| 1 |
#include <cstdlib> |
| 2 |
#include <cstdio> |
| 3 |
#include <cstring> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "ForceFields.hpp" |
| 9 |
#include "SRI.hpp" |
| 10 |
|
| 11 |
|
| 12 |
TraPPE_ExFF::TraPPE_ExFF(){ |
| 13 |
|
| 14 |
char fileName[200]; |
| 15 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 16 |
char* ffPath; |
| 17 |
char temp[200]; |
| 18 |
|
| 19 |
// generate the force file name |
| 20 |
|
| 21 |
|
| 22 |
strcpy( fileName, "TraPPE_Ex.frc" ); |
| 23 |
fprintf( stderr,"Trying to open %s\n", fileName ); |
| 24 |
|
| 25 |
// attempt to open the file in the current directory first. |
| 26 |
|
| 27 |
frcFile = fopen( fileName, "r" ); |
| 28 |
|
| 29 |
if( frcFile == NULL ){ |
| 30 |
|
| 31 |
// next see if the force path enviorment variable is set |
| 32 |
|
| 33 |
ffPath = getenv( ffPath_env ); |
| 34 |
if( ffPath == NULL ) { |
| 35 |
fprintf( stderr, |
| 36 |
"Error opening the force field parameter file: %s\n" |
| 37 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 38 |
"vairable?\n", |
| 39 |
fileName ); |
| 40 |
exit( 8 ); |
| 41 |
} |
| 42 |
|
| 43 |
|
| 44 |
strcpy( temp, ffPath ); |
| 45 |
strcat( temp, "/" ); |
| 46 |
strcat( temp, fileName ); |
| 47 |
strcpy( fileName, temp ); |
| 48 |
|
| 49 |
frcFile = fopen( fileName, "r" ); |
| 50 |
|
| 51 |
if( frcFile == NULL ){ |
| 52 |
|
| 53 |
fprintf( stderr, |
| 54 |
"Error opening the force field parameter file: %s\n" |
| 55 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 56 |
"vairable?\n", |
| 57 |
fileName ); |
| 58 |
exit( 8 ); |
| 59 |
} |
| 60 |
} |
| 61 |
} |
| 62 |
|
| 63 |
TraPPE_ExFF::~TraPPE_ExFF(){ |
| 64 |
|
| 65 |
fclose( frcFile ); |
| 66 |
} |
| 67 |
|
| 68 |
void TraPPE_ExFF::initializeAtoms( void ){ |
| 69 |
|
| 70 |
class LinkedType { |
| 71 |
public: |
| 72 |
LinkedType(){ |
| 73 |
next = NULL; |
| 74 |
name[0] = '\0'; |
| 75 |
} |
| 76 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 77 |
|
| 78 |
LinkedType* find(char* key){ |
| 79 |
if( !strcmp(name, key) ) return this; |
| 80 |
if( next != NULL ) return next->find(key); |
| 81 |
return NULL; |
| 82 |
} |
| 83 |
|
| 84 |
char name[15]; |
| 85 |
int isDipole; |
| 86 |
double mass; |
| 87 |
double epslon; |
| 88 |
double sigma; |
| 89 |
double dipole; |
| 90 |
LinkedType* next; |
| 91 |
}; |
| 92 |
|
| 93 |
LinkedType* headAtomType; |
| 94 |
LinkedType* currentAtomType; |
| 95 |
LinkedType* tempAtomType; |
| 96 |
|
| 97 |
char readLine[500]; |
| 98 |
char* the_token; |
| 99 |
char* eof_test; |
| 100 |
int foundAtom = 0; |
| 101 |
int lineNum = 0; |
| 102 |
int i; |
| 103 |
|
| 104 |
////////////////////////////////////////////////// |
| 105 |
// a quick water fix |
| 106 |
|
| 107 |
double waterI[3][3]; |
| 108 |
waterI[0][0] = 1.76958347772500; |
| 109 |
waterI[0][1] = 0.0; |
| 110 |
waterI[0][2] = 0.0; |
| 111 |
|
| 112 |
waterI[1][0] = 0.0; |
| 113 |
waterI[1][1] = 0.614537057924513; |
| 114 |
waterI[1][2] = 0.0; |
| 115 |
|
| 116 |
waterI[2][0] = 0.0; |
| 117 |
waterI[2][1] = 0.0; |
| 118 |
waterI[2][2] = 1.15504641980049; |
| 119 |
|
| 120 |
|
| 121 |
double headI[3][3]; |
| 122 |
headI[0][0] = 1125; |
| 123 |
headI[0][1] = 0.0; |
| 124 |
headI[0][2] = 0.0; |
| 125 |
|
| 126 |
headI[1][0] = 0.0; |
| 127 |
headI[1][1] = 1125; |
| 128 |
headI[1][2] = 0.0; |
| 129 |
|
| 130 |
headI[2][0] = 0.0; |
| 131 |
headI[2][1] = 0.0; |
| 132 |
headI[2][2] = 250; |
| 133 |
|
| 134 |
|
| 135 |
|
| 136 |
////////////////////////////////////////////////// |
| 137 |
|
| 138 |
Atom** the_atoms; |
| 139 |
