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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Thermo.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Thermo.cpp (file contents), Revision 445 by gezelter, Thu Apr 3 19:58:24 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   }
155  
156   double Thermo::getPressure(){
157 +  // returns pressure in units amu*fs^-2*Ang^-1
158 +  // routine derived via viral theorem description in:
159 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
160  
129 – //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
130 – // 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
132 –
161    return 0.0;
162   }
163  
# Line 140 | Line 168 | void Thermo::velocitize() {
168    double jx, jy, jz;
169    int i, vr, vd; // velocity randomizer loop counters
170    double vdrift[3];
143 –  double mtot = 0.0;
171    double vbar;
172    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
173    double av2;
174    double kebar;
175 <  int ndf; // number of degrees of freedom
176 <  int ndfRaw; // the raw number of degrees of freedom
175 >  int ndf, ndf_local; // number of degrees of freedom
176 >  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
177    int n_atoms;
178    Atom** atoms;
179    DirectionalAtom* dAtom;
# Line 160 | Line 187 | void Thermo::velocitize() {
187    n_oriented    = entry_plug->n_oriented;
188    n_constraints = entry_plug->n_constraints;
189    
190 +  // Raw degrees of freedom that we have to set
191 +  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
192  
193 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
194 <  ndf = ndfRaw - n_constraints - 3;
193 >  // Degrees of freedom that can contain kinetic energy
194 >  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
195 >    - entry_plug->n_constraints;
196 >  
197 > #ifdef IS_MPI
198 >  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
199 >  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
200 > #else
201 >  ndfRaw = ndfRaw_local;
202 >  ndf = ndf_local;
203 > #endif
204 >  ndf = ndf - 3;
205 >
206    kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
207    
208    for(vr = 0; vr < n_atoms; vr++){
# Line 171 | Line 211 | void Thermo::velocitize() {
211  
212      av2 = 2.0 * kebar / atoms[vr]->getMass();
213      vbar = sqrt( av2 );
214 <
214 >
215   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
216      
217      // picks random velocities from a gaussian distribution
# Line 185 | Line 225 | void Thermo::velocitize() {
225      atoms[vr]->set_vy( vy );
226      atoms[vr]->set_vz( vz );
227    }
228 +
229 +  // Get the Center of Mass drift velocity.
230 +
231 +  getCOMVel(vdrift);
232    
233    //  Corrects for the center of mass drift.
234    // 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 –  
235  
236    for(vd = 0; vd < n_atoms; vd++){
237      
238      vx = atoms[vd]->get_vx();
239      vy = atoms[vd]->get_vy();
240      vz = atoms[vd]->get_vz();
241 <    
216 <    
241 >        
242      vx -= vdrift[0];
243      vy -= vdrift[1];
244      vz -= vdrift[2];
# Line 246 | Line 271 | void Thermo::velocitize() {
271      }  
272    }
273   }
274 +
275 + void Thermo::getCOMVel(double vdrift[3]){
276 +
277 +  double mtot, mtot_local;
278 +  double vdrift_local[3];
279 +  int vd, n_atoms;
280 +  Atom** atoms;
281 +
282 +  // We are very careless here with the distinction between n_atoms and n_local
283 +  // We should really fix this before someone pokes an eye out.
284 +
285 +  n_atoms = entry_plug->n_atoms;  
286 +  atoms   = entry_plug->atoms;
287 +
288 +  mtot_local = 0.0;
289 +  vdrift_local[0] = 0.0;
290 +  vdrift_local[1] = 0.0;
291 +  vdrift_local[2] = 0.0;
292 +  
293 +  for(vd = 0; vd < n_atoms; vd++){
294 +    
295 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
296 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
297 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
298 +    
299 +    mtot_local += atoms[vd]->getMass();
300 +  }
301 +
302 + #ifdef IS_MPI
303 +  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
304 +  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
305 + #else
306 +  mtot = mtot_local;
307 +  for(vd = 0; vd < 3; vd++) {
308 +    vdrift[vd] = vdrift_local[vd];
309 +  }
310 + #endif
311 +    
312 +  for (vd = 0; vd < 3; vd++) {
313 +    vdrift[vd] = vdrift[vd] / mtot;
314 +  }
315 +  
316 + }
317 +

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