90 |
|
int nComponents; |
91 |
|
double latticeConstant; |
92 |
|
std::vector<double> lc; |
93 |
< |
double mass; |
93 |
> |
double mass; |
94 |
|
const double rhoConvertConst = 1.661; |
95 |
|
double density; |
96 |
|
double particleRadius; |
130 |
|
|
131 |
|
|
132 |
|
/*calculate lattice constant (in Angstrom) |
133 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
134 |
< |
1.0 / 3.0);*/ |
133 |
> |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
134 |
> |
1.0 / 3.0);*/ |
135 |
|
|
136 |
|
latticeConstant = args_info.latticeCnst_arg; |
137 |
|
particleRadius = args_info.radius_arg; |
162 |
|
/* Get number of lattice sites */ |
163 |
|
numSites = nanoParticleSites.size(); |
164 |
|
|
165 |
< |
//std::cout <<"numSites are %d "<<numSites<<std::endl; |
166 |
< |
// std::cout <<"nComponents are %d "<<nComponents<<std::endl; |
165 |
> |
//std::cout <<"numSites are %d "<<numSites<<std::endl; |
166 |
> |
// std::cout <<"nComponents are %d "<<nComponents<<std::endl; |
167 |
|
numMol = new int[nComponents]; |
168 |
|
|
169 |
|
|
184 |
|
} |
185 |
|
numMol[nComponents-1] = numSites - totComponents; |
186 |
|
|
187 |
< |
/* do the iPod thing, Shuffle da vector */ |
188 |
< |
std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end()); |
187 |
> |
/* do the iPod thing, Shuffle da vector */ |
188 |
> |
std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end()); |
189 |
|
} else{ /*Handle core-shell with multiple components.*/ |
190 |
|
std::cout << "Creating a core-shell nanoparticle." << std::endl; |
191 |
|
if (nComponents != args_info.ShellRadius_given + 1){ |
195 |
|
|
196 |
|
} |
197 |
|
|
198 |
< |
|
199 |
< |
//get the orientation of the cell sites |
198 |
> |
|
199 |
> |
//get the orientation of the cell sites |
200 |
|
//for the same type of molecule in same lattice, it will not change |
201 |
< |
latticeOrt = nanoParticle.getPointsOrt(); |
202 |
< |
std::cout<<"Orientational vector Size: "<< std::endl; |
203 |
< |
std::cout<<latticeOrt.size()<< std::endl; |
204 |
< |
|
201 |
> |
latticeOrt = nanoParticle.getPointsOrt(); |
202 |
> |
std::cout<<"Orientational vector Size: "<< std::endl; |
203 |
> |
std::cout<<latticeOrt.size()<< std::endl; |
204 |
|
|
206 |
– |
|
207 |
– |
// needed for writing out new md file. |
205 |
|
|
206 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
207 |
< |
outMdFileName = outPrefix + ".md"; |
206 |
> |
|
207 |
> |
// needed for writing out new md file. |
208 |
|
|
209 |
< |
//creat new .md file on fly which corrects the number of molecule |
210 |
< |
createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
209 |
> |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
210 |
> |
outMdFileName = outPrefix + ".md"; |
211 |
|
|
212 |
+ |
//creat new .md file on fly which corrects the number of molecule |
213 |
+ |
createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
214 |
+ |
|
215 |
|
if (oldInfo != NULL) |
216 |
|
delete oldInfo; |
217 |
|
|
219 |
|
// We need to read in new siminfo object. |
220 |
|
//parse md file and set up the system |
221 |
|
//SimCreator NewCreator; |
222 |
< |
SimCreator newCreator; |
222 |
> |
SimCreator newCreator; |
223 |
|
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
224 |
|
|
225 |
|
|
227 |
|
Molecule* mol; |
228 |
|
SimInfo::MoleculeIterator mi; |
229 |
|
mol = NewInfo->beginMolecule(mi); |
230 |
< |
int l = 0; |
231 |
< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
232 |
< |
locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
233 |
< |
l++; |
230 |
> |
int l = 0; |
231 |
> |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
232 |
> |
locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
233 |
> |
l++; |
234 |
|
} |
235 |
|
|
236 |
|
|
297 |
|
|
298 |
|
//correct molecule number |
299 |
|
if (strstr(buffer, "nMol") != NULL) { |
300 |
< |
if(i<components){ |
301 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
302 |
< |
newMdFile << buffer << std::endl; |
303 |
< |
i++; |
304 |
< |
} |
300 |
> |
if(i<components){ |
301 |
> |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
302 |
> |
newMdFile << buffer << std::endl; |
303 |
> |
i++; |
304 |
> |
} |
305 |
|
} else |
306 |
|
newMdFile << buffer << std::endl; |
307 |
|
|