int nAtoms; |
| 140 |
the_atoms = entry_plug->atoms; |
| 141 |
nAtoms = entry_plug->n_atoms; |
| 142 |
|
| 143 |
// read in the atom types. |
| 144 |
|
| 145 |
rewind( frcFile ); |
| 146 |
headAtomType = new LinkedType; |
| 147 |
currentAtomType = headAtomType; |
| 148 |
|
| 149 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 150 |
lineNum++; |
| 151 |
if( eof_test == NULL ){ |
| 152 |
fprintf( stderr, "Error in reading Atoms from force file.\n" ); |
| 153 |
exit(8); |
| 154 |
} |
| 155 |
|
| 156 |
|
| 157 |
while( !foundAtom ){ |
| 158 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 159 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 160 |
lineNum++; |
| 161 |
} |
| 162 |
if( eof_test == NULL ){ |
| 163 |
fprintf( stderr, |
| 164 |
"Error in reading Atoms from force file at line %d.\n", |
| 165 |
lineNum ); |
| 166 |
exit(8); |
| 167 |
} |
| 168 |
|
| 169 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 170 |
foundAtom = !strcmp( "AtomTypes", the_token ); |
| 171 |
|
| 172 |
if( !foundAtom ){ |
| 173 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 174 |
lineNum++; |
| 175 |
|
| 176 |
if( eof_test == NULL ){ |
| 177 |
fprintf( stderr, |
| 178 |
"Error in reading Atoms from force file at line %d.\n", |
| 179 |
lineNum ); |
| 180 |
exit(8); |
| 181 |
} |
| 182 |
} |
| 183 |
} |
| 184 |
|
| 185 |
// we are now at the AtomTypes section. |
| 186 |
|
| 187 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 188 |
lineNum++; |
| 189 |
|
| 190 |
if( eof_test == NULL ){ |
| 191 |
fprintf( stderr, |
| 192 |
"Error in reading Atoms from force file at line %d.\n", |
| 193 |
lineNum ); |
| 194 |
exit(8); |
| 195 |
} |
| 196 |
|
| 197 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 198 |
|
| 199 |
if( readLine[0] != '!' ){ |
| 200 |
|
| 201 |
the_token = strtok( readLine, " \n\t,;" ); |
| 202 |
if( the_token != NULL ){ |
| 203 |
|
| 204 |
strcpy( currentAtomType->name, the_token ); |
| 205 |
|
| 206 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 207 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 208 |
exit(8); |
| 209 |
} |
| 210 |
|
| 211 |
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
| 212 |
|
| 213 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 214 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 215 |
exit(8); |
| 216 |
} |
| 217 |
|
| 218 |
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
| 219 |
|
| 220 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 221 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 222 |
exit(8); |
| 223 |
} |
| 224 |
|
| 225 |
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
| 226 |
|
| 227 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 228 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 229 |
exit(8); |
| 230 |
} |
| 231 |
|
| 232 |
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
| 233 |
|
| 234 |
if( currentAtomType->isDipole ){ |
| 235 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 236 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 237 |
exit(8); |
| 238 |
} |
| 239 |
|
| 240 |
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
| 241 |
} |
| 242 |
} |
| 243 |
} |
| 244 |
|
| 245 |
tempAtomType = new LinkedType; |
| 246 |
currentAtomType->next = tempAtomType; |
| 247 |
currentAtomType = tempAtomType; |
| 248 |
|
| 249 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 250 |
lineNum++; |
| 251 |
} |
| 252 |
|
| 253 |
|
| 254 |
// initialize the atoms |
| 255 |
|
| 256 |
DirectionalAtom* dAtom; |
| 257 |
|
| 258 |
