| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <stdlib.h> |
| 43 |
#include <stdio.h> |
| 44 |
#include <string.h> |
| 45 |
#include <iostream> |
| 46 |
|
| 47 |
#include "types/MoleculeStamp.hpp" |
| 48 |
|
| 49 |
char MoleculeStamp::errMsg[500]; |
| 50 |
|
| 51 |
MoleculeStamp::MoleculeStamp(){ |
| 52 |
|
| 53 |
n_atoms = 0; |
| 54 |
n_bonds = 0; |
| 55 |
n_bends = 0; |
| 56 |
n_torsions = 0; |
| 57 |
n_rigidbodies = 0; |
| 58 |
n_cutoffgroups = 0; |
| 59 |
n_integrable = 0; |
| 60 |
|
| 61 |
unhandled = NULL; |
| 62 |
atoms = NULL; |
| 63 |
bonds = NULL; |
| 64 |
bends = NULL; |
| 65 |
torsions = NULL; |
| 66 |
rigidBodies = NULL; |
| 67 |
cutoffGroups = NULL; |
| 68 |
|
| 69 |
have_name = 0; |
| 70 |
have_atoms = 0; |
| 71 |
have_bonds = 0; |
| 72 |
have_bends = 0; |
| 73 |
have_torsions = 0; |
| 74 |
have_rigidbodies = 0; |
| 75 |
have_cutoffgroups = 0; |
| 76 |
|
| 77 |
} |
| 78 |
|
| 79 |
MoleculeStamp::~MoleculeStamp(){ |
| 80 |
int i; |
| 81 |
|
| 82 |
if( unhandled != NULL) delete unhandled; |
| 83 |
|
| 84 |
if( rigidBodies != NULL ) { |
| 85 |
for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i]; |
| 86 |
} |
| 87 |
delete[] rigidBodies; |
| 88 |
|
| 89 |
if( cutoffGroups != NULL ) { |
| 90 |
for( i=0; i<n_cutoffgroups; i++ ) delete cutoffGroups[i]; |
| 91 |
} |
| 92 |
delete[] cutoffGroups; |
| 93 |
|
| 94 |
if( atoms != NULL ){ |
| 95 |
for( i=0; i<n_atoms; i++ ) delete atoms[i]; |
| 96 |
} |
| 97 |
delete[] atoms; |
| 98 |
|
| 99 |
if( bonds != NULL ){ |
| 100 |
for( i=0; i<n_bonds; i++ ) delete bonds[i]; |
| 101 |
} |
| 102 |
delete[] bonds; |
| 103 |
|
| 104 |
if( bends != NULL ){ |
| 105 |
for( i=0; i<n_bends; i++ ) delete bends[i]; |
| 106 |
} |
| 107 |
delete[] bends; |
| 108 |
|
| 109 |
if( torsions != NULL ){ |
| 110 |
for( i=0; i<n_torsions; i++ ) delete torsions[i]; |
| 111 |
} |
| 112 |
delete[] torsions; |
| 113 |
|
| 114 |
|
| 115 |
|
| 116 |
|
| 117 |
} |
| 118 |
|
| 119 |
char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
| 120 |
|
| 121 |
if( !strcmp( lhs, "name" ) ){ |
| 122 |
strcpy( name, rhs ); |
| 123 |
have_name = 1; |
| 124 |
} |
| 125 |
else{ |
| 126 |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
| 127 |
else unhandled->add( lhs, rhs ); |
| 128 |
have_extras = 1; |
| 129 |
} |
| 130 |
return NULL; |
| 131 |
} |
| 132 |
|
| 133 |
char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
| 134 |
int i; |
| 135 |
|
| 136 |
if( !strcmp( lhs, "nAtoms" ) ){ |
| 137 |
n_atoms = (int)rhs; |
| 138 |
|
| 139 |
if( have_atoms ){ |
| 140 |
sprintf( errMsg, |
| 141 |
"MoleculeStamp error, n_atoms already declared" |
| 142 |
" for molecule: %s\n", |
| 143 |
name); |
| 144 |
return strdup( errMsg ); |
| 145 |
} |
| 146 |
have_atoms = 1; |
| 147 |
atoms = new AtomStamp*[n_atoms]; |
| 148 |
for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
| 149 |
} |
| 150 |
|
| 151 |
else if( !strcmp( lhs, "nBonds" ) ){ |
| 152 |
n_bonds = (int)rhs; |
| 153 |
|
| 154 |
if( have_bonds ){ |
| 155 |
sprintf( errMsg, |
| 156 |
"MoleculeStamp error, n_bonds already declared for" |
| 157 |
" molecule: %s\n", |
| 158 |
name); |
| 159 |
return strdup( errMsg ); |
| 160 |
} |
| 161 |
have_bonds = 1; |
| 162 |
bonds = new BondStamp*[n_bonds]; |
| 163 |
for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
| 164 |
} |
| 165 |
|
| 166 |
else if( !strcmp( lhs, "nBends" ) ){ |
| 167 |
n_bends = (int)rhs; |
| 168 |
