| 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
#include "selection/SelectionManager.hpp" |
| 42 |
|
#include "visitors/OtherVisitor.hpp" |
| 44 |
|
#include "primitives/RigidBody.hpp" |
| 45 |
|
#include "primitives/Molecule.hpp" |
| 46 |
|
#include "brains/SimInfo.hpp" |
| 47 |
< |
namespace oopse { |
| 47 |
> |
namespace OpenMD { |
| 48 |
|
|
| 49 |
|
void WrappingVisitor::visit(Atom *atom) { |
| 50 |
|
internalVisit(atom); |
| 235 |
|
if (!evaluator.isDynamic()) { |
| 236 |
|
seleMan.setSelectionSet(evaluator.evaluate()); |
| 237 |
|
} |
| 238 |
< |
|
| 238 |
> |
posOnly_ = false; |
| 239 |
|
} |
| 240 |
|
|
| 241 |
|
XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) : |
| 248 |
|
if (!evaluator.isDynamic()) { |
| 249 |
|
seleMan.setSelectionSet(evaluator.evaluate()); |
| 250 |
|
} |
| 251 |
< |
|
| 251 |
> |
posOnly_ = false; |
| 252 |
|
} |
| 253 |
|
|
| 254 |
|
void XYZVisitor::visit(Atom *atom) { |
| 291 |
|
} else |
| 292 |
|
return; |
| 293 |
|
|
| 294 |
< |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 295 |
< |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 296 |
< |
sprintf(buffer, |
| 297 |
< |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
| 298 |
< |
atomInfo->atomTypeName.c_str(), |
| 299 |
< |
atomInfo->pos[0], |
| 300 |
< |
atomInfo->pos[1], |
| 301 |
< |
atomInfo->pos[2], |
| 302 |
< |
atomInfo->dipole[0], |
| 303 |
< |
atomInfo->dipole[1], |
| 304 |
< |
atomInfo->dipole[2]); |
| 305 |
< |
frame.push_back(buffer); |
| 294 |
> |
AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType(); |
| 295 |
> |
std::string bn = baseTypeName(at); |
| 296 |
> |
|
| 297 |
> |
if (posOnly_){ |
| 298 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 299 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 300 |
> |
if (atomInfo->hasCharge) { |
| 301 |
> |
sprintf(buffer, |
| 302 |
> |
"%s%15.8f%15.8f%15.8f%15.8f", |
| 303 |
> |
bn.c_str(), |
| 304 |
> |
atomInfo->pos[0], |
| 305 |
> |
atomInfo->pos[1], |
| 306 |
> |
atomInfo->pos[2], |
| 307 |
> |
atomInfo->charge); |
| 308 |
> |
} else { |
| 309 |
> |
sprintf(buffer, |
| 310 |
> |
"%s%15.8f%15.8f%15.8f", |
| 311 |
> |
bn.c_str(), |
| 312 |
> |
atomInfo->pos[0], |
| 313 |
> |
atomInfo->pos[1], |
| 314 |
> |
atomInfo->pos[2]); |
| 315 |
> |
} |
| 316 |
> |
frame.push_back(buffer); |
| 317 |
> |
} |
| 318 |
> |
}else{ |
| 319 |
> |
for( atomInfo = atomData->beginAtomInfo(i); atomInfo; |
| 320 |
> |
atomInfo = atomData->nextAtomInfo(i) ) { |
| 321 |
> |
if (atomInfo->hasCharge) { |
| 322 |
> |
sprintf(buffer, |
| 323 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
| 324 |
> |
bn.c_str(), |
| 325 |
> |
atomInfo->pos[0], |
| 326 |
> |
atomInfo->pos[1], |
| 327 |
> |
atomInfo->pos[2], |
| 328 |
> |
atomInfo->charge, |
| 329 |
> |
atomInfo->dipole[0], |
| 330 |
> |
atomInfo->dipole[1], |
| 331 |
> |
atomInfo->dipole[2]); |
| 332 |
> |
} else { |
| 333 |
> |
sprintf(buffer, |
| 334 |
> |
"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f", |
| 335 |
> |
bn.c_str(), |
| 336 |
> |
atomInfo->pos[0], |
| 337 |
> |
atomInfo->pos[1], |
| 338 |
> |
atomInfo->pos[2], |
| 339 |
> |
atomInfo->dipole[0], |
| 340 |
> |
atomInfo->dipole[1], |
| 341 |
> |
atomInfo->dipole[2]); |
| 342 |
> |
} |
| 343 |
> |
frame.push_back(buffer); |
| 344 |
> |
} |
| 345 |
|
} |
| 346 |
|
} |
| 347 |
|
|
| 376 |
|
outStream << *i << std::endl; |
| 377 |
|
} |
| 378 |
|
|
| 379 |
+ |
std::string XYZVisitor::trimmedName(const std::string&atomTypeName) { |
| 380 |
+ |
return atomTypeName.substr(0, atomTypeName.find('-')); |
| 381 |
+ |
} |
| 382 |
+ |
|
| 383 |
+ |
std::string XYZVisitor::baseTypeName(AtomType* at) { |
| 384 |
+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 385 |
+ |
return ayb[ayb.size()-1]->getName(); |
| 386 |
+ |
} |
| 387 |
+ |
|
| 388 |
|
const std::string XYZVisitor::toString() { |
| 389 |
|
char buffer[65535]; |
| 390 |
|
std::string result; |
| 552 |
|
return result; |
| 553 |
|
} |
| 554 |
|
|
| 555 |
< |
} //namespace oopse |
| 555 |
> |
} //namespace OpenMD |