for( i=0; i<nAtoms; i++ ){ |
| 259 |
|
| 260 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 261 |
if( currentAtomType == NULL ){ |
| 262 |
fprintf( stderr, "AtomType error, %s not found in force file.\n", |
| 263 |
the_atoms[i]->getType() ); |
| 264 |
exit(8); |
| 265 |
} |
| 266 |
|
| 267 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 268 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 269 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 270 |
the_atoms[i]->setLJ(); |
| 271 |
|
| 272 |
if( currentAtomType->isDipole ){ |
| 273 |
if( the_atoms[i]->isDirectional() ){ |
| 274 |
|
| 275 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 276 |
dAtom->setMu( currentAtomType->dipole ); |
| 277 |
dAtom->setHasDipole( 1 ); |
| 278 |
dAtom->setJx( 0.0 ); |
| 279 |
dAtom->setJy( 0.0 ); |
| 280 |
dAtom->setJz( 0.0 ); |
| 281 |
|
| 282 |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
| 283 |
dAtom->setI( waterI ); |
| 284 |
dAtom->setSSD( 1 ); |
| 285 |
} |
| 286 |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
| 287 |
dAtom->setI( headI ); |
| 288 |
dAtom->setSSD( 0 ); |
| 289 |
} |
| 290 |
else{ |
| 291 |
fprintf(stderr, |
| 292 |
"AtmType error, %s does not have a moment of inertia set.\n", |
| 293 |
the_atoms[i]->getType() ); |
| 294 |
exit(8); |
| 295 |
} |
| 296 |
entry_plug->n_dipoles++; |
| 297 |
} |
| 298 |
else{ |
| 299 |
std::cerr |
| 300 |
<< "TraPPE_ExFF error: Atom \"" |
| 301 |
<< currentAtomType->name << "\" is a dipole, yet no standard" |
| 302 |
<< " orientation was specifed in the BASS file.\n"; |
| 303 |
exit(8); |
| 304 |
} |
| 305 |
} |
| 306 |
else{ |
| 307 |
if( the_atoms[i]->isDirectional() ){ |
| 308 |
std::cerr |
| 309 |
<< "TraPPE_ExFF error: Atom \"" |
| 310 |
<< currentAtomType->name << "\" was given a standard orientation" |
| 311 |
<< " in the BASS file, yet it is not a dipole.\n"; |
| 312 |
exit(8); |
| 313 |
} |
| 314 |
} |
| 315 |
} |
| 316 |
|
| 317 |
|
| 318 |
// clean up the memory |
| 319 |
|
| 320 |
delete headAtomType; |
| 321 |
} |
| 322 |
|
| 323 |
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
| 324 |
|
| 325 |
class LinkedType { |
| 326 |
public: |
| 327 |
LinkedType(){ |
| 328 |
next = NULL; |
| 329 |
nameA[0] = '\0'; |
| 330 |
nameB[0] = '\0'; |
| 331 |
type[0] = '\0'; |
| 332 |
} |
| 333 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 334 |
|
| 335 |
LinkedType* find(char* key1, char* key2){ |
| 336 |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
| 337 |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
| 338 |
if( next != NULL ) return next->find(key1, key2); |
| 339 |
return NULL; |
| 340 |
} |
| 341 |
|
| 342 |
char nameA[15]; |
| 343 |
char nameB[15]; |
| 344 |
char type[30]; |
| 345 |
double d0; |
| 346 |
|
| 347 |
LinkedType* next; |
| 348 |
}; |
| 349 |
|
| 350 |
|
| 351 |
|
| 352 |
LinkedType* headBondType; |
| 353 |
LinkedType* currentBondType; |
| 354 |
LinkedType* tempBondType; |
| 355 |
|
| 356 |
char readLine[500]; |
| 357 |
char* the_token; |
| 358 |
char* eof_test; |
| 359 |
int foundBond = 0; |
| 360 |
int lineNum = 0; |
| 361 |
int i, a, b; |
| 362 |
char* atomA; |
| 363 |
char* atomB; |
| 364 |
|
| 365 |
SRI **the_sris; |
| 366 |
Atom** the_atoms; |
| 367 |
int nBonds; |
| 368 |
the_sris = entry_plug->sr_interactions; |
| 369 |
the_atoms = entry_plug->atoms; |
| 370 |
nBonds = entry_plug->n_bonds; |
| 371 |
|
| 372 |
// read in the bond types. |
| 373 |
|
| 374 |
rewind( frcFile ); |
| 375 |
headBondType = new LinkedType; |
| 376 |
currentBondType = headBondType; |
