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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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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 1133 by gezelter, Mon Apr 26 14:29:18 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 > inline double roundMe( double x ){
21 >          return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22 > }
23 >
24 > Thermo::Thermo( SimInfo* the_info ) {
25 >  info = the_info;
26 >  int baseSeed = the_info->getSeed();
27    
28    gaussStream = new gaussianSPRNG( baseSeed );
29   }
# Line 27 | 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  
35 –  DirectionalAtom *dAtom;
36 –
37 –  int n_atoms;
43    double kinetic_global;
44 <  Atom** atoms;
40 <
44 >  vector<StuntDouble *> integrableObjects = info->integrableObjects;
45    
42 –  n_atoms = entry_plug->n_atoms;
43 –  atoms = entry_plug->atoms;
44 –
46    kinetic = 0.0;
47    kinetic_global = 0.0;
47 –  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::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
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 77 | Line 82 | double Thermo::getPotential(){
82  
83   double Thermo::getPotential(){
84    
85 +  double potential_local;
86    double potential;
81 –  double potential_global;
87    int el, nSRI;
88 <  SRI** sris;
88 >  Molecule* molecules;
89  
90 <  sris = entry_plug->sr_interactions;
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_global = 0.0;
90 <  potential += entry_plug->lrPot;
95 >  potential_local += info->lrPot;
96  
97 <  for( el=0; el<nSRI; el++ ){
98 <    
94 <    potential += sris[el]->get_potential();
97 >  for( el=0; el<info->n_mol; el++ ){    
98 >    potential_local += molecules[el].getPotential();
99    }
100  
101    // Get total potential for entire system from MPI.
102   #ifdef IS_MPI
103 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
104 <  potential = potential_global;
105 <
103 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
104 >                MPI_SUM, MPI_COMM_WORLD);
105 > #else
106 >  potential = potential_local;
107   #endif // is_mpi
108  
109    return potential;
# Line 114 | 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;
119 –  
120 –  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 –    - entry_plug->n_constraints - 3;
124  
125 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
125 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126    return temperature;
127   }
128  
129 < double Thermo::getPressure(){
129 > double Thermo::getVolume() {
130  
131 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
132 < // 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
131 >  return info->boxVol;
132 > }
133  
134 <  return 0.0;
134 > double Thermo::getPressure() {
135 >
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 >  this->getPressureTensor(press);
143 >
144 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
145 >
146 >  return pressure;
147   }
148  
149 < void Thermo::velocitize() {
149 > double Thermo::getPressureX() {
150 >
151 >  // Relies on the calculation of the full molecular pressure tensor
152    
153 <  double x,y;
154 <  double vx, vy, vz;
155 <  double jx, jy, jz;
141 <  int i, vr, vd; // velocity randomizer loop counters
142 <  double vdrift[3];
143 <  double mtot = 0.0;
144 <  double vbar;
145 <  const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
146 <  double av2;
147 <  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;
153 <  double temperature;
154 <  int n_oriented;
155 <  int n_constraints;
153 >  const double p_convert = 1.63882576e8;
154 >  double press[3][3];
155 >  double pressureX;
156  
157 <  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;
157 >  this->getPressureTensor(press);
158 >
159 >  pressureX = p_convert * press[0][0];
160 >
161 >  return pressureX;
162 > }
163 >
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[3][3];
170 +  double pressureY;
171  
172 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
173 <  ndf = ndfRaw - n_constraints - 3;
174 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
172 >  this->getPressureTensor(press);
173 >
174 >  pressureY = p_convert * press[1][1];
175 >
176 >  return pressureY;
177 > }
178 >
179 > double Thermo::getPressureZ() {
180 >
181 >  // Relies on the calculation of the full molecular pressure tensor
182    
183 <  for(vr = 0; vr < n_atoms; vr++){
184 <    
185 <    // uses equipartition theory to solve for vbar in angstrom/fs
183 >  const double p_convert = 1.63882576e8;
184 >  double press[3][3];
185 >  double pressureZ;
186  
187 <    av2 = 2.0 * kebar / atoms[vr]->getMass();
173 <    vbar = sqrt( av2 );
187 >  this->getPressureTensor(press);
188  
189 < //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
176 <    
177 <    // picks random velocities from a gaussian distribution
178 <    // centered on vbar
189 >  pressureZ = p_convert * press[2][2];
190  
191 <    vx = vbar * gaussStream->getGaussian();
192 <    vy = vbar * gaussStream->getGaussian();
182 <    vz = vbar * gaussStream->getGaussian();
191 >  return pressureZ;
192 > }
193  
194 <    atoms[vr]->set_vx( vx );
195 <    atoms[vr]->set_vy( vy );
196 <    atoms[vr]->set_vz( vz );
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
199 >
200 >  const double e_convert = 4.184e-4;
201 >
202 >  double molmass, volume;
203 >  double vcom[3], pcom[3], fcom[3], scaled[3];
204 >  double p_local[9], p_global[9];
205 >  int i, j, k, nMols;
206 >  Molecule* molecules;
207 >
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++) {    
214 >    p_local[i] = 0.0;
215 >    p_global[i] = 0.0;
216    }
217 <  
218 <  //  Corrects for the center of mass drift.
