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root/group/trunk/mdtools/md_code/Thermo.cpp
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Comparing:
branches/mmeineke/mdtools/md_code/Thermo.cpp (file contents), Revision 10 by mmeineke, Tue Jul 9 18:40:59 2002 UTC vs.
trunk/mdtools/md_code/Thermo.cpp (file contents), Revision 264 by chuckv, Tue Feb 4 20:16:08 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 17 | Line 36 | double Thermo::getKinetic(){
36    DirectionalAtom *dAtom;
37  
38    int n_atoms;
39 +  double kinetic_global;
40    Atom** atoms;
41 +
42    
43    n_atoms = entry_plug->n_atoms;
44    atoms = entry_plug->atoms;
45  
46    kinetic = 0.0;
47 +  kinetic_global = 0.0;
48    for( kl=0; kl < n_atoms; kl++ ){
49  
50      vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
# Line 44 | Line 66 | double Thermo::getKinetic(){
66          + (jz2 / dAtom->getIzz());
67      }
68    }
69 <  
69 > #ifdef IS_MPI
70 >  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
71 >  kinetic = kinetic_global;
72 > #endif //is_mpi
73 >
74    kinetic = kinetic * 0.5 / e_convert;
75  
76    return kinetic;
# Line 53 | Line 79 | double Thermo::getPotential(){
79   double Thermo::getPotential(){
80    
81    double potential;
82 +  double potential_global;
83    int el, nSRI;
84    SRI** sris;
85  
# Line 60 | Line 87 | double Thermo::getPotential(){
87    nSRI = entry_plug->n_SRI;
88  
89    potential = 0.0;
90 +  potential_global = 0.0;
91 +  potential += entry_plug->lrPot;
92  
64 –  potential += entry_plug->longRange->get_potential();;
65 –
93    // std::cerr << "long range potential: " << potential << "\n";
67 –
94    for( el=0; el<nSRI; el++ ){
95      
96      potential += sris[el]->get_potential();
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 +
104 + #endif // is_mpi
105 +
106    return potential;
107   }
108  
# Line 83 | Line 116 | double Thermo::getTemperature(){
116  
117   double Thermo::getTemperature(){
118  
119 <  const double kb = 1.88E-3; // boltzman's constant in kcal/(mol K)
119 >  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
120    double temperature;
121    
122    int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
# Line 95 | Line 128 | double Thermo::getPressure(){
128  
129   double Thermo::getPressure(){
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
133 <  const double conv_A_m = 1.0E-10; //convert A -> m
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
133 > //  const double conv_A_m = 1.0E-10; //convert A -> m
134  
135    return 0.0;
136   }
# Line 145 | Line 178 | void Thermo::velocitize() {
178      
179      // picks random velocities from a gaussian distribution
180      // centered on vbar
181 <    
181 > #ifndef USE_SPRNG
182 >    /* If we are using mpi, we need to use the SPRNG random
183 >       generator. The non drand48 generator will just repeat
184 >       the same numbers for every node creating a non-gaussian
185 >       distribution for the simulation. drand48 is fine for the
186 >       single processor version of the code, but SPRNG should
187 >       still be preferred for consistency.
188 >    */
189 >
190 > #ifdef IS_MPI
191 > #error "SPRNG random number generator must be used for MPI"
192 > #else
193 >    // warning "Using drand48 for random number generation"
194 > #endif  // is_mpi
195 >
196      x = drand48();
197      y = drand48();
198      vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
# Line 157 | Line 204 | void Thermo::velocitize() {
204      x = drand48();
205      y = drand48();
206      vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
207 <    
207 >
208 > #endif // use_spring
209 >
210 > #ifdef USE_SPRNG
211 >    vx = vbar * gaussStream->getGaussian();
212 >    vy = vbar * gaussStream->getGaussian();
213 >    vz = vbar * gaussStream->getGaussian();
214 > #endif // use_spring
215 >
216      atoms[vr]->set_vx( vx );
217      atoms[vr]->set_vy( vy );
218      atoms[vr]->set_vz( vz );
# Line 205 | Line 260 | void Thermo::velocitize() {
260        if( atoms[i]->isDirectional() ){
261          
262          dAtom = (DirectionalAtom *)atoms[i];
263 +
264 + #ifndef USE_SPRNG
265 +
266 + #ifdef IS_MPI
267 + #error "SPRNG random number generator must be used for MPI"
268 + #else  // is_mpi
269 +        //warning "Using drand48 for random number generation"
270 + #endif   // is_MPI
271          
272          vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
273          x = drand48();
# Line 220 | Line 283 | void Thermo::velocitize() {
283          x = drand48();
284          y = drand48();
285          jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
286 +
287 + #else //use_sprng
288 +
289 +        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
290 +        jx = vbar * gaussStream->getGaussian();
291 +
292 +        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
293 +        jy = vbar * gaussStream->getGaussian();
294 +
295 +        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
296 +        jz = vbar * gaussStream->getGaussian();
297 + #endif //use_sprng
298          
299          dAtom->setJx( jx );
300          dAtom->setJy( jy );

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