| 377 |
|
| 378 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 379 |
lineNum++; |
| 380 |
if( eof_test == NULL ){ |
| 381 |
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
| 382 |
exit(8); |
| 383 |
} |
| 384 |
|
| 385 |
|
| 386 |
while( !foundBond ){ |
| 387 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 388 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 389 |
lineNum++; |
| 390 |
} |
| 391 |
if( eof_test == NULL ){ |
| 392 |
fprintf( stderr, |
| 393 |
"Error in reading Bonds from force file at line %d.\n", |
| 394 |
lineNum ); |
| 395 |
exit(8); |
| 396 |
} |
| 397 |
|
| 398 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 399 |
foundBond = !strcmp( "BondTypes", the_token ); |
| 400 |
|
| 401 |
if( !foundBond ){ |
| 402 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 403 |
lineNum++; |
| 404 |
|
| 405 |
if( eof_test == NULL ){ |
| 406 |
fprintf( stderr, |
| 407 |
"Error in reading Bonds from force file at line %d.\n", |
| 408 |
lineNum ); |
| 409 |
exit(8); |
| 410 |
} |
| 411 |
} |
| 412 |
} |
| 413 |
|
| 414 |
// we are now at the BondTypes section. |
| 415 |
|
| 416 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 417 |
lineNum++; |
| 418 |
|
| 419 |
if( eof_test == NULL ){ |
| 420 |
fprintf( stderr, |
| 421 |
"Error in reading Bonds from force file at line %d.\n", |
| 422 |
lineNum ); |
| 423 |
exit(8); |
| 424 |
} |
| 425 |
|
| 426 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 427 |
|
| 428 |
if( readLine[0] != '!' ){ |
| 429 |
|
| 430 |
the_token = strtok( readLine, " \n\t,;" ); |
| 431 |
if( the_token != NULL ){ |
| 432 |
|
| 433 |
strcpy( currentBondType->nameA, the_token ); |
| 434 |
|
| 435 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 436 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
| 437 |
exit(8); |
| 438 |
} |
| 439 |
|
| 440 |
strcpy( currentBondType->nameB, the_token ); |
| 441 |
|
| 442 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 443 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
| 444 |
exit(8); |
| 445 |
} |
| 446 |
|
| 447 |
strcpy( currentBondType->type, the_token ); |
| 448 |
|
| 449 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
| 450 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 451 |
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
| 452 |
exit(8); |
| 453 |
} |
| 454 |
|
| 455 |
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
| 456 |
} |
| 457 |
|
| 458 |
else{ |
| 459 |
fprintf(stderr, |
| 460 |
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
| 461 |
currentBondType->type, |
| 462 |
lineNum ); |
| 463 |
exit(8); |
| 464 |
} |
| 465 |
} |
| 466 |
} |
| 467 |
|
| 468 |
tempBondType = new LinkedType; |
| 469 |
currentBondType->next = tempBondType; |
| 470 |
currentBondType = tempBondType; |
| 471 |
|
| 472 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 473 |
lineNum++; |
| 474 |
} |
| 475 |
|
| 476 |
|
| 477 |
// initialize the Bonds |
| 478 |
|
| 479 |
|
| 480 |
for( i=0; i<nBonds; i++ ){ |
| 481 |
|
| 482 |
a = the_bonds[i].a; |
| 483 |
b = the_bonds[i].b; |
| 484 |
|
| 485 |
atomA = the_atoms[a]->getType(); |
| 486 |
atomB = the_atoms[b]->getType(); |
| 487 |
currentBondType = headBondType->find( atomA, atomB ); |
| 488 |
if( currentBondType == NULL ){ |
| 489 |
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
| 490 |
atomA, atomB ); |
| 491 |
exit(8); |
| 492 |
} |
| 493 |
|
| 494 |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
| 495 |
|
| 496 |
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
