| 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; |
