| 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, 234107 (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> |
| 65 |
|
#include "utils/StringUtils.hpp" |
| 66 |
|
|
| 67 |
|
using namespace std; |
| 68 |
< |
using namespace oopse; |
| 68 |
> |
using namespace OpenMD; |
| 69 |
|
void createMdFile(const std::string&oldMdFileName, |
| 70 |
|
const std::string&newMdFileName, |
| 71 |
|
std::vector<int> numMol); |
| 72 |
|
|
| 73 |
|
int main(int argc, char *argv []) { |
| 74 |
|
|
| 74 |
– |
//register force fields |
| 75 |
– |
registerForceFields(); |
| 75 |
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registerLattice(); |
| 76 |
|
|
| 77 |
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gengetopt_args_info args_info; |
| 78 |
|
std::string latticeType; |
| 79 |
|
std::string inputFileName; |
| 80 |
|
std::string outputFileName; |
| 82 |
– |
|
| 81 |
|
MoLocator* locator; |
| 82 |
|
int nComponents; |
| 83 |
|
double latticeConstant; |
| 86 |
– |
std::vector<double> lc; |
| 87 |
– |
|
| 84 |
|
RealType particleRadius; |
| 89 |
– |
|
| 85 |
|
Mat3x3d hmat; |
| 91 |
– |
std::vector<Vector3d> latticePos; |
| 92 |
– |
std::vector<Vector3d> latticeOrt; |
| 93 |
– |
|
| 86 |
|
DumpWriter *writer; |
| 87 |
|
|
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|
// Parse Command Line Arguments |
| 118 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
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vector<Vector3d> sites = nanoParticle.getSites(); |
| 120 |
|
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
| 121 |
< |
std::vector<int> vacancyTargets; |
| 121 |
> |
|
| 122 |
> |
|
| 123 |
> |
std::vector<std::size_t> vacancyTargets; |
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|
vector<bool> isVacancy; |
| 125 |
|
|
| 126 |
|
Vector3d myLoc; |
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|
RealType myR; |
| 128 |
|
|
| 129 |
< |
for (int i = 0; i < sites.size(); i++) |
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> |
for (unsigned int i = 0; i < sites.size(); i++) |
| 130 |
|
isVacancy.push_back(false); |
| 131 |
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|
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if (args_info.vacancyPercent_given) { |
| 133 |
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if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) { |
| 134 |
< |
sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value."); |
| 134 |
> |
sprintf(painCave.errMsg, |
| 135 |
> |
"vacancyPercent was set to a non-sensical value."); |
| 136 |
|
painCave.isFatal = 1; |
| 137 |
|
simError(); |
| 138 |
|
} else { |
| 151 |
|
} |
| 152 |
|
if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) { |
| 153 |
|
|
| 154 |
< |
for (int i = 0; i < sites.size(); i++) { |
| 154 |
> |
for (std::size_t 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) { |
| 165 |
|
|
| 166 |
|
|
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|
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
| 168 |
< |
"\tsites between %lf and %lf.", vacancyTargets.size(), |
| 168 |
> |
"\tsites between %lf and %lf.", (int) vacancyTargets.size(), |
| 169 |
|
vIR, vOR); |
| 170 |
|
painCave.isFatal = 0; |
| 171 |
+ |
painCave.severity = OPENMD_INFO; |
| 172 |
|
simError(); |
| 173 |
|
|
| 174 |
|
isVacancy.clear(); |
| 175 |
< |
for (int i = 0; i < sites.size(); i++) { |
| 175 |
> |
for (std::size_t i = 0; i < sites.size(); i++) { |
| 176 |
|
bool vac = false; |
| 177 |
< |
for (int j = 0; j < vacancyTargets.size(); j++) { |
| 177 |
> |
for (std::size_t j = 0; j < vacancyTargets.size(); j++) { |
| 178 |
|
if (i == vacancyTargets[j]) vac = true; |
| 179 |
|
} |
| 180 |
|
isVacancy.push_back(vac); |
| 190 |
|
} |
| 191 |
|
|
| 192 |
|
/* Get number of lattice sites */ |
| 193 |
< |
int nSites = sites.size() - vacancyTargets.size(); |
| 193 |
> |
std::size_t nSites = sites.size() - vacancyTargets.size(); |
| 194 |
|
|
| 195 |
|
std::vector<Component*> components = simParams->getComponents(); |
| 196 |
|
std::vector<RealType> molFractions; |
| 197 |
|
std::vector<RealType> shellRadii; |
| 202 |
– |
std::vector<RealType> molecularMasses; |
| 198 |
|
