| 1 |
#include <stdlib.h> |
| 2 |
#include <string.h> |
| 3 |
#include <math.h> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "SimInfo.hpp" |
| 9 |
#define __C |
| 10 |
#include "fSimulation.h" |
| 11 |
#include "simError.h" |
| 12 |
|
| 13 |
#include "fortranWrappers.hpp" |
| 14 |
|
| 15 |
#include "MatVec3.h" |
| 16 |
|
| 17 |
#ifdef IS_MPI |
| 18 |
#include "mpiSimulation.hpp" |
| 19 |
#endif |
| 20 |
|
| 21 |
inline double roundMe( double x ){ |
| 22 |
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 23 |
} |
| 24 |
|
| 25 |
inline double min( double a, double b ){ |
| 26 |
return (a < b ) ? a : b; |
| 27 |
} |
| 28 |
|
| 29 |
SimInfo* currentInfo; |
| 30 |
|
| 31 |
SimInfo::SimInfo(){ |
| 32 |
|
| 33 |
n_constraints = 0; |
| 34 |
nZconstraints = 0; |
| 35 |
n_oriented = 0; |
| 36 |
n_dipoles = 0; |
| 37 |
ndf = 0; |
| 38 |
ndfRaw = 0; |
| 39 |
nZconstraints = 0; |
| 40 |
the_integrator = NULL; |
| 41 |
setTemp = 0; |
| 42 |
thermalTime = 0.0; |
| 43 |
currentTime = 0.0; |
| 44 |
rCut = 0.0; |
| 45 |
ecr = 0.0; |
| 46 |
est = 0.0; |
| 47 |
|
| 48 |
haveRcut = 0; |
| 49 |
haveEcr = 0; |
| 50 |
boxIsInit = 0; |
| 51 |
|
| 52 |
resetTime = 1e99; |
| 53 |
|
| 54 |
orthoRhombic = 0; |
| 55 |
orthoTolerance = 1E-6; |
| 56 |
useInitXSstate = true; |
| 57 |
|
| 58 |
usePBC = 0; |
| 59 |
useLJ = 0; |
| 60 |
useSticky = 0; |
| 61 |
useCharges = 0; |
| 62 |
useDipoles = 0; |
| 63 |
useReactionField = 0; |
| 64 |
useGB = 0; |
| 65 |
useEAM = 0; |
| 66 |
|
| 67 |
excludes = Exclude::Instance(); |
| 68 |
|
| 69 |
myConfiguration = new SimState(); |
| 70 |
|
| 71 |
has_minimizer = false; |
| 72 |
the_minimizer =NULL; |
| 73 |
|
| 74 |
wrapMeSimInfo( this ); |
| 75 |
} |
| 76 |
|
| 77 |
|
| 78 |
SimInfo::~SimInfo(){ |
| 79 |
|
| 80 |
delete myConfiguration; |
| 81 |
|
| 82 |
map<string, GenericData*>::iterator i; |
| 83 |
|
| 84 |
for(i = properties.begin(); i != properties.end(); i++) |
| 85 |
delete (*i).second; |
| 86 |
|
| 87 |
} |
| 88 |
|
| 89 |
void SimInfo::setBox(double newBox[3]) { |
| 90 |
|
| 91 |
int i, j; |
| 92 |
double tempMat[3][3]; |
| 93 |
|
| 94 |
for(i=0; i<3; i++) |
| 95 |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
| 96 |
|
| 97 |
tempMat[0][0] = newBox[0]; |
| 98 |
tempMat[1][1] = newBox[1]; |
| 99 |
tempMat[2][2] = newBox[2]; |
| 100 |
|
| 101 |
setBoxM( tempMat ); |
| 102 |
|
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} |
| 104 |
|
| 105 |
void SimInfo::setBoxM( double theBox[3][3] ){ |
| 106 |
|
| 107 |
int i, j; |
| 108 |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
| 109 |
// ordering in the array is as follows: |
| 110 |
// [ 0 3 6 ] |
| 111 |
// [ 1 4 7 ] |
| 112 |
// [ 2 5 8 ] |
| 113 |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
| 114 |
|
| 115 |
if( !boxIsInit ) boxIsInit = 1; |
| 116 |
|
| 117 |
for(i=0; i < 3; i++) |
| 118 |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
| 119 |
|
| 120 |
calcBoxL(); |
| 121 |
calcHmatInv(); |
| 122 |
|
| 123 |
for(i=0; i < 3; i++) { |
| 124 |
for (j=0; j < 3; j++) { |
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FortranHmat[3*j + i] = Hmat[i][j]; |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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} |
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} |
| 129 |
|
| 130 |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
| 131 |
|