|
| 169 |
if( have_bends ){ |
| 170 |
sprintf( errMsg, |
| 171 |
"MoleculeStamp error, n_bends already declared for" |
| 172 |
" molecule: %s\n", |
| 173 |
name); |
| 174 |
return strdup( errMsg ); |
| 175 |
} |
| 176 |
have_bends = 1; |
| 177 |
bends = new BendStamp*[n_bends]; |
| 178 |
for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
| 179 |
} |
| 180 |
|
| 181 |
else if( !strcmp( lhs, "nTorsions" ) ){ |
| 182 |
n_torsions = (int)rhs; |
| 183 |
|
| 184 |
if( have_torsions ){ |
| 185 |
sprintf( errMsg, |
| 186 |
"MoleculeStamp error, n_torsions already declared for" |
| 187 |
" molecule: %s\n", |
| 188 |
name ); |
| 189 |
return strdup( errMsg ); |
| 190 |
} |
| 191 |
have_torsions = 1; |
| 192 |
torsions = new TorsionStamp*[n_torsions]; |
| 193 |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
| 194 |
} |
| 195 |
|
| 196 |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
| 197 |
n_rigidbodies = (int)rhs; |
| 198 |
|
| 199 |
if( have_rigidbodies ){ |
| 200 |
sprintf( errMsg, |
| 201 |
"MoleculeStamp error, n_rigidbodies already declared for" |
| 202 |
" molecule: %s\n", |
| 203 |
name ); |
| 204 |
return strdup( errMsg ); |
| 205 |
} |
| 206 |
have_rigidbodies = 1; |
| 207 |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
| 208 |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
| 209 |
} |
| 210 |
|
| 211 |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
| 212 |
n_cutoffgroups = (int)rhs; |
| 213 |
|
| 214 |
if( have_cutoffgroups ){ |
| 215 |
sprintf( errMsg, |
| 216 |
"MoleculeStamp error, n_cutoffgroups already declared for" |
| 217 |
" molecule: %s\n", |
| 218 |
name ); |
| 219 |
return strdup( errMsg ); |
| 220 |
} |
| 221 |
have_cutoffgroups = 1; |
| 222 |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
| 223 |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
| 224 |
} |
| 225 |
|
| 226 |
else{ |
| 227 |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
| 228 |
else unhandled->add( lhs, rhs ); |
| 229 |
have_extras = 1; |
| 230 |
} |
| 231 |
return NULL; |
| 232 |
} |
| 233 |
|
| 234 |
char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
| 235 |
int i; |
| 236 |
|
| 237 |
if( !strcmp( lhs, "nAtoms" ) ){ |
| 238 |
n_atoms = rhs; |
| 239 |
|
| 240 |
if( have_atoms ){ |
| 241 |
sprintf( errMsg, |
| 242 |
"MoleculeStamp error, n_atoms already declared for" |
| 243 |
" molecule: %s\n", |
| 244 |
name); |
| 245 |
return strdup( errMsg ); |
| 246 |
} |
| 247 |
have_atoms = 1; |
| 248 |
atoms = new AtomStamp*[n_atoms]; |
| 249 |
for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
| 250 |
} |
| 251 |
|
| 252 |
else if( !strcmp( lhs, "nBonds" ) ){ |
| 253 |
n_bonds = rhs; |
| 254 |
|
| 255 |
if( have_bonds ){ |
| 256 |
sprintf( errMsg, |
| 257 |
"MoleculeStamp error, n_bonds already declared for" |
| 258 |
" molecule: %s\n", |
| 259 |
name); |
| 260 |
return strdup( errMsg ); |
| 261 |
} |
| 262 |
have_bonds = 1; |
| 263 |
bonds = new BondStamp*[n_bonds]; |
| 264 |
for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
| 265 |
} |
| 266 |
|
| 267 |
else if( !strcmp( lhs, "nBends" ) ){ |
| 268 |
n_bends = rhs; |
| 269 |
|
| 270 |
if( have_bends ){ |
| 271 |
sprintf( errMsg, |
| 272 |
"MoleculeStamp error, n_bends already declared for" |
| 273 |
" molecule: %s\n", |
| 274 |
name ); |
| 275 |
return strdup( errMsg ); |
| 276 |
} |
| 277 |
have_bends = 1; |
| 278 |
bends = new BendStamp*[n_bends]; |