219 <  // sums all the momentum and divides by total mass.
220 <  
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++){
217 >
218 >  for (i=0; i < info->integrableObjects.size(); i++) {
219 >
220 >    molmass = info->integrableObjects[i]->getMass();
221      
222 <    vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
223 <    vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
224 <    vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
225 <    
226 <    mtot += atoms[vd]->getMass();
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]) + fcom[0]*pcom[0]*eConvert;
236 >    p_local[1] += molmass * (vcom[0] * vcom[1]) + fcom[0]*pcom[1]*eConvert;
237 >    p_local[2] += molmass * (vcom[0] * vcom[2]) + fcom[0]*pcom[2]*eConvert;
238 >    p_local[3] += molmass * (vcom[1] * vcom[0]) + fcom[1]*pcom[0]*eConvert;
239 >    p_local[4] += molmass * (vcom[1] * vcom[1]) + fcom[1]*pcom[1]*eConvert;
240 >    p_local[5] += molmass * (vcom[1] * vcom[2]) + fcom[1]*pcom[2]*eConvert;
241 >    p_local[6] += molmass * (vcom[2] * vcom[0]) + fcom[2]*pcom[0]*eConvert;
242 >    p_local[7] += molmass * (vcom[2] * vcom[1]) + fcom[2]*pcom[1]*eConvert;
243 >    p_local[8] += molmass * (vcom[2] * vcom[2]) + fcom[2]*pcom[2]*eConvert;
244 >    
245    }
246 +
247 +  // Get total for entire system from MPI.
248 +
249 + #ifdef IS_MPI
250 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
251 + #else
252 +  for (i=0; i<9; i++) {
253 +    p_global[i] = p_local[i];
254 +  }
255 + #endif // is_mpi
256 +
257 +  volume = this->getVolume();
258 +
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] /  volume;
263 +
264 +    }
265 +  }
266 + }
267 +
268 + void Thermo::velocitize() {
269    
270 <  for (vd = 0; vd < 3; vd++) {
271 <    vdrift[vd] = vdrift[vd] / mtot;
270 >  double aVel[3], aJ[3], I[3][3];
271 >  int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
272 >  double vdrift[3];
273 >  double vbar;
274 >  const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
275 >  double av2;
276 >  double kebar;
277 >  double temperature;
278 >  int nobj;
279 >
280 >  nobj = info->integrableObjects.size();
281 >  
282 >  temperature   = info->target_temp;
283 >  
284 >  kebar = kb * temperature * (double)info->ndfRaw /
285 >    ( 2.0 * (double)info->ndf );
286 >  
287 >  for(vr = 0; vr < nobj; vr++){
288 >    
289 >    // uses equipartition theory to solve for vbar in angstrom/fs
290 >
291 >    av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
292 >    vbar = sqrt( av2 );
293 >
294 >    // picks random velocities from a gaussian distribution
295 >    // centered on vbar
296 >
297 >    for (j=0; j<3; j++)
298 >      aVel[j] = vbar * gaussStream->getGaussian();
299 >    
300 >    info->integrableObjects[vr]->setVel( aVel );
301 >    
302 >    if(info->integrableObjects[vr]->isDirectional()){
303 >
304 >      info->integrableObjects[vr]->getI( I );
305 >
306 >      if (info->integrableObjects[vr]->isLinear()) {
307 >
308 >        l= info->integrableObjects[vr]->linearAxis();
309 >        m = (l+1)%3;
310 >        n = (l+2)%3;
311 >
312 >        aJ[l] = 0.0;
313 >        vbar = sqrt( 2.0 * kebar * I[m][m] );
314 >        aJ[m] = vbar * gaussStream->getGaussian();
315 >        vbar = sqrt( 2.0 * kebar * I[n][n] );
316 >        aJ[n] = vbar * gaussStream->getGaussian();
317 >        
318 >      } else {
319 >        for (j = 0 ; j < 3; j++) {
320 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
321 >          aJ[j] = vbar * gaussStream->getGaussian();
322 >        }      
323 >      } // else isLinear
324 >
325 >      info->integrableObjects[vr]->setJ( aJ );
326 >      
327 >    }//isDirectional
328 >
329    }
330 +
331 +  // Get the Center of Mass drift velocity.
332 +
333 +  getCOMVel(vdrift);
334    
335 +  //  Corrects for the center of mass drift.
336 +  // sums all the momentum and divides by total mass.
