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#include "SRI.hpp" |
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#include "simError.h" |
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#include <fortranWrappers.hpp> |
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|
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// Declare the structures that will be passed by the parser and MPI |
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|
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typedef struct{ |
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char name[15]; |
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double mass; |
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double epslon; |
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double sigma; |
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int ident; |
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int last; // 0 -> default |
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// 1 -> in MPI: tells nodes to stop listening |
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} atomStruct; |
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|
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int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ); |
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|
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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#endif // is_mpi |
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|
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MPI_Datatype mpiAtomStructType; |
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|
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#endif |
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|
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namespace { |
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|
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// declaration of functions needed to wrap the fortran module |
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// Declare the structures that will be passed by the parser and MPI |
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|
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typedef struct{ |
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char name[15]; |
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double mass; |
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double epslon; |
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double sigma; |
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int ident; |
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int last; // 0 -> default |
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// 1 -> in MPI: tells nodes to stop listening |
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} atomStruct; |
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|
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extern "C" { |
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void forcefactory_( char* forceName, |
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int* status, |
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void (*wrapFunction)( void (*p1)( int* ident, |
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double* mass, |
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double* epslon, |
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double* sigma, |
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int* status ), |
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void (*p2)( int *nLocal, |
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int *identArray, |
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int *isError ), |
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void (*p3)( double* positionArray, |
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double* forceArray, |
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double* potentialEnergy, |
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double* tau, |
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short int* doPotentialCalc, |
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int* isError)), |
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int forceNameLength ); |
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int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
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|
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#ifdef IS_MPI |
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|
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MPI_Datatype mpiAtomStructType; |
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|
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#endif |
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} |
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|
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|
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void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
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double* sigma, int* status ), |
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void (*p2)( int *nLocal, int *identArray, int *isError ), |
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void (*p3)( double* positionArray,double* forceArray, |
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double* potentialEnergy, double* tau, |
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short int* doPotentialCalc, int* isError ) ); |
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|
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void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma, |
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int* status ); |
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|
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void (*initLJfortran) ( int *nLocal, int *identArray, int *isError ); |
