FindAllAtomsInsideSphere

This function creates a cluster out of all the atoms that are in a sphere of radius R around the central atom in a crystal lattice.

Syntax: FindAllAtomsInsideSphere(Crystal basis, Lattice parameters, position of central atom, R)

• Crystal basis: List of all Atoms creating the basis of the crystal lattice including the name, position and type and name of the valence orbitals
• Lattice parameters: List of the three real-space lattice vectors
• position of central atom: vector
• R: Float

• Cluster: List of all Atoms of the cluster including the name, position and type and name of the valence orbitals

In this example, a cluster of a UO_2 crystal is created using the results of a DFT calculation. The central atom is chosen to be the Uranium ion at position (0,0,0). The radius of 5 Bohr radii is chosen to include the nearest neighbor oxygen atoms, hence forming a UO_8 cluster.

Example.Quanty

-- read the output of FPLO
print("--Read FPLO output--\n")
FPLOOut = FileReadDresdenFPLO("DFT/out.wan")
 
 
-- from the DFT output we can create a tight binding Hamiltonian
print("--Create the Tight Binding Hamiltonian--\n")
print("Create the tight binding Hamiltonian for the crystal\n")
TB = TightBindingDefFromDresdenFPLO(FPLOOut)
print("Basis")
print(TB.Atoms)
print("Cell")
print(TB.Cell)
 
print("Define a cluster")
 
NewCluster = FindAllAtomsInsideSphere(TB.Atoms,TB.Cell,{0,0,0},5)
print("Quanty detected the following cluster:")
print("Cluster")
print(NewCluster)

--Read FPLO output--
 
--Create the Tight Binding Hamiltonian--
 
Create the tight binding Hamiltonian for the crystal
 
Basis
{ { U , 
  { 0 , 0 , 0 } , 
  { { 5f , 
  { f_{y^3-3x^2y} , f_{xyz} , f_{5z^2y-yr^2} , f_{5z^3-3zr^2} , f_{5z^2x-xr^2} , f_{x^2z-y^2z} , f_{x^3-3xy^2} } } } } , 
  { O , 
  { 2.5842004759287 , 2.5842004759287 , 2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { -2.5842004759287 , -2.5842004759287 , -2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } }
Cell
{ { 0 , 5.1684009518575 , 5.1684009518575 } , 
  { 5.1684009518575 , 0 , 5.1684009518575 } , 
  { 5.1684009518575 , 5.1684009518575 , 0 } }
Define a cluster
Quanty detected the following cluster:
Cluster
{ { O , 
  { 2.5842004759287 , -2.5842004759287 , -2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { -2.5842004759287 , 2.5842004759287 , -2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { -2.5842004759287 , -2.5842004759287 , 2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { U , 
  { 0 , 0 , 0 } , 
  { { 5f , 
  { f_{y^3-3x^2y} , f_{xyz} , f_{5z^2y-yr^2} , f_{5z^3-3zr^2} , f_{5z^2x-xr^2} , f_{x^2z-y^2z} , f_{x^3-3xy^2} } } } } , 
  { O , 
  { 2.5842004759287 , 2.5842004759287 , 2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { -2.5842004759287 , -2.5842004759287 , -2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { 2.5842004759287 , 2.5842004759287 , -2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { 2.5842004759287 , -2.5842004759287 , 2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } , 
  { O , 
  { -2.5842004759287 , 2.5842004759287 , 2.5842004759287 } , 
  { { 2p , 
  { p_y , p_z , p_x } } } } }