337  
338 <  for(vd = 0; vd < n_atoms; vd++){
338 >  for(vd = 0; vd < nobj; vd++){
339      
340 <    vx = atoms[vd]->get_vx();
213 <    vy = atoms[vd]->get_vy();
214 <    vz = atoms[vd]->get_vz();
340 >    info->integrableObjects[vd]->getVel(aVel);
341      
342 +    for (j=0; j < 3; j++)
343 +      aVel[j] -= vdrift[j];
344 +        
345 +    info->integrableObjects[vd]->setVel( aVel );
346 +  }
347 +
348 + }
349 +
350 + void Thermo::getCOMVel(double vdrift[3]){
351 +
352 +  double mtot, mtot_local;
353 +  double aVel[3], amass;
354 +  double vdrift_local[3];
355 +  int vd, j;
356 +  int nobj;
357 +
358 +  nobj   = info->integrableObjects.size();
359 +
360 +  mtot_local = 0.0;
361 +  vdrift_local[0] = 0.0;
362 +  vdrift_local[1] = 0.0;
363 +  vdrift_local[2] = 0.0;
364 +  
365 +  for(vd = 0; vd < nobj; vd++){
366      
367 <    vx -= vdrift[0];
368 <    vy -= vdrift[1];
369 <    vz -= vdrift[2];
367 >    amass = info->integrableObjects[vd]->getMass();
368 >    info->integrableObjects[vd]->getVel( aVel );
369 >
370 >    for(j = 0; j < 3; j++)
371 >      vdrift_local[j] += aVel[j] * amass;
372      
373 <    atoms[vd]->set_vx(vx);
222 <    atoms[vd]->set_vy(vy);
223 <    atoms[vd]->set_vz(vz);
373 >    mtot_local += amass;
374    }
375 <  if( n_oriented ){
375 >
376 > #ifdef IS_MPI
377 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
378 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
379 > #else
380 >  mtot = mtot_local;
381 >  for(vd = 0; vd < 3; vd++) {
382 >    vdrift[vd] = vdrift_local[vd];
383 >  }
384 > #endif
385 >    
386 >  for (vd = 0; vd < 3; vd++) {
387 >    vdrift[vd] = vdrift[vd] / mtot;
388 >  }
389    
390 <    for( i=0; i<n_atoms; i++ ){
228 <      
229 <      if( atoms[i]->isDirectional() ){
230 <        
231 <        dAtom = (DirectionalAtom *)atoms[i];
390 > }
391  
392 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
234 <        jx = vbar * gaussStream->getGaussian();
392 > void Thermo::getCOM(double COM[3]){
393  
394 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
395 <        jy = vbar * gaussStream->getGaussian();
394 >  double mtot, mtot_local;
395 >  double aPos[3], amass;
396 >  double COM_local[3];
397 >  int i, j;
398 >  int nobj;
399  
400 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
401 <        jz = vbar * gaussStream->getGaussian();
402 <        
403 <        dAtom->setJx( jx );
404 <        dAtom->setJy( jy );
405 <        dAtom->setJz( jz );
406 <      }
407 <    }  
400 >  mtot_local = 0.0;
401 >  COM_local[0] = 0.0;
402 >  COM_local[1] = 0.0;
403 >  COM_local[2] = 0.0;
404 >
405 >  nobj = info->integrableObjects.size();
406 >  for(i = 0; i < nobj; i++){
407 >    
408 >    amass = info->integrableObjects[i]->getMass();
409 >    info->integrableObjects[i]->getPos( aPos );
410 >
411 >    for(j = 0; j < 3; j++)
412 >      COM_local[j] += aPos[j] * amass;
413 >    
414 >    mtot_local += amass;
415    }
416 +
417 + #ifdef IS_MPI
418 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
419 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
420 + #else
421 +  mtot = mtot_local;
422 +  for(i = 0; i < 3; i++) {
423 +    COM[i] = COM_local[i];
424 +  }
425 + #endif
426 +    
427 +  for (i = 0; i < 3; i++) {
428 +    COM[i] = COM[i] / mtot;
429 +  }
430   }
431 +
432 + void Thermo::removeCOMdrift() {
433 +  double vdrift[3], aVel[3];
434 +  int vd, j, nobj;
435 +
436 +  nobj = info->integrableObjects.size();
437 +
438 +  // Get the Center of Mass drift velocity.
439 +
440 +  getCOMVel(vdrift);
441 +  
442 +  //  Corrects for the center of mass drift.
443 +  // sums all the momentum and divides by total mass.
444 +
445 +  for(vd = 0; vd < nobj; vd++){
446 +    
447 +    info->integrableObjects[vd]->getVel(aVel);
448 +    
449 +    for (j=0; j < 3; j++)
450 +      aVel[j] -= vdrift[j];
451 +        
452 +    info->integrableObjects[vd]->setVel( aVel );
453 +  }
454 + }

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