| 35 |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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* Created by Kelsey M. Stocker on 2/9/12. |
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#include "config.h" |
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#include "shapedLatticeRod.hpp" |
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#include "shapedLatticeEllipsoid.hpp" |
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#include "nanorodBuilderCmd.h" |
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#include "lattice/LatticeFactory.hpp" |
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#include "utils/MoLocator.hpp" |
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int main(int argc, char *argv []) { |
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//register force fields |
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registerForceFields(); |
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registerLattice(); |
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gengetopt_args_info args_info; |
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std::string latticeType; |
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std::string inputFileName; |
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std::string outputFileName; |
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MoLocator* locator; |
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int nComponents; |
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double latticeConstant; |
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std::vector<double> lc; |
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RealType rodRadius; |
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RealType rodLength; |
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Mat3x3d hmat; |
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std::vector<Vector3d> latticePos; |
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std::vector<Vector3d> latticeOrt; |
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DumpWriter *writer; |
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// Parse Command Line Arguments |
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rodLength = args_info.length_arg; |
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Globals* simParams = oldInfo->getSimParams(); |
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/* Create nanorod */ |
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shapedLatticeRod nanoRod(latticeConstant, latticeType, |
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rodRadius, rodLength); |
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< |
/* Build a lattice and get lattice points for this lattice constant */ |
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vector<Vector3d> sites = nanoRod.getSites(); |
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vector<Vector3d> orientations = nanoRod.getOrientations(); |
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> |
vector<Vector3d> sites; |
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vector<Vector3d> orientations; |
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> |
|
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> |
if (args_info.ellipsoid_flag) { |
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shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType, |
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rodLength, rodRadius); |
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sites = nanoEllipsoid.getSites(); |
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orientations = nanoEllipsoid.getOrientations(); |
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} else { |
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> |
|
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/* Create nanorod */ |
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shapedLatticeRod nanoRod(latticeConstant, latticeType, |
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rodRadius, rodLength); |
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> |
/* Build a lattice and get lattice points for this lattice constant */ |
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sites = nanoRod.getSites(); |
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orientations = nanoRod.getOrientations(); |
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> |
} |
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> |
|
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std::vector<int> vacancyTargets; |
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vector<bool> isVacancy; |
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Vector3d myLoc; |
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RealType myR; |
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for (int i = 0; i < sites.size(); i++) |
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> |
for (unsigned int i = 0; i < sites.size(); i++) |
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isVacancy.push_back(false); |
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< |
|
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> |
|
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// cerr << "checking vacancyPercent" << "\n"; |
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if (args_info.vacancyPercent_given) { |
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// cerr << "vacancyPercent given" << "\n"; |
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} |
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if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) { |
