| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
#include "selection/SelectionManager.hpp" |
| 43 |
|
#include "visitors/OtherVisitor.hpp" |
| 45 |
|
#include "primitives/RigidBody.hpp" |
| 46 |
|
#include "primitives/Molecule.hpp" |
| 47 |
|
#include "brains/SimInfo.hpp" |
| 48 |
< |
namespace oopse { |
| 48 |
> |
#include "brains/Thermo.hpp" |
| 49 |
|
|
| 50 |
+ |
namespace OpenMD { |
| 51 |
+ |
|
| 52 |
|
void WrappingVisitor::visit(Atom *atom) { |
| 53 |
|
internalVisit(atom); |
| 54 |
|
} |
| 79 |
|
|
| 80 |
|
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 81 |
|
|
| 82 |
< |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) { |
| 82 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 83 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 84 |
> |
|
| 85 |
|
Vector3d newPos = atomInfo->pos - origin_; |
| 86 |
|
currSnapshot->wrapVector(newPos); |
| 87 |
|
atomInfo->pos = newPos; |
| 88 |
+ |
|
| 89 |
|
} |
| 90 |
|
} |
| 91 |
|
|
| 92 |
|
void WrappingVisitor::update() { |
| 93 |
|
if (useCom_){ |
| 94 |
< |
origin_ = info->getCom(); |
| 94 |
> |
Thermo thermo(info); |
| 95 |
> |
origin_ = thermo.getCom(); |
| 96 |
|
} |
| 97 |
|
} |
| 98 |
|
|
| 185 |
|
std::vector<AtomInfo *>::iterator i; |
| 186 |
|
|
| 187 |
|
for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) { |
| 188 |
< |
for( i = infoList.begin(); i != infoList.end(); i++ ) { |
| 188 |
> |
for( i = infoList.begin(); i != infoList.end(); ++i ) { |
| 189 |
|
newAtomInfo = new AtomInfo(); |
| 190 |
|
*newAtomInfo = *(*i); |
| 191 |
|
|
| 200 |
|
const std::string ReplicateVisitor::toString() { |
| 201 |
|
char buffer[65535]; |
| 202 |
|
std::string result; |
| 196 |
– |
std::set<std::string>::iterator i; |
| 203 |
|
|
| 204 |
+ |
|
| 205 |
|
sprintf(buffer, |
| 206 |
< |
"------------------------------------------------------------------\n"); |
| 206 |
> |
"--------------------------------------------------------------\n"); |
| 207 |
|
result += buffer; |
| 208 |
|
|
| 209 |
|
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 224 |
|
result += buffer; |
| 225 |
|
|
| 226 |
|
sprintf(buffer, |
| 227 |
< |
"------------------------------------------------------------------\n"); |
| 227 |
> |
"--------------------------------------------------------------\n"); |
| 228 |
|
result += buffer; |
| 229 |
|
|
| 230 |
|
return result; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
< |
//----------------------------------------------------------------------------// |
| 233 |
> |
//------------------------------------------------------------------------// |
| 234 |
|
|
| 235 |
< |
XYZVisitor::XYZVisitor(SimInfo *info) : |
| 236 |
< |
BaseVisitor(), seleMan(info), evaluator(info){ |
| 237 |
< |
this->info = info; |
| 238 |
< |
visitorName = "XYZVisitor"; |
| 239 |
< |
|
| 240 |
< |
evaluator.loadScriptString("select all"); |
| 241 |
< |
|
| 242 |
< |
if (!evaluator.isDynamic()) { |
| 243 |
< |
seleMan.setSelectionSet(evaluator.evaluate()); |
| 244 |
< |
} |
| 245 |
< |
|
| 246 |
< |
} |
| 247 |
< |
|
| 235 |
> |
XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info), |
| 236 |
> |
evaluator(info), doPositions_(true), |
| 237 |
> |
doVelocities_(false), |
| 238 |
> |
doForces_(false), doVectors_(false), |
| 239 |
