| 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 |
| 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 |
|
|
| 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<entry_plug->n_mol; el++ ){ |
| 100 |
< |
potential_local += entry_plug->molecules[el]->get_potential(); |
| 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 |
|
} |
| 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 |
| 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 |
|
|
| 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 |
– |
|
| 154 |
|
return 0.0; |
| 155 |
|
} |
| 156 |
|
|
| 188 |
|
- entry_plug->n_constraints; |
| 189 |
|
|
| 190 |
|
#ifdef IS_MPI |
| 191 |
< |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
| 192 |
< |
MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM); |
| 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; |
| 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 |
| 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++) { |
