| 1 |
< |
#include <cstdlib> |
| 1 |
> |
#include <iostream> |
| 2 |
|
|
| 3 |
+ |
using namespace std; |
| 4 |
+ |
|
| 5 |
+ |
|
| 6 |
+ |
#include <stdlib.h> |
| 7 |
+ |
|
| 8 |
|
#ifdef IS_MPI |
| 9 |
|
#include <mpi.h> |
| 10 |
|
#endif // is_mpi |
| 26 |
|
|
| 27 |
|
//calc rCut and rList |
| 28 |
|
|
| 29 |
< |
entry_plug->rCut = 2.5 * bigSigma; |
| 30 |
< |
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)) |
| 28 |
< |
entry_plug->rCut = entry_plug->box_y / 2.0; |
| 29 |
< |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
| 30 |
< |
entry_plug->rCut = entry_plug->box_z / 2.0; |
| 31 |
< |
|
| 32 |
< |
entry_plug->rList = entry_plug->rCut + 1.0; |
| 33 |
< |
|
| 29 |
> |
entry_plug->setDefaultRcut( 2.5 * bigSigma ); |
| 30 |
> |
|
| 31 |
|
} |
| 32 |
|
|
| 33 |
|
void ForceFields::doForces( int calcPot, int calcStress ){ |
| 36 |
|
double* frc; |
| 37 |
|
double* pos; |
| 38 |
|
double* trq; |
| 42 |
– |
double* tau; |
| 39 |
|
double* A; |
| 40 |
|
double* u_l;; |
| 41 |
< |
DirectionalAtom* dAtom; |
| 41 |
> |
SimState* config; |
| 42 |
|
|
| 47 |
– |
double ut[3]; |
| 48 |
– |
|
| 49 |
– |
//u_l = new double[entry_plug->n_atoms]; |
| 50 |
– |
|
| 43 |
|
short int passedCalcPot = (short int)calcPot; |
| 44 |
|
short int passedCalcStress = (short int)calcStress; |
| 45 |
|
|
| 46 |
< |
// forces are zeroed here, before any are acumulated. |
| 46 |
> |
// forces are zeroed here, before any are accumulated. |
| 47 |
|
// NOTE: do not rezero the forces in Fortran. |
| 48 |
|
|
| 57 |
– |
|
| 49 |
|
for(i=0; i<entry_plug->n_atoms; i++){ |
| 50 |
< |
entry_plug->atoms[i]->zeroForces(); |
| 60 |
< |
|
| 61 |
< |
// if( entry_plug->atoms[i]->isDirectional() ){ |
| 62 |
< |
// dAtom = (DirectionalAtom *)entry_plug->atoms[i]; |
| 63 |
< |
// dAtom->getU(ut); |
| 64 |
< |
|
| 65 |
< |
|
| 66 |
< |
// if(dAtom->getIndex()== 1){ |
| 67 |
< |
// std::cerr << "atom 2's u_l = " << ut[0] << ", " << ut[1] |
| 68 |
< |
// << ", " << ut[2] << "\n"; |
| 69 |
< |
// } |
| 70 |
< |
// } |
| 71 |
< |
|
| 50 |
> |
entry_plug->atoms[i]->zeroForces(); |
| 51 |
|
} |
| 52 |
|
|
| 53 |
|
for(i=0; i<entry_plug->n_mol; i++ ){ |
| 54 |
|
entry_plug->molecules[i].calcForces(); |
| 55 |
|
} |
| 56 |
|
|
| 57 |
< |
frc = Atom::getFrcArray(); |
| 79 |
< |
pos = Atom::getPosArray(); |
| 80 |
< |
trq = Atom::getTrqArray(); |
| 81 |
< |
A = Atom::getAmatArray(); |
| 82 |
< |
u_l = Atom::getUlArray(); |
| 83 |
< |
tau = entry_plug->tau; |
| 84 |
< |
|
| 57 |
> |
config = entry_plug->getConfiguration(); |
| 58 |
|
|
| 59 |
+ |
frc = config->getFrcArray(); |
| 60 |
+ |
pos = config->getPosArray(); |
| 61 |
+ |
trq = config->getTrqArray(); |
| 62 |
+ |
A = config->getAmatArray(); |
| 63 |
+ |
u_l = config->getUlArray(); |
| 64 |
+ |
|
| 65 |
|
isError = 0; |
| 66 |
|
entry_plug->lrPot = 0.0; |
| 67 |
|
|
| 68 |
+ |
for (i=0; i<9; i++) { |
| 69 |
+ |
entry_plug->tau[i] = 0.0; |
| 70 |
+ |
} |
| 71 |
|
|
| 72 |
< |
|
| 72 |
> |
std::cerr << "before\n" |
| 73 |
> |
<< " force[0] = " << frc[0] << "\n" |
| 74 |
> |
<< " pos[0] = " << pos[0] << "\n" |
| 75 |
> |
<< " trq[0] = " << trq[0] << "\n" |
| 76 |
> |
<< " A[0] = " << A[0] << "\n" |
| 77 |
> |
<< " tau = " << entry_plug->tau[0] << ", " << entry_plug->tau[1] << ", " << entry_plug->tau[2] << "\n" |
| 78 |
> |
<< " " << entry_plug->tau[3] << ", " << entry_plug->tau[4] << ", " << entry_plug->tau[5] << "\n" |
| 79 |
> |
<< " " << entry_plug->tau[6] << ", " << entry_plug->tau[7] << ", " << entry_plug->tau[8] << "\n\n"; |
| 80 |
> |
|
| 81 |
|
fortranForceLoop( pos, |
| 82 |
|
A, |
| 83 |
|
u_l, |
| 84 |
|
frc, |
| 85 |
|
trq, |
| 86 |
< |
tau, |
| 86 |
> |
entry_plug->tau, |
| 87 |
|
&(entry_plug->lrPot), |
| 88 |
|
&passedCalcPot, |
| 89 |
|
&passedCalcStress, |
| 90 |
|
&isError ); |
| 91 |
|
|
| 92 |
|
|
| 93 |
< |
// delete[] u_l; |
| 93 |
> |
std::cerr << "after\n" |
| 94 |
> |
<< " force[0] = " << frc[0] << "\n" |
| 95 |
> |
<< " pos[0] = " << pos[0] << "\n" |
| 96 |
> |
<< " trq[0] = " << trq[0] << "\n" |
| 97 |
> |
<< " A[0] = " << A[0] << "\n" |
| 98 |
> |
<< " tau = " << entry_plug->tau[0] << ", " << entry_plug->tau[1] << ", " << entry_plug->tau[2] << "\n" |
| 99 |
> |
<< " " << entry_plug->tau[3] << ", " << entry_plug->tau[4] << ", " << entry_plug->tau[5] << "\n" |
| 100 |
> |
<< " " << entry_plug->tau[6] << ", " << entry_plug->tau[7] << ", " << entry_plug->tau[8] << "\n\n"; |
| 101 |
|
|
| 102 |
|
if( isError ){ |
| 103 |
|
sprintf( painCave.errMsg, |
| 111 |
|
"returned from the force calculation.\n" ); |
| 112 |
|
MPIcheckPoint(); |
| 113 |
|
#endif // is_mpi |
| 114 |
+ |
|
| 115 |
|
|
| 116 |
|
} |
| 117 |
|
|
