| 15 |
|
|
| 16 |
|
#ifdef IS_MPI |
| 17 |
|
double tempBig = bigSigma; |
| 18 |
< |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 18 |
> |
MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX, |
| 19 |
> |
MPI_COMM_WORLD); |
| 20 |
|
#endif //is_mpi |
| 21 |
|
|
| 22 |
|
//calc rCut and rList |
| 23 |
|
|
| 24 |
< |
entry_plug->rCut = 2.5 bigSigma; |
| 24 |
> |
entry_plug->rCut = 2.5 * bigSigma; |
| 25 |
|
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
| 26 |
|
entry_plug->rCut = entry_plug->box_x / 2.0; |
| 27 |
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
| 39 |
|
double* frc; |
| 40 |
|
double* pos; |
| 41 |
|
double* trq; |
| 41 |
– |
double* tau; |
| 42 |
|
double* A; |
| 43 |
< |
double* u_l; |
| 43 |
> |
double* u_l;; |
| 44 |
> |
DirectionalAtom* dAtom; |
| 45 |
|
|
| 46 |
+ |
double ut[3]; |
| 47 |
|
|
| 48 |
+ |
//u_l = new double[entry_plug->n_atoms]; |
| 49 |
+ |
|
| 50 |
|
short int passedCalcPot = (short int)calcPot; |
| 51 |
|
short int passedCalcStress = (short int)calcStress; |
| 52 |
|
|
| 53 |
|
// forces are zeroed here, before any are acumulated. |
| 54 |
|
// NOTE: do not rezero the forces in Fortran. |
| 55 |
|
|
| 56 |
+ |
|
| 57 |
|
for(i=0; i<entry_plug->n_atoms; i++){ |
| 58 |
|
entry_plug->atoms[i]->zeroForces(); |
| 59 |
+ |
|
| 60 |
+ |
// if( entry_plug->atoms[i]->isDirectional() ){ |
| 61 |
+ |
// dAtom = (DirectionalAtom *)entry_plug->atoms[i]; |
| 62 |
+ |
// dAtom->getU(ut); |
| 63 |
+ |
|
| 64 |
+ |
|
| 65 |
+ |
// if(dAtom->getIndex()== 1){ |
| 66 |
+ |
// std::cerr << "atom 2's u_l = " << ut[0] << ", " << ut[1] |
| 67 |
+ |
// << ", " << ut[2] << "\n"; |
| 68 |
+ |
// } |
| 69 |
+ |
// } |
| 70 |
+ |
|
| 71 |
|
} |
| 72 |
|
|
| 73 |
|
for(i=0; i<entry_plug->n_mol; i++ ){ |
| 74 |
< |
entry_plug->molecules[i]->calc_forces(); |
| 74 |
> |
entry_plug->molecules[i].calcForces(); |
| 75 |
|
} |
| 76 |
|
|
| 77 |
|
frc = Atom::getFrcArray(); |
| 79 |
|
trq = Atom::getTrqArray(); |
| 80 |
|
A = Atom::getAmatArray(); |
| 81 |
|
u_l = Atom::getUlArray(); |
| 65 |
– |
tau = entry_plug->tau; |
| 82 |
|
|
| 83 |
|
|
| 84 |
|
isError = 0; |
| 85 |
|
entry_plug->lrPot = 0.0; |
| 86 |
|
|
| 87 |
< |
|
| 87 |
> |
for (i=0; i<9; i++) { |
| 88 |
> |
entry_plug->tau[i] = 0.0; |
| 89 |
> |
} |
| 90 |
> |
|
| 91 |
|
fortranForceLoop( pos, |
| 92 |
|
A, |
| 93 |
|
u_l, |
| 94 |
|
frc, |
| 95 |
|
trq, |
| 96 |
< |
tau, |
| 96 |
> |
entry_plug->tau, |
| 97 |
|
&(entry_plug->lrPot), |
| 98 |
|
&passedCalcPot, |
| 99 |
|
&passedCalcStress, |
| 100 |
|
&isError ); |
| 101 |
|
|
| 102 |
+ |
// delete[] u_l; |
| 103 |
|
|
| 104 |
|
if( isError ){ |
| 105 |
|
sprintf( painCave.errMsg, |
