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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 428 by mmeineke, Thu Mar 27 21:07:14 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 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   #ifdef IS_MPI
15   #define __C
16   #include "mpiSimulation.hpp"
17   #endif // is_mpi
18  
19 <
20 < #define BASE_SEED 123456789
21 <
22 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  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 33 | 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 45 | 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  
55 –    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
56 –    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
57 –    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
58 –
59 –    v_sqr = vx2 + vy2 + vz2;
60 –    kinetic += atoms[kl]->getMass() * v_sqr;
61 –
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();
68 <      jz2 = dAtom->getJz() * dAtom->getJz();
65 >      for (j=0; j<3; j++)
66 >        kinetic += aJ[j]*aJ[j] / I[j][j];
67        
70 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
71 –        + (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 88 | Line 85 | double Thermo::getPotential(){
85    int el, nSRI;
86    Molecule* molecules;
87  
88 <  molecules = entry_plug->molecules;
89 <  nSRI = entry_plug->n_SRI;
88 >  molecules = info->molecules;
89 >  nSRI = info->n_SRI;
90  
91    potential_local = 0.0;
92 <  potential_local += entry_plug->lrPot;
92 >  potential = 0.0;
93 >  potential_local += info->lrPot;
94  
95 <  for( el=0; el<entry_plug->n_mol; el++ ){    
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_local,&potential,1,MPI_DOUBLE,MPI_SUM);
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 118 | 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;
123 –  int ndf_local, ndf;
128    
129 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
130 <    - entry_plug->n_constraints;
129 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130 >  return temperature;
131 > }
132  
133 < #ifdef IS_MPI
129 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
130 < #else
131 <  ndf = ndf_local;
132 < #endif
133 > double Thermo::getVolume() {
134  
135 <  ndf = ndf - 3;
135 >  return info->boxVol;
136 > }
137 >
138 > double Thermo::getPressure() {
139 >
140 >  // Relies on the calculation of the full molecular pressure tensor
141    
142 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
143 <  return temperature;
142 >  const double p_convert = 1.63882576e8;
143 >  double press[3][3];
144 >  double pressure;
145 >
146 >  this->getPressureTensor(press);
147 >
148 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
149 >
150 >  return pressure;
151   }
152  
153 < double Thermo::getPressure(){
153 > double Thermo::getPressureX() {
154  
155 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
156 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
157 < //  const double conv_A_m = 1.0E-10; //convert A -> m
155 >  // Relies on the calculation of the full molecular pressure tensor
156 >  
157 >  const double p_convert = 1.63882576e8;
158 >  double press[3][3];
159 >  double pressureX;
160  
161 <  return 0.0;
161 >  this->getPressureTensor(press);
162 >
163 >  pressureX = p_convert * press[0][0];
164 >
165 >  return pressureX;
166   }
167  
168 + double Thermo::getPressureY() {
169 +
170 +  // Relies on the calculation of the full molecular pressure tensor
171 +  
172 +  const double p_convert = 1.63882576e8;
173 +  double press[3][3];
174 +  double pressureY;
175 +
176 +  this->getPressureTensor(press);
177 +
178 +  pressureY = p_convert * press[1][1];
179 +
180 +  return pressureY;
181 + }
182 +
183 + double Thermo::getPressureZ() {
184 +
185 +  // Relies on the calculation of the full molecular pressure tensor
186 +  
187 +  const double p_convert = 1.63882576e8;
188 +  double press[3][3];
189 +  double pressureZ;
190 +
191 +  this->getPressureTensor(press);
192 +
193 +  pressureZ = p_convert * press[2][2];
194 +
195 +  return pressureZ;
196 + }
197 +
198 +
199 + void Thermo::getPressureTensor(double press[3][3]){
200 +  // returns pressure tensor in units amu*fs^-2*Ang^-1
201 +  // routine derived via viral theorem description in:
202 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
203 +
204 +  const double e_convert = 4.184e-4;
205 +
206 +  double molmass, volume;
207 +  double vcom[3];
208 +  double p_local[9], p_global[9];
209 +  int i, j, k, nMols;
210 +  Molecule* molecules;
211 +
212 +  nMols = info->n_mol;
213 +  molecules = info->molecules;
214 +  //tau = info->tau;
215 +
216 +  // use velocities of molecular centers of mass and molecular masses:
217 +  for (i=0; i < 9; i++) {    
218 +    p_local[i] = 0.0;
219 +    p_global[i] = 0.0;
220 +  }
221 +
222 +  for (i=0; i < nMols; i++) {
223 +    molmass = molecules[i].getCOMvel(vcom);
224 +
225 +    p_local[0] += molmass * (vcom[0] * vcom[0]);
226 +    p_local[1] += molmass * (vcom[0] * vcom[1]);
227 +    p_local[2] += molmass * (vcom[0] * vcom[2]);
228 +    p_local[3] += molmass * (vcom[1] * vcom[0]);
229 +    p_local[4] += molmass * (vcom[1] * vcom[1]);
230 +    p_local[5] += molmass * (vcom[1] * vcom[2]);
231 +    p_local[6] += molmass * (vcom[2] * vcom[0]);
232 +    p_local[7] += molmass * (vcom[2] * vcom[1]);
233 +    p_local[8] += molmass * (vcom[2] * vcom[2]);
234 +  }
235 +
236 +  // Get total for entire system from MPI.