std::vector<int> nMol; |
| 199 |
|
std::map<int, int> componentFromSite; |
| 200 |
|
nComponents = components.size(); |
| 271 |
|
totalFraction += molFractions.at(i); |
| 272 |
|
} |
| 273 |
|
if (abs(totalFraction - 1.0) > 1e-6) { |
| 274 |
< |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 274 |
> |
sprintf(painCave.errMsg, |
| 275 |
> |
"The sum of molFractions was not close enough to 1.0"); |
| 276 |
|
painCave.isFatal = 1; |
| 277 |
|
simError(); |
| 278 |
|
} |
| 286 |
|
|
| 287 |
|
// recompute actual mol fractions and perform final sanity check: |
| 288 |
|
|
| 289 |
< |
int totalMolecules = 0; |
| 289 |
> |
std::size_t totalMolecules = 0; |
| 290 |
|
for (int i=0; i < nComponents; i++) { |
| 291 |
|
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 292 |
|
totalMolecules += nMol.at(i); |
| 293 |
|
} |
| 294 |
|
|
| 295 |
|
if (totalMolecules != nSites) { |
| 296 |
< |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 296 |
> |
sprintf(painCave.errMsg, |
| 297 |
> |
"Computed total number of molecules is not equal " |
| 298 |
|
"to the number of lattice sites!"); |
| 299 |
|
painCave.isFatal = 1; |
| 300 |
|
simError(); |
| 301 |
|
} |
| 302 |
|
} else { |
| 303 |
|
|
| 304 |
< |
for (int i = 0; i < shellRadii.size(); i++) { |
| 304 |
> |
for (unsigned int i = 0; i < shellRadii.size(); i++) { |
| 305 |
|
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
| 306 |
< |
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
| 306 |
> |
sprintf(painCave.errMsg, |
| 307 |
> |
"One of the shellRadius values exceeds the particle Radius."); |
| 308 |
|
painCave.isFatal = 1; |
| 309 |
|
simError(); |
| 310 |
|
} |
| 311 |
|
if (shellRadii.at(i) <= 0.0 ) { |
| 312 |
< |
sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
| 312 |
> |
sprintf(painCave.errMsg, |
| 313 |
> |
"One of the shellRadius values is smaller than zero!"); |
| 314 |
|
painCave.isFatal = 1; |
| 315 |
|
simError(); |
| 316 |
|
} |
| 321 |
|
if ((int)args_info.molFraction_given){ |
| 322 |
|
sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle."); |
| 323 |
|
painCave.isFatal = 0; |
| 324 |
+ |
painCave.severity = OPENMD_INFO; |
| 325 |
|
simError(); |
| 326 |
|
/* Random particle is the default case*/ |
| 327 |
|
|
| 328 |
< |
for (int i = 0; i < sites.size(); i++) |
| 328 |
> |
for (unsigned int i = 0; i < sites.size(); i++) |
| 329 |
|
if (!isVacancy[i]) ids.push_back(i); |
| 330 |
|
|
| 331 |
|
std::random_shuffle(ids.begin(), ids.end()); |
| 333 |
|
} else{ |
| 334 |
|
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
| 335 |
|
painCave.isFatal = 0; |
| 336 |
+ |
painCave.severity = OPENMD_INFO; |
| 337 |
|
simError(); |
| 338 |
|
|
| 339 |
|
RealType smallestSoFar; |
| 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; |
| 365 |
|
//creat new .md file on fly which corrects the number of molecule |
| 366 |
|
createMdFile(inputFileName, outputFileName, nMol); |
| 367 |
|
|
| 368 |
< |
if (oldInfo != NULL) |
| 368 |
< |
delete oldInfo; |
| 368 |
> |
delete oldInfo; |
| 369 |
|
|
| 370 |
|
SimCreator newCreator; |
| 371 |
|
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 376 |
|
mol = NewInfo->beginMolecule(mi); |
| 377 |
|
|
| 378 |
|
int l = 0; |
| 379 |
– |
int whichSite = 0; |
| 379 |
|
|
| 380 |
|
for (int i = 0; i < nComponents; i++){ |
| 381 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 382 |
|
NewInfo->getForceField()); |
| 383 |
|
|
| 384 |
|
if (!args_info.molFraction_given) { |
| 385 |
< |
for (int n = 0; n < sites.size(); n++) { |
| 385 |
> |
for (unsigned int n = 0; n < sites.size(); n++) { |
| 386 |
|
if (!isVacancy[n]) { |
| 387 |
|
if (componentFromSite[n] == i) { |
| 388 |
|
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 433 |
|
delete writer; |
| 434 |
|
|
| 435 |
|
// cleanup a by calling sim error..... |
| 436 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 436 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 437 |
|
"generated.\n", outputFileName.c_str()); |
| 438 |
|
painCave.isFatal = 0; |
| 439 |
+ |
painCave.severity = OPENMD_INFO; |
| 440 |
|
simError(); |
| 441 |
|
return 0; |
| 442 |
|
} |
| 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 |