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} |
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|
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|
| 135 |
void SimInfo::getBoxM (double theBox[3][3]) { |
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|
| 137 |
int i, j; |
| 138 |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
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} |
| 141 |
|
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|
| 143 |
void SimInfo::scaleBox(double scale) { |
| 144 |
double theBox[3][3]; |
| 145 |
int i, j; |
| 146 |
|
| 147 |
// cerr << "Scaling box by " << scale << "\n"; |
| 148 |
|
| 149 |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
| 151 |
|
| 152 |
setBoxM(theBox); |
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|
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} |
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|
| 156 |
void SimInfo::calcHmatInv( void ) { |
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|
| 158 |
int oldOrtho; |
| 159 |
int i,j; |
| 160 |
double smallDiag; |
| 161 |
double tol; |
| 162 |
double sanity[3][3]; |
| 163 |
|
| 164 |
invertMat3( Hmat, HmatInv ); |
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|
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// check to see if Hmat is orthorhombic |
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|
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oldOrtho = orthoRhombic; |
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|
| 170 |
smallDiag = fabs(Hmat[0][0]); |
| 171 |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
| 172 |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
| 173 |
tol = smallDiag * orthoTolerance; |
| 174 |
|
| 175 |
orthoRhombic = 1; |
| 176 |
|
| 177 |
for (i = 0; i < 3; i++ ) { |
| 178 |
for (j = 0 ; j < 3; j++) { |
| 179 |
if (i != j) { |
| 180 |
if (orthoRhombic) { |
| 181 |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
| 182 |
} |
| 183 |
} |
| 184 |
} |
| 185 |
} |
| 186 |
|
| 187 |
if( oldOrtho != orthoRhombic ){ |
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|
| 189 |
if( orthoRhombic ){ |
| 190 |
sprintf( painCave.errMsg, |
| 191 |
"OOPSE is switching from the default Non-Orthorhombic\n" |
| 192 |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 193 |
"\tThis is usually a good thing, but if you wan't the\n" |
| 194 |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 195 |
"\tvariable ( currently set to %G ) smaller.\n", |
| 196 |
orthoTolerance); |
| 197 |
simError(); |
| 198 |
} |
| 199 |
else { |
| 200 |
sprintf( painCave.errMsg, |
| 201 |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 202 |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 203 |
"\tThis is usually because the box has deformed under\n" |
| 204 |
"\tNPTf integration. If you wan't to live on the edge with\n" |
| 205 |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 206 |
"\tvariable ( currently set to %G ) larger.\n", |
| 207 |
orthoTolerance); |
| 208 |
simError(); |
| 209 |
} |
| 210 |
} |
| 211 |
} |
| 212 |
|
| 213 |
void SimInfo::calcBoxL( void ){ |
| 214 |
|
| 215 |
double dx, dy, dz, dsq; |
| 216 |
|
| 217 |
// boxVol = Determinant of Hmat |
| 218 |
|
| 219 |
boxVol = matDet3( Hmat ); |
| 220 |
|
| 221 |
// boxLx |
| 222 |
|
| 223 |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
| 224 |