237 +
238 + #ifdef IS_MPI
239 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
240 + #else
241 +  for (i=0; i<9; i++) {
242 +    p_global[i] = p_local[i];
243 +  }
244 + #endif // is_mpi
245 +
246 +  volume = this->getVolume();
247 +
248 +  for(i = 0; i < 3; i++) {
249 +    for (j = 0; j < 3; j++) {
250 +      k = 3*i + j;
251 +      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
252 +
253 +    }
254 +  }
255 + }
256 +
257   void Thermo::velocitize() {
258    
259 <  double x,y;
260 <  double vx, vy, vz;
153 <  double jx, jy, jz;
154 <  int i, vr, vd; // velocity randomizer loop counters
259 >  double aVel[3], aJ[3], I[3][3];
260 >  int i, j, vr, vd; // velocity randomizer loop counters
261    double vdrift[3];
262    double vbar;
263    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
264    double av2;
265    double kebar;
160 –  int ndf, ndf_local; // number of degrees of freedom
161 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
266    int n_atoms;
267    Atom** atoms;
268    DirectionalAtom* dAtom;
# Line 166 | Line 270 | void Thermo::velocitize() {
270    int n_oriented;
271    int n_constraints;
272  
273 <  atoms         = entry_plug->atoms;
274 <  n_atoms       = entry_plug->n_atoms;
275 <  temperature   = entry_plug->target_temp;
276 <  n_oriented    = entry_plug->n_oriented;
277 <  n_constraints = entry_plug->n_constraints;
273 >  atoms         = info->atoms;
274 >  n_atoms       = info->n_atoms;
275 >  temperature   = info->target_temp;
276 >  n_oriented    = info->n_oriented;
277 >  n_constraints = info->n_constraints;
278    
279 <  // Raw degrees of freedom that we have to set
280 <  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
177 <
178 <  // Degrees of freedom that can contain kinetic energy
179 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
180 <    - entry_plug->n_constraints;
279 >  kebar = kb * temperature * (double)info->ndfRaw /
280 >    ( 2.0 * (double)info->ndf );
281    
182 – #ifdef IS_MPI
183 –  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
184 –  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
185 – #else
186 –  ndfRaw = ndfRaw_local;
187 –  ndf = ndf_local;
188 – #endif
189 –  ndf = ndf - 3;
190 –
191 –  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
192 –  
282    for(vr = 0; vr < n_atoms; vr++){
283      
284      // uses equipartition theory to solve for vbar in angstrom/fs
285  
286      av2 = 2.0 * kebar / atoms[vr]->getMass();
287      vbar = sqrt( av2 );
288 <
288 >
289   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
290      
291      // picks random velocities from a gaussian distribution
292      // centered on vbar
293  
294 <    vx = vbar * gaussStream->getGaussian();
295 <    vy = vbar * gaussStream->getGaussian();
296 <    vz = vbar * gaussStream->getGaussian();
294 >    for (j=0; j<3; j++)
295 >      aVel[j] = vbar * gaussStream->getGaussian();
296 >    
297 >    atoms[vr]->setVel( aVel );
298  
209 –    atoms[vr]->set_vx( vx );
210 –    atoms[vr]->set_vy( vy );
211 –    atoms[vr]->set_vz( vz );
299    }
300  
301    // Get the Center of Mass drift velocity.