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|
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LJ_FF* currentLJwrap; |
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|
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|
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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char errMsg[1000]; |
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|
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// do the funtion wrapping |
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currentLJwrap = this; |
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wrapMe(); |
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wrapMeFF( this ); |
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|
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#ifdef IS_MPI |
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int i; |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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|
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void LJ_FF::wrapMe( void ){ |
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|
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char* currentFF = "LJ"; |
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int isError = 0; |
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|
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forcefactory_( currentFF, &isError, LJfunctionWrapper, strlen(currentFF) ); |
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|
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if( isError ){ |
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|
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sprintf( painCave.errMsg, |
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"LJ_FF error: an error was returned from fortran when the " |
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"the functions were being wrapped.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, "LJ_FF functions succesfully wrapped." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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|
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|
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void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, |
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double* sigma, int* status ), |
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void (*p2)( int*, int*, int* ), |
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void (*p3)( double* positionArray,double* forceArray, |
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double* potentialEnergy, |
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short int* doPotentialCalc ) ){ |
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|
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|
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newLJtype = p1; |
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initLJfortran = p2; |
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currentLJwrap->setLJfortran( p3 ); |
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} |
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|
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|
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// call new A_types in fortran |
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|
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int isError; |
339 |
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|
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// dummy variables |
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int isLJ = 1; |
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int isDipole = 0; |
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int isSSD = 0; |
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int isGB = 0; |
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double w0 = 0.0; |
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double v0 = 0.0; |
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double dipole = 0.0; |
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|
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|
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currentAtomType = headAtomType; |
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while( currentAtomType != NULL ){ |
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|
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if( currentAtomType->name[0] != '\0' ){ |
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isError = 0; |
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< |
newLJtype( &(currentAtomType->ident), |
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< |
&(currentAtomType->mass), |
357 |
< |
&(currentAtomType->epslon), |
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< |
&(currentAtomType->sigma), |
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< |
&isError ); |
355 |
> |
newAtype( &(currentAtomType->ident), |
356 |
> |
&(currentAtomType->mass), |
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> |
&(currentAtomType->epslon), |
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> |
&(currentAtomType->sigma), |
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&isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &dipole, |
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&isError ); |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error initializing the \"%s\" atom type in fortran\n", |
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|
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initFortran(); |
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entry_plug->refreshSim(); |
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< |
|
431 |
> |
|
432 |
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} |
