| 1 |
#include "visitors/OtherVisitor.hpp" |
| 2 |
#include "primitives/DirectionalAtom.hpp" |
| 3 |
#include "primitives/RigidBody.hpp" |
| 4 |
#include "primitives/Molecule.hpp" |
| 5 |
#include "brains/SimInfo.hpp" |
| 6 |
namespace oopse { |
| 7 |
|
| 8 |
//----------------------------------------------------------------------------// |
| 9 |
void IgnoreVisitor::visit(Atom *atom) { |
| 10 |
if (isIgnoreType(atom->getType())) |
| 11 |
internalVisit(atom); |
| 12 |
} |
| 13 |
|
| 14 |
void IgnoreVisitor::visit(DirectionalAtom *datom) { |
| 15 |
if (isIgnoreType(datom->getType())) |
| 16 |
internalVisit(datom); |
| 17 |
} |
| 18 |
|
| 19 |
void IgnoreVisitor::visit(RigidBody *rb) { |
| 20 |
std::vector<Atom *> myAtoms; |
| 21 |
std::vector<Atom *>::iterator atomIter; |
| 22 |
AtomInfo * atomInfo; |
| 23 |
|
| 24 |
if (isIgnoreType(rb->getType())) { |
| 25 |
internalVisit(rb); |
| 26 |
|
| 27 |
myAtoms = rb->getAtoms(); |
| 28 |
|
| 29 |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
| 30 |
internalVisit(*atomIter); |
| 31 |
} |
| 32 |
} |
| 33 |
|
| 34 |
bool IgnoreVisitor::isIgnoreType(const std::string&name) { |
| 35 |
return itList.find(name) != itList.end() ? true : false; |
| 36 |
} |
| 37 |
|
| 38 |
void IgnoreVisitor::internalVisit(StuntDouble *sd) { |
| 39 |
GenericData *data; |
| 40 |
data = sd->getPropertyByName("IGNORE"); |
| 41 |
|
| 42 |
//if this stuntdoulbe is already marked as ignore just skip it |
| 43 |
if (data == NULL) { |
| 44 |
data = new GenericData; |
| 45 |
data->setID("IGNORE"); |
| 46 |
sd->addProperty(data); |
| 47 |
} |
| 48 |
} |
| 49 |
|
| 50 |
const std::string IgnoreVisitor::toString() { |
| 51 |
char buffer[65535]; |
| 52 |
std::string result; |
| 53 |
std::set<std::string>::iterator i; |
| 54 |
|
| 55 |
sprintf(buffer, |
| 56 |
"------------------------------------------------------------------\n"); |
| 57 |
result += buffer; |
| 58 |
|
| 59 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 60 |
result += buffer; |
| 61 |
|
| 62 |
sprintf(buffer, "Visitor Description: ignore stuntdoubles\n"); |
| 63 |
result += buffer; |
| 64 |
|
| 65 |
//print the ignore type list |
| 66 |
sprintf(buffer, "Ignore type list contains below types:\n"); |
| 67 |
result += buffer; |
| 68 |
|
| 69 |
for( i = itList.begin(); i != itList.end(); ++i ) { |
| 70 |
sprintf(buffer, "%s\t", i->c_str()); |
| 71 |
result += buffer; |
| 72 |
} |
| 73 |
|
| 74 |
sprintf(buffer, "\n"); |
| 75 |
result += buffer; |
| 76 |
|
| 77 |
sprintf(buffer, |
| 78 |
"------------------------------------------------------------------\n"); |
| 79 |
result += buffer; |
| 80 |
|
| 81 |
return result; |
| 82 |
} |
| 83 |
|
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//----------------------------------------------------------------------------// |
| 85 |
|
| 86 |
void WrappingVisitor::visit(Atom *atom) { |
| 87 |
internalVisit(atom); |
| 88 |
} |
| 89 |
|
| 90 |
void WrappingVisitor::visit(DirectionalAtom *datom) { |
| 91 |
internalVisit(datom); |
| 92 |
} |
| 93 |
|
| 94 |
void WrappingVisitor::visit(RigidBody *rb) { |
| 95 |
internalVisit(rb); |
| 96 |
} |
| 97 |
|
| 98 |
void WrappingVisitor::internalVisit(StuntDouble *sd) { |
| 99 |
GenericData * data; |
| 100 |
AtomData * atomData; |
| 101 |
AtomInfo * atomInfo; |
| 102 |
std::vector<AtomInfo *>::iterator i; |
| 103 |
|
| 104 |
data = sd->getPropertyByName("ATOMDATA"); |
| 105 |
|
| 106 |
if (data != NULL) { |
| 107 |
atomData = dynamic_cast<AtomData *>(data); |