> |
doCharges_(false), |
| 240 |
> |
doElectricFields_(false) { |
| 241 |
> |
this->info = info; |
| 242 |
> |
visitorName = "XYZVisitor"; |
| 243 |
> |
|
| 244 |
> |
evaluator.loadScriptString("select all"); |
| 245 |
> |
|
| 246 |
> |
if (!evaluator.isDynamic()) { |
| 247 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
| 248 |
> |
} |
| 249 |
> |
} |
| 250 |
> |
|
| 251 |
|
XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
| 252 |
< |
BaseVisitor(), seleMan(info), evaluator(info) { |
| 253 |
< |
this->info = info; |
| 254 |
< |
visitorName = "XYZVisitor"; |
| 255 |
< |
|
| 256 |
< |
evaluator.loadScriptString(script); |
| 257 |
< |
|
| 258 |
< |
if (!evaluator.isDynamic()) { |
| 259 |
< |
seleMan.setSelectionSet(evaluator.evaluate()); |
| 260 |
< |
} |
| 261 |
< |
|
| 252 |
> |
BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true), |
| 253 |
> |
doVelocities_(false), doForces_(false), doVectors_(false), |
| 254 |
> |
doCharges_(false), doElectricFields_(false) { |
| 255 |
> |
|
| 256 |
> |
this->info = info; |
| 257 |
> |
visitorName = "XYZVisitor"; |
| 258 |
> |
|
| 259 |
> |
evaluator.loadScriptString(script); |
| 260 |
> |
|
| 261 |
> |
if (!evaluator.isDynamic()) { |
| 262 |
> |
seleMan.setSelectionSet(evaluator.evaluate()); |
| 263 |
|
} |
| 264 |
+ |
} |
| 265 |
|
|
| 266 |
|
void XYZVisitor::visit(Atom *atom) { |
| 267 |
|
if (isSelected(atom)) |
| 272 |
|
if (isSelected(datom)) |
| 273 |
|
internalVisit(datom); |
| 274 |
|
} |
| 275 |
< |
|
| 275 |
> |
|
| 276 |
|
void XYZVisitor::visit(RigidBody *rb) { |
| 277 |
|
if (isSelected(rb)) |
| 278 |
|
internalVisit(rb); |
| 279 |
|
} |
| 280 |
< |
|
| 280 |
> |
|
| 281 |
|
void XYZVisitor::update() { |
| 282 |
|
//if dynamic, we need to re-evaluate the selection |
| 283 |
|
if (evaluator.isDynamic()) { |
| 284 |
|
seleMan.setSelectionSet(evaluator.evaluate()); |
| 285 |
|
} |
| 286 |
|
} |
| 287 |
< |
|
| 287 |
> |
|
| 288 |
|
void XYZVisitor::internalVisit(StuntDouble *sd) { |
| 289 |
|
GenericData * data; |
| 290 |
|
AtomData * atomData; |
| 291 |
|
AtomInfo * atomInfo; |
| 292 |
|
std::vector<AtomInfo *>::iterator i; |
| 293 |
|
char buffer[1024]; |
| 294 |
< |
|
| 294 |
> |
|
| 295 |
|
//if there is not atom data, just skip it |
| 296 |
|
data = sd->getPropertyByName("ATOMDATA"); |
| 297 |
< |
|
| 297 |
> |
|
| 298 |
|
if (data != NULL) { |
| 299 |
|
atomData = dynamic_cast<AtomData *>(data); |
| 300 |
< |
|
| 300 |
> |
|
| 301 |
|
if (atomData == NULL) |
| 302 |
|
return; |
| 303 |
|
} else |
| 304 |
|
return; |
| 305 |
|
|
| 306 |
|
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 307 |
< |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 308 |
< |
sprintf(buffer, |
| 309 |
< |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
| 310 |
< |
atomInfo->atomTypeName.c_str(), |
| 311 |
< |
atomInfo->pos[0], |
| 312 |
< |
atomInfo->pos[1], |
| 313 |
< |
atomInfo->pos[2], |
| 314 |
< |
atomInfo->dipole[0], |
| 315 |
< |
atomInfo->dipole[1], |
| 316 |
< |
atomInfo->dipole[2]); |
| 317 |
< |
frame.push_back(buffer); |
| 318 |
< |
} |
| 307 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 308 |
> |
|
| 309 |
> |
std::string line; |
| 310 |
> |
sprintf(buffer, "%s", atomInfo->atomTypeName.c_str()); |
| 311 |
> |
