| 1 | #include <cstdlib> | 
| 2 | #include <cstdio> | 
| 3 |  | 
| 4 | #include "MakeStamps.hpp" | 
| 5 | #include "MoleculeStamp.hpp" | 
| 6 | #include "simError.h" | 
| 7 | #ifdef IS_MPI | 
| 8 | #include "mpiBASS.h" | 
| 9 | #endif // is_mpi | 
| 10 |  | 
| 11 | LinkedMolStamp::~LinkedMolStamp(){ | 
| 12 | if( mol_stamp != NULL ) delete mol_stamp; | 
| 13 | if( next != NULL ) delete next; | 
| 14 | } | 
| 15 |  | 
| 16 | void LinkedMolStamp::add( LinkedMolStamp* newbie ){ | 
| 17 |  | 
| 18 | if( next != NULL ) next->add( newbie ); | 
| 19 | else{ | 
| 20 | next = newbie; | 
| 21 | next->setPrev( this ); | 
| 22 | } | 
| 23 | } | 
| 24 |  | 
| 25 | MoleculeStamp* LinkedMolStamp::match( char* id ){ | 
| 26 |  | 
| 27 | if( mol_stamp != NULL ){ | 
| 28 | if(!strcmp( mol_stamp->getID(), id )){ | 
| 29 |  | 
| 30 | // make sure we aren't hiding somebody else with the same name | 
| 31 | if(next != NULL ){ | 
| 32 | if( next->match( id ) != NULL){ | 
| 33 | sprintf( painCave.errMsg, | 
| 34 | "Molecule Stamp Error. Two separate of declarations of " | 
| 35 | "%s present.\n", | 
| 36 | id ); | 
| 37 | painCave.isFatal = 1; | 
| 38 | simError(); | 
| 39 | #ifdef IS_MPI | 
| 40 | if( painCave.isEventLoop ){ | 
| 41 | if( worldRank == 0 ) mpiInterfaceExit(); | 
| 42 | } | 
| 43 | #endif //is_mpi | 
| 44 | } | 
| 45 | else return mol_stamp; | 
| 46 | } | 
| 47 | else  return mol_stamp; | 
| 48 | } | 
| 49 | } | 
| 50 |  | 
| 51 | if( next != NULL ) return next->match( id ); | 
| 52 |  | 
| 53 | return NULL; | 
| 54 | } | 
| 55 |  | 
| 56 | LinkedMolStamp* LinkedMolStamp::extract( char* id ){ | 
| 57 |  | 
| 58 | if( mol_stamp != NULL ){ | 
| 59 | if(!strcmp( mol_stamp->getID(), id )){ | 
| 60 |  | 
| 61 | // make sure we aren't hiding somebody else with the same name | 
| 62 | if(next != NULL ){ | 
| 63 | if( next->match( id ) != NULL){ | 
| 64 | sprintf( painCave.errMsg, | 
| 65 | "Molecule Stamp Error. Two separate of declarations of " | 
| 66 | "%s present.\n", | 
| 67 | id ); | 
| 68 | painCave.isFatal = 1; | 
| 69 | simError(); | 
| 70 | #ifdef IS_MPI | 
| 71 | if( painCave.isEventLoop ){ | 
| 72 | if( worldRank == 0 ) mpiInterfaceExit(); | 
| 73 | } | 
| 74 | #endif //is_mpi | 
| 75 | } | 
| 76 | } | 
| 77 |  | 
| 78 | prev->setNext( next ); | 
| 79 | if( next != NULL ) next->setPrev( prev ); | 
| 80 | return this; | 
| 81 | } | 
| 82 | } | 
| 83 |  | 
| 84 | if( next != NULL ) return next->extract( id ); | 
| 85 |  | 
| 86 | return NULL; | 
| 87 | } | 
| 88 |  | 
| 89 | MakeStamps::MakeStamps(){ | 
| 90 |  | 
| 91 | int i; | 
| 92 |  | 
| 93 | hash_size = 47; | 
| 94 | hash_shift = 4; | 
| 95 |  | 
| 96 | my_mols = new LinkedMolStamp*[hash_size]; | 
| 97 | for( i=0; i<hash_size; i++ ){ | 
| 98 | my_mols[i] = new LinkedMolStamp(); | 
| 99 | } | 
| 100 |  | 