| 108 |
|
| 109 |
if (atomData == NULL) |
| 110 |
return; |
| 111 |
} else |
| 112 |
return; |
| 113 |
|
| 114 |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 115 |
|
| 116 |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) { |
| 117 |
currSnapshot->wrapVector(atomInfo->pos); |
| 118 |
} |
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} |
| 120 |
|
| 121 |
const std::string WrappingVisitor::toString() { |
| 122 |
char buffer[65535]; |
| 123 |
std::string result; |
| 124 |
|
| 125 |
sprintf(buffer, |
| 126 |
"------------------------------------------------------------------\n"); |
| 127 |
result += buffer; |
| 128 |
|
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sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 130 |
result += buffer; |
| 131 |
|
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sprintf(buffer, |
| 133 |
"Visitor Description: wrapping atoms back to periodic box\n"); |
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result += buffer; |
| 135 |
|
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sprintf(buffer, |
| 137 |
"------------------------------------------------------------------\n"); |
| 138 |
result += buffer; |
| 139 |
|
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return result; |
| 141 |
} |
| 142 |
|
| 143 |
//----------------------------------------------------------------------------// |
| 144 |
|
| 145 |
ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) : |
| 146 |
BaseVisitor() { |
| 147 |
this->info = info; |
| 148 |
visitorName = "ReplicateVisitor"; |
| 149 |
this->replicateOpt = opt; |
| 150 |
|
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//generate the replicate directions |
| 152 |
for( int i = 0; i <= replicateOpt[0]; i++ ) { |
| 153 |
for( int j = 0; j <= replicateOpt[1]; j++ ) { |
| 154 |
for( int k = 0; k <= replicateOpt[2]; k++ ) { |
| 155 |
//skip original frame |
| 156 |
if (i == 0 && j == 0 && k == 0) { |
| 157 |
continue; |
| 158 |
} else { |
| 159 |
dir.push_back(Vector3i(i, j, k)); |
| 160 |
} |
| 161 |
} |
| 162 |
} |
| 163 |
} |
| 164 |
|
| 165 |
} |
| 166 |
|
| 167 |
void ReplicateVisitor::visit(Atom *atom) { |
| 168 |
internalVisit(atom); |
| 169 |
} |
| 170 |
|
| 171 |
void ReplicateVisitor::visit(DirectionalAtom *datom) { |
| 172 |
internalVisit(datom); |
| 173 |
} |
| 174 |
|
| 175 |
void ReplicateVisitor::visit(RigidBody *rb) { |
| 176 |
internalVisit(rb); |
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} |
| 178 |
|
| 179 |
void ReplicateVisitor::internalVisit(StuntDouble *sd) { |
| 180 |
GenericData * data; |
| 181 |
AtomData * atomData; |
| 182 |
|
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//if there is not atom data, just skip it |
| 184 |
data = sd->getPropertyByName("ATOMDATA"); |
| 185 |
|
| 186 |
if (data != NULL) { |
| 187 |
atomData = dynamic_cast<AtomData *>(data); |
| 188 |
|
| 189 |
if (atomData == NULL) { |
| 190 |
return; |
| 191 |
} |
| 192 |
} else { |
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return; |
| 194 |
} |
| 195 |
|
| 196 |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 197 |
Mat3x3d box = currSnapshot->getHmat(); |
| 198 |
|
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std::vector<AtomInfo *> atomInfoList = atomData->getData(); |
| 200 |
|
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replicate(atomInfoList, atomData, box); |
| 202 |
} |
| 203 |
|
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void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) { |