| 497 |
*the_atoms[b], |
| 498 |
currentBondType->d0 ); |
| 499 |
entry_plug->n_constraints++; |
| 500 |
} |
| 501 |
} |
| 502 |
|
| 503 |
|
| 504 |
// clean up the memory |
| 505 |
|
| 506 |
delete headBondType; |
| 507 |
|
| 508 |
} |
| 509 |
|
| 510 |
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
| 511 |
|
| 512 |
class LinkedType { |
| 513 |
public: |
| 514 |
LinkedType(){ |
| 515 |
next = NULL; |
| 516 |
nameA[0] = '\0'; |
| 517 |
nameB[0] = '\0'; |
| 518 |
nameC[0] = '\0'; |
| 519 |
type[0] = '\0'; |
| 520 |
} |
| 521 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 522 |
|
| 523 |
LinkedType* find( char* key1, char* key2, char* key3 ){ |
| 524 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
| 525 |
&& !strcmp( nameC, key3 ) ) return this; |
| 526 |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
| 527 |
&& !strcmp( nameC, key1 ) ) return this; |
| 528 |
if( next != NULL ) return next->find(key1, key2, key3); |
| 529 |
return NULL; |
| 530 |
} |
| 531 |
|
| 532 |
char nameA[15]; |
| 533 |
char nameB[15]; |
| 534 |
char nameC[15]; |
| 535 |
char type[30]; |
| 536 |
double k1, k2, k3, t0; |
| 537 |
|
| 538 |
LinkedType* next; |
| 539 |
}; |
| 540 |
|
| 541 |
LinkedType* headBendType; |
| 542 |
LinkedType* currentBendType; |
| 543 |
LinkedType* tempBendType; |
| 544 |
|
| 545 |
char readLine[500]; |
| 546 |
char* the_token; |
| 547 |
char* eof_test; |
| 548 |
int foundBend = 0; |
| 549 |
int lineNum = 0; |
| 550 |
int i, a, b, c, index; |
| 551 |
char* atomA; |
| 552 |
char* atomB; |
| 553 |
char* atomC; |
| 554 |
QuadraticBend* qBend; |
| 555 |
|
| 556 |
SRI **the_sris; |
| 557 |
Atom** the_atoms; |
| 558 |
int nBends; |
| 559 |
the_sris = entry_plug->sr_interactions; |
| 560 |
the_atoms = entry_plug->atoms; |
| 561 |
nBends = entry_plug->n_bends; |
| 562 |
|
| 563 |
// read in the bend types. |
| 564 |
|
| 565 |
rewind( frcFile ); |
| 566 |
headBendType = new LinkedType; |
| 567 |
currentBendType = headBendType; |
| 568 |
|
| 569 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 570 |
lineNum++; |
| 571 |
if( eof_test == NULL ){ |
| 572 |
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
| 573 |
exit(8); |
| 574 |
} |
| 575 |
|
| 576 |
|
| 577 |
while( !foundBend ){ |
| 578 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 579 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 580 |
lineNum++; |
| 581 |
} |
| 582 |
if( eof_test == NULL ){ |
| 583 |
fprintf( stderr, |
| 584 |
"Error in reading Bends from force file at line %d.\n", |
| 585 |
lineNum ); |
| 586 |
exit(8); |
| 587 |
} |
| 588 |
|
| 589 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 590 |
foundBend = !strcmp( "BendTypes", the_token ); |
| 591 |
|
| 592 |
if( !foundBend ){ |
| 593 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 594 |
lineNum++; |
| 595 |
|
| 596 |
if( eof_test == NULL ){ |
| 597 |
fprintf( stderr, |
| 598 |
"Error in reading Bends from force file at line %d.\n", |
| 599 |
lineNum ); |
| 600 |
exit(8); |
| 601 |
} |
| 602 |
} |
| 603 |
} |
| 604 |
|
| 605 |
// we are now at the BendTypes section. |
| 606 |
|
| 607 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 608 |
lineNum++; |
| 609 |
|
| 610 |
if( eof_test == NULL ){ |
| 611 |
fprintf( stderr, |
| 612 |
"Error in reading Bends from force file at line %d.\n", |
| 613 |
lineNum ); |
| 614 |
exit(8); |
| 615 |
} |
| 616 |
|
| 617 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 618 |
|
| 619 |
if( readLine[0] != '!' ){ |
| 620 |
|
| 621 |