dsq = dx*dx + dy*dy + dz*dz; |
| 225 |
boxL[0] = sqrt( dsq ); |
| 226 |
//maxCutoff = 0.5 * boxL[0]; |
| 227 |
|
| 228 |
// boxLy |
| 229 |
|
| 230 |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
| 231 |
dsq = dx*dx + dy*dy + dz*dz; |
| 232 |
boxL[1] = sqrt( dsq ); |
| 233 |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
| 234 |
|
| 235 |
|
| 236 |
// boxLz |
| 237 |
|
| 238 |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
| 239 |
dsq = dx*dx + dy*dy + dz*dz; |
| 240 |
boxL[2] = sqrt( dsq ); |
| 241 |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
| 242 |
|
| 243 |
//calculate the max cutoff |
| 244 |
maxCutoff = calcMaxCutOff(); |
| 245 |
|
| 246 |
checkCutOffs(); |
| 247 |
|
| 248 |
} |
| 249 |
|
| 250 |
|
| 251 |
double SimInfo::calcMaxCutOff(){ |
| 252 |
|
| 253 |
double ri[3], rj[3], rk[3]; |
| 254 |
double rij[3], rjk[3], rki[3]; |
| 255 |
double minDist; |
| 256 |
|
| 257 |
ri[0] = Hmat[0][0]; |
| 258 |
ri[1] = Hmat[1][0]; |
| 259 |
ri[2] = Hmat[2][0]; |
| 260 |
|
| 261 |
rj[0] = Hmat[0][1]; |
| 262 |
rj[1] = Hmat[1][1]; |
| 263 |
rj[2] = Hmat[2][1]; |
| 264 |
|
| 265 |
rk[0] = Hmat[0][2]; |
| 266 |
rk[1] = Hmat[1][2]; |
| 267 |
rk[2] = Hmat[2][2]; |
| 268 |
|
| 269 |
crossProduct3(ri, rj, rij); |
| 270 |
distXY = dotProduct3(rk,rij) / norm3(rij); |
| 271 |
|
| 272 |
crossProduct3(rj,rk, rjk); |
| 273 |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
| 274 |
|
| 275 |
crossProduct3(rk,ri, rki); |
| 276 |
distZX = dotProduct3(rj,rki) / norm3(rki); |
| 277 |
|
| 278 |
minDist = min(min(distXY, distYZ), distZX); |
| 279 |
return minDist/2; |
| 280 |
|
| 281 |
} |
| 282 |
|
| 283 |
void SimInfo::wrapVector( double thePos[3] ){ |
| 284 |
|
| 285 |
int i; |
| 286 |
double scaled[3]; |
| 287 |
|
| 288 |
if( !orthoRhombic ){ |
| 289 |
// calc the scaled coordinates. |
| 290 |
|
| 291 |
|
| 292 |
matVecMul3(HmatInv, thePos, scaled); |
| 293 |
|
| 294 |
for(i=0; i<3; i++) |
| 295 |
scaled[i] -= roundMe(scaled[i]); |
| 296 |
|
| 297 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 298 |
|
| 299 |
matVecMul3(Hmat, scaled, thePos); |
| 300 |
|
| 301 |
} |
| 302 |
else{ |
| 303 |
// calc the scaled coordinates. |
| 304 |
|
| 305 |
for(i=0; i<3; i++) |
| 306 |
scaled[i] = thePos[i]*HmatInv[i][i]; |
| 307 |
|
| 308 |
// wrap the scaled coordinates |
| 309 |
|
| 310 |
for(i=0; i<3; i++) |
| 311 |
scaled[i] -= roundMe(scaled[i]); |
| 312 |
|
| 313 |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 314 |
|
| 315 |
for(i=0; i<3; i++) |
| 316 |
thePos[i] = scaled[i]*Hmat[i][i]; |
| 317 |
} |
| 318 |
|
| 319 |
} |
| 320 |
|
| 321 |
|
| 322 |
int SimInfo::getNDF(){ |
| 323 |
int ndf_local; |
| 324 |
|
| 325 |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 326 |
ndf_local += 3; |
| 327 |
if (integrableObjects[i]->isDirectional()) |
| 328 |
ndf_local += 3; |
| 329 |
} |
| 330 |
|
| 331 |
// n_constraints is local, so subtract them on each processor: |
| 332 |
|
| 333 |
ndf_local -= n_constraints; |
| 334 |
|
| 335 |
#ifdef IS_MPI |
| 336 |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 337 |
#else |
| 338 |
ndf = ndf_local; |
| 339 |
#endif |
| 340 |
|
| 341 |
// nZconstraints is global, as are the 3 COM translations for the |
| 342 |
// entire system: |
| 343 |
|
| 344 |
ndf = ndf - 3 - nZconstraints; |
| 345 |
|
| 346 |
return ndf; |
| 347 |
} |
| 348 |
|
| 349 |
int SimInfo::getNDFraw() { |
