| 65 |
|
if( !strcmp( info.name, name ) ){ |
| 66 |
|
sprintf( painCave.errMsg, |
| 67 |
|
"Duplicate LJ atom type \"%s\" found in " |
| 68 |
< |
"the LJ_FF param file./n", |
| 68 |
> |
"the LJFF param file./n", |
| 69 |
|
name ); |
| 70 |
|
painCave.isFatal = 1; |
| 71 |
|
simError(); |
| 117 |
|
//**************************************************************** |
| 118 |
|
|
| 119 |
|
|
| 120 |
< |
LJ_FF::LJ_FF(){ |
| 120 |
> |
LJFF::LJFF(){ |
| 121 |
|
|
| 122 |
|
char fileName[200]; |
| 123 |
|
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 124 |
|
char* ffPath; |
| 125 |
|
char temp[200]; |
| 126 |
– |
char errMsg[1000]; |
| 126 |
|
|
| 127 |
|
headAtomType = NULL; |
| 128 |
|
currentAtomType = NULL; |
| 161 |
|
|
| 162 |
|
// generate the force file name |
| 163 |
|
|
| 164 |
< |
strcpy( fileName, "LJ_FF.frc" ); |
| 165 |
< |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
| 164 |
> |
strcpy( fileName, "LJFF.frc" ); |
| 165 |
> |
fprintf( stderr,"Trying to open %s\n", fileName ); |
| 166 |
|
|
| 167 |
|
// attempt to open the file in the current directory first. |
| 168 |
|
|
| 200 |
|
#ifdef IS_MPI |
| 201 |
|
} |
| 202 |
|
|
| 203 |
< |
sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
| 203 |
> |
sprintf( checkPointMsg, "LJFF file opened sucessfully." ); |
| 204 |
|
MPIcheckPoint(); |
| 205 |
|
|
| 206 |
|
#endif // is_mpi |
| 207 |
|
} |
| 208 |
|
|
| 209 |
|
|
| 210 |
< |
LJ_FF::~LJ_FF(){ |
| 210 |
> |
LJFF::~LJFF(){ |
| 211 |
|
|
| 212 |
|
if( headAtomType != NULL ) delete headAtomType; |
| 213 |
|
|
| 222 |
|
#endif // is_mpi |
| 223 |
|
} |
| 224 |
|
|
| 225 |
< |
void LJ_FF::initForceField( int ljMixRule ){ |
| 225 |
> |
void LJFF::initForceField( int ljMixRule ){ |
| 226 |
|
|
| 227 |
|
initFortran( ljMixRule, 0 ); |
| 228 |
|
} |
| 229 |
|
|
| 230 |
< |
void LJ_FF::cleanMe( void ){ |
| 230 |
> |
void LJFF::cleanMe( void ){ |
| 231 |
|
|
| 232 |
|
#ifdef IS_MPI |
| 233 |
|
|
| 242 |
|
#endif // is_mpi |
| 243 |
|
} |
| 244 |
|
|
| 245 |
< |
void LJ_FF::readParams( void ){ |
| 245 |
> |
void LJFF::readParams( void ){ |
| 246 |
|
|
| 247 |
|
atomStruct info; |
| 248 |
|
info.last = 1; // initialize last to have the last set. |
| 249 |
|
// if things go well, last will be set to 0 |
| 250 |
|
|
| 252 |
– |
int i; |
| 251 |
|
int identNum; |
| 252 |
|
|
| 253 |
|
|
| 301 |
|
// send out the linked list to all the other processes |
| 302 |
|
|
| 303 |
|
sprintf( checkPointMsg, |
| 304 |
< |
"LJ_FF atom structures read successfully." ); |
| 304 |
> |
"LJFF atom structures read successfully." ); |
| 305 |
|
MPIcheckPoint(); |
| 306 |
|
|
| 307 |
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 355 |
|
int isDipole = 0; |
| 356 |
|
int isSSD = 0; |
| 357 |
|
int isGB = 0; |
| 358 |
+ |
int isEAM = 0; |
| 359 |
|
double dipole = 0.0; |
| 360 |
|
|
| 361 |
|
currentAtomType = headAtomType; |
| 368 |
|
&isSSD, |
| 369 |
|
&isDipole, |
| 370 |
|
&isGB, |
| 371 |
+ |
&isEAM, |
| 372 |
|
&(currentAtomType->epslon), |
| 373 |
|
&(currentAtomType->sigma), |
| 374 |
|
&dipole, |
| 388 |
|
|
| 389 |
|
#ifdef IS_MPI |
| 390 |
|
sprintf( checkPointMsg, |
| 391 |
< |
"LJ_FF atom structures successfully sent to fortran\n" ); |
| 391 |
> |
"LJFF atom structures successfully sent to fortran\n" ); |
| 392 |
|
MPIcheckPoint(); |
| 393 |
|
#endif // is_mpi |
| 394 |
|
|
| 395 |
|
} |
| 396 |
|
|
| 397 |
|
|
| 398 |
< |
void LJ_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 398 |
> |
void LJFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 399 |
|
|
| 400 |
|
int i; |
| 401 |
|
|
| 402 |
|
// initialize the atoms |
| 403 |
|
|
| 404 |
|
|
| 405 |
– |
Atom* thisAtom; |
| 406 |
– |
|
| 405 |
|
for( i=0; i<nAtoms; i++ ){ |
| 406 |
|
|
| 407 |
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 423 |
|
} |
| 424 |
|
} |
| 425 |
|
|
| 426 |
< |
void LJ_FF::initializeBonds( int nBonds, Bond** BondArray, |
| 426 |
> |
void LJFF::initializeBonds( int nBonds, Bond** BondArray, |
| 427 |
|
bond_pair* the_bonds ){ |
| 428 |
|
|
| 429 |
|
if( nBonds ){ |
| 430 |
|
sprintf( painCave.errMsg, |
| 431 |
< |
"LJ_FF does not support bonds.\n" ); |
| 431 |
> |
"LJFF does not support bonds.\n" ); |
| 432 |
|
painCave.isFatal = 1; |
| 433 |
|
simError(); |
| 434 |
|
} |
| 435 |
|
} |
| 436 |
|
|
| 437 |
< |
void LJ_FF::initializeBends( int nBends, Bend** bendArray, |
| 437 |
> |
void LJFF::initializeBends( int nBends, Bend** bendArray, |
| 438 |
|
bend_set* the_bends ){ |
| 439 |
|
|
| 440 |
|
if( nBends ){ |
| 441 |
|
sprintf( painCave.errMsg, |
| 442 |
< |
"LJ_FF does not support bends.\n" ); |
| 442 |
> |
"LJFF does not support bends.\n" ); |
| 443 |
|
painCave.isFatal = 1; |
| 444 |
|
simError(); |
| 445 |
|
} |
| 446 |
|
} |
| 447 |
|
|
| 448 |
< |
void LJ_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
| 448 |
> |
void LJFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
| 449 |
|
torsion_set* the_torsions ){ |
| 450 |
|
|
| 451 |
|
if( nTorsions ){ |
| 452 |
|
sprintf( painCave.errMsg, |
| 453 |
< |
"LJ_FF does not support torsions.\n" ); |
| 453 |
> |
"LJFF does not support torsions.\n" ); |
| 454 |
|
painCave.isFatal = 1; |
| 455 |
|
simError(); |
| 456 |
|
} |
| 457 |
|
} |
| 458 |
|
|
| 459 |
< |
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
| 459 |
> |
void LJFF::fastForward( char* stopText, char* searchOwner ){ |
| 460 |
|
|
| 461 |
|
int foundText = 0; |
| 462 |
|
char* the_token; |
