| 10 |
|
#include "Thermo.hpp" |
| 11 |
|
#include "SRI.hpp" |
| 12 |
|
#include "Integrator.hpp" |
| 13 |
+ |
#include "simError.h" |
| 14 |
|
|
| 15 |
|
#ifdef IS_MPI |
| 16 |
|
#define __C |
| 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 |
+ |
#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_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
| 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 |
|
|
| 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 |
|
|
| 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 |
| 145 |
– |
|
| 161 |
|
return 0.0; |
| 162 |
|
} |
| 163 |
|
|
| 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 |