| 279 |
for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
| 280 |
} |
| 281 |
|
| 282 |
else if( !strcmp( lhs, "nTorsions" ) ){ |
| 283 |
n_torsions = rhs; |
| 284 |
|
| 285 |
if( have_torsions ){ |
| 286 |
sprintf( errMsg, |
| 287 |
"MoleculeStamp error, n_torsions already declared for" |
| 288 |
" molecule: %s\n", |
| 289 |
name); |
| 290 |
return strdup( errMsg ); |
| 291 |
} |
| 292 |
have_torsions = 1; |
| 293 |
torsions = new TorsionStamp*[n_torsions]; |
| 294 |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
| 295 |
} |
| 296 |
|
| 297 |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
| 298 |
n_rigidbodies = rhs; |
| 299 |
|
| 300 |
if( have_rigidbodies ){ |
| 301 |
sprintf( errMsg, |
| 302 |
"MoleculeStamp error, n_rigidbodies already declared for" |
| 303 |
" molecule: %s\n", |
| 304 |
name); |
| 305 |
return strdup( errMsg ); |
| 306 |
} |
| 307 |
have_rigidbodies = 1; |
| 308 |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
| 309 |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
| 310 |
} |
| 311 |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
| 312 |
n_cutoffgroups = rhs; |
| 313 |
|
| 314 |
if( have_cutoffgroups ){ |
| 315 |
sprintf( errMsg, |
| 316 |
"MoleculeStamp error, n_cutoffgroups already declared for" |
| 317 |
" molecule: %s\n", |
| 318 |
name); |
| 319 |
return strdup( errMsg ); |
| 320 |
} |
| 321 |
have_cutoffgroups = 1; |
| 322 |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
| 323 |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
| 324 |
} |
| 325 |
else{ |
| 326 |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
| 327 |
else unhandled->add( lhs, rhs ); |
| 328 |
have_extras = 1; |
| 329 |
} |
| 330 |
return NULL; |
| 331 |
} |
| 332 |
|
| 333 |
char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
| 334 |
|
| 335 |
if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
| 336 |
else { |
| 337 |
if( have_atoms ){ |
| 338 |
sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
| 339 |
atomIndex ); |
| 340 |
return strdup( errMsg ); |
| 341 |
} |
| 342 |
else return strdup("MoleculeStamp error, nAtoms not given before" |
| 343 |
" first atom declaration." ); |
| 344 |
} |
| 345 |
|
| 346 |
return NULL; |
| 347 |
} |
| 348 |
|
| 349 |
char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
| 350 |
int rigidBodyIndex ){ |
| 351 |
|
| 352 |
if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
| 353 |
rigidBodies[rigidBodyIndex] = the_rigidbody; |
| 354 |
else { |
| 355 |
if( have_rigidbodies ){ |
| 356 |
sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
| 357 |
rigidBodyIndex ); |
| 358 |
return strdup( errMsg ); |
| 359 |
} |
| 360 |
else return strdup("MoleculeStamp error, nRigidBodies not given before" |
| 361 |
" first rigidBody declaration." ); |
| 362 |
} |
| 363 |
|
| 364 |
return NULL; |
| 365 |
} |
| 366 |
|
| 367 |
char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, |
| 368 |
int cutoffGroupIndex ){ |
| 369 |
|
| 370 |
if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) |
| 371 |
cutoffGroups[cutoffGroupIndex] = the_cutoffgroup; |
| 372 |
else { |
| 373 |
if( have_cutoffgroups ){ |
| 374 |
sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", |
| 375 |
cutoffGroupIndex ); |
| 376 |
return strdup( errMsg ); |
| 377 |
} |
| 378 |
else return strdup("MoleculeStamp error, nCutoffGroups not given before" |
| 379 |
