| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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< |
* 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 |
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* 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 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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). |
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*/ |
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|
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#include <cstdlib> |
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#include "utils/StringUtils.hpp" |
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|
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using namespace std; |
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< |
using namespace oopse; |
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> |
using namespace OpenMD; |
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void createMdFile(const std::string&oldMdFileName, |
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const std::string&newMdFileName, |
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std::vector<int> numMol); |
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|
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int main(int argc, char *argv []) { |
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|
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– |
//register force fields |
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– |
registerForceFields(); |
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registerLattice(); |
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|
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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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– |
|
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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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– |
|
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RealType particleRadius; |
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– |
|
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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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– |
|
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DumpWriter *writer; |
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|
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// Parse Command Line Arguments |
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/* Build a lattice and get lattice points for this lattice constant */ |
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vector<Vector3d> sites = nanoParticle.getSites(); |
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vector<Vector3d> orientations = nanoParticle.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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|
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Vector3d myLoc; |
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RealType myR; |
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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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isVacancy.push_back(false); |
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|
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if (args_info.vacancyPercent_given) { |
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} |
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if (vIR >= 0.0 && vOR <= particleRadius && 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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|
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|
|
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|
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
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< |
"\tsites between %lf and %lf.", vacancyTargets.size(), |
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> |
"\tsites between %lf and %lf.", (int) vacancyTargets.size(), |
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|
vIR, vOR); |
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painCave.isFatal = 0; |
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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++) { |
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> |
for (unsigned int i = 0; i < sites.size(); i++) { |
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|
bool vac = false; |
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< |
for (int j = 0; j < vacancyTargets.size(); j++) { |
| 175 |
> |
for (unsigned int j = 0; j < vacancyTargets.size(); j++) { |
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|
if (i == vacancyTargets[j]) vac = true; |
| 177 |
|
} |
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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; |
| 196 |
|
std::vector<int> nMol; |
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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 { |
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|
|
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< |
for (int i = 0; i < shellRadii.size(); i++) { |
| 300 |
> |
for (unsigned int i = 0; i < shellRadii.size(); i++) { |
| 301 |
|
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
| 302 |
|
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
| 303 |
|
painCave.isFatal = 1; |
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|
simError(); |
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|
/* Random particle is the default case*/ |
| 320 |
|
|
| 321 |
< |
for (int i = 0; i < sites.size(); i++) |
| 321 |
> |
for (unsigned int i = 0; i < sites.size(); i++) |
| 322 |
|
if (!isVacancy[i]) ids.push_back(i); |
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|
|
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std::random_shuffle(ids.begin(), ids.end()); |
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nMol.clear(); |
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nMol.resize(nComponents); |
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|
|
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< |
for (int i = 0; i < sites.size(); i++) { |
| 336 |
> |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 337 |
|
myLoc = sites[i]; |
| 338 |
|
myR = myLoc.length(); |
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smallestSoFar = particleRadius; |
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|
//creat new .md file on fly which corrects the number of molecule |
| 358 |
|
createMdFile(inputFileName, outputFileName, nMol); |
| 359 |
|
|
| 360 |
< |
if (oldInfo != NULL) |
| 368 |
< |
delete oldInfo; |
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> |
delete oldInfo; |
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|
|
| 362 |
|
SimCreator newCreator; |
| 363 |
|
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 368 |
|
mol = NewInfo->beginMolecule(mi); |
| 369 |
|
|
| 370 |
|
int l = 0; |
| 379 |
– |
int whichSite = 0; |
| 371 |
|
|
| 372 |
|
for (int i = 0; i < nComponents; i++){ |
| 373 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 374 |
|
NewInfo->getForceField()); |
| 375 |
|
|
| 376 |
|
if (!args_info.molFraction_given) { |
| 377 |
< |
for (int n = 0; n < sites.size(); n++) { |
| 377 |
> |
for (unsigned int n = 0; n < sites.size(); n++) { |
| 378 |
|
if (!isVacancy[n]) { |
| 379 |
|
if (componentFromSite[n] == i) { |
| 380 |
|
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 425 |
|
delete writer; |
| 426 |
|
|
| 427 |
|
// cleanup a by calling sim error..... |
| 428 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 428 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 429 |
|
"generated.\n", outputFileName.c_str()); |
| 430 |
|
painCave.isFatal = 0; |
| 431 |
|
simError(); |
| 445 |
|
newMdFile.open(newMdFileName.c_str()); |
| 446 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 447 |
|
|
| 448 |
< |
int i = 0; |
| 448 |
> |
unsigned int i = 0; |
| 449 |
|
while (!oldMdFile.eof()) { |
| 450 |
|
|
| 451 |
|
//correct molecule number |
