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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 24 |
|
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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// A modifier creating a triangle with the incremental builder. |
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template <class HDS> |
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class Build_nanorod : public CGAL::Modifier_base<HDS> { |
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< |
public: |
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> |
public: |
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Vertex_handle end1; |
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Vertex_handle neight1; |
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< |
Vertex_handle end2; |
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> |
Vertex_handle end2; |
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Vertex_handle neight2; |
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|
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Build_nanorod() {} |
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|
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bool GeometryBuilder::isInsidePolyhedron(double x, double y, double z) { |
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|
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< |
Point_3 point(x,y,z); |
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> |
Point_3 point(x,y,z); |
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Plane_iterator i; |
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Facet_iterator j; |
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for ( i =nanoRodPolyhedron.planes_begin(), j = nanoRodPolyhedron.facets_begin(); i != nanoRodPolyhedron.planes_end() && j !=nanoRodPolyhedron.facets_end(); ++i, ++j) { |
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|
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|
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GeometryBuilder::GeometryBuilder(double length,double width) { |
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// Create the geometry for nanorod |
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> |
// Create the geometry for nanorod |
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Build_nanorod<HalfedgeDS> nanorod; |
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|
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nanoRodPolyhedron.delegate( nanorod); |
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|
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< |
double y1 = nanorod.end1->point().y() - nanorod.neight1->point().y(); |
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< |
double y2 = nanorod.end2->point().y() - nanorod.neight2->point().y(); |
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< |
|
| 274 |
< |
CGAL::Aff_transformation_3<Kernel> aff_tranformation( width, |
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< |
0.0, |
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< |
0.0, |
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< |
0.0, |
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< |
0.0, |
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< |
length, |
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< |
0.0, |
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< |
0.0, |
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< |
0.0, |
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< |
0.0, |
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< |
width, |
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< |
0.0); |
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< |
std::transform( nanoRodPolyhedron.points_begin(), nanoRodPolyhedron.points_end(), nanoRodPolyhedron.points_begin(), aff_tranformation); |
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> |
double y1 = nanorod.end1->point().y() - nanorod.neight1->point().y(); |
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> |
double y2 = nanorod.end2->point().y() - nanorod.neight2->point().y(); |
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|
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< |
Point_3 point1(nanorod.end1->point().x(), y1 + nanorod.neight1->point().y(), nanorod.end1->point().z()); |
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< |
Point_3 point2(nanorod.end2->point().x(), y2+ nanorod.neight2->point().y(), nanorod.end2->point().z()); |
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< |
nanorod.end1->point() = point1; |
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< |
nanorod.end2->point() = point2; |
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> |
CGAL::Aff_transformation_3<Kernel> aff_tranformation( width, |
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> |
0.0, |
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> |
0.0, |
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> |
0.0, |
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> |
0.0, |
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> |
length, |
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> |
0.0, |
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> |
0.0, |
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> |
0.0, |
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> |
0.0, |
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> |
width, |
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> |
0.0); |
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> |
std::transform( nanoRodPolyhedron.points_begin(), nanoRodPolyhedron.points_end(), nanoRodPolyhedron.points_begin(), aff_tranformation); |
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|
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< |
// Construct normal vector for each face. |
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< |
std::transform( nanoRodPolyhedron.facets_begin(), nanoRodPolyhedron.facets_end(), nanoRodPolyhedron.planes_begin(), |
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< |
Normal_vector()); |
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> |
Point_3 point1(nanorod.end1->point().x(), y1 + nanorod.neight1->point().y(), nanorod.end1->point().z()); |
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> |
Point_3 point2(nanorod.end2->point().x(), y2+ nanorod.neight2->point().y(), nanorod.end2->point().z()); |
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> |
nanorod.end1->point() = point1; |
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> |
nanorod.end2->point() = point2; |
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> |
|
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> |
// Construct normal vector for each face. |
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> |
std::transform( nanoRodPolyhedron.facets_begin(), nanoRodPolyhedron.facets_end(), nanoRodPolyhedron.planes_begin(), |
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> |
Normal_vector()); |
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|
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|
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|