| 101 | } | 
| 102 |  | 
| 103 | MakeStamps::~MakeStamps(){ | 
| 104 |  | 
| 105 | int i; | 
| 106 |  | 
| 107 | for( i=0; i<hash_size; i++ ){ | 
| 108 | if( my_mols[i] != NULL ) delete my_mols[i]; | 
| 109 | } | 
| 110 | delete[] my_mols; | 
| 111 | } | 
| 112 |  | 
| 113 | int MakeStamps::hash( char* text ){ | 
| 114 |  | 
| 115 | register unsigned short int i = 0; // loop counter | 
| 116 | int key = 0; // the hash key | 
| 117 |  | 
| 118 | while( text[i] != '\0' ){ | 
| 119 |  | 
| 120 | key = ( ( key << hash_shift ) + text[i] ) % hash_size; | 
| 121 |  | 
| 122 | i++; | 
| 123 | } | 
| 124 |  | 
| 125 | if( key < 0 ){ | 
| 126 |  | 
| 127 | // if the key is less than zero, we've had an overflow error | 
| 128 |  | 
| 129 | sprintf( painCave.errMsg, | 
| 130 | "There has been an overflow error in the MakeStamps hash key."); | 
| 131 | painCave.isFatal = 1; | 
| 132 | simError(); | 
| 133 | #ifdef IS_MPI | 
| 134 | if( painCave.isEventLoop ){ | 
| 135 | if( worldRank == 0 ) mpiInterfaceExit(); | 
| 136 | } | 
| 137 | #endif //is_mpi | 
| 138 | } | 
| 139 |  | 
| 140 | return key; | 
| 141 | } | 
| 142 |  | 
| 143 | LinkedMolStamp* MakeStamps::extractMolStamp( char* the_id ){ | 
| 144 | int key; | 
| 145 |  | 
| 146 | key = hash( the_id ); | 
| 147 | if( my_mols[key] != NULL ){ | 
| 148 | return my_mols[key]->extract( the_id ); | 
| 149 | } | 
| 150 |  | 
| 151 | return NULL; | 
| 152 | } | 
| 153 |  | 
| 154 | void MakeStamps::addMolStamp( MoleculeStamp* the_stamp ){ | 
| 155 |  | 
| 156 | int key; | 
| 157 | LinkedMolStamp* linked_mol; | 
| 158 |  | 
| 159 | key = hash( the_stamp->getID() ); | 
| 160 |  | 
| 161 | linked_mol = new LinkedMolStamp; | 
| 162 | linked_mol->setStamp( the_stamp ); | 
| 163 |  | 
| 164 | my_mols[key]->add( linked_mol ); | 
| 165 |  | 
| 166 | } | 
| 167 |  | 
| 168 |  | 
| 169 | int MakeStamps::newMolecule( event* the_event ){ | 
| 170 |  | 
| 171 | current_mol = new MoleculeStamp; | 
| 172 | return 1; | 
| 173 | } | 
| 174 |  | 
| 175 | int MakeStamps::moleculeAssign( event* the_event ){ | 
| 176 |  | 
| 177 | switch( the_event->evt.asmt.asmt_type ){ | 
| 178 |  | 
| 179 | case STRING: | 
| 180 | the_event->err_msg = current_mol->assignString( the_event->evt.asmt.lhs, | 
| 181 | the_event->evt.asmt.rhs.sval ); | 
| 182 | break; | 
| 183 |  | 
| 184 | case DOUBLE: | 
| 185 | the_event->err_msg = current_mol->assignDouble( the_event->evt.asmt.lhs, | 
| 186 | the_event->evt.asmt.rhs.dval ); | 
| 187 | break; | 
| 188 |  | 
| 189 | case INT: | 
| 190 | the_event->err_msg = current_mol->assignInt( the_event->evt.asmt.lhs, | 
| 191 | the_event->evt.asmt.rhs.ival ); | 
| 192 | break; | 
| 193 |  | 
| 194 | default: | 
| 195 | the_event->err_msg = strdup( "MakeStamp error. Invalid molecule" | 
| 196 | " assignment type" ); | 
| 197 | return 0; | 
