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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 447 by mmeineke, Thu Apr 3 20:21:54 2003 UTC

# Line 4 | Line 4 | 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 ) {
# Line 66 | Line 72 | double Thermo::getKinetic(){
72      }
73    }
74   #ifdef IS_MPI
75 <  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
75 >  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
76 >                MPI_SUM, MPI_COMM_WORLD);
77    kinetic = kinetic_global;
78   #endif //is_mpi
79  
# 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    // Get total potential for entire system from MPI.
104   #ifdef IS_MPI
105 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
106 <  potential = potential_global;
107 <
105 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
106 >                MPI_SUM, MPI_COMM_WORLD);
107 > #else
108 >  potential = potential_local;
109   #endif // is_mpi
110  
111 + #ifdef IS_MPI
112 +  /*
113 +  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
114 +  */
115 + #endif
116 +
117    return potential;
118   }
119  
# Line 116 | Line 129 | double Thermo::getTemperature(){
129  
130    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131    double temperature;
132 +  int ndf_local, ndf;
133    
134 <  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
135 <    - entry_plug->n_constraints - 3;
134 >  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
135 >    - entry_plug->n_constraints;
136  
137 + #ifdef IS_MPI
138 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
139 + #else
140 +  ndf = ndf_local;
141 + #endif
142 +
143 +  ndf = ndf - 3;
144 +  
145    temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
146    return temperature;
147   }
148  
149   double Thermo::getPressure(){
150 +  // returns pressure in units amu*fs^-2*Ang^-1
151 +  // routine derived via viral theorem description in:
152 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
153  
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 –
154    return 0.0;
155   }
156  
# Line 140 | Line 161 | void Thermo::velocitize() {
161    double jx, jy, jz;
162    int i, vr, vd; // velocity randomizer loop counters
163    double vdrift[3];
143 –  double mtot = 0.0;
164    double vbar;
165    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
166    double av2;
167    double kebar;
168 <  int ndf; // number of degrees of freedom
169 <  int ndfRaw; // the raw number of degrees of freedom
168 >  int ndf, ndf_local; // number of degrees of freedom
169 >  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
170    int n_atoms;
171    Atom** atoms;
172    DirectionalAtom* dAtom;
# Line 160 | Line 180 | void Thermo::velocitize() {
180    n_oriented    = entry_plug->n_oriented;
181    n_constraints = entry_plug->n_constraints;
182    
183 +  // Raw degrees of freedom that we have to set
184 +  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
185  
186 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
187 <  ndf = ndfRaw - n_constraints - 3;
186 >  // Degrees of freedom that can contain kinetic energy
187 >  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
188 >    - entry_plug->n_constraints;
189 >  
190 > #ifdef IS_MPI
191 >  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
192 >  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
193 > #else
194 >  ndfRaw = ndfRaw_local;
195 >  ndf = ndf_local;
196 > #endif
197 >  ndf = ndf - 3;
198 >
199    kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
200    
201    for(vr = 0; vr < n_atoms; vr++){
# Line 171 | Line 204 | void Thermo::velocitize() {
204  
205      av2 = 2.0 * kebar / atoms[vr]->getMass();
206      vbar = sqrt( av2 );
207 <
207 >
208   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
209      
210      // picks random velocities from a gaussian distribution
# Line 185 | Line 218 | void Thermo::velocitize() {
218      atoms[vr]->set_vy( vy );
219      atoms[vr]->set_vz( vz );
220    }
221 +
222 +  // Get the Center of Mass drift velocity.
223 +
224 +  getCOMVel(vdrift);
225    
226    //  Corrects for the center of mass drift.
227    // 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 –  
228  
229    for(vd = 0; vd < n_atoms; vd++){
230      
231      vx = atoms[vd]->get_vx();
232      vy = atoms[vd]->get_vy();
233      vz = atoms[vd]->get_vz();
234 <    
216 <    
234 >        
235      vx -= vdrift[0];
236      vy -= vdrift[1];
237      vz -= vdrift[2];
# Line 246 | Line 264 | void Thermo::velocitize() {
264      }  
265    }
266   }
267 +
268 + void Thermo::getCOMVel(double vdrift[3]){
269 +
270 +  double mtot, mtot_local;
271 +  double vdrift_local[3];
272 +  int vd, n_atoms;
273 +  Atom** atoms;
274 +
275 +  // We are very careless here with the distinction between n_atoms and n_local
276 +  // We should really fix this before someone pokes an eye out.
277 +
278 +  n_atoms = entry_plug->n_atoms;  
279 +  atoms   = entry_plug->atoms;
280 +
281 +  mtot_local = 0.0;
282 +  vdrift_local[0] = 0.0;
283 +  vdrift_local[1] = 0.0;
284 +  vdrift_local[2] = 0.0;
285 +  
286 +  for(vd = 0; vd < n_atoms; vd++){
287 +    
288 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
289 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
290 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
291 +    
292 +    mtot_local += atoms[vd]->getMass();
293 +  }
294 +
295 + #ifdef IS_MPI
296 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
297 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
298 + #else
299 +  mtot = mtot_local;
300 +  for(vd = 0; vd < 3; vd++) {
301 +    vdrift[vd] = vdrift_local[vd];
302 +  }
303 + #endif
304 +    
305 +  for (vd = 0; vd < 3; vd++) {
306 +    vdrift[vd] = vdrift[vd] / mtot;
307 +  }
308 +  
309 + }
310 +

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