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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 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC

# Line 10 | Line 10 | using namespace std;
10   #include "Thermo.hpp"
11   #include "SRI.hpp"
12   #include "Integrator.hpp"
13 + #include "simError.h"
14  
15 + #ifdef IS_MPI
16 + #define __C
17 + #include "mpiSimulation.hpp"
18 + #endif // is_mpi
19 +
20 +
21   #define BASE_SEED 123456789
22  
23   Thermo::Thermo( SimInfo* the_entry_plug ) {
# Line 77 | Line 84 | double Thermo::getPotential(){
84  
85   double Thermo::getPotential(){
86    
87 +  double potential_local;
88    double potential;
81 –  double potential_global;
89    int el, nSRI;
90 <  SRI** sris;
90 >  Molecule* molecules;
91  
92 <  sris = entry_plug->sr_interactions;
92 >  molecules = entry_plug->molecules;
93    nSRI = entry_plug->n_SRI;
94  
95 +  potential_local = 0.0;
96    potential = 0.0;
97 <  potential_global = 0.0;
90 <  potential += entry_plug->lrPot;
97 >  potential_local += entry_plug->lrPot;
98  
99 <  for( el=0; el<nSRI; el++ ){
100 <    
94 <    potential += sris[el]->get_potential();
99 >  for( el=0; el<entry_plug->n_mol; el++ ){    
100 >    potential_local += molecules[el].getPotential();
101    }
102  
103 + #ifdef IS_MPI
104 +  /*
105 +  std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot
106 +            << "; pot_local = " << potential_local
107 +            << "; pot = " << potential << "\n";
108 +  */
109 + #endif
110 +
111    // Get total potential for entire system from MPI.
112   #ifdef IS_MPI
113 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
114 <  potential = potential_global;
115 <
113 >  MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM);
114 > #else
115 >  potential = potential_local;
116   #endif // is_mpi
117  
118 + #ifdef IS_MPI
119 +  /*
120 +  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
121 +  */
122 + #endif
123 +
124    return potential;
125   }
126  
# Line 116 | Line 136 | double Thermo::getTemperature(){
136  
137    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
138    double temperature;
139 +  int ndf_local, ndf;
140    
141 <  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
142 <    - entry_plug->n_constraints - 3;
141 >  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
142 >    - entry_plug->n_constraints;
143  
144 + #ifdef IS_MPI
145 +  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
146 + #else
147 +  ndf = ndf_local;
148 + #endif
149 +
150 +  ndf = ndf - 3;
151 +  
152    temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
153    return temperature;
154   }
# Line 140 | Line 169 | void Thermo::velocitize() {
169    double jx, jy, jz;
170    int i, vr, vd; // velocity randomizer loop counters
171    double vdrift[3];
143 –  double mtot = 0.0;
172    double vbar;
173    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
174    double av2;
175    double kebar;
176 <  int ndf; // number of degrees of freedom
177 <  int ndfRaw; // the raw number of degrees of freedom
176 >  int ndf, ndf_local; // number of degrees of freedom
177 >  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
178    int n_atoms;
179    Atom** atoms;
180    DirectionalAtom* dAtom;
# Line 160 | Line 188 | void Thermo::velocitize() {
188    n_oriented    = entry_plug->n_oriented;
189    n_constraints = entry_plug->n_constraints;
190    
191 +  // Raw degrees of freedom that we have to set
192 +  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
193  
194 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
195 <  ndf = ndfRaw - n_constraints - 3;
194 >  // Degrees of freedom that can contain kinetic energy
195 >  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
196 >    - entry_plug->n_constraints;
197 >  
198 > #ifdef IS_MPI
199 >  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
200 >  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
201 > #else
202 >  ndfRaw = ndfRaw_local;
203 >  ndf = ndf_local;
204 > #endif
205 >  ndf = ndf - 3;
206 >
207    kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
208    
209    for(vr = 0; vr < n_atoms; vr++){
# Line 185 | Line 226 | void Thermo::velocitize() {
226      atoms[vr]->set_vy( vy );
227      atoms[vr]->set_vz( vz );
228    }
229 +
230 +  // Get the Center of Mass drift velocity.
231 +
232 +  getCOMVel(vdrift);
233    
234    //  Corrects for the center of mass drift.
235    // 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 –  
236  
237    for(vd = 0; vd < n_atoms; vd++){
238      
239      vx = atoms[vd]->get_vx();
240      vy = atoms[vd]->get_vy();
241      vz = atoms[vd]->get_vz();
242 <    
216 <    
242 >        
243      vx -= vdrift[0];
244      vy -= vdrift[1];
245      vz -= vdrift[2];
# Line 246 | Line 272 | void Thermo::velocitize() {
272      }  
273    }
274   }
275 +
276 + void Thermo::getCOMVel(double vdrift[3]){
277 +
278 +  double mtot, mtot_local;
279 +  double vdrift_local[3];
280 +  int vd, n_atoms;
281 +  Atom** atoms;
282 +
283 +  // We are very careless here with the distinction between n_atoms and n_local
284 +  // We should really fix this before someone pokes an eye out.
285 +
286 +  n_atoms = entry_plug->n_atoms;  
287 +  atoms   = entry_plug->atoms;
288 +
289 +  mtot_local = 0.0;
290 +  vdrift_local[0] = 0.0;
291 +  vdrift_local[1] = 0.0;
292 +  vdrift_local[2] = 0.0;
293 +  
294 +  for(vd = 0; vd < n_atoms; vd++){
295 +    
296 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
297 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
298 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
299 +    
300 +    mtot_local += atoms[vd]->getMass();
301 +  }
302 +
303 + #ifdef IS_MPI
304 +  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
305 +  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
306 + #else
307 +  mtot = mtot_local;
308 +  for(vd = 0; vd < 3; vd++) {
309 +    vdrift[vd] = vdrift_local[vd];
310 +  }
311 + #endif
312 +    
313 +  for (vd = 0; vd < 3; vd++) {
314 +    vdrift[vd] = vdrift[vd] / mtot;
315 +  }
316 +  
317 + }
318 +

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