| 198 | break; | 
| 199 | } | 
| 200 | if( the_event->err_msg != NULL ) return 0; | 
| 201 | return 1; | 
| 202 | } | 
| 203 |  | 
| 204 | int MakeStamps::moleculeEnd( event* the_event ){ | 
| 205 |  | 
| 206 | the_event->err_msg = current_mol->checkMe(); | 
| 207 | // if err_msg is set, then something is wrong | 
| 208 | if( the_event->err_msg != NULL ) return 0; | 
| 209 |  | 
| 210 | addMolStamp( current_mol ); | 
| 211 | return 1; | 
| 212 | } | 
| 213 |  | 
| 214 | int MakeStamps::newAtom( event* the_event ){ | 
| 215 |  | 
| 216 | current_atom = new AtomStamp; | 
| 217 |  | 
| 218 | the_event->err_msg = current_mol->addAtom( current_atom, | 
| 219 | the_event->evt.blk_index ); | 
| 220 | if( the_event->err_msg != NULL ) return 0; | 
| 221 | return 1; | 
| 222 | } | 
| 223 |  | 
| 224 | int MakeStamps::atomPosition( event* the_event ){ | 
| 225 |  | 
| 226 | current_atom->setPosition( the_event->evt.pos.x, | 
| 227 | the_event->evt.pos.y, | 
| 228 | the_event->evt.pos.z ); | 
| 229 | return 1; | 
| 230 | } | 
| 231 |  | 
| 232 |  | 
| 233 | int MakeStamps::atomOrientation( event* the_event ){ | 
| 234 |  | 
| 235 | current_atom->setOrientation( the_event->evt.ornt.x, | 
| 236 | the_event->evt.ornt.y, | 
| 237 | the_event->evt.ornt.z ); | 
| 238 | return 1; | 
| 239 | } | 
| 240 |  | 
| 241 | int MakeStamps::atomAssign( event* the_event ){ | 
| 242 |  | 
| 243 | switch( the_event->evt.asmt.asmt_type ){ | 
| 244 |  | 
| 245 | case STRING: | 
| 246 | the_event->err_msg = | 
| 247 | current_atom->assignString( the_event->evt.asmt.lhs, | 
| 248 | the_event->evt.asmt.rhs.sval ); | 
| 249 | if( the_event->err_msg != NULL ) return 0; | 
| 250 | return 1; | 
| 251 | break; | 
| 252 |  | 
| 253 | case DOUBLE: | 
| 254 | the_event->err_msg = | 
| 255 | current_atom->assignDouble( the_event->evt.asmt.lhs, | 
| 256 | the_event->evt.asmt.rhs.dval ); | 
| 257 | if( the_event->err_msg != NULL ) return 0; | 
| 258 | return 1; | 
| 259 | break; | 
| 260 |  | 
| 261 | case INT: | 
| 262 | the_event->err_msg = | 
| 263 | current_atom->assignInt( the_event->evt.asmt.lhs, | 
| 264 | the_event->evt.asmt.rhs.ival ); | 
| 265 | if( the_event->err_msg != NULL ) return 0; | 
| 266 | return 1; | 
| 267 | break; | 
| 268 |  | 
| 269 | default: | 
| 270 | the_event->err_msg = strdup( "MakeStamp error. Invalid atom" | 
| 271 | " assignment type" ); | 
| 272 | return 0; | 
| 273 | break; | 
| 274 | } | 
| 275 | return 0; | 
| 276 | } | 
| 277 |  | 
| 278 | int MakeStamps::atomEnd( event* the_event ){ | 
| 279 |  | 
| 280 | the_event->err_msg = current_atom->checkMe(); | 
| 281 | if( the_event->err_msg != NULL ) return 0; | 
| 282 |  | 
| 283 | return 1; | 
| 284 | } | 
| 285 |  | 
| 286 | int MakeStamps::newBond( event* the_event ){ | 
| 287 |  | 
| 288 | current_bond = new BondStamp; | 