| 350 |
int ndfRaw_local; |
| 351 |
|
| 352 |
// Raw degrees of freedom that we have to set |
| 353 |
|
| 354 |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 355 |
ndfRaw_local += 3; |
| 356 |
if (integrableObjects[i]->isDirectional()) |
| 357 |
ndfRaw_local += 3; |
| 358 |
} |
| 359 |
|
| 360 |
#ifdef IS_MPI |
| 361 |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 362 |
#else |
| 363 |
ndfRaw = ndfRaw_local; |
| 364 |
#endif |
| 365 |
|
| 366 |
return ndfRaw; |
| 367 |
} |
| 368 |
|
| 369 |
int SimInfo::getNDFtranslational() { |
| 370 |
int ndfTrans_local; |
| 371 |
|
| 372 |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
| 373 |
|
| 374 |
|
| 375 |
#ifdef IS_MPI |
| 376 |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 377 |
#else |
| 378 |
ndfTrans = ndfTrans_local; |
| 379 |
#endif |
| 380 |
|
| 381 |
ndfTrans = ndfTrans - 3 - nZconstraints; |
| 382 |
|
| 383 |
return ndfTrans; |
| 384 |
} |
| 385 |
|
| 386 |
void SimInfo::refreshSim(){ |
| 387 |
|
| 388 |
simtype fInfo; |
| 389 |
int isError; |
| 390 |
int n_global; |
| 391 |
int* excl; |
| 392 |
|
| 393 |
fInfo.dielect = 0.0; |
| 394 |
|
| 395 |
if( useDipoles ){ |
| 396 |
if( useReactionField )fInfo.dielect = dielectric; |
| 397 |
} |
| 398 |
|
| 399 |
fInfo.SIM_uses_PBC = usePBC; |
| 400 |
//fInfo.SIM_uses_LJ = 0; |
| 401 |
fInfo.SIM_uses_LJ = useLJ; |
| 402 |
fInfo.SIM_uses_sticky = useSticky; |
| 403 |
//fInfo.SIM_uses_sticky = 0; |
| 404 |
fInfo.SIM_uses_charges = useCharges; |
| 405 |
fInfo.SIM_uses_dipoles = useDipoles; |
| 406 |
//fInfo.SIM_uses_dipoles = 0; |
| 407 |
fInfo.SIM_uses_RF = useReactionField; |
| 408 |
//fInfo.SIM_uses_RF = 0; |
| 409 |
fInfo.SIM_uses_GB = useGB; |
| 410 |
fInfo.SIM_uses_EAM = useEAM; |
| 411 |
|
| 412 |
n_exclude = excludes->getSize(); |
| 413 |
excl = excludes->getFortranArray(); |
| 414 |
|
| 415 |
#ifdef IS_MPI |
| 416 |
n_global = mpiSim->getTotAtoms(); |
| 417 |
#else |
| 418 |
n_global = n_atoms; |
| 419 |
#endif |
| 420 |
|
| 421 |
isError = 0; |
| 422 |
|
| 423 |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 424 |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 425 |
&isError ); |
| 426 |
|
| 427 |
if( isError ){ |
| 428 |
|
| 429 |
sprintf( painCave.errMsg, |
| 430 |
"There was an error setting the simulation information in fortran.\n" ); |
| 431 |
painCave.isFatal = 1; |
| 432 |
simError(); |
| 433 |
} |
| 434 |
|
| 435 |
#ifdef IS_MPI |
| 436 |
sprintf( checkPointMsg, |
| 437 |
"succesfully sent the simulation information to fortran.\n"); |
| 438 |
MPIcheckPoint(); |
| 439 |
#endif // is_mpi |
| 440 |
|
| 441 |
this->ndf = this->getNDF(); |
| 442 |
this->ndfRaw = this->getNDFraw(); |
| 443 |
this->ndfTrans = this->getNDFtranslational(); |
| 444 |
} |
| 445 |
|
| 446 |
void SimInfo::setDefaultRcut( double theRcut ){ |
| 447 |
|
| 448 |
haveRcut = 1; |
| 449 |
rCut = theRcut; |
| 450 |
|
| 451 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 452 |
|
| 453 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 454 |
} |
| 455 |
|
| 456 |
void SimInfo::setDefaultEcr( double theEcr ){ |
| 457 |
|
| 458 |
haveEcr = 1; |
| 459 |
ecr = theEcr; |
| 460 |
|
| 461 |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 462 |
|
| 463 |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 464 |
} |
| 465 |
|
| 466 |
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
| 467 |
