| 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 |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#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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|
| 77 |
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gengetopt_args_info args_info; |
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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) { |
| 159 |
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|
| 160 |
< |
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]; |
| 162 |
|
myR = myLoc.length(); |
| 163 |
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if (myR >= vIR && myR <= vOR) { |
| 171 |
|
|
| 172 |
|
|
| 173 |
|
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(), |
| 175 |
|
vIR, vOR); |
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|
painCave.isFatal = 0; |
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simError(); |
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|
|
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|
isVacancy.clear(); |
| 180 |
< |
for (int i = 0; i < sites.size(); i++) { |
| 180 |
> |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 181 |
|
bool vac = false; |
| 182 |
< |
for (int j = 0; j < vacancyTargets.size(); j++) { |
| 182 |
> |
for (unsigned int j = 0; j < vacancyTargets.size(); j++) { |
| 183 |
|
if (i == vacancyTargets[j]) vac = true; |
| 184 |
|
} |
| 185 |
|
isVacancy.push_back(vac); |
| 305 |
|
} |
| 306 |
|
} else { |
| 307 |
|
|
| 308 |
< |
for (int i = 0; i < shellRadii.size(); i++) { |
| 308 |
> |
for (unsigned int i = 0; i < shellRadii.size(); i++) { |
| 309 |
|
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
| 310 |
|
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
| 311 |
|
painCave.isFatal = 1; |
| 326 |
|
simError(); |
| 327 |
|
/* Random particle is the default case*/ |
| 328 |
|
|
| 329 |
< |
for (int i = 0; i < sites.size(); i++) |
| 329 |
> |
for (unsigned int i = 0; i < sites.size(); i++) |
| 330 |
|
if (!isVacancy[i]) ids.push_back(i); |
| 331 |
|
|
| 332 |
|
std::random_shuffle(ids.begin(), ids.end()); |
| 341 |
|
nMol.clear(); |
| 342 |
|
nMol.resize(nComponents); |
| 343 |
|
|
| 344 |
< |
for (int i = 0; i < sites.size(); i++) { |
| 344 |
> |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 345 |
|
myLoc = sites[i]; |
| 346 |
|
myR = myLoc.length(); |
| 347 |
|
smallestSoFar = particleRadius; |
| 377 |
|
mol = NewInfo->beginMolecule(mi); |
| 378 |
|
|
| 379 |
|
int l = 0; |
| 379 |
– |
int whichSite = 0; |
| 380 |
|
|
| 381 |
|
for (int i = 0; i < nComponents; i++){ |
| 382 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 383 |
|
NewInfo->getForceField()); |
| 384 |
|
|
| 385 |
|
if (!args_info.molFraction_given) { |
| 386 |
< |
for (int n = 0; n < sites.size(); n++) { |
| 386 |
> |
for (unsigned int n = 0; n < sites.size(); n++) { |
| 387 |
|
if (!isVacancy[n]) { |
| 388 |
|
if (componentFromSite[n] == i) { |
| 389 |
|
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 434 |
|
delete writer; |
| 435 |
|
|
| 436 |
|
// cleanup a by calling sim error..... |
| 437 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 437 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 438 |
|
"generated.\n", outputFileName.c_str()); |
| 439 |
|
painCave.isFatal = 0; |
| 440 |
|
simError(); |
| 454 |
|
newMdFile.open(newMdFileName.c_str()); |
| 455 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 456 |
|
|
| 457 |
< |
int i = 0; |
| 457 |
> |
unsigned int i = 0; |
| 458 |
|
while (!oldMdFile.eof()) { |
| 459 |
|
|
| 460 |
|
//correct molecule number |