| 289 |  | 
| 290 | the_event->err_msg = current_mol->addBond( current_bond, | 
| 291 | the_event->evt.blk_index ); | 
| 292 | if( the_event->err_msg != NULL ) return 0; | 
| 293 |  | 
| 294 | return 1; | 
| 295 | } | 
| 296 |  | 
| 297 | int MakeStamps::bondAssign( event* the_event ){ | 
| 298 |  | 
| 299 | switch( the_event->evt.asmt.asmt_type ){ | 
| 300 |  | 
| 301 | case STRING: | 
| 302 | current_bond->assignString( the_event->evt.asmt.lhs, | 
| 303 | the_event->evt.asmt.rhs.sval ); | 
| 304 | return 1; | 
| 305 | break; | 
| 306 |  | 
| 307 | case DOUBLE: | 
| 308 | current_bond->assignDouble( the_event->evt.asmt.lhs, | 
| 309 | the_event->evt.asmt.rhs.dval ); | 
| 310 | return 1; | 
| 311 | break; | 
| 312 |  | 
| 313 | case INT: | 
| 314 | current_bond->assignInt( the_event->evt.asmt.lhs, | 
| 315 | the_event->evt.asmt.rhs.ival ); | 
| 316 | return 1; | 
| 317 | break; | 
| 318 |  | 
| 319 | default: | 
| 320 | the_event->err_msg = strdup( "MakeStamp error. Invalid bond" | 
| 321 | " assignment type" ); | 
| 322 | return 0; | 
| 323 | break; | 
| 324 | } | 
| 325 | return 0; | 
| 326 | } | 
| 327 |  | 
| 328 | int MakeStamps::bondMember( event* the_event ){ | 
| 329 |  | 
| 330 | current_bond->members( the_event->evt.mbr.a, | 
| 331 | the_event->evt.mbr.b ); | 
| 332 | return 1; | 
| 333 | } | 
| 334 |  | 
| 335 | int MakeStamps::bondConstraint( event* the_event ){ | 
| 336 |  | 
| 337 | current_bond->constrain( the_event->evt.cnstr ); | 
| 338 | return 1; | 
| 339 | } | 
| 340 |  | 
| 341 | int MakeStamps::bondEnd( event* the_event ){ | 
| 342 |  | 
| 343 | the_event->err_msg = current_bond->checkMe(); | 
| 344 | if( the_event->err_msg != NULL ) return 0; | 
| 345 |  | 
| 346 | return 1; | 
| 347 | } | 
| 348 |  | 
| 349 | int MakeStamps::newBend( event* the_event ){ | 
| 350 |  | 
| 351 | current_bend = new BendStamp; | 
| 352 |  | 
| 353 | the_event->err_msg = current_mol->addBend( current_bend, | 
| 354 | the_event->evt.blk_index ); | 
| 355 | if( the_event->err_msg != NULL ) return 0; | 
| 356 |  | 
| 357 | return 1; | 
| 358 | } | 
| 359 |  | 
| 360 | int MakeStamps::bendAssign( event* the_event ){ | 
| 361 |  | 
| 362 | switch( the_event->evt.asmt.asmt_type ){ | 
| 363 |  | 
| 364 | case STRING: | 
| 365 | current_bend->assignString( the_event->evt.asmt.lhs, | 
| 366 | the_event->evt.asmt.rhs.sval ); | 
| 367 | return 1; | 
| 368 | break; | 
| 369 |  | 
| 370 | case DOUBLE: | 
| 371 | current_bend->assignDouble( the_event->evt.asmt.lhs, | 
| 372 | the_event->evt.asmt.rhs.dval ); | 
| 373 | return 1; | 
| 374 | break; | 
| 375 |  | 
| 376 | case INT: | 
| 377 | current_bend->assignInt( the_event->evt.asmt.lhs, | 
| 378 | the_event->evt.asmt.rhs.ival ); | 
| 379 | return 1; | 
| 380 | break; | 
| 381 |  | 
| 382 | default: | 
