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root/group/branches/no-template-branch/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 454 by gezelter, Fri Apr 4 01:57:11 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 112 | Line 125 | double Thermo::getTotalE(){
125    return total;
126   }
127  
128 + int Thermo::getNDF(){
129 +  int ndf_local, ndf;
130 +  
131 +  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
132 +    - entry_plug->n_constraints;
133 +
134 + #ifdef IS_MPI
135 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
136 + #else
137 +  ndf = ndf_local;
138 + #endif
139 +
140 +  ndf = ndf - 3;
141 +
142 +  return ndf;
143 + }
144 +
145 + int Thermo::getNDFraw() {
146 +  int ndfRaw_local, ndfRaw;
147 +
148 +  // Raw degrees of freedom that we have to set
149 +  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
150 +  
151 + #ifdef IS_MPI
152 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
153 + #else
154 +  ndfRaw = ndfRaw_local;
155 + #endif
156 +
157 +  return ndfRaw;
158 + }
159 +
160 +
161   double Thermo::getTemperature(){
162  
163    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
164    double temperature;
165    
166 <  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 <    - entry_plug->n_constraints - 3;
122 <
123 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
166 >  temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * kb );
167    return temperature;
168   }
169  
170   double Thermo::getPressure(){
171 <
172 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
173 < // 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
171 >  // returns pressure in units amu*fs^-2*Ang^-1
172 >  // routine derived via viral theorem description in:
173 >  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
174  
175    return 0.0;
176   }
# Line 140 | Line 182 | void Thermo::velocitize() {
182    double jx, jy, jz;
183    int i, vr, vd; // velocity randomizer loop counters
184    double vdrift[3];
143 –  double mtot = 0.0;
185    double vbar;
186    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
187    double av2;
188    double kebar;
189 <  int ndf; // number of degrees of freedom
190 <  int ndfRaw; // the raw number of degrees of freedom
189 >  int ndf, ndf_local; // number of degrees of freedom
190 >  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
191    int n_atoms;
192    Atom** atoms;
193    DirectionalAtom* dAtom;
# Line 160 | Line 201 | void Thermo::velocitize() {
201    n_oriented    = entry_plug->n_oriented;
202    n_constraints = entry_plug->n_constraints;
203    
204 <
205 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
204 >  kebar = kb * temperature * (double)this->getNDF() /
205 >    ( 2.0 * (double)this->getNDFraw() );
206    
207    for(vr = 0; vr < n_atoms; vr++){
208      
# Line 171 | Line 210 | void Thermo::velocitize() {
210  
211      av2 = 2.0 * kebar / atoms[vr]->getMass();
212      vbar = sqrt( av2 );
213 <
213 >
214   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
215      
216      // picks random velocities from a gaussian distribution
# Line 185 | Line 224 | void Thermo::velocitize() {
224      atoms[vr]->set_vy( vy );
225      atoms[vr]->set_vz( vz );
226    }
227 +
228 +  // Get the Center of Mass drift velocity.
229 +
230 +  getCOMVel(vdrift);
231    
232    //  Corrects for the center of mass drift.
233    // 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 –  
234  
235    for(vd = 0; vd < n_atoms; vd++){
236      
237      vx = atoms[vd]->get_vx();
238      vy = atoms[vd]->get_vy();
239      vz = atoms[vd]->get_vz();
240 <    
216 <    
240 >        
241      vx -= vdrift[0];
242      vy -= vdrift[1];
243      vz -= vdrift[2];
# Line 235 | Line 259 | void Thermo::velocitize() {
259  
260          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
261          jy = vbar * gaussStream->getGaussian();
262 <
262 >        
263          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
264          jz = vbar * gaussStream->getGaussian();
265          
# Line 246 | Line 270 | void Thermo::velocitize() {
270      }  
271    }
272   }
273 +
274 + void Thermo::getCOMVel(double vdrift[3]){
275 +
276 +  double mtot, mtot_local;
277 +  double vdrift_local[3];
278 +  int vd, n_atoms;
279 +  Atom** atoms;
280 +
281 +  // We are very careless here with the distinction between n_atoms and n_local
282 +  // We should really fix this before someone pokes an eye out.
283 +
284 +  n_atoms = entry_plug->n_atoms;  
285 +  atoms   = entry_plug->atoms;
286 +
287 +  mtot_local = 0.0;
288 +  vdrift_local[0] = 0.0;
289 +  vdrift_local[1] = 0.0;
290 +  vdrift_local[2] = 0.0;
291 +  
292 +  for(vd = 0; vd < n_atoms; vd++){
293 +    
294 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
295 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
296 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
297 +    
298 +    mtot_local += atoms[vd]->getMass();
299 +  }
300 +
301 + #ifdef IS_MPI
302 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
303 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
304 + #else
305 +  mtot = mtot_local;
306 +  for(vd = 0; vd < 3; vd++) {
307 +    vdrift[vd] = vdrift_local[vd];
308 +  }
309 + #endif
310 +    
311 +  for (vd = 0; vd < 3; vd++) {
312 +    vdrift[vd] = vdrift[vd] / mtot;
313 +  }
314 +  
315 + }
316 +

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