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|
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< |
for (int i = 0; i < sites.size(); i++) { |
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> |
for (unsigned int i = 0; i < sites.size(); i++) { |
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myLoc = sites[i]; |
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myR = myLoc.length(); |
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if (myR >= vIR && myR <= vOR) { |
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simError(); |
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|
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isVacancy.clear(); |
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< |
for (int i = 0; i < sites.size(); i++) { |
| 191 |
> |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 192 |
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bool vac = false; |
| 193 |
< |
for (int j = 0; j < vacancyTargets.size(); j++) { |
| 193 |
> |
for (unsigned int j = 0; j < vacancyTargets.size(); j++) { |
| 194 |
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if (i == vacancyTargets[j]) vac = true; |
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} |
| 196 |
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isVacancy.push_back(vac); |
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std::vector<Component*> components = simParams->getComponents(); |
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std::vector<RealType> molFractions; |
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std::vector<RealType> shellRadii; |
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std::vector<RealType> molecularMasses; |
| 218 |
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std::vector<int> nMol; |
| 219 |
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std::map<int, int> componentFromSite; |
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nComponents = components.size(); |
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} |
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} else { |
| 321 |
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|
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< |
for (int i = 0; i < shellRadii.size(); i++) { |
| 322 |
> |
for (unsigned int i = 0; i < shellRadii.size(); i++) { |
| 323 |
|
if (shellRadii.at(i) > rodRadius + 1e-6 ) { |
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sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod Radius."); |
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painCave.isFatal = 1; |
| 341 |
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simError(); |
| 342 |
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/* Random rod is the default case*/ |
| 343 |
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|
| 344 |
< |
for (int i = 0; i < sites.size(); i++) |
| 344 |
> |
for (unsigned int i = 0; i < sites.size(); i++) |
| 345 |
|
if (!isVacancy[i]) ids.push_back(i); |
| 346 |
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|
| 347 |
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std::random_shuffle(ids.begin(), ids.end()); |
| 351 |
|
painCave.isFatal = 0; |
| 352 |
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simError(); |
| 353 |
|
|
| 354 |
< |
RealType smallestSoFar; |
| 354 |
> |
// RealType smallestSoFar; |
| 355 |
|
int myComponent = -1; |
| 356 |
|
nMol.clear(); |
| 357 |
|
nMol.resize(nComponents); |
| 358 |
|
|
| 359 |
|
// cerr << "shellRadii[0] " << shellRadii[0] << "\n"; |
| 360 |
< |
// cerr << "rodRadius " << rodRadius << "\n"; |
| 360 |
> |
// cerr << "rodRadius " << rodRadius << "\n"; |
| 361 |
|
|
| 362 |
< |
for (int i = 0; i < sites.size(); i++) { |
| 362 |
> |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 363 |
|
myLoc = sites[i]; |
| 364 |
|
myR = myLoc.length(); |
| 365 |
< |
smallestSoFar = rodRadius; |
| 366 |
< |
//cerr << "vac = " << isVacancy[i]<< "\n"; |
| 365 |
> |
// smallestSoFar = rodRadius; |
| 366 |
> |
// cerr << "vac = " << isVacancy[i]<< "\n"; |
| 367 |
|
|
| 368 |
|
if (!isVacancy[i]) { |
| 369 |
|
|
| 391 |
|
|
| 392 |
|
createMdFile(inputFileName, outputFileName, nMol); |
| 393 |
|
|
| 394 |
< |
if (oldInfo != NULL) |
| 393 |
< |
delete oldInfo; |
| 394 |
> |
delete oldInfo; |
| 395 |
|
|
| 396 |
|
SimCreator newCreator; |
| 397 |
|
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 402 |
|
mol = NewInfo->beginMolecule(mi); |
| 403 |
|
|
| 404 |
|
int l = 0; |
| 404 |
– |
int whichSite = 0; |
| 405 |
|
|
| 406 |
< |
for (int i = 0; i < nComponents; i++){ |
| 406 |
> |
for (unsigned int i = 0; i < nComponents; i++){ |
| 407 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 408 |
|
NewInfo->getForceField()); |
| 409 |
|
|
| 410 |
|
// cerr << "nMol = " << nMol.at(i) << "\n"; |
| 411 |
|
if (!args_info.molFraction_given) { |
| 412 |
< |
for (int n = 0; n < sites.size(); n++) { |
| 412 |
> |
for (unsigned int n = 0; n < sites.size(); n++) { |
| 413 |
|
if (!isVacancy[n]) { |
| 414 |
|
if (componentFromSite[n] == i) { |
| 415 |
|
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 419 |
|
} |
| 420 |
|
} |
| 421 |
|
} else { |
| 422 |
< |
for (int n = 0; n < nMol.at(i); n++) { |
| 422 |
> |
for (unsigned int n = 0; n < nMol.at(i); n++) { |
| 423 |
|
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 424 |
|
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 425 |
|
l++; |
| 480 |
|
newMdFile.open(newMdFileName.c_str()); |
| 481 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 482 |
|
|
| 483 |
< |
int i = 0; |
| 483 |
> |
unsigned int i = 0; |
| 484 |
|
while (!oldMdFile.eof()) { |
| 485 |
|
|
| 486 |
|
//correct molecule number |