# Line 220 | Line 307 | void Thermo::velocitize() {
307  
308    for(vd = 0; vd < n_atoms; vd++){
309      
310 <    vx = atoms[vd]->get_vx();
224 <    vy = atoms[vd]->get_vy();
225 <    vz = atoms[vd]->get_vz();
226 <        
227 <    vx -= vdrift[0];
228 <    vy -= vdrift[1];
229 <    vz -= vdrift[2];
310 >    atoms[vd]->getVel(aVel);
311      
312 <    atoms[vd]->set_vx(vx);
313 <    atoms[vd]->set_vy(vy);
314 <    atoms[vd]->set_vz(vz);
312 >    for (j=0; j < 3; j++)
313 >      aVel[j] -= vdrift[j];
314 >        
315 >    atoms[vd]->setVel( aVel );
316    }
317    if( n_oriented ){
318    
# Line 239 | Line 321 | void Thermo::velocitize() {
321        if( atoms[i]->isDirectional() ){
322          
323          dAtom = (DirectionalAtom *)atoms[i];
324 +        dAtom->getI( I );
325 +        
326 +        for (j = 0 ; j < 3; j++) {
327  
328 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
329 <        jx = vbar * gaussStream->getGaussian();
328 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
329 >          aJ[j] = vbar * gaussStream->getGaussian();
330  
331 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
247 <        jy = vbar * gaussStream->getGaussian();
331 >        }      
332  
333 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
334 <        jz = vbar * gaussStream->getGaussian();
251 <        
252 <        dAtom->setJx( jx );
253 <        dAtom->setJy( jy );
254 <        dAtom->setJz( jz );
333 >        dAtom->setJ( aJ );
334 >
335        }
336      }  
337    }
# Line 260 | Line 340 | void Thermo::getCOMVel(double vdrift[3]){
340   void Thermo::getCOMVel(double vdrift[3]){
341  
342    double mtot, mtot_local;
343 +  double aVel[3], amass;
344    double vdrift_local[3];
345 <  int vd, n_atoms;
345 >  int vd, n_atoms, j;
346    Atom** atoms;
347  
348    // We are very careless here with the distinction between n_atoms and n_local
349    // We should really fix this before someone pokes an eye out.
350  
351 <  n_atoms = entry_plug->n_atoms;  
352 <  atoms   = entry_plug->atoms;
351 >  n_atoms = info->n_atoms;  
352 >  atoms   = info->atoms;
353  
354    mtot_local = 0.0;
355    vdrift_local[0] = 0.0;
# Line 277 | Line 358 | void Thermo::getCOMVel(double vdrift[3]){
358    
359    for(vd = 0; vd < n_atoms; vd++){
360      
361 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
362 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
363 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
361 >    amass = atoms[vd]->getMass();
362 >    atoms[vd]->getVel( aVel );
363 >
364 >    for(j = 0; j < 3; j++)
365 >      vdrift_local[j] += aVel[j] * amass;
366      
367 <    mtot_local += atoms[vd]->getMass();
367 >    mtot_local += amass;
368    }
369  
370   #ifdef IS_MPI
371 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
372 <  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
371 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
372 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
373   #else
374    mtot = mtot_local;
375    for(vd = 0; vd < 3; vd++) {
# Line 300 | Line 383 | void Thermo::getCOMVel(double vdrift[3]){
383    
384   }
385  
386 + void Thermo::getCOM(double COM[3]){
387 +
388 +  double mtot, mtot_local;
389 +  double aPos[3], amass;
390 +  double COM_local[3];
391 +  int i, n_atoms, j;
392 +  Atom** atoms;
393 +
394 +  // We are very careless here with the distinction between n_atoms and n_local
395 +  // We should really fix this before someone pokes an eye out.
396 +
397 +  n_atoms = info->n_atoms;  
398 +  atoms   = info->atoms;
399 +
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 +  for(i = 0; i < n_atoms; i++){
406 +    
407 +    amass = atoms[i]->getMass();
408 +    atoms[i]->getPos( aPos );
409 +
410 +    for(j = 0; j < 3; j++)
411 +      COM_local[j] += aPos[j] * amass;
412 +    
413 +    mtot_local += amass;
414 +  }
415 +
416 + #ifdef IS_MPI
417 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
418 +  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
419 + #else
420 +  mtot = mtot_local;
421 +  for(i = 0; i < 3; i++) {
422 +    COM[i] = COM_local[i];
423 +  }
424 + #endif
425 +    
426 +  for (i = 0; i < 3; i++) {
427 +    COM[i] = COM[i] / mtot;
428 +  }
429 + }

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