line += buffer; |
| 312 |
> |
|
| 313 |
> |
if (doPositions_){ |
| 314 |
> |
sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0], |
| 315 |
> |
atomInfo->pos[1], atomInfo->pos[2]); |
| 316 |
> |
line += buffer; |
| 317 |
> |
} |
| 318 |
> |
if (doCharges_ && atomInfo->hasCharge) { |
| 319 |
> |
sprintf(buffer, "%15.8f", atomInfo->charge); |
| 320 |
> |
line += buffer; |
| 321 |
> |
} |
| 322 |
> |
if (doVectors_ && atomInfo->hasVector) { |
| 323 |
> |
sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0], |
| 324 |
> |
atomInfo->vec[1], atomInfo->vec[2]); |
| 325 |
> |
line += buffer; |
| 326 |
> |
} |
| 327 |
> |
if (doVelocities_ && atomInfo->hasVelocity) { |
| 328 |
> |
sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0], |
| 329 |
> |
atomInfo->vel[1], atomInfo->vel[2]); |
| 330 |
> |
line += buffer; |
| 331 |
> |
} |
| 332 |
> |
if (doForces_ && atomInfo->hasForce) { |
| 333 |
> |
sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0], |
| 334 |
> |
atomInfo->frc[1], atomInfo->frc[2]); |
| 335 |
> |
line += buffer; |
| 336 |
> |
} |
| 337 |
> |
if (doElectricFields_ && atomInfo->hasElectricField) { |
| 338 |
> |
sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->eField[0], |
| 339 |
> |
atomInfo->eField[1], atomInfo->eField[2]); |
| 340 |
> |
line += buffer; |
| 341 |
> |
} |
| 342 |
> |
frame.push_back(line); |
| 343 |
> |
} |
| 344 |
|
} |
| 345 |
|
|
| 346 |
|
bool XYZVisitor::isSelected(StuntDouble *sd) { |
| 350 |
|
void XYZVisitor::writeFrame(std::ostream &outStream) { |
| 351 |
|
std::vector<std::string>::iterator i; |
| 352 |
|
char buffer[1024]; |
| 353 |
< |
|
| 354 |
< |
if (frame.size() == 0) |
| 353 |
> |
|
| 354 |
> |
if (frame.empty()) |
| 355 |
|
std::cerr << "Current Frame does not contain any atoms" << std::endl; |
| 356 |
< |
|
| 356 |
> |
|
| 357 |
|
//total number of atoms |
| 358 |
|
outStream << frame.size() << std::endl; |
| 359 |
< |
|
| 359 |
> |
|
| 360 |
|
//write comment line |
| 361 |
|
Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 362 |
|
Mat3x3d box = currSnapshot->getHmat(); |
| 367 |
|
box(0, 0), box(0, 1), box(0, 2), |
| 368 |
|
box(1, 0), box(1, 1), box(1, 2), |
| 369 |
|
box(2, 0), box(2, 1), box(2, 2)); |
| 370 |
< |
|
| 370 |
> |
|
| 371 |
|
outStream << buffer << std::endl; |
| 372 |
< |
|
| 372 |
> |
|
| 373 |
|
for( i = frame.begin(); i != frame.end(); ++i ) |
| 374 |
|
outStream << *i << std::endl; |
| 375 |
|
} |
| 376 |
< |
|
| 376 |
> |
|
| 377 |
> |
std::string XYZVisitor::trimmedName(const std::string&atomTypeName) { |
| 378 |
> |
return atomTypeName.substr(0, atomTypeName.find('-')); |
| 379 |
> |
} |
| 380 |
> |
|
| 381 |
|
const std::string XYZVisitor::toString() { |
| 382 |
|
char buffer[65535]; |
| 383 |
|
std::string result; |
| 384 |
< |
|
| 384 |
> |
|
| 385 |
|
sprintf(buffer, |
| 386 |
|
"------------------------------------------------------------------\n"); |
| 387 |
|
result += buffer; |
| 388 |
< |
|
| 388 |
> |
|
| 389 |
|
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 390 |
|
result += buffer; |
| 391 |
< |
|
| 391 |
> |
|
| 392 |
|
sprintf(buffer, |
| 393 |
|
"Visitor Description: assemble the atom data and output xyz file\n"); |
| 394 |
|
result += buffer; |
| 396 |
|
sprintf(buffer, |
| 397 |
|