the_token = strtok( readLine, " \n\t,;" ); |
| 622 |
if( the_token != NULL ){ |
| 623 |
|
| 624 |
strcpy( currentBendType->nameA, the_token ); |
| 625 |
|
| 626 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 627 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 628 |
exit(8); |
| 629 |
} |
| 630 |
|
| 631 |
strcpy( currentBendType->nameB, the_token ); |
| 632 |
|
| 633 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 634 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 635 |
exit(8); |
| 636 |
} |
| 637 |
|
| 638 |
strcpy( currentBendType->nameC, the_token ); |
| 639 |
|
| 640 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 641 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 642 |
exit(8); |
| 643 |
} |
| 644 |
|
| 645 |
strcpy( currentBendType->type, the_token ); |
| 646 |
|
| 647 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
| 648 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 649 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 650 |
exit(8); |
| 651 |
} |
| 652 |
|
| 653 |
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
| 654 |
|
| 655 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 656 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 657 |
exit(8); |
| 658 |
} |
| 659 |
|
| 660 |
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
| 661 |
|
| 662 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 663 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 664 |
exit(8); |
| 665 |
} |
| 666 |
|
| 667 |
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
| 668 |
|
| 669 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 670 |
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
| 671 |
exit(8); |
| 672 |
} |
| 673 |
|
| 674 |
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
| 675 |
} |
| 676 |
|
| 677 |
else{ |
| 678 |
fprintf(stderr, |
| 679 |
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
| 680 |
currentBendType->type, |
| 681 |
lineNum ); |
| 682 |
exit(8); |
| 683 |
} |
| 684 |
} |
| 685 |
} |
| 686 |
|
| 687 |
tempBendType = new LinkedType; |
| 688 |
currentBendType->next = tempBendType; |
| 689 |
currentBendType = tempBendType; |
| 690 |
|
| 691 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 692 |
lineNum++; |
| 693 |
} |
| 694 |
|
| 695 |
|
| 696 |
// initialize the Bends |
| 697 |
|
| 698 |
for( i=0; i<nBends; i++ ){ |
| 699 |
|
| 700 |
a = the_bends[i].a; |
| 701 |
b = the_bends[i].b; |
| 702 |
c = the_bends[i].c; |
| 703 |
|
| 704 |
atomA = the_atoms[a]->getType(); |
| 705 |
atomB = the_atoms[b]->getType(); |
| 706 |
atomC = the_atoms[c]->getType(); |
| 707 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
| 708 |
if( currentBendType == NULL ){ |
| 709 |
fprintf( stderr, "BendType error, %s - %s - %s not found" |
| 710 |
" in force file.\n", |
| 711 |
atomA, atomB, atomC ); |
| 712 |
exit(8); |
| 713 |
} |
| 714 |
|
| 715 |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
| 716 |
|
| 717 |
index = i + entry_plug->n_bonds; |
| 718 |
qBend = new QuadraticBend( *the_atoms[a], |
| 719 |
*the_atoms[b], |
| 720 |
*the_atoms[c] ); |
| 721 |
qBend->setConstants( currentBendType->k1, |
| 722 |
currentBendType->k2, |
| 723 |
currentBendType->k3, |
| 724 |
currentBendType->t0 ); |
| 725 |
the_sris[index] = qBend; |
| 726 |
} |
| 727 |
} |
| 728 |
|
| 729 |
|
| 730 |
// clean up the memory |
| 731 |
|
| 732 |
delete headBendType; |
| 733 |
|
| 734 |
} |
| 735 |
|
| 736 |
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
| 737 |
|
| 738 |
class LinkedType { |
| 739 |