| 383 | the_event->err_msg = strdup( "MakeStamp error. Invalid bend" | 
| 384 | " assignment type" ); | 
| 385 | return 0; | 
| 386 | break; | 
| 387 | } | 
| 388 | return 0; | 
| 389 | } | 
| 390 |  | 
| 391 | int MakeStamps::bendMember( event* the_event ){ | 
| 392 |  | 
| 393 | current_bend->members( the_event->evt.mbr.a, | 
| 394 | the_event->evt.mbr.b, | 
| 395 | the_event->evt.mbr.c ); | 
| 396 | return 1; | 
| 397 | } | 
| 398 |  | 
| 399 | int MakeStamps::bendConstraint( event* the_event ){ | 
| 400 |  | 
| 401 | current_bend->constrain( the_event->evt.cnstr ); | 
| 402 | return 1; | 
| 403 | } | 
| 404 |  | 
| 405 | int MakeStamps::bendEnd( event* the_event ){ | 
| 406 |  | 
| 407 | the_event->err_msg = current_bend->checkMe(); | 
| 408 | if( the_event->err_msg != NULL ) return 0; | 
| 409 |  | 
| 410 | return 1; | 
| 411 | } | 
| 412 |  | 
| 413 | int MakeStamps::newTorsion( event* the_event ){ | 
| 414 |  | 
| 415 | current_torsion = new TorsionStamp; | 
| 416 |  | 
| 417 | the_event->err_msg = current_mol->addTorsion( current_torsion, | 
| 418 | the_event->evt.blk_index ); | 
| 419 | if( the_event->err_msg != NULL ) return 0; | 
| 420 |  | 
| 421 | return 1; | 
| 422 | } | 
| 423 |  | 
| 424 | int MakeStamps::torsionAssign( event* the_event ){ | 
| 425 |  | 
| 426 | switch( the_event->evt.asmt.asmt_type ){ | 
| 427 |  | 
| 428 | case STRING: | 
| 429 | current_torsion->assignString( the_event->evt.asmt.lhs, | 
| 430 | the_event->evt.asmt.rhs.sval ); | 
| 431 | return 1; | 
| 432 | break; | 
| 433 |  | 
| 434 | case DOUBLE: | 
| 435 | current_torsion->assignDouble( the_event->evt.asmt.lhs, | 
| 436 | the_event->evt.asmt.rhs.dval ); | 
| 437 | return 1; | 
| 438 | break; | 
| 439 |  | 
| 440 | case INT: | 
| 441 | current_torsion->assignInt( the_event->evt.asmt.lhs, | 
| 442 | the_event->evt.asmt.rhs.ival ); | 
| 443 | return 1; | 
| 444 | break; | 
| 445 |  | 
| 446 | default: | 
| 447 | the_event->err_msg = strdup( "MakeStamp error. Invalid torsion" | 
| 448 | " assignment type" ); | 
| 449 | return 0; | 
| 450 | break; | 
| 451 | } | 
| 452 | return 0; | 
| 453 | } | 
| 454 |  | 
| 455 | int MakeStamps::torsionMember( event* the_event ){ | 
| 456 |  | 
| 457 | current_torsion->members( the_event->evt.mbr.a, | 
| 458 | the_event->evt.mbr.b, | 
| 459 | the_event->evt.mbr.c, | 
| 460 | the_event->evt.mbr.d ); | 
| 461 | return 1; | 
| 462 | } | 
| 463 |  | 
| 464 | int MakeStamps::torsionConstraint( event* the_event ){ | 
| 465 |  | 
| 466 | current_torsion->constrain( the_event->evt.cnstr ); | 
| 467 | return 1; | 
| 468 | } | 
| 469 |  | 
| 470 | int MakeStamps::torsionEnd( event* the_event ){ | 
| 471 |  | 
| 472 | the_event->err_msg = current_torsion->checkMe(); | 
| 473 | if( the_event->err_msg != NULL ) return 0; | 
| 474 |  | 
| 475 | return 1; | 
| 476 | } |