147 |
|
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
148 |
|
} |
149 |
|
|
150 |
+ |
std::cout <<"Before build shaped lattice. "<<std::endl; |
151 |
|
|
151 |
– |
|
152 |
|
/* create Molocators */ |
153 |
|
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
154 |
|
|
155 |
|
/* Create nanoparticle */ |
156 |
|
shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
157 |
+ |
|
158 |
+ |
std::cout <<"Before build getPoints. "<<std::endl; |
159 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
160 |
|
vector<Vector3d> nanoParticleSites = nanoParticle.getPoints(); |
161 |
+ |
|
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; |
167 |
|
numMol = new int[nComponents]; |
168 |
|
|
169 |
|
|
197 |
|
//get the orientation of the cell sites |
198 |
|
//for the same type of molecule in same lattice, it will not change |
199 |
|
latticeOrt = nanoParticle.getPointsOrt(); |
200 |
< |
|
201 |
< |
|
200 |
> |
std::cout<<"Orientational vector Size: "<< std::endl; |
201 |
> |
std::cout<<latticeOrt.size()<< std::endl; |
202 |
> |
|
203 |
|
|
204 |
+ |
|
205 |
|
// needed for writing out new md file. |
206 |
|
|
207 |
|
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
227 |
|
mol = NewInfo->beginMolecule(mi); |
228 |
|
int l = 0; |
229 |
|
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
230 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
230 |
> |
locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
231 |
|
l++; |
232 |
|
} |
233 |
+ |
|
234 |
|
|
235 |
|
|
228 |
– |
|
229 |
– |
|
230 |
– |
|
236 |
|
|
237 |
|
//fill Hmat |
238 |
|
hmat(0, 0)= latticeConstant; |