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void | setup (Parameter_Map ¶m_map, const Atom_List &atlist) |
| | setup from command line parameters. Typically, an Atom_List has to be set up anyway, so use if it possible
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void | setup (Parameter_Map ¶m_map) |
| | If not, the set up Atom_List temporarliy and drop it when Neighbor_List is set up.
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void | add (const Atom_List &atlist, const Neighborhood_Criterion &criterion, double boxwidth=-1.) |
| | calculate neighbors from Atom_List according to the specified Neighborhood_Criterion, then add them to the existing neighbors
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void | add_shifted (const Atom_List &atlist, const Neighborhood_Criterion &criterion, const Vec3d &shift, double boxwidth=-1.) |
| | Same as 'add' but shift the atom positions before checking if the Neighborhood_Criterion is fulfilled. Used for periodic boundaries.
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void | calculate (const Atom_List &atlist, const Neighborhood_Criterion &criterion, const std::vector< Vec3d > &periodic_vec=std::vector< Vec3d >(), double boxwidth=-1.) |
| | Clear existing data and 'add'.
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void | calculate (const Atom_List &atlist, const Lattice &lat, const std::vector< Vec3d > &periodic_vec=std::vector< Vec3d >(), double tolerance=0.20) |
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void | calculate_unrelaxed (const Atom_List &atlist, const Lattice &lat, double tolerance=0.2) |
| | Same as 'calculate', but set the bond vector 'D' of each 'Neighbor' to one matching a neighbor in an equilibirum lattice bond.
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void | setup_unrelaxed_from_relaxed (const Atom_List &atlist, const Neighbor_List &neilist_relaxed, const TB_Parameter_List &parlist) |
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bool | calcualte_unrelaxed_single (const Neighbor_List &other, size_t index, size_t n, const Lattice &lat, double tolerance=0.2, const Vec3d &shift=Vec3d()) |
| | If there is more than one material, there is more than one equilibrium lattice. Thus, we have to go through all atoms individually to get the correct equilibirum distance vectors. Returns false if neighbor is not found.
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size_t | get_max_neighbors_per_atom () const |
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void | read (const std::string &filename, const Atom_List &atlist) |
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void | print (const std::string &filename) const |
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void | print_withD (const std::string &filename) const |
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void | check_consistency () const |
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| Neighbor_List (const Atom_List &atlist, const Neighborhood_Criterion &criterion, const std::vector< Vec3d > &periodic_vec=std::vector< Vec3d >(), double boxwidth=-1.) |
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| Neighbor_List (const Atom_List &atlist, const Lattice &lat, const std::vector< Vec3d > &periodic_vec=std::vector< Vec3d >(), double tolerance=0.2) |
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std::vector< Neighbor > & | operator[] (size_t i) |
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const std::vector< Neighbor > & | operator[] (size_t i) const |
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size_t | size () const |
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virtual void | resize (size_t i) |
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virtual void | reserve (size_t i) |
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virtual void | push_back (const std::vector< Neighbor > &value) |
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virtual void | clear () |
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List_Class< std::vector< Neighbor > > & | operator= (const std::vector< std::vector< Neighbor > > &Tvec) |
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int | find (std::vector< Neighbor >element) const |
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int | find_check (std::vector< Neighbor >element) const |
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void | add_if_new (std::vector< Neighbor >element) |
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void | add_if_new_check (std::vector< Neighbor >element) |
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Public Member Functions inherited from List_Class< std::vector< Neighbor > >
1.8.11
