| 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). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
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| 43 |
|
#include <iostream> |
| 64 |
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| 65 |
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using namespace OpenMD; |
| 66 |
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| 67 |
+ |
using namespace std; |
| 68 |
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int main(int argc, char* argv[]){ |
| 69 |
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| 68 |
– |
//register force fields |
| 69 |
– |
registerForceFields(); |
| 70 |
– |
|
| 70 |
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gengetopt_args_info args_info; |
| 71 |
< |
std::string dumpFileName; |
| 72 |
< |
std::string xyzFileName; |
| 73 |
< |
bool printVel; |
| 74 |
< |
bool printFrc; |
| 75 |
< |
bool printVec; |
| 76 |
< |
bool printChrg; |
| 71 |
> |
string dumpFileName; |
| 72 |
> |
string xyzFileName; |
| 73 |
> |
|
| 74 |
> |
bool printVel(false); |
| 75 |
> |
bool printFrc(false); |
| 76 |
> |
bool printVec(false); |
| 77 |
> |
bool printChrg(false); |
| 78 |
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| 79 |
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//parse the command line option |
| 80 |
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if (cmdline_parser (argc, argv, &args_info) != 0) { |
| 85 |
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if (args_info.input_given){ |
| 86 |
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dumpFileName = args_info.input_arg; |
| 87 |
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} else { |
| 88 |
< |
std::cerr << "Does not have input file name" << std::endl; |
| 88 |
> |
cerr << "Does not have input file name" << endl; |
| 89 |
|
exit(1); |
| 90 |
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} |
| 91 |
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|
| 138 |
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if (args_info.basetype_flag) { |
| 139 |
|
AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info); |
| 140 |
|
compositeVisitor->addVisitor(atomNameVisitor, 550); |
| 141 |
< |
std::cout << compositeVisitor->toString(); |
| 141 |
> |
cout << compositeVisitor->toString(); |
| 142 |
|
} |
| 143 |
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|
| 144 |
|
//create ZconsVisitor |
| 180 |
|
args_info.refsele_arg), |
| 181 |
|
250); |
| 182 |
|
} else if (args_info.refsele_given || args_info.originsele_given) { |
| 183 |
< |
std::cerr << "Both of --refsele and --originsele should appear by pair" |
| 184 |
< |
<< std::endl; |
| 183 |
> |
cerr << "Both of --refsele and --originsele should appear by pair" |
| 184 |
> |
<< endl; |
| 185 |
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exit(1); |
| 186 |
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} |
| 187 |
|
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| 220 |
|
DumpReader* dumpReader = new DumpReader(info, dumpFileName); |
| 221 |
|
int nframes = dumpReader->getNFrames(); |
| 222 |
|
|
| 223 |
< |
std::ofstream xyzStream(xyzFileName.c_str()); |
| 223 |
> |
ofstream xyzStream(xyzFileName.c_str()); |
| 224 |
|
|
| 225 |
|
SimInfo::MoleculeIterator miter; |
| 226 |
|
Molecule::IntegrableObjectIterator iiter; |
| 227 |
|
Molecule::RigidBodyIterator rbIter; |
| 228 |
|
Molecule* mol; |
| 229 |
< |
StuntDouble* integrableObject; |
| 229 |
> |
StuntDouble* sd; |
| 230 |
|
RigidBody* rb; |
| 231 |
|
Vector3d molCom; |
| 232 |
|
Vector3d newMolCom; |
| 244 |
|
currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 245 |
|
for (mol = info->beginMolecule(miter); mol != NULL; |
| 246 |
|
mol = info->nextMolecule(miter)) { |
| 247 |
< |
molCom = mol->getCom(); |
| 248 |
< |
newMolCom = molCom; |
| 249 |
< |
currentSnapshot->wrapVector(newMolCom); |
| 250 |
< |
displacement = newMolCom - molCom; |
| 251 |
< |
for (integrableObject = mol->beginIntegrableObject(iiter); |
| 252 |
< |
integrableObject != NULL; |
| 253 |
< |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 254 |
< |
integrableObject->setPos(integrableObject->getPos() + displacement); |
| 247 |
> |
|
| 248 |
> |
molCom = mol->getCom(); |
| 249 |
> |
newMolCom = molCom; |
| 250 |
> |
currentSnapshot->wrapVector(newMolCom); |
| 251 |
> |
displacement = newMolCom - molCom; |
| 252 |
> |
|
| 253 |
> |
for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
| 254 |
> |
sd = mol->nextIntegrableObject(iiter)) { |
| 255 |
> |
|
| 256 |
> |
sd->setPos(sd->getPos() + displacement); |
| 257 |
> |
|
| 258 |
|
} |
| 259 |
|
} |
| 260 |
|
} |
| 261 |
+ |
|
| 262 |
|
//update atoms of rigidbody |
| 263 |
|
for (mol = info->beginMolecule(miter); mol != NULL; |
| 264 |
|
mol = info->nextMolecule(miter)) { |
| 266 |
|
//change the positions of atoms which belong to the rigidbodies |
| 267 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 268 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 269 |
+ |
|
| 270 |
|
rb->updateAtoms(); |
| 271 |
|
if (printVel) rb->updateAtomVel(); |
| 272 |
+ |
|
| 273 |
|
} |
| 274 |
|
} |
| 275 |
|
|
| 276 |
|
//prepare visit |
| 277 |
|
for (mol = info->beginMolecule(miter); mol != NULL; |
| 278 |
|
mol = info->nextMolecule(miter)) { |
| 279 |
< |
for (integrableObject = mol->beginIntegrableObject(iiter); |
| 280 |
< |
integrableObject != NULL; |
| 281 |
< |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 282 |
< |
integrableObject->accept(prepareVisitor); |
| 279 |
> |
|
| 280 |
> |
for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
| 281 |
> |
sd = mol->nextIntegrableObject(iiter)) { |
| 282 |
> |
|
| 283 |
> |
sd->accept(prepareVisitor); |
| 284 |
> |
|
| 285 |
|
} |
| 286 |
|
} |
| 287 |
|
|
| 292 |
|
//visit stuntdouble |
| 293 |
|
for (mol = info->beginMolecule(miter); mol != NULL; |
| 294 |
|
mol = info->nextMolecule(miter)) { |
| 295 |
< |
for (integrableObject = mol->beginIntegrableObject(iiter); |
| 296 |
< |
integrableObject != NULL; |
| 297 |
< |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 298 |
< |
integrableObject->accept(compositeVisitor); |
| 295 |
> |
|
| 296 |
> |
for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
| 297 |
> |
sd = mol->nextIntegrableObject(iiter)) { |
| 298 |
> |
|
| 299 |
> |
sd->accept(compositeVisitor); |
| 300 |
> |
|
| 301 |
|
} |
| 302 |
|
} |
| 303 |
|
|