public: |
| 740 |
LinkedType(){ |
| 741 |
next = NULL; |
| 742 |
nameA[0] = '\0'; |
| 743 |
nameB[0] = '\0'; |
| 744 |
nameC[0] = '\0'; |
| 745 |
type[0] = '\0'; |
| 746 |
} |
| 747 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 748 |
|
| 749 |
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
| 750 |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
| 751 |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
| 752 |
|
| 753 |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
| 754 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
| 755 |
|
| 756 |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
| 757 |
return NULL; |
| 758 |
} |
| 759 |
|
| 760 |
char nameA[15]; |
| 761 |
char nameB[15]; |
| 762 |
char nameC[15]; |
| 763 |
char nameD[15]; |
| 764 |
char type[30]; |
| 765 |
double k1, k2, k3, k4; |
| 766 |
|
| 767 |
LinkedType* next; |
| 768 |
}; |
| 769 |
|
| 770 |
LinkedType* headTorsionType; |
| 771 |
LinkedType* currentTorsionType; |
| 772 |
LinkedType* tempTorsionType; |
| 773 |
|
| 774 |
char readLine[500]; |
| 775 |
char* the_token; |
| 776 |
char* eof_test; |
| 777 |
int foundTorsion = 0; |
| 778 |
int lineNum = 0; |
| 779 |
int i, a, b, c, d, index; |
| 780 |
char* atomA; |
| 781 |
char* atomB; |
| 782 |
char* atomC; |
| 783 |
char* atomD; |
| 784 |
CubicTorsion* cTors; |
| 785 |
|
| 786 |
SRI **the_sris; |
| 787 |
Atom** the_atoms; |
| 788 |
int nTorsions; |
| 789 |
the_sris = entry_plug->sr_interactions; |
| 790 |
the_atoms = entry_plug->atoms; |
| 791 |
nTorsions = entry_plug->n_torsions; |
| 792 |
|
| 793 |
// read in the torsion types. |
| 794 |
|
| 795 |
rewind( frcFile ); |
| 796 |
headTorsionType = new LinkedType; |
| 797 |
currentTorsionType = headTorsionType; |
| 798 |
|
| 799 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 800 |
lineNum++; |
| 801 |
if( eof_test == NULL ){ |
| 802 |
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
| 803 |
exit(8); |
| 804 |
} |
| 805 |
|
| 806 |
|
| 807 |
while( !foundTorsion ){ |
| 808 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 809 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 810 |
lineNum++; |
| 811 |
} |
| 812 |
if( eof_test == NULL ){ |
| 813 |
fprintf( stderr, |
| 814 |
"Error in reading Torsions from force file at line %d.\n", |
| 815 |
lineNum ); |
| 816 |
exit(8); |
| 817 |
} |
| 818 |
|
| 819 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 820 |
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
| 821 |
|
| 822 |
if( !foundTorsion ){ |
| 823 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 824 |
lineNum++; |
| 825 |
|
| 826 |
if( eof_test == NULL ){ |
| 827 |
fprintf( stderr, |
| 828 |
"Error in reading Torsions from force file at line %d.\n", |
| 829 |
lineNum ); |
| 830 |
exit(8); |
| 831 |
} |
| 832 |
} |
| 833 |
} |
| 834 |
|
| 835 |
// we are now at the TorsionTypes section. |
| 836 |
|
| 837 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 838 |
lineNum++; |
| 839 |
|
| 840 |
if( eof_test == NULL ){ |
| 841 |
fprintf( stderr, |
| 842 |
"Error in reading Torsions from force file at line %d.\n", |
| 843 |
lineNum ); |
| 844 |
exit(8); |
| 845 |
} |
| 846 |
|
| 847 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 848 |
|
| 849 |
if( readLine[0] != '!' ){ |
| 850 |
|
| 851 |
the_token = strtok( readLine, " \n\t,;" ); |
| 852 |
if( the_token != NULL ){ |
| 853 |
|
| 854 |
strcpy( currentTorsionType->nameA, the_token ); |
| 855 |
|
| 856 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 857 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