" first CutoffGroup declaration." ); |
| 380 |
} |
| 381 |
|
| 382 |
return NULL; |
| 383 |
} |
| 384 |
|
| 385 |
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
| 386 |
|
| 387 |
|
| 388 |
if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
| 389 |
else{ |
| 390 |
if( have_bonds ){ |
| 391 |
sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
| 392 |
bondIndex ); |
| 393 |
return strdup( errMsg ); |
| 394 |
} |
| 395 |
else return strdup("MoleculeStamp error, nBonds not given before" |
| 396 |
"first bond declaration." ); |
| 397 |
} |
| 398 |
|
| 399 |
return NULL; |
| 400 |
} |
| 401 |
|
| 402 |
char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
| 403 |
|
| 404 |
|
| 405 |
if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
| 406 |
else{ |
| 407 |
if( have_bends ){ |
| 408 |
sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
| 409 |
bendIndex ); |
| 410 |
return strdup( errMsg ); |
| 411 |
} |
| 412 |
else return strdup("MoleculeStamp error, nBends not given before" |
| 413 |
"first bend declaration." ); |
| 414 |
} |
| 415 |
|
| 416 |
return NULL; |
| 417 |
} |
| 418 |
|
| 419 |
char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
| 420 |
|
| 421 |
|
| 422 |
if( have_torsions && torsionIndex < n_torsions ) |
| 423 |
torsions[torsionIndex] = the_torsion; |
| 424 |
else{ |
| 425 |
if( have_torsions ){ |
| 426 |
sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
| 427 |
torsionIndex ); |
| 428 |
return strdup( errMsg ); |
| 429 |
} |
| 430 |
else return strdup("MoleculeStamp error, nTorsions not given before" |
| 431 |
"first torsion declaration." ); |
| 432 |
} |
| 433 |
|
| 434 |
return NULL; |
| 435 |
} |
| 436 |
|
| 437 |
char* MoleculeStamp::checkMe( void ){ |
| 438 |
|
| 439 |
int i; |
| 440 |
short int no_atom, no_rigidbody, no_cutoffgroup; |
| 441 |
|
| 442 |
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
| 443 |
" was not given.\n" ); |
| 444 |
|
| 445 |
if( !have_atoms ){ |
| 446 |
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
| 447 |
} |
| 448 |
|
| 449 |
no_rigidbody = 0; |
| 450 |
for( i=0; i<n_rigidbodies; i++ ){ |
| 451 |
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
| 452 |
} |
| 453 |
|
| 454 |
if( no_rigidbody ){ |
| 455 |
sprintf( errMsg, |
| 456 |
"MoleculeStamp error. Not all of the RigidBodies were" |
| 457 |
" declared in molecule \"%s\".\n", name ); |
| 458 |
return strdup( errMsg ); |
| 459 |
} |
| 460 |
|
| 461 |
no_cutoffgroup = 0; |
| 462 |
for( i=0; i<n_cutoffgroups; i++ ){ |
| 463 |
if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1; |
| 464 |
} |
| 465 |
|
| 466 |
if( no_cutoffgroup ){ |
| 467 |
sprintf( errMsg, |
| 468 |
"MoleculeStamp error. Not all of the CutoffGroups were" |
| 469 |
" declared in molecule \"%s\".\n", name ); |
| 470 |
return strdup( errMsg ); |
| 471 |
} |
| 472 |
|
| 473 |
no_atom = 0; |
| 474 |
for( i=0; i<n_atoms; i++ ){ |
| 475 |
if( atoms[i] == NULL ) no_atom = 1; |
| 476 |
} |
| 477 |
|
| 478 |
if( no_atom ){ |
| 479 |
sprintf( errMsg, |
| 480 |
"MoleculeStamp error. Not all of the atoms were" |
| 481 |
" declared in molecule \"%s\".\n", name ); |
| 482 |
return strdup( errMsg ); |
| 483 |
} |
| 484 |
|
| 485 |
n_integrable = n_atoms; |
| 486 |
for (i = 0; i < n_rigidbodies; i++) |
| 487 |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
| 488 |
|
| 489 |
if (n_integrable <= 0 || n_integrable > n_atoms) { |
| 490 |
sprintf( errMsg, |
