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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 401 by chuckv, Tue Mar 25 22:54:16 2003 UTC vs.
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"
16 > #include "mpiSimulation.hpp"
17 > #endif // is_mpi
18  
19 +
20   #define BASE_SEED 123456789
21  
22   Thermo::Thermo( SimInfo* the_entry_plug ) {
# Line 68 | 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 82 | Line 87 | double Thermo::getPotential(){
87    double potential_local;
88    double potential;
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_local += entry_plug->lrPot;
98  
99 <  for( el=0; el<nSRI; el++ ){    
100 <    potential_local += 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_local,&potential,1,MPI_DOUBLE,MPI_SUM);
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 122 | Line 135 | double Thermo::getTemperature(){
135      - entry_plug->n_constraints;
136  
137   #ifdef IS_MPI
138 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
138 >  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
139   #else
140    ndf = ndf_local;
141   #endif
# Line 134 | Line 147 | double Thermo::getPressure(){
147   }
148  
149   double Thermo::getPressure(){
150 <
151 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
152 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
140 < //  const double conv_A_m = 1.0E-10; //convert A -> m
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  
154    return 0.0;
155   }
# Line 148 | Line 160 | void Thermo::velocitize() {
160    double vx, vy, vz;
161    double jx, jy, jz;
162    int i, vr, vd; // velocity randomizer loop counters
163 <  double *vdrift;
163 >  double vdrift[3];
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 168 | 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 179 | 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 196 | Line 221 | void Thermo::velocitize() {
221  
222    // Get the Center of Mass drift velocity.
223  
224 <  vdrift = getCOMVel();
224 >  getCOMVel(vdrift);
225    
226    //  Corrects for the center of mass drift.
227    // sums all the momentum and divides by total mass.
# Line 240 | Line 265 | double* Thermo::getCOMVel(){
265    }
266   }
267  
268 < double* Thermo::getCOMVel(){
268 > void Thermo::getCOMVel(double vdrift[3]){
269  
270    double mtot, mtot_local;
246 –  double* vdrift;
271    double vdrift_local[3];
272    int vd, n_atoms;
273    Atom** atoms;
274  
251 –  vdrift = new double[3];
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  
# Line 270 | Line 293 | double* Thermo::getCOMVel(){
293    }
294  
295   #ifdef IS_MPI
296 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
297 <  MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM);
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++) {
# Line 283 | Line 306 | double* Thermo::getCOMVel(){
306      vdrift[vd] = vdrift[vd] / mtot;
307    }
308    
286 –  return vdrift;
309   }
310  

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