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|
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void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
473 |
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|
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} |
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|
476 |
+ |
void LJ_FF::doForces( int calcPot ){ |
477 |
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|
478 |
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int i, isError; |
479 |
+ |
double* frc; |
480 |
+ |
double* pos; |
481 |
+ |
double* trq; |
482 |
+ |
double* tau; |
483 |
+ |
short int passedCalcPot = (short int)calcPot; |
484 |
+ |
|
485 |
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// forces are zeroed here, before any are acumulated. |
486 |
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// NOTE: do not rezero the forces in Fortran. |
487 |
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|
488 |
+ |
for(i=0; i<entry_plug->n_atoms; i++){ |
489 |
+ |
entry_plug->atoms[i]->zeroForces(); |
490 |
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} |
491 |
+ |
|
492 |
+ |
frc = Atom::getFrcArray(); |
493 |
+ |
pos = Atom::getPosArray(); |
494 |
+ |
trq = Atom::getTrqArray(); |
495 |
+ |
tau = entry_plug->tau; |
496 |
+ |
|
497 |
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// dummy variables |
498 |
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// NOTE: THIS IS A MAJOR POTENTIAL BUG!!!!!! be careful. |
499 |
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// that said, here we go anyway. |
500 |
+ |
|
501 |
+ |
double* A = NULL; |
502 |
+ |
double* mu = NULL; |
503 |
+ |
double* u_l = NULL; |
504 |
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|
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isError = 0; |
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fortranForceLoop( pos, A, mu, u_l, frc, trq, tau, &(entry_plug->lrPot), |
507 |
+ |
&passedCalcPot, &isError ); |
508 |
+ |
|
509 |
+ |
|
510 |
+ |
if( isError ){ |
511 |
+ |
sprintf( painCave.errMsg, |
512 |
+ |
"Error returned from the fortran force calculation.\n" ); |
513 |
+ |
painCave.isFatal = 1; |
514 |
+ |
simError(); |
515 |
+ |
} |
516 |
+ |
|
517 |
+ |
#ifdef IS_MPI |
518 |
+ |
sprintf( checkPointMsg, |
519 |
+ |
"returned from the force calculation.\n" ); |
520 |
+ |
MPIcheckPoint(); |
521 |
+ |
#endif // is_mpi |
522 |
+ |
|
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
void LJ_FF::initFortran( void ){ |
526 |
+ |
|
527 |
+ |
int nLocal = entry_plug->n_atoms; |
528 |
+ |
int *ident; |
529 |
+ |
int isError; |
530 |
+ |
int i; |
531 |
+ |
|
532 |
+ |
ident = new int[nLocal]; |
533 |
+ |
|
534 |
+ |
for(i=0; i<nLocal; i++){ |
535 |
+ |
ident[i] = entry_plug->atoms[i]->getIdent(); |
536 |
+ |
} |
537 |
+ |
|
538 |
+ |
isError = 0; |
539 |
+ |
initfortran( &nLocal, ident, &isError ); |
540 |
+ |
|
541 |
+ |
if(isError){ |
542 |
+ |
sprintf( painCave.errMsg, |
543 |
+ |
"LJ_FF error: There was an error initializing the component list in fortran.\n" ); |
544 |
+ |
painCave.isFatal = 1; |
545 |
+ |
simError(); |
546 |
+ |
} |
547 |
+ |
|
548 |
+ |
|
549 |
+ |
#ifdef IS_MPI |
550 |
+ |
sprintf( checkPointMsg, "LJ_FF successfully initialized the fortran component list.\n" ); |
551 |
+ |
MPIcheckPoint(); |
552 |
+ |
#endif // is_mpi |
553 |
+ |
|
554 |
+ |
delete[] ident; |
555 |
+ |
|
556 |
+ |
} |
557 |
+ |
|
558 |
+ |
|
559 |
|
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
560 |
|
|
561 |
|
int foundText = 0; |
612 |
|
|
613 |
|
|
614 |
|
|
615 |
< |
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){ |
615 |
> |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
616 |
|
|
617 |
|
char* the_token; |
618 |
|
|
652 |
|
} |
653 |
|
else return 0; |
654 |
|
} |
629 |
– |
|
630 |
– |
|
631 |
– |
void LJ_FF::doForces( int calcPot ){ |
632 |
– |
|
633 |
– |
int i, isError; |
634 |
– |
double* frc; |
635 |
– |
double* pos; |
636 |
– |
double* tau; |
637 |
– |
short int passedCalcPot = (short int)calcPot; |
638 |
– |
|
639 |
– |
// forces are zeroed here, before any are acumulated. |
640 |
– |
// NOTE: do not rezero the forces in Fortran. |
641 |
– |
|
642 |
– |
for(i=0; i<entry_plug->n_atoms; i++){ |
643 |
– |
entry_plug->atoms[i]->zeroForces(); |
644 |
– |
} |
645 |
– |
|
646 |
– |
frc = Atom::getFrcArray(); |
647 |
– |
pos = Atom::getPosArray(); |
648 |
– |
tau = entry_plug->tau; |
649 |
– |
|
650 |
– |
isError = 0; |
651 |
– |
doLJfortran( pos, frc, &(entry_plug->lrPot), tau, &passedCalcPot, &isError ); |
652 |
– |
|
653 |
– |
|
654 |
– |
if( isError ){ |
655 |
– |
sprintf( painCave.errMsg, |
656 |
– |
"Error returned from the fortran force calculation.\n" ); |
657 |
– |
painCave.isFatal = 1; |
658 |
– |
simError(); |
659 |
– |
} |
660 |
– |
|
661 |
– |
#ifdef IS_MPI |
662 |
– |
sprintf( checkPointMsg, |
663 |
– |
"returned from the force calculation.\n" ); |
664 |
– |
MPIcheckPoint(); |
665 |
– |
#endif // is_mpi |
666 |
– |
|
667 |
– |
} |
668 |
– |
|
669 |
– |
void LJ_FF::initFortran( void ){ |
670 |
– |
|
671 |
– |
int nLocal = entry_plug->n_atoms; |
672 |
– |
int *ident; |
673 |
– |
int isError; |
674 |
– |
int i; |
675 |
– |
|
676 |
– |
ident = new int[nLocal]; |
677 |
– |
|
678 |
– |
for(i=0; i<nLocal; i++){ |
679 |
– |
ident[i] = entry_plug->atoms[i]->getIdent(); |
680 |
– |
} |
681 |
– |
|
682 |
– |
isError = 0; |
683 |
– |
initLJfortran( &nLocal, ident, &isError ); |
684 |
– |
|
685 |
– |
if(isError){ |
686 |
– |
sprintf( painCave.errMsg, |
687 |
– |
"LJ_FF error: There was an error initializing the component list in fortran.\n" ); |
688 |
– |
painCave.isFatal = 1; |
689 |
– |
simError(); |
690 |
– |
} |
691 |
– |
|
692 |
– |
|
693 |
– |
#ifdef IS_MPI |
694 |
– |
sprintf( checkPointMsg, "LJ_FF successfully initialized the fortran component list.\n" ); |
695 |
– |
MPIcheckPoint(); |
696 |
– |
#endif // is_mpi |
697 |
– |
|
698 |
– |
delete[] ident; |
699 |
– |
|
700 |
– |
} |
701 |
– |
|