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AtomInfo* newAtomInfo; |
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std::vector<Vector3i>::iterator dirIter; |
| 207 |
std::vector<AtomInfo *>::iterator i; |
| 208 |
|
| 209 |
for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
| 210 |
for( i = infoList.begin(); i != infoList.end(); i++ ) { |
| 211 |
newAtomInfo = new AtomInfo(); |
| 212 |
*newAtomInfo = *(*i); |
| 213 |
|
| 214 |
for( int j = 0; j < 3; j++ ) |
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newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2); |
| 216 |
|
| 217 |
data->addAtomInfo(newAtomInfo); |
| 218 |
} |
| 219 |
} // end for(dirIter) |
| 220 |
} |
| 221 |
|
| 222 |
const std::string ReplicateVisitor::toString() { |
| 223 |
char buffer[65535]; |
| 224 |
std::string result; |
| 225 |
std::set<std::string>::iterator i; |
| 226 |
|
| 227 |
sprintf(buffer, |
| 228 |
"------------------------------------------------------------------\n"); |
| 229 |
result += buffer; |
| 230 |
|
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sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 232 |
result += buffer; |
| 233 |
|
| 234 |
sprintf(buffer, |
| 235 |
"Visitor Description: replicate the atoms in different direction\n"); |
| 236 |
result += buffer; |
| 237 |
|
| 238 |
//print the replicate direction |
| 239 |
sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]); |
| 240 |
result += buffer; |
| 241 |
|
| 242 |
sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]); |
| 243 |
result += buffer; |
| 244 |
|
| 245 |
sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]); |
| 246 |
result += buffer; |
| 247 |
|
| 248 |
sprintf(buffer, |
| 249 |
"------------------------------------------------------------------\n"); |
| 250 |
result += buffer; |
| 251 |
|
| 252 |
return result; |
| 253 |
} |
| 254 |
|
| 255 |
//----------------------------------------------------------------------------// |
| 256 |
|
| 257 |
XYZVisitor::XYZVisitor(SimInfo *info, bool printDipole) : |
| 258 |
BaseVisitor() { |
| 259 |
this->info = info; |
| 260 |
visitorName = "XYZVisitor"; |
| 261 |
this->printDipole = printDipole; |
| 262 |
} |
| 263 |
|
| 264 |
void XYZVisitor::visit(Atom *atom) { |
| 265 |
if (!isIgnore(atom)) |
| 266 |
internalVisit(atom); |
| 267 |
} |
| 268 |
|
| 269 |
void XYZVisitor::visit(DirectionalAtom *datom) { |
| 270 |
if (!isIgnore(datom)) |
| 271 |
internalVisit(datom); |
| 272 |
} |
| 273 |
|
| 274 |
void XYZVisitor::visit(RigidBody *rb) { |
| 275 |
if (!isIgnore(rb)) |
| 276 |
internalVisit(rb); |
| 277 |
} |
| 278 |
|
| 279 |
void XYZVisitor::internalVisit(StuntDouble *sd) { |
| 280 |
GenericData * data; |
| 281 |
AtomData * atomData; |
| 282 |
AtomInfo * atomInfo; |
| 283 |
std::vector<AtomInfo *>::iterator i; |
| 284 |
char buffer[1024]; |
| 285 |
|
| 286 |
//if there is not atom data, just skip it |
| 287 |
data = sd->getPropertyByName("ATOMDATA"); |
| 288 |
|
| 289 |
if (data != NULL) { |
| 290 |
atomData = dynamic_cast<AtomData *>(data); |
| 291 |
|
| 292 |
if (atomData == NULL) |
| 293 |
return; |
| 294 |
} else |
| 295 |
return; |
| 296 |
|
| 297 |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 298 |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 299 |
if (printDipole) |
| 300 |
sprintf(buffer, |
| 301 |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
| 302 |
atomInfo->AtomType.c_str(), |
| 303 |
atomInfo->pos[0], |
| 304 |
