Synopsys: create_H_from_xyz(x,y,z,number_of_orbitals,onsite_energy,hopping_parameter, bond_to_bond_distance,number_of_bonds)
The command create the Hamiltonian matrix expressed in the VHF (Vides Hamiltonian Format), to be included in the Hamiltonian class and to compute transport in the defined material.
If N is the number of total atoms, as input it requires:
- x (array of double N long): the x coordinate of each atom expressed in Angstrom
- y (array of double N long): the y coordinate of each atom expressed in Angstrom
- z (array of double N long): the z coordinate of each atom expressed in Angstrom
- number_of_orbitals (integer): the number of the considered orbitals
- onsite_energy (double): the value of the onsite energy in correspondence of the atoms of the elementary cell, if number_of_orbitals = 1
- hopping_parameter (double): the value of the hopping parameter, if number_of_orbitals = 1
- d_bond (double): the bond-to-bond distance expressed in Angstrom, needed in order to compute the first neighbors of each atom.
- Nbond (int): the number of nearest neighbours
As outputs it provides three quantities: H,n,Nc
- H, The Hamiltonian Matrix
- n, the number of atoms in each slice
- Nc, the number of slices
- x,y,z, the modified coordinates (This since release 1.5)