| 858 |
exit(8); |
| 859 |
} |
| 860 |
|
| 861 |
strcpy( currentTorsionType->nameB, the_token ); |
| 862 |
|
| 863 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 864 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
| 865 |
exit(8); |
| 866 |
} |
| 867 |
|
| 868 |
strcpy( currentTorsionType->nameC, the_token ); |
| 869 |
|
| 870 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 871 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
| 872 |
exit(8); |
| 873 |
} |
| 874 |
|
| 875 |
strcpy( currentTorsionType->nameD, the_token ); |
| 876 |
|
| 877 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 878 |
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
| 879 |
exit(8); |
| 880 |
} |
| 881 |
|
| 882 |
strcpy( currentTorsionType->type, the_token ); |
| 883 |
|
| 884 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
| 885 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 886 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 887 |
exit(8); |
| 888 |
} |
| 889 |
|
| 890 |
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
| 891 |
|
| 892 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 893 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 894 |
exit(8); |
| 895 |
} |
| 896 |
|
| 897 |
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
| 898 |
|
| 899 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 900 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 901 |
exit(8); |
| 902 |
} |
| 903 |
|
| 904 |
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
| 905 |
|
| 906 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 907 |
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
| 908 |
exit(8); |
| 909 |
} |
| 910 |
|
| 911 |
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
| 912 |
} |
| 913 |
|
| 914 |
else{ |
| 915 |
fprintf(stderr, |
| 916 |
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
| 917 |
currentTorsionType->type, |
| 918 |
lineNum ); |
| 919 |
exit(8); |
| 920 |
} |
| 921 |
} |
| 922 |
} |
| 923 |
|
| 924 |
tempTorsionType = new LinkedType; |
| 925 |
currentTorsionType->next = tempTorsionType; |
| 926 |
currentTorsionType = tempTorsionType; |
| 927 |
|
| 928 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 929 |
lineNum++; |
| 930 |
} |
| 931 |
|
| 932 |
|
| 933 |
// initialize the Torsions |
| 934 |
|
| 935 |
for( i=0; i<nTorsions; i++ ){ |
| 936 |
|
| 937 |
a = the_torsions[i].a; |
| 938 |
b = the_torsions[i].b; |
| 939 |
c = the_torsions[i].c; |
| 940 |
d = the_torsions[i].d; |
| 941 |
|
| 942 |
atomA = the_atoms[a]->getType(); |
| 943 |
atomB = the_atoms[b]->getType(); |
| 944 |
atomC = the_atoms[c]->getType(); |
| 945 |
atomD = the_atoms[d]->getType(); |
| 946 |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
| 947 |
if( currentTorsionType == NULL ){ |
| 948 |
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
| 949 |
" in force file.\n", |
| 950 |
atomA, atomB, atomC, atomD ); |
| 951 |
exit(8); |
| 952 |
} |
| 953 |
|
| 954 |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
| 955 |
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
| 956 |
|
| 957 |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
| 958 |
*the_atoms[c], *the_atoms[d] ); |
| 959 |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
| 960 |
currentTorsionType->k3, currentTorsionType->k4 ); |
| 961 |
the_sris[index] = cTors; |
| 962 |
} |
| 963 |
} |
| 964 |
|
| 965 |
|
| 966 |
// clean up the memory |
| 967 |
|
| 968 |
delete headTorsionType; |
| 969 |
|
| 970 |
} |
