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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 403 by chuckv, Wed Mar 26 15:37:05 2003 UTC vs.
Revision 477 by gezelter, Tue Apr 8 14:34:30 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
# Line 72 | 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 86 | 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 120 | Line 129 | double Thermo::getTemperature(){
129  
130    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131    double temperature;
123 –  int ndf_local, ndf;
132    
133 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
126 <    - entry_plug->n_constraints;
127 <
128 < #ifdef IS_MPI
129 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
130 < #else
131 <  ndf = ndf_local;
132 < #endif
133 <
134 <  ndf = ndf - 3;
135 <  
136 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
133 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
134    return temperature;
135   }
136  
137   double Thermo::getPressure(){
138 +  // returns pressure in units amu*fs^-2*Ang^-1
139 +  // routine derived via viral theorem description in:
140 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
141  
142 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
143 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
144 < //  const double conv_A_m = 1.0E-10; //convert A -> m
142 >  const double e_convert = 4.184e-4;
143 >  const double p_convert = 1.63882576e8;
144 >  double molmass;
145 >  double vcom[3];
146 >  double p_local, p_sum, p_mol, virial;
147 >  double theBox[3];
148 >  double* tau;
149 >  int i, nMols;
150 >  Molecule* molecules;
151  
152 <  return 0.0;
152 >  nMols = entry_plug->n_mol;
153 >  molecules = entry_plug->molecules;
154 >  tau = entry_plug->tau;
155 >
156 >  // use velocities of molecular centers of mass and molecular masses:
157 >  p_local = 0.0;
158 >
159 >  for (i=0; i < nMols; i++) {
160 >    molmass = molecules[i].getCOMvel(vcom);
161 >    p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass;
162 >  }
163 >
164 >  // Get total for entire system from MPI.
165 > #ifdef IS_MPI
166 >  MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
167 > #else
168 >  p_sum = p_local;
169 > #endif // is_mpi
170 >
171 >  virial = tau[0] + tau[4] + tau[8];
172 >  entry_plug->getBox(theBox);
173 >
174 >  p_mol = p_convert * (p_sum - virial*e_convert) /
175 >    (3.0 * theBox[0] * theBox[1]* theBox[2]);
176 >
177 >  return p_mol;
178   }
179  
180   void Thermo::velocitize() {
# Line 157 | Line 188 | void Thermo::velocitize() {
188    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
189    double av2;
190    double kebar;
160 –  int ndf, ndf_local; // number of degrees of freedom
161 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
191    int n_atoms;
192    Atom** atoms;
193    DirectionalAtom* dAtom;
# Line 172 | Line 201 | void Thermo::velocitize() {
201    n_oriented    = entry_plug->n_oriented;
202    n_constraints = entry_plug->n_constraints;
203    
204 <  // Raw degrees of freedom that we have to set
205 <  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
177 <
178 <  // Degrees of freedom that can contain kinetic energy
179 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
180 <    - entry_plug->n_constraints;
204 >  kebar = kb * temperature * (double)entry_plug->ndf /
205 >    ( 2.0 * (double)entry_plug->ndfRaw );
206    
182 – #ifdef IS_MPI
183 –  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
184 –  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
185 – #else
186 –  ndfRaw = ndfRaw_local;
187 –  ndf = ndf_local;
188 – #endif
189 –  ndf = ndf - 3;
190 –
191 –  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
192 –  
207    for(vr = 0; vr < n_atoms; vr++){
208      
209      // uses equipartition theory to solve for vbar in angstrom/fs
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 245 | 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 285 | Line 299 | void Thermo::getCOMVel(double vdrift[3]){
299    }
300  
301   #ifdef IS_MPI
302 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
303 <  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
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++) {

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