====== 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)
###

===== Input =====

  * 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

===== Output =====

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

===== Example =====

###
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.
###

==== Input ====
<code Quanty 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)
</code>

==== Result ====
<file Quanty_Output>
--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 } } } } }

</file>

===== Table of contents =====
{{indexmenu>.#1}}