ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/mdtools/md_code/Thermo.cpp
(Generate patch)

Comparing trunk/mdtools/md_code/Thermo.cpp (file contents):
Revision 218 by chuckv, Sun Dec 29 19:11:05 2002 UTC vs.
Revision 261 by chuckv, Mon Feb 3 21:15:59 2003 UTC

# Line 1 | Line 1
1   #include <cmath>
2 + #include <iostream>
3 + using namespace std;
4 +
5 + #ifdef IS_MPI
6 + #include <mpi.h>
7   #include <mpi++.h>
8 + #endif //is_mpi
9  
10   #include "Thermo.hpp"
11   #include "SRI.hpp"
12   #include "LRI.hpp"
13   #include "Integrator.hpp"
14  
15 + #define BASE_SEED 123456789
16  
17 + Thermo::Thermo( SimInfo* the_entry_plug ) {
18 +  entry_plug = the_entry_plug;
19 +  int baseSeed = BASE_SEED;
20 +  
21 +  gaussStream = new gaussianSPRNG( baseSeed );
22 + }
23 +
24 + Thermo::~Thermo(){
25 +  delete gaussStream;
26 + }
27 +
28   double Thermo::getKinetic(){
29  
30    const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
# Line 49 | Line 67 | double Thermo::getKinetic(){
67      }
68    }
69   #ifdef IS_MPI
70 <  MPI_COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
70 >  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
71    kinetic = kinetic_global;
72 < #endif
72 > #endif //is_mpi
73  
74    kinetic = kinetic * 0.5 / e_convert;
75  
# Line 70 | Line 88 | double Thermo::getPotential(){
88  
89    potential = 0.0;
90    potential_global = 0.0;
91 <  potential += entry_plug->longRange->get_potential();;
91 >  potential += entry_plug->lrPot;
92  
93    // std::cerr << "long range potential: " << potential << "\n";
94    for( el=0; el<nSRI; el++ ){
# Line 80 | Line 98 | double Thermo::getPotential(){
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);
101 >  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
102    potential = potential_global;
103 < #endif
103 > #endif // is_mpi
104  
105    return potential;
106   }
# Line 159 | Line 177 | void Thermo::velocitize() {
177      
178      // picks random velocities from a gaussian distribution
179      // centered on vbar
180 <    
180 > #ifndef USE_SPRNG
181 >    /* If we are using mpi, we need to use the SPRNG random
182 >       generator. The non drand48 generator will just repeat
183 >       the same numbers for every node creating a non-gaussian
184 >       distribution for the simulation. drand48 is fine for the
185 >       single processor version of the code, but SPRNG should
186 >       still be preferred for consistency.
187 >    */
188 >
189 > #ifdef IS_MPI
190 > #error "SPRNG random number generator must be used for MPI"
191 > #else
192 >    // warning "Using drand48 for random number generation"
193 > #endif  // is_mpi
194 >
195      x = drand48();
196      y = drand48();
197      vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
# Line 171 | Line 203 | void Thermo::velocitize() {
203      x = drand48();
204      y = drand48();
205      vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
206 <    
206 >
207 > #endif // use_spring
208 >
209 > #ifdef USE_SPRNG
210 >    vx = vbar * gaussStream->getGaussian();
211 >    vy = vbar * gaussStream->getGaussian();
212 >    vz = vbar * gaussStream->getGaussian();
213 > #endif // use_spring
214 >
215      atoms[vr]->set_vx( vx );
216      atoms[vr]->set_vy( vy );
217      atoms[vr]->set_vz( vz );
# Line 219 | Line 259 | void Thermo::velocitize() {
259        if( atoms[i]->isDirectional() ){
260          
261          dAtom = (DirectionalAtom *)atoms[i];
262 +
263 + #ifndef USE_SPRNG
264 +
265 + #ifdef IS_MPI
266 + #error "SPRNG random number generator must be used for MPI"
267 + #else  // is_mpi
268 +        //warning "Using drand48 for random number generation"
269 + #endif   // is_MPI
270          
271          vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
272          x = drand48();
# Line 234 | Line 282 | void Thermo::velocitize() {
282          x = drand48();
283          y = drand48();
284          jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
285 +
286 + #else //use_sprng
287 +
288 +        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
289 +        jx = vbar * gaussStream->getGaussian();
290 +
291 +        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
292 +        jy = vbar * gaussStream->getGaussian();
293 +
294 +        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
295 +        jz = vbar * gaussStream->getGaussian();
296 + #endif //use_sprng
297          
298          dAtom->setJx( jx );
299          dAtom->setJy( jy );

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines