| 1 |
#include <stdlib.h> |
| 2 |
#include <stdio.h> |
| 3 |
#include <string.h> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#ifdef IS_MPI |
| 9 |
#include <mpi.h> |
| 10 |
#endif //is_mpi |
| 11 |
|
| 12 |
#include "UseTheForce/ForceFields.hpp" |
| 13 |
#include "primitives/SRI.hpp" |
| 14 |
#include "utils/simError.h" |
| 15 |
|
| 16 |
#include "UseTheForce/fortranWrappers.hpp" |
| 17 |
|
| 18 |
#ifdef IS_MPI |
| 19 |
#include "UseTheForce/mpiForceField.h" |
| 20 |
#endif // is_mpi |
| 21 |
|
| 22 |
Shapes_FF::Shapes_FF() { |
| 23 |
Shapes_FF(""); |
| 24 |
} |
| 25 |
|
| 26 |
Shapes_FF::Shapes_FF(char* the_variant){ |
| 27 |
|
| 28 |
char fileName[200]; |
| 29 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 30 |
char* ffPath; |
| 31 |
char temp[200]; |
| 32 |
|
| 33 |
// do the funtion wrapping |
| 34 |
wrapMeFF( this ); |
| 35 |
|
| 36 |
#ifdef IS_MPI |
| 37 |
if( worldRank == 0 ){ |
| 38 |
#endif |
| 39 |
|
| 40 |
// generate the force file name |
| 41 |
|
| 42 |
strcpy( fileName, "Shapes" ); |
| 43 |
|
| 44 |
if (strlen(the_variant) > 0) { |
| 45 |
has_variant = 1; |
| 46 |
strcpy( variant, the_variant); |
| 47 |
strcat( fileName, "."); |
| 48 |
strcat( fileName, variant ); |
| 49 |
|
| 50 |
sprintf( painCave.errMsg, |
| 51 |
"Using %s variant of Shapes force field.\n", |
| 52 |
variant ); |
| 53 |
painCave.severity = OOPSE_INFO; |
| 54 |
painCave.isFatal = 0; |
| 55 |
simError(); |
| 56 |
} |
| 57 |
strcat( fileName, ".frc"); |
| 58 |
|
| 59 |
// attempt to open the file in the current directory first. |
| 60 |
|
| 61 |
frcFile = fopen( fileName, "r" ); |
| 62 |
|
| 63 |
if( frcFile == NULL ){ |
| 64 |
|
| 65 |
// next see if the force path enviorment variable is set |
| 66 |
|
| 67 |
ffPath = getenv( ffPath_env ); |
| 68 |
if( ffPath == NULL ) { |
| 69 |
STR_DEFINE(ffPath, FRC_PATH ); |
| 70 |
} |
| 71 |
|
| 72 |
|
| 73 |
strcpy( temp, ffPath ); |
| 74 |
strcat( temp, "/" ); |
| 75 |
strcat( temp, fileName ); |
| 76 |
strcpy( fileName, temp ); |
| 77 |
|
| 78 |
frcFile = fopen( fileName, "r" ); |
| 79 |
|
| 80 |
if( frcFile == NULL ){ |
| 81 |
|
| 82 |
sprintf( painCave.errMsg, |
| 83 |
"Error opening the force field parameter file:\n" |
| 84 |
"\t%s\n" |
| 85 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 86 |
"variable?\n", |
| 87 |
fileName ); |
| 88 |
painCave.severity = OOPSE_ERROR; |
| 89 |
painCave.isFatal = 1; |
| 90 |
simError(); |
| 91 |
} |
| 92 |
} |
| 93 |
|
| 94 |
|
| 95 |
#ifdef IS_MPI |
| 96 |
} |
| 97 |
|
| 98 |
sprintf( checkPointMsg, "Shapes_FF file opened sucessfully." ); |
| 99 |
MPIcheckPoint(); |
| 100 |
|
| 101 |
#endif // is_mpi |
| 102 |
} |
| 103 |
|
| 104 |
|
| 105 |
Shapes_FF::~Shapes_FF(){ |
| 106 |
|
| 107 |
#ifdef IS_MPI |
| 108 |
if( worldRank == 0 ){ |
| 109 |
#endif // is_mpi |
| 110 |
|
| 111 |
fclose( frcFile ); |
| 112 |
|
| 113 |
#ifdef IS_MPI |
| 114 |
} |
| 115 |
#endif // is_mpi |
| 116 |
} |
| 117 |
|
| 118 |
|
| 119 |
void Shapes_FF::calcRcut( void ){ |
| 120 |
|
| 121 |
#ifdef IS_MPI |
| 122 |
double tempShapesRcut = shapesRcut; |
| 123 |
MPI_Allreduce( &tempShapesRcut, &shapesRcut, 1, MPI_DOUBLE, MPI_MAX, |
| 124 |
MPI_COMM_WORLD); |
| 125 |
#endif //is_mpi |
| 126 |
entry_plug->setDefaultRcut(shapesRcut); |
| 127 |
} |
| 128 |
|
| 129 |
|
| 130 |
void Shapes_FF::initForceField(int ljMixRule){ |
| 131 |
initFortran(ljMixRule, 0); |
| 132 |
} |
| 133 |
|
| 134 |
|
| 135 |
void Shapes_FF::readParams( void ){ |
| 136 |
|
| 137 |
char shapePotFile[1000]; |
| 138 |
|
| 139 |
#ifdef IS_MPI |
| 140 |
if( worldRank == 0 ){ |
| 141 |
#endif |
| 142 |
|
| 143 |
// read in the atom types. |
| 144 |
|
| 145 |
fastForward( "AtomTypes", "eam atom readParams" ); |
| 146 |
|
| 147 |
// we are now at the AtomTypes section. |
| 148 |
|
| 149 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 150 |
lineNum++; |
| 151 |
|
| 152 |
|
| 153 |
// read a line, and start parseing out the atom types |
| 154 |
|
| 155 |
if( eof_test == NULL ){ |
| 156 |
sprintf( painCave.errMsg, |
| 157 |
"Error in reading Atoms from force file at line %d.\n", |
| 158 |
lineNum ); |
| 159 |
painCave.isFatal = 1; |
| 160 |
simError(); |
| 161 |
} |
| 162 |
|
| 163 |
identNum = 1; |
| 164 |
// stop reading at end of file, or at next section |
| 165 |
|
| 166 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 167 |
|
| 168 |
// toss comment lines |
| 169 |
if( readLine[0] != '!' ){ |
| 170 |
|
| 171 |
// the parser returns 0 if the line was blank |
| 172 |
if( parseAtom( readLine, lineNum, info, eamPotFile ) ){ |
| 173 |
parseEAM(info,eamPotFile, &eam_rvals, |
| 174 |
&eam_rhovals, &eam_Frhovals); |
| 175 |
info.ident = identNum; |
| 176 |
headAtomType->add( info, eam_rvals, |
| 177 |
eam_rhovals,eam_Frhovals ); |
| 178 |
identNum++; |
| 179 |
} |
| 180 |
} |
| 181 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 182 |
lineNum++; |
| 183 |
} |
| 184 |
|
| 185 |
|
| 186 |
|
| 187 |
#ifdef IS_MPI |
| 188 |
|
| 189 |
|
| 190 |
// send out the linked list to all the other processes |
| 191 |
|
| 192 |
sprintf( checkPointMsg, |
| 193 |
"Shapes_FF atom structures read successfully." ); |
| 194 |
MPIcheckPoint(); |
| 195 |
|
| 196 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 197 |
while( currentAtomType != NULL ){ |
| 198 |
currentAtomType->duplicate( info ); |
| 199 |
|
| 200 |
|
| 201 |
|
| 202 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 203 |
|
| 204 |
// We have to now broadcast the Arrays |
| 205 |
MPI_Bcast(currentAtomType->eam_rvals, |
| 206 |
currentAtomType->eam_nr, |
| 207 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
| 208 |
MPI_Bcast(currentAtomType->eam_rhovals, |
| 209 |
currentAtomType->eam_nr, |
| 210 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
| 211 |
MPI_Bcast(currentAtomType->eam_Frhovals, |
| 212 |
currentAtomType->eam_nrho, |
| 213 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
| 214 |
|
| 215 |
sprintf( checkPointMsg, |
| 216 |
"successfully sent EAM force type: \"%s\"\n", |
| 217 |
info.name ); |
| 218 |
MPIcheckPoint(); |
| 219 |
|
| 220 |
currentAtomType = currentAtomType->next; |
| 221 |
} |
| 222 |
info.last = 1; |
| 223 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 224 |
|
| 225 |
} |
| 226 |
|
| 227 |
else{ |
| 228 |
|
| 229 |
// listen for node 0 to send out the force params |
| 230 |
|
| 231 |
MPIcheckPoint(); |
| 232 |
|
| 233 |
headAtomType = new LinkedAtomType; |
| 234 |
receiveFrcStruct( &info, mpiAtomStructType ); |
| 235 |
|
| 236 |
while( !info.last ){ |
| 237 |
|
| 238 |
// allocate the arrays |
| 239 |
|
| 240 |
eam_rvals = new double[info.eam_nr]; |
| 241 |
eam_rhovals = new double[info.eam_nr]; |
| 242 |
eam_Frhovals = new double[info.eam_nrho]; |
| 243 |
|
| 244 |
// We have to now broadcast the Arrays |
| 245 |
MPI_Bcast(eam_rvals, |
| 246 |
info.eam_nr, |
| 247 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
| 248 |
MPI_Bcast(eam_rhovals, |
| 249 |
info.eam_nr, |
| 250 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
| 251 |
MPI_Bcast(eam_Frhovals, |
| 252 |
info.eam_nrho, |
| 253 |
MPI_DOUBLE,0,MPI_COMM_WORLD); |
| 254 |
|
| 255 |
|
| 256 |
headAtomType->add( info, eam_rvals, eam_rhovals, eam_Frhovals ); |
| 257 |
|
| 258 |
MPIcheckPoint(); |
| 259 |
|
| 260 |
receiveFrcStruct( &info, mpiAtomStructType ); |
| 261 |
|
| 262 |
|
| 263 |
} |
| 264 |
} |
| 265 |
#endif // is_mpi |
| 266 |
|
| 267 |
// call new A_types in fortran |
| 268 |
|
| 269 |
int isError; |
| 270 |
|
| 271 |
// dummy variables |
| 272 |
int isLJ = 0; |
| 273 |
int isDipole = 0; |
| 274 |
int isSSD = 0; |
| 275 |
int isGB = 0; |
| 276 |
int isEAM = 1; |
| 277 |
int isCharge = 0; |
| 278 |
double dipole = 0.0; |
| 279 |
double charge = 0.0; |
| 280 |
double eamSigma = 0.0; |
| 281 |
double eamEpslon = 0.0; |
| 282 |
|
| 283 |
currentAtomType = headAtomType->next; |
| 284 |
while( currentAtomType != NULL ){ |
| 285 |
|
| 286 |
if( currentAtomType->name[0] != '\0' ){ |
| 287 |
isError = 0; |
| 288 |
makeAtype( &(currentAtomType->ident), |
| 289 |
&isLJ, |
| 290 |
&isSSD, |
| 291 |
&isDipole, |
| 292 |
&isGB, |
| 293 |
&isEAM, |
| 294 |
&isCharge, |
| 295 |
&eamEpslon, |
| 296 |
&eamSigma, |
| 297 |
&charge, |
| 298 |
&dipole, |
| 299 |
&isError ); |
| 300 |
if( isError ){ |
| 301 |
sprintf( painCave.errMsg, |
| 302 |
"Error initializing the \"%s\" atom type in fortran\n", |
| 303 |
currentAtomType->name ); |
| 304 |
painCave.isFatal = 1; |
| 305 |
simError(); |
| 306 |
} |
| 307 |
} |
| 308 |
currentAtomType = currentAtomType->next; |
| 309 |
} |
| 310 |
|
| 311 |
entry_plug->useLJ = 0; |
| 312 |
entry_plug->useEAM = 1; |
| 313 |
// Walk down again and send out EAM type |
| 314 |
currentAtomType = headAtomType->next; |
| 315 |
while( currentAtomType != NULL ){ |
| 316 |
|
| 317 |
if( currentAtomType->name[0] != '\0' ){ |
| 318 |
isError = 0; |
| 319 |
|
| 320 |
newEAMtype( &(currentAtomType->lattice_constant), |
| 321 |
&(currentAtomType->eam_nrho), |
| 322 |
&(currentAtomType->eam_drho), |
| 323 |
&(currentAtomType->eam_nr), |
| 324 |
&(currentAtomType->eam_dr), |
| 325 |
&(currentAtomType->eam_rcut), |
| 326 |
currentAtomType->eam_rvals, |
| 327 |
currentAtomType->eam_rhovals, |
| 328 |
currentAtomType->eam_Frhovals, |
| 329 |
&(currentAtomType->eam_ident), |
| 330 |
&isError); |
| 331 |
|
| 332 |
if( isError ){ |
| 333 |
sprintf( painCave.errMsg, |
| 334 |
"Error initializing the \"%s\" atom type in fortran EAM\n", |
| 335 |
currentAtomType->name ); |
| 336 |
painCave.isFatal = 1; |
| 337 |
simError(); |
| 338 |
} |
| 339 |
} |
| 340 |
currentAtomType = currentAtomType->next; |
| 341 |
} |
| 342 |
|
| 343 |
|
| 344 |
|
| 345 |
#ifdef IS_MPI |
| 346 |
sprintf( checkPointMsg, |
| 347 |
"Shapes_FF atom structures successfully sent to fortran\n" ); |
| 348 |
MPIcheckPoint(); |
| 349 |
#endif // is_mpi |
| 350 |
|
| 351 |
|
| 352 |
|
| 353 |
} |
| 354 |
|
| 355 |
|
| 356 |
void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 357 |
|
| 358 |
int i; |
| 359 |
|
| 360 |
// initialize the atoms |
| 361 |
|
| 362 |
for( i=0; i<nAtoms; i++ ){ |
| 363 |
|
| 364 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 365 |
if( currentAtomType == NULL ){ |
| 366 |
sprintf( painCave.errMsg, |
| 367 |
"AtomType error, %s not found in force file.\n", |
| 368 |
the_atoms[i]->getType() ); |
| 369 |
painCave.isFatal = 1; |
| 370 |
simError(); |
| 371 |
} |
| 372 |
|
| 373 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 374 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 375 |
|
| 376 |
if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut; |
| 377 |
|
| 378 |
} |
| 379 |
} |
| 380 |
|
| 381 |
void Shapes_FF::initializeBonds( int nBonds, Bond** BondArray, |
| 382 |
bond_pair* the_bonds ){ |
| 383 |
|
| 384 |
if( nBonds ){ |
| 385 |
sprintf( painCave.errMsg, |
| 386 |
"LJ_FF does not support bonds.\n" ); |
| 387 |
painCave.isFatal = 1; |
| 388 |
simError(); |
| 389 |
} |
| 390 |
} |
| 391 |
|
| 392 |
void Shapes_FF::initializeBends( int nBends, Bend** bendArray, |
| 393 |
bend_set* the_bends ){ |
| 394 |
|
| 395 |
if( nBends ){ |
| 396 |
sprintf( painCave.errMsg, |
| 397 |
"LJ_FF does not support bends.\n" ); |
| 398 |
painCave.isFatal = 1; |
| 399 |
simError(); |
| 400 |
} |
| 401 |
} |
| 402 |
|
| 403 |
void Shapes_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
| 404 |
torsion_set* the_torsions ){ |
| 405 |
|
| 406 |
if( nTorsions ){ |
| 407 |
sprintf( painCave.errMsg, |
| 408 |
"LJ_FF does not support torsions.\n" ); |
| 409 |
painCave.isFatal = 1; |
| 410 |
simError(); |
| 411 |
} |
| 412 |
} |
| 413 |
|
| 414 |
void Shapes_FF::fastForward( char* stopText, char* searchOwner ){ |
| 415 |
|
| 416 |
int foundText = 0; |
| 417 |
char* the_token; |
| 418 |
|
| 419 |
rewind( frcFile ); |
| 420 |
lineNum = 0; |
| 421 |
|
| 422 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 423 |
lineNum++; |
| 424 |
if( eof_test == NULL ){ |
| 425 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 426 |
" file is empty.\n", |
| 427 |
searchOwner ); |
| 428 |
painCave.isFatal = 1; |
| 429 |
simError(); |
| 430 |
} |
| 431 |
|
| 432 |
|
| 433 |
while( !foundText ){ |
| 434 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 435 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 436 |
lineNum++; |
| 437 |
} |
| 438 |
if( eof_test == NULL ){ |
| 439 |
sprintf( painCave.errMsg, |
| 440 |
"Error fast forwarding force file for %s at " |
| 441 |
"line %d: file ended unexpectedly.\n", |
| 442 |
searchOwner, |
| 443 |
lineNum ); |
| 444 |
painCave.isFatal = 1; |
| 445 |
simError(); |
| 446 |
} |
| 447 |
|
| 448 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 449 |
foundText = !strcmp( stopText, the_token ); |
| 450 |
|
| 451 |
if( !foundText ){ |
| 452 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 453 |
lineNum++; |
| 454 |
|
| 455 |
if( eof_test == NULL ){ |
| 456 |
sprintf( painCave.errMsg, |
| 457 |
"Error fast forwarding force file for %s at " |
| 458 |
"line %d: file ended unexpectedly.\n", |
| 459 |
searchOwner, |
| 460 |
lineNum ); |
| 461 |
painCave.isFatal = 1; |
| 462 |
simError(); |
| 463 |
} |
| 464 |
} |
| 465 |
} |
| 466 |
} |
| 467 |
|
| 468 |
|
| 469 |
|
| 470 |
int EAM_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info, char *eamPotFile ){ |
| 471 |
|
| 472 |
char* the_token; |
| 473 |
|
| 474 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 475 |
if( the_token != NULL ){ |
| 476 |
|
| 477 |
strcpy( info.name, the_token ); |
| 478 |
|
| 479 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 480 |
sprintf( painCave.errMsg, |
| 481 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 482 |
painCave.isFatal = 1; |
| 483 |
simError(); |
| 484 |
} |
| 485 |
|
| 486 |
info.mass = atof( the_token ); |
| 487 |
|
| 488 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 489 |
sprintf( painCave.errMsg, |
| 490 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 491 |
painCave.isFatal = 1; |
| 492 |
simError(); |
| 493 |
} |
| 494 |
|
| 495 |
strcpy( eamPotFile, the_token ); |
| 496 |
return 1; |
| 497 |
} |
| 498 |
else return 0; |
| 499 |
} |
| 500 |
|
| 501 |
int EAM_NS::parseEAM(atomStruct &info, char *eamPotFile, |
| 502 |
double **eam_rvals, |
| 503 |
double **eam_rhovals, |
| 504 |
double **eam_Frhovals){ |
| 505 |
double* myEam_rvals; |
| 506 |
double* myEam_rhovals; |
| 507 |
double* myEam_Frhovals; |
| 508 |
|
| 509 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 510 |
char* ffPath; |
| 511 |
char* the_token; |
| 512 |
char* eam_eof_test; |
| 513 |
FILE *eamFile; |
| 514 |
const int BUFFERSIZE = 3000; |
| 515 |
|
| 516 |
char temp[200]; |
| 517 |
int linenumber; |
| 518 |
int nReadLines; |
| 519 |
char eam_read_buffer[BUFFERSIZE]; |
| 520 |
|
| 521 |
|
| 522 |
int i,j; |
| 523 |
|
| 524 |
linenumber = 0; |
| 525 |
|
| 526 |
// Open eam file |
| 527 |
eamFile = fopen( eamPotFile, "r" ); |
| 528 |
|
| 529 |
|
| 530 |
if( eamFile == NULL ){ |
| 531 |
|
| 532 |
// next see if the force path enviorment variable is set |
| 533 |
|
| 534 |
ffPath = getenv( ffPath_env ); |
| 535 |
if( ffPath == NULL ) { |
| 536 |
STR_DEFINE(ffPath, FRC_PATH ); |
| 537 |
} |
| 538 |
|
| 539 |
|
| 540 |
strcpy( temp, ffPath ); |
| 541 |
strcat( temp, "/" ); |
| 542 |
strcat( temp, eamPotFile ); |
| 543 |
strcpy( eamPotFile, temp ); |
| 544 |
|
| 545 |
eamFile = fopen( eamPotFile, "r" ); |
| 546 |
|
| 547 |
|
| 548 |
|
| 549 |
if( eamFile == NULL ){ |
| 550 |
|
| 551 |
sprintf( painCave.errMsg, |
| 552 |
"Error opening the EAM force parameter file: %s\n" |
| 553 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 554 |
"variable?\n", |
| 555 |
eamPotFile ); |
| 556 |
painCave.isFatal = 1; |
| 557 |
simError(); |
| 558 |
} |
| 559 |
} |
| 560 |
|
| 561 |
// First line is a comment line, read and toss it.... |
| 562 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
| 563 |
linenumber++; |
| 564 |
if(eam_eof_test == NULL){ |
| 565 |
sprintf( painCave.errMsg, |
| 566 |
"error in reading commment in %s\n", eamPotFile); |
| 567 |
painCave.isFatal = 1; |
| 568 |
simError(); |
| 569 |
} |
| 570 |
|
| 571 |
|
| 572 |
|
| 573 |
// The Second line contains atomic number, atomic mass and a lattice constant |
| 574 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
| 575 |
linenumber++; |
| 576 |
if(eam_eof_test == NULL){ |
| 577 |
sprintf( painCave.errMsg, |
| 578 |
"error in reading Identifier line in %s\n", eamPotFile); |
| 579 |
painCave.isFatal = 1; |
| 580 |
simError(); |
| 581 |
} |
| 582 |
|
| 583 |
|
| 584 |
|
| 585 |
|
| 586 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
| 587 |
sprintf( painCave.errMsg, |
| 588 |
"Error parsing EAM ident line in %s\n", eamPotFile ); |
| 589 |
painCave.isFatal = 1; |
| 590 |
simError(); |
| 591 |
} |
| 592 |
|
| 593 |
info.eam_ident = atoi( the_token ); |
| 594 |
|
| 595 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 596 |
sprintf( painCave.errMsg, |
| 597 |
"Error parsing EAM mass in %s\n", eamPotFile ); |
| 598 |
painCave.isFatal = 1; |
| 599 |
simError(); |
| 600 |
} |
| 601 |
info.mass = atof( the_token); |
| 602 |
|
| 603 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 604 |
sprintf( painCave.errMsg, |
| 605 |
"Error parsing EAM Lattice Constant %s\n", eamPotFile ); |
| 606 |
painCave.isFatal = 1; |
| 607 |
simError(); |
| 608 |
} |
| 609 |
info.lattice_constant = atof( the_token); |
| 610 |
|
| 611 |
// Next line is nrho, drho, nr, dr and rcut |
| 612 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
| 613 |
if(eam_eof_test == NULL){ |
| 614 |
sprintf( painCave.errMsg, |
| 615 |
"error in reading number of points line in %s\n", eamPotFile); |
| 616 |
painCave.isFatal = 1; |
| 617 |
simError(); |
| 618 |
} |
| 619 |
|
| 620 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
| 621 |
sprintf( painCave.errMsg, |
| 622 |
"Error parseing EAM nrho: line in %s\n", eamPotFile ); |
| 623 |
painCave.isFatal = 1; |
| 624 |
simError(); |
| 625 |
} |
| 626 |
|
| 627 |
info.eam_nrho = atoi( the_token ); |
| 628 |
|
| 629 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 630 |
sprintf( painCave.errMsg, |
| 631 |
"Error parsing EAM drho in %s\n", eamPotFile ); |
| 632 |
painCave.isFatal = 1; |
| 633 |
simError(); |
| 634 |
} |
| 635 |
info.eam_drho = atof( the_token); |
| 636 |
|
| 637 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 638 |
sprintf( painCave.errMsg, |
| 639 |
"Error parsing EAM # r in %s\n", eamPotFile ); |
| 640 |
painCave.isFatal = 1; |
| 641 |
simError(); |
| 642 |
} |
| 643 |
info.eam_nr = atoi( the_token); |
| 644 |
|
| 645 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 646 |
sprintf( painCave.errMsg, |
| 647 |
"Error parsing EAM dr in %s\n", eamPotFile ); |
| 648 |
painCave.isFatal = 1; |
| 649 |
simError(); |
| 650 |
} |
| 651 |
info.eam_dr = atof( the_token); |
| 652 |
|
| 653 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 654 |
sprintf( painCave.errMsg, |
| 655 |
"Error parsing EAM rcut in %s\n", eamPotFile ); |
| 656 |
painCave.isFatal = 1; |
| 657 |
simError(); |
| 658 |
} |
| 659 |
info.eam_rcut = atof( the_token); |
| 660 |
|
| 661 |
|
| 662 |
|
| 663 |
|
| 664 |
|
| 665 |
// Ok now we have to allocate point arrays and read in number of points |
| 666 |
// Index the arrays for fortran, starting at 1 |
| 667 |
myEam_Frhovals = new double[info.eam_nrho]; |
| 668 |
myEam_rvals = new double[info.eam_nr]; |
| 669 |
myEam_rhovals = new double[info.eam_nr]; |
| 670 |
|
| 671 |
// Parse F of rho vals. |
| 672 |
|
| 673 |
// Assume for now that we have a complete number of lines |
| 674 |
nReadLines = int(info.eam_nrho/5); |
| 675 |
|
| 676 |
|
| 677 |
|
| 678 |
for (i=0;i<nReadLines;i++){ |
| 679 |
j = i*5; |
| 680 |
|
| 681 |
// Read next line |
| 682 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
| 683 |
linenumber++; |
| 684 |
if(eam_eof_test == NULL){ |
| 685 |
sprintf( painCave.errMsg, |
| 686 |
"error in reading EAM file %s at line %d\n", |
| 687 |
eamPotFile,linenumber); |
| 688 |
painCave.isFatal = 1; |
| 689 |
simError(); |
| 690 |
} |
| 691 |
|
| 692 |
// Parse 5 values on each line into array |
| 693 |
// Value 1 |
| 694 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
| 695 |
sprintf( painCave.errMsg, |
| 696 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 697 |
painCave.isFatal = 1; |
| 698 |
simError(); |
| 699 |
} |
| 700 |
|
| 701 |
myEam_Frhovals[j+0] = atof( the_token ); |
| 702 |
|
| 703 |
// Value 2 |
| 704 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 705 |
sprintf( painCave.errMsg, |
| 706 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 707 |
painCave.isFatal = 1; |
| 708 |
simError(); |
| 709 |
} |
| 710 |
|
| 711 |
myEam_Frhovals[j+1] = atof( the_token ); |
| 712 |
|
| 713 |
// Value 3 |
| 714 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 715 |
sprintf( painCave.errMsg, |
| 716 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 717 |
painCave.isFatal = 1; |
| 718 |
simError(); |
| 719 |
} |
| 720 |
|
| 721 |
myEam_Frhovals[j+2] = atof( the_token ); |
| 722 |
|
| 723 |
// Value 4 |
| 724 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 725 |
sprintf( painCave.errMsg, |
| 726 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 727 |
painCave.isFatal = 1; |
| 728 |
simError(); |
| 729 |
} |
| 730 |
|
| 731 |
myEam_Frhovals[j+3] = atof( the_token ); |
| 732 |
|
| 733 |
// Value 5 |
| 734 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 735 |
sprintf( painCave.errMsg, |
| 736 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 737 |
painCave.isFatal = 1; |
| 738 |
simError(); |
| 739 |
} |
| 740 |
|
| 741 |
myEam_Frhovals[j+4] = atof( the_token ); |
| 742 |
|
| 743 |
} |
| 744 |
// Parse Z of r vals |
| 745 |
|
| 746 |
// Assume for now that we have a complete number of lines |
| 747 |
nReadLines = int(info.eam_nr/5); |
| 748 |
|
| 749 |
for (i=0;i<nReadLines;i++){ |
| 750 |
j = i*5; |
| 751 |
|
| 752 |
// Read next line |
| 753 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
| 754 |
linenumber++; |
| 755 |
if(eam_eof_test == NULL){ |
| 756 |
sprintf( painCave.errMsg, |
| 757 |
"error in reading EAM file %s at line %d\n", |
| 758 |
eamPotFile,linenumber); |
| 759 |
painCave.isFatal = 1; |
| 760 |
simError(); |
| 761 |
} |
| 762 |
|
| 763 |
// Parse 5 values on each line into array |
| 764 |
// Value 1 |
| 765 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
| 766 |
sprintf( painCave.errMsg, |
| 767 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 768 |
painCave.isFatal = 1; |
| 769 |
simError(); |
| 770 |
} |
| 771 |
|
| 772 |
myEam_rvals[j+0] = atof( the_token ); |
| 773 |
|
| 774 |
// Value 2 |
| 775 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 776 |
sprintf( painCave.errMsg, |
| 777 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 778 |
painCave.isFatal = 1; |
| 779 |
simError(); |
| 780 |
} |
| 781 |
|
| 782 |
myEam_rvals[j+1] = atof( the_token ); |
| 783 |
|
| 784 |
// Value 3 |
| 785 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 786 |
sprintf( painCave.errMsg, |
| 787 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 788 |
painCave.isFatal = 1; |
| 789 |
simError(); |
| 790 |
} |
| 791 |
|
| 792 |
myEam_rvals[j+2] = atof( the_token ); |
| 793 |
|
| 794 |
// Value 4 |
| 795 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 796 |
sprintf( painCave.errMsg, |
| 797 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 798 |
painCave.isFatal = 1; |
| 799 |
simError(); |
| 800 |
} |
| 801 |
|
| 802 |
myEam_rvals[j+3] = atof( the_token ); |
| 803 |
|
| 804 |
// Value 5 |
| 805 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 806 |
sprintf( painCave.errMsg, |
| 807 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 808 |
painCave.isFatal = 1; |
| 809 |
simError(); |
| 810 |
} |
| 811 |
|
| 812 |
myEam_rvals[j+4] = atof( the_token ); |
| 813 |
|
| 814 |
} |
| 815 |
// Parse rho of r vals |
| 816 |
|
| 817 |
// Assume for now that we have a complete number of lines |
| 818 |
|
| 819 |
for (i=0;i<nReadLines;i++){ |
| 820 |
j = i*5; |
| 821 |
|
| 822 |
// Read next line |
| 823 |
eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile); |
| 824 |
linenumber++; |
| 825 |
if(eam_eof_test == NULL){ |
| 826 |
sprintf( painCave.errMsg, |
| 827 |
"error in reading EAM file %s at line %d\n", |
| 828 |
eamPotFile,linenumber); |
| 829 |
painCave.isFatal = 1; |
| 830 |
simError(); |
| 831 |
} |
| 832 |
|
| 833 |
// Parse 5 values on each line into array |
| 834 |
// Value 1 |
| 835 |
if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){ |
| 836 |
sprintf( painCave.errMsg, |
| 837 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 838 |
painCave.isFatal = 1; |
| 839 |
simError(); |
| 840 |
} |
| 841 |
|
| 842 |
myEam_rhovals[j+0] = atof( the_token ); |
| 843 |
|
| 844 |
// Value 2 |
| 845 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 846 |
sprintf( painCave.errMsg, |
| 847 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 848 |
painCave.isFatal = 1; |
| 849 |
simError(); |
| 850 |
} |
| 851 |
|
| 852 |
myEam_rhovals[j+1] = atof( the_token ); |
| 853 |
|
| 854 |
// Value 3 |
| 855 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 856 |
sprintf( painCave.errMsg, |
| 857 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 858 |
painCave.isFatal = 1; |
| 859 |
simError(); |
| 860 |
} |
| 861 |
|
| 862 |
myEam_rhovals[j+2] = atof( the_token ); |
| 863 |
|
| 864 |
// Value 4 |
| 865 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 866 |
sprintf( painCave.errMsg, |
| 867 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 868 |
painCave.isFatal = 1; |
| 869 |
simError(); |
| 870 |
} |
| 871 |
|
| 872 |
myEam_rhovals[j+3] = atof( the_token ); |
| 873 |
|
| 874 |
// Value 5 |
| 875 |
if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){ |
| 876 |
sprintf( painCave.errMsg, |
| 877 |
"Error parsing EAM nrho: line in %s\n", eamPotFile ); |
| 878 |
painCave.isFatal = 1; |
| 879 |
simError(); |
| 880 |
} |
| 881 |
|
| 882 |
myEam_rhovals[j+4] = atof( the_token ); |
| 883 |
|
| 884 |
} |
| 885 |
*eam_rvals = myEam_rvals; |
| 886 |
*eam_rhovals = myEam_rhovals; |
| 887 |
*eam_Frhovals = myEam_Frhovals; |
| 888 |
|
| 889 |
fclose(eamFile); |
| 890 |
return 0; |
| 891 |
} |