"------------------------------------------------------------------\n"); |
| 398 |
|
result += buffer; |
| 399 |
< |
|
| 399 |
> |
|
| 400 |
|
return result; |
| 401 |
|
} |
| 402 |
< |
|
| 402 |
> |
|
| 403 |
|
//----------------------------------------------------------------------------// |
| 404 |
< |
|
| 404 |
> |
|
| 405 |
|
void PrepareVisitor::internalVisit(Atom *atom) { |
| 406 |
|
GenericData *data; |
| 407 |
< |
AtomData * atomData; |
| 367 |
< |
|
| 407 |
> |
|
| 408 |
|
//if visited property is existed, remove it |
| 409 |
|
data = atom->getPropertyByName("VISITED"); |
| 410 |
< |
|
| 410 |
> |
|
| 411 |
|
if (data != NULL) { |
| 412 |
|
atom->removeProperty("VISITED"); |
| 413 |
|
} |
| 414 |
< |
|
| 414 |
> |
|
| 415 |
|
//remove atomdata |
| 416 |
|
data = atom->getPropertyByName("ATOMDATA"); |
| 417 |
|
|
| 418 |
|
if (data != NULL) { |
| 419 |
< |
atomData = dynamic_cast<AtomData *>(data); |
| 419 |
> |
AtomData* atomData = dynamic_cast<AtomData *>(data); |
| 420 |
|
|
| 421 |
|
if (atomData != NULL) |
| 422 |
|
atom->removeProperty("ATOMDATA"); |
| 480 |
|
visitorName = "WaterTypeVisitor"; |
| 481 |
|
waterTypeList.insert("TIP3P_RB_0"); |
| 482 |
|
waterTypeList.insert("TIP4P_RB_0"); |
| 483 |
+ |
waterTypeList.insert("TIP4P-Ew_RB_0"); |
| 484 |
|
waterTypeList.insert("TIP5P_RB_0"); |
| 485 |
+ |
waterTypeList.insert("TIP5P-E_RB_0"); |
| 486 |
|
waterTypeList.insert("SPCE_RB_0"); |
| 487 |
+ |
waterTypeList.insert("SPC_RB_0"); |
| 488 |
|
} |
| 489 |
|
|
| 490 |
|
void WaterTypeVisitor::visit(RigidBody *rb) { |
| 491 |
|
std::string rbName; |
| 492 |
|
std::vector<Atom *> myAtoms; |
| 493 |
|
std::vector<Atom *>::iterator atomIter; |
| 451 |
– |
GenericData* data; |
| 452 |
– |
AtomData* atomData; |
| 453 |
– |
AtomInfo* atomInfo; |
| 494 |
|
std::vector<AtomInfo *>::iterator i; |
| 495 |
+ |
AtomData* atomData; |
| 496 |
|
|
| 497 |
|
rbName = rb->getType(); |
| 498 |
< |
|
| 498 |
> |
|
| 499 |
|
if (waterTypeList.find(rbName) != waterTypeList.end()) { |
| 500 |
|
myAtoms = rb->getAtoms(); |
| 501 |
< |
|
| 501 |
> |
|
| 502 |
|
for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); |
| 503 |
|
++atomIter ) { |
| 504 |
< |
data = (*atomIter)->getPropertyByName("ATOMDATA"); |
| 505 |
< |
|
| 504 |
> |
GenericData* data = (*atomIter)->getPropertyByName("ATOMDATA"); |
| 505 |
> |
|
| 506 |
|
if (data != NULL) { |
| 507 |
|
atomData = dynamic_cast<AtomData *>(data); |
| 508 |
< |
|
| 508 |
> |
|
| 509 |
|
if (atomData == NULL) |
| 510 |
|
continue; |
| 511 |
|
} else |
| 512 |
|
continue; |
| 513 |
< |
|
| 514 |
< |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 513 |
> |
|
| 514 |
> |
for( AtomInfo* atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 515 |
|
atomInfo = atomData->nextAtomInfo(i) ) { |
| 516 |
|
atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName); |
| 517 |
< |
} //end for(atomInfo) |
| 518 |
< |
} //end for(atomIter) |
| 519 |
< |
} //end if (waterTypeList.find(rbName) != waterTypeList.end()) |
| 517 |
> |
} |
| 518 |
> |
} |
| 519 |
> |
} |
| 520 |
|
} |
| 521 |
|
|
| 522 |
|
std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) { |
| 545 |
|
return result; |
| 546 |
|
} |
| 547 |
|
|
| 548 |
< |
} //namespace oopse |
| 548 |
> |
} //namespace OpenMD |