atomInfo->pos[1], |
| 305 |
atomInfo->pos[2], |
| 306 |
atomInfo->dipole[0], |
| 307 |
atomInfo->dipole[1], |
| 308 |
atomInfo->dipole[2]); else |
| 309 |
sprintf(buffer, "%s%15.8f%15.8f%15.8f", |
| 310 |
atomInfo->AtomType.c_str(), atomInfo->pos[0], |
| 311 |
atomInfo->pos[1], atomInfo->pos[2]); |
| 312 |
|
| 313 |
frame.push_back(buffer); |
| 314 |
} |
| 315 |
} |
| 316 |
|
| 317 |
bool XYZVisitor::isIgnore(StuntDouble *sd) { |
| 318 |
GenericData *data; |
| 319 |
|
| 320 |
data = sd->getPropertyByName("IGNORE"); |
| 321 |
return data == NULL ? false : true; |
| 322 |
} |
| 323 |
|
| 324 |
void XYZVisitor::writeFrame(ostream &outStream) { |
| 325 |
std::vector<std::string>::iterator i; |
| 326 |
char buffer[1024]; |
| 327 |
|
| 328 |
if (frame.size() == 0) |
| 329 |
cerr << "Current Frame does not contain any atoms" << endl; |
| 330 |
|
| 331 |
//total number of atoms |
| 332 |
outStream << frame.size() << endl; |
| 333 |
|
| 334 |
//write comment line |
| 335 |
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 336 |
Mat3x3d box = currSnapshot->getHmat(); |
| 337 |
|
| 338 |
sprintf(buffer, |
| 339 |
"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f", |
| 340 |
currSnapshot->getTime(), |
| 341 |
box(0, 0), box(0, 1), box(0, 2), |
| 342 |
box(1, 0), box(1, 1), box(1, 2), |
| 343 |
box(2, 0), box(2, 1), box(2, 2)); |
| 344 |
|
| 345 |
outStream << buffer << endl; |
| 346 |
|
| 347 |
for( i = frame.begin(); i != frame.end(); ++i ) |
| 348 |
outStream << *i << endl; |
| 349 |
} |
| 350 |
|
| 351 |
const std::string XYZVisitor::toString() { |
| 352 |
char buffer[65535]; |
| 353 |
std::string result; |
| 354 |
|
| 355 |
sprintf(buffer, |
| 356 |
"------------------------------------------------------------------\n"); |
| 357 |
result += buffer; |
| 358 |
|
| 359 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 360 |
result += buffer; |
| 361 |
|
| 362 |
sprintf(buffer, |
| 363 |
"Visitor Description: assemble the atom data and output xyz file\n"); |
| 364 |
result += buffer; |
| 365 |
|
| 366 |
sprintf(buffer, |
| 367 |
"------------------------------------------------------------------\n"); |
| 368 |
result += buffer; |
| 369 |
|
| 370 |
return result; |
| 371 |
} |
| 372 |
|
| 373 |
//----------------------------------------------------------------------------// |
| 374 |
|
| 375 |
void PrepareVisitor::internalVisit(Atom *atom) { |
| 376 |
GenericData *data; |
| 377 |
AtomData * atomData; |
| 378 |
|
| 379 |
//if visited property is existed, remove it |
| 380 |
data = atom->getPropertyByName("VISITED"); |
| 381 |
|
| 382 |
if (data != NULL) { |
| 383 |
atom->removeProperty("VISITED"); |
| 384 |
} |
| 385 |
|
| 386 |
//remove atomdata |
| 387 |
data = atom->getPropertyByName("ATOMDATA"); |
| 388 |
|
| 389 |
if (data != NULL) { |
| 390 |
atomData = dynamic_cast<AtomData *>(data); |
| 391 |
|
| 392 |
if (atomData != NULL) |
| 393 |
atom->removeProperty("ATOMDATA"); |
| 394 |
} |
| 395 |
} |
| 396 |
|
| 397 |
void PrepareVisitor::internalVisit(RigidBody *rb) { |
| 398 |
GenericData* data; |
| 399 |
AtomData* atomData; |
| 400 |
std::vector<Atom *> myAtoms; |
| 401 |
std::vector<Atom *>::iterator atomIter; |
| 402 |
|
| 403 |
//if visited property is existed, remove it |
| 404 |
data = rb->getPropertyByName("VISITED"); |
| 405 |
|
| 406 |
if (data != NULL) { |
| 407 |
rb->removeProperty("VISITED"); |
| 408 |
} |
| 409 |
|
| 410 |
//remove atomdata |
| 411 |
data = rb->getPropertyByName("ATOMDATA"); |
| 412 |
|