| 491 |
"MoleculeStamp error. n_integrable is either <= 0 or" |
| 492 |
" greater than n_atoms in molecule \"%s\".\n", name ); |
| 493 |
return strdup( errMsg ); |
| 494 |
} |
| 495 |
|
| 496 |
return NULL; |
| 497 |
} |
| 498 |
|
| 499 |
|
| 500 |
//Function Name: isBondInSameRigidBody |
| 501 |
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
| 502 |
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
| 503 |
int rbA; |
| 504 |
int rbB; |
| 505 |
int consAtomA; |
| 506 |
int consAtomB; |
| 507 |
|
| 508 |
if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA)) |
| 509 |
return false; |
| 510 |
|
| 511 |
if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) ) |
| 512 |
return false; |
| 513 |
|
| 514 |
if(rbB == rbA) |
| 515 |
return true; |
| 516 |
else |
| 517 |
return false; |
| 518 |
} |
| 519 |
|
| 520 |
// Function Name: isAtomInRigidBody |
| 521 |
//return false if atom does not belong to a rigid body, otherwise return true |
| 522 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
| 523 |
int whichRigidBody; |
| 524 |
int consAtomIndex; |
| 525 |
|
| 526 |
return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex); |
| 527 |
|
| 528 |
} |
| 529 |
|
| 530 |
// Function Name: isAtomInRigidBody |
| 531 |
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody |
| 532 |
//and consAtomIndex |
| 533 |
//atomIndex : the index of atom in component |
| 534 |
//whichRigidBody: the index of rigidbody in component |
| 535 |
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
| 536 |
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
| 537 |
RigidBodyStamp* rbStamp; |
| 538 |
int numRb; |
| 539 |
int numAtom; |
| 540 |
|
| 541 |
whichRigidBody = -1; |
| 542 |
consAtomIndex = -1; |
| 543 |
|
| 544 |
numRb = this->getNRigidBodies(); |
| 545 |
|
| 546 |
for(int i = 0 ; i < numRb; i++){ |
| 547 |
rbStamp = this->getRigidBody(i); |
| 548 |
numAtom = rbStamp->getNMembers(); |
| 549 |
for(int j = 0; j < numAtom; j++) |
| 550 |
if (rbStamp->getMember(j) == atomIndex){ |
| 551 |
whichRigidBody = i; |
| 552 |
consAtomIndex = j; |
| 553 |
return true; |
| 554 |
} |
| 555 |
} |
| 556 |
|
| 557 |
return false; |
| 558 |
|
| 559 |
} |
| 560 |
|
| 561 |
//return the position of joint atom apears in rigidbody's definition |
| 562 |
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2) |
| 563 |
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first |
| 564 |
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){ |
| 565 |
RigidBodyStamp* rbStamp1; |
| 566 |
RigidBodyStamp* rbStamp2; |
| 567 |
int natomInRb1; |
| 568 |
int natomInRb2; |
| 569 |
int atomIndex1; |
| 570 |
int atomIndex2; |
| 571 |
std::vector<std::pair<int, int> > jointAtomIndexPair; |
| 572 |
|
| 573 |
rbStamp1 = this->getRigidBody(rb1); |
| 574 |
natomInRb1 =rbStamp1->getNMembers(); |
| 575 |
|
| 576 |
rbStamp2 = this->getRigidBody(rb2); |
| 577 |
natomInRb2 =rbStamp2->getNMembers(); |
| 578 |
|
| 579 |
for(int i = 0; i < natomInRb1; i++){ |
| 580 |
atomIndex1 = rbStamp1->getMember(i); |
| 581 |
|
| 582 |
for(int j= 0; j < natomInRb1; j++){ |
| 583 |
atomIndex2 = rbStamp2->getMember(j); |
| 584 |
|
| 585 |
if(atomIndex1 == atomIndex2){ |
| 586 |
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
| 587 |
break; |
| 588 |
} |
| 589 |
|
| 590 |
}//end for(j =0) |
| 591 |
|
| 592 |
}//end for (i = 0) |
| 593 |
|
| 594 |
return jointAtomIndexPair; |
| 595 |
} |
