 <  atoms         = entry_plug->atoms;
268 <  n_atoms       = entry_plug->n_atoms;
269 <  temperature   = entry_plug->target_temp;
270 <  n_oriented    = entry_plug->n_oriented;
271 <  n_constraints = entry_plug->n_constraints;
267 >  atoms         = info->atoms;
268 >  n_atoms       = info->n_atoms;
269 >  temperature   = info->target_temp;
270 >  n_oriented    = info->n_oriented;
271 >  n_constraints = info->n_constraints;
272    
273 <
274 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
273 >  kebar = kb * temperature * (double)info->ndfRaw /
274 >    ( 2.0 * (double)info->ndf );
275    
276    for(vr = 0; vr < n_atoms; vr++){
277      
# Line 172 | Line 280 | void Thermo::velocitize() {
280      av2 = 2.0 * kebar / atoms[vr]->getMass();
281      vbar = sqrt( av2 );
282  
175 – //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
176 –    
283      // picks random velocities from a gaussian distribution
284      // centered on vbar
285  
286 <    vx = vbar * gaussStream->getGaussian();
287 <    vy = vbar * gaussStream->getGaussian();
288 <    vz = vbar * gaussStream->getGaussian();
286 >    for (j=0; j<3; j++)
287 >      aVel[j] = vbar * gaussStream->getGaussian();
288 >    
289 >    atoms[vr]->setVel( aVel );
290  
184 –    atoms[vr]->set_vx( vx );
185 –    atoms[vr]->set_vy( vy );
186 –    atoms[vr]->set_vz( vz );
291    }
292 +
293 +  // Get the Center of Mass drift velocity.
294 +
295 +  getCOMVel(vdrift);
296    
297    //  Corrects for the center of mass drift.
298    // 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 –  
299  
300    for(vd = 0; vd < n_atoms; vd++){
301      
302 <    vx = atoms[vd]->get_vx();
213 <    vy = atoms[vd]->get_vy();
214 <    vz = atoms[vd]->get_vz();
302 >    atoms[vd]->getVel(aVel);
303      
304 <    
305 <    vx -= vdrift[0];
306 <    vy -= vdrift[1];
307 <    vz -= vdrift[2];
220 <    
221 <    atoms[vd]->set_vx(vx);
222 <    atoms[vd]->set_vy(vy);
223 <    atoms[vd]->set_vz(vz);
304 >    for (j=0; j < 3; j++)
305 >      aVel[j] -= vdrift[j];
306 >        
307 >    atoms[vd]->setVel( aVel );
308    }
309    if( n_oriented ){
310    
# Line 229 | Line 313 | void Thermo::velocitize() {
313        if( atoms[i]->isDirectional() ){
314          
315          dAtom = (DirectionalAtom *)atoms[i];
316 +        dAtom->getI( I );
317 +        
318 +        for (j = 0 ; j < 3; j++) {
319  
320 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
321 <        jx = vbar * gaussStream->getGaussian();
320 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
321 >          aJ[j] = vbar * gaussStream->getGaussian();
322  
323 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
237 <        jy = vbar * gaussStream->getGaussian();
323 >        }      
324  
325 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
326 <        jz = vbar * gaussStream->getGaussian();
241 <        
242 <        dAtom->setJx( jx );
243 <        dAtom->setJy( jy );
244 <        dAtom->setJz( jz );
325 >        dAtom->setJ( aJ );
326 >
327        }
328      }  
329    }
330   }
331 +
332 + void Thermo::getCOMVel(double vdrift[3]){
333 +
334 +  double mtot, mtot_local;
335 +  double aVel[3], amass;
336 +  double vdrift_local[3];
337 +  int vd, n_atoms, j;
338 +  Atom** atoms;
339 +
340 +  // We are very careless here with the distinction between n_atoms and n_local
341 +  // We should really fix this before someone pokes an eye out.
342 +
343 +  n_atoms = info->n_atoms;  
344 +  atoms   = info->atoms;
345 +
346 +  mtot_local = 0.0;
347 +  vdrift_local[0] = 0.0;
348 +  vdrift_local[1] = 0.0;
349 +  vdrift_local[2] = 0.0;
350 +  
351 +  for(vd = 0; vd < n_atoms; vd++){
352 +    
353 +    amass = atoms[vd]->getMass();
354 +    atoms[vd]->getVel( aVel );
355 +
356 +    for(j = 0; j < 3; j++)
357 +      vdrift_local[j] += aVel[j] * amass;
358 +    
359 +    mtot_local += amass;
360 +  }
361 +
362 + #ifdef IS_MPI
363 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
364 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
365 + #else
366 +  mtot = mtot_local;
367 +  for(vd = 0; vd < 3; vd++) {
368 +    vdrift[vd] = vdrift_local[vd];
369 +  }
370 + #endif
371 +    
372 +  for (vd = 0; vd < 3; vd++) {
373 +    vdrift[vd] = vdrift[vd] / mtot;
374 +  }
375 +  
376 + }
377 +
378 + void Thermo::getCOM(double COM[3]){
379 +
380 +  double mtot, mtot_local;
381 +  double aPos[3], amass;
382 +  double COM_local[3];
383 +  int i, n_atoms, j;
384 +  Atom** atoms;
385 +
386 +  // We are very careless here with the distinction between n_atoms and n_local
387 +  // We should really fix this before someone pokes an eye out.
388 +
389 +  n_atoms = info->n_atoms;  
390 +  atoms   = info->atoms;
391 +
392 +  mtot_local = 0.0;
393 +  COM_local[0] = 0.0;
394 +  COM_local[1] = 0.0;
395 +  COM_local[2] = 0.0;
396 +  
397 +  for(i = 0; i < n_atoms; i++){
398 +    
399 +    amass = atoms[i]->getMass();
400 +    atoms[i]->getPos( aPos );
401 +
402 +    for(j = 0; j < 3; j++)
403 +      COM_local[j] += aPos[j] * amass;
404 +    
405 +    mtot_local += amass;
406 +  }
407 +
408 + #ifdef IS_MPI
409 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
410 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
411 + #else
412 +  mtot = mtot_local;
413 +  for(i = 0; i < 3; i++) {
414 +    COM[i] = COM_local[i];
415 +  }
416 + #endif
417 +    
418 +  for (i = 0; i < 3; i++) {
419 +    COM[i] = COM[i] / mtot;
420 +  }
421 + }

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