| 413 |
if (data != NULL) { |
| 414 |
atomData = dynamic_cast<AtomData *>(data); |
| 415 |
|
| 416 |
if (atomData != NULL) |
| 417 |
rb->removeProperty("ATOMDATA"); |
| 418 |
} |
| 419 |
|
| 420 |
myAtoms = rb->getAtoms(); |
| 421 |
|
| 422 |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter ) |
| 423 |
internalVisit(*atomIter); |
| 424 |
} |
| 425 |
|
| 426 |
const std::string PrepareVisitor::toString() { |
| 427 |
char buffer[65535]; |
| 428 |
std::string result; |
| 429 |
|
| 430 |
sprintf(buffer, |
| 431 |
"------------------------------------------------------------------\n"); |
| 432 |
result += buffer; |
| 433 |
|
| 434 |
sprintf(buffer, "Visitor name: %s", visitorName.c_str()); |
| 435 |
result += buffer; |
| 436 |
|
| 437 |
sprintf(buffer, |
| 438 |
"Visitor Description: prepare for operation of other vistors\n"); |
| 439 |
result += buffer; |
| 440 |
|
| 441 |
sprintf(buffer, |
| 442 |
"------------------------------------------------------------------\n"); |
| 443 |
result += buffer; |
| 444 |
|
| 445 |
return result; |
| 446 |
} |
| 447 |
|
| 448 |
//----------------------------------------------------------------------------// |
| 449 |
|
| 450 |
WaterTypeVisitor::WaterTypeVisitor() { |
| 451 |
visitorName = "WaterTypeVisitor"; |
| 452 |
waterTypeList.insert("TIP3P_RB_0"); |
| 453 |
waterTypeList.insert("TIP4P_RB_0"); |
| 454 |
waterTypeList.insert("TIP5P_RB_0"); |
| 455 |
waterTypeList.insert("SPCE_RB_0"); |
| 456 |
} |
| 457 |
|
| 458 |
void WaterTypeVisitor::visit(RigidBody *rb) { |
| 459 |
std::string rbName; |
| 460 |
std::vector<Atom *> myAtoms; |
| 461 |
std::vector<Atom *>::iterator atomIter; |
| 462 |
GenericData* data; |
| 463 |
AtomData* atomData; |
| 464 |
AtomInfo* atomInfo; |
| 465 |
std::vector<AtomInfo *>::iterator i; |
| 466 |
|
| 467 |
rbName = rb->getType(); |
| 468 |
|
| 469 |
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
| 470 |
myAtoms = rb->getAtoms(); |
| 471 |
|
| 472 |
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
| 473 |
++atomIter ) { |
| 474 |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
| 475 |
|
| 476 |
if (data != NULL) { |
| 477 |
atomData = dynamic_cast<AtomData *>(data); |
| 478 |
|
| 479 |
if (atomData == NULL) |
| 480 |
continue; |
| 481 |
} else |
| 482 |
continue; |
| 483 |
|
| 484 |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 485 |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 486 |
replaceType(atomInfo->AtomType); |
| 487 |
} //end for(atomInfo) |
| 488 |
} //end for(atomIter) |
| 489 |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
| 490 |
} |
| 491 |
|
| 492 |
void WaterTypeVisitor::replaceType(std::string&atomType) { |
| 493 |
atomType = atomType.substr(0, atomType.find('_')); |
| 494 |
} |
| 495 |
|
| 496 |
const std::string WaterTypeVisitor::toString() { |
| 497 |
char buffer[65535]; |
| 498 |
std::string result; |
| 499 |
|
| 500 |
sprintf(buffer, |
| 501 |
"------------------------------------------------------------------\n"); |
| 502 |
result += buffer; |
| 503 |
|
| 504 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 505 |
result += buffer; |
| 506 |
|
| 507 |
sprintf(buffer, |
| 508 |
"Visitor Description: Replace the atom type in water model\n"); |
| 509 |
result += buffer; |
| 510 |
|
| 511 |
sprintf(buffer, |
| 512 |
"------------------------------------------------------------------\n"); |
| 513 |
result += buffer; |
| 514 |
|
| 515 |
return result; |
| 516 |
} |
| 517 |
|
| 518 |
} //namespace oopse |