|
| 468 |
est = theEst; |
| 469 |
setDefaultEcr( theEcr ); |
| 470 |
} |
| 471 |
|
| 472 |
|
| 473 |
void SimInfo::checkCutOffs( void ){ |
| 474 |
|
| 475 |
if( boxIsInit ){ |
| 476 |
|
| 477 |
//we need to check cutOffs against the box |
| 478 |
|
| 479 |
if( rCut > maxCutoff ){ |
| 480 |
sprintf( painCave.errMsg, |
| 481 |
"LJrcut is too large for the current periodic box.\n" |
| 482 |
"\tCurrent Value of LJrcut = %G at time %G\n " |
| 483 |
"\tThis is larger than half of at least one of the\n" |
| 484 |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 485 |
"\n, %G" |
| 486 |
"\t[ %G %G %G ]\n" |
| 487 |
"\t[ %G %G %G ]\n" |
| 488 |
"\t[ %G %G %G ]\n", |
| 489 |
rCut, currentTime, maxCutoff, |
| 490 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 491 |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 492 |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 493 |
painCave.isFatal = 1; |
| 494 |
simError(); |
| 495 |
} |
| 496 |
|
| 497 |
if( haveEcr ){ |
| 498 |
if( ecr > maxCutoff ){ |
| 499 |
sprintf( painCave.errMsg, |
| 500 |
"electrostaticCutoffRadius is too large for the current\n" |
| 501 |
"\tperiodic box.\n\n" |
| 502 |
"\tCurrent Value of ECR = %G at time %G\n " |
| 503 |
"\tThis is larger than half of at least one of the\n" |
| 504 |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 505 |
"\n" |
| 506 |
"\t[ %G %G %G ]\n" |
| 507 |
"\t[ %G %G %G ]\n" |
| 508 |
"\t[ %G %G %G ]\n", |
| 509 |
ecr, currentTime, |
| 510 |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 511 |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 512 |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 513 |
painCave.isFatal = 1; |
| 514 |
simError(); |
| 515 |
} |
| 516 |
} |
| 517 |
} else { |
| 518 |
// initialize this stuff before using it, OK? |
| 519 |
sprintf( painCave.errMsg, |
| 520 |
"Trying to check cutoffs without a box.\n" |
| 521 |
"\tOOPSE should have better programmers than that.\n" ); |
| 522 |
painCave.isFatal = 1; |
| 523 |
simError(); |
| 524 |
} |
| 525 |
|
| 526 |
} |
| 527 |
|
| 528 |
void SimInfo::addProperty(GenericData* prop){ |
| 529 |
|
| 530 |
map<string, GenericData*>::iterator result; |
| 531 |
result = properties.find(prop->getID()); |
| 532 |
|
| 533 |
//we can't simply use properties[prop->getID()] = prop, |
| 534 |
//it will cause memory leak if we already contain a propery which has the same name of prop |
| 535 |
|
| 536 |
if(result != properties.end()){ |
| 537 |
|
| 538 |
delete (*result).second; |
| 539 |
(*result).second = prop; |
| 540 |
|
| 541 |
} |
| 542 |
else{ |
| 543 |
|
| 544 |
properties[prop->getID()] = prop; |
| 545 |
|
| 546 |
} |
| 547 |
|
| 548 |
} |
| 549 |
|
| 550 |
GenericData* SimInfo::getProperty(const string& propName){ |
| 551 |
|
| 552 |
map<string, GenericData*>::iterator result; |
| 553 |
|
| 554 |
//string lowerCaseName = (); |
| 555 |
|
| 556 |
result = properties.find(propName); |
| 557 |
|
| 558 |
if(result != properties.end()) |
| 559 |
return (*result).second; |
| 560 |
else |
| 561 |
return NULL; |
| 562 |
} |
| 563 |
|
| 564 |
vector<GenericData*> SimInfo::getProperties(){ |
| 565 |
|
| 566 |
vector<GenericData*> result; |
| 567 |
map<string, GenericData*>::iterator i; |
| 568 |
|
| 569 |
for(i = properties.begin(); i != properties.end(); i++) |
| 570 |
result.push_back((*i).second); |
| 571 |
|
| 572 |
return result; |
| 573 |
} |
