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documentation:language_reference:functions:findallatomsinsidesphere [2018/09/25 13:38] – created Simon Heinzedocumentation:language_reference:functions:findallatomsinsidesphere [2024/07/23 18:00] (current) – Henrik hahn
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 ### ###
-alligned paragraph text+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 ===== ===== Input =====
  
-  * bla : Integer +  * 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 
-  * bla2 : Real+  * Lattice parameters: List of the three real-space lattice vectors  
 +  * position of central atom: vector 
 +  * R: Float
  
 ===== Output ===== ===== Output =====
  
-  * bla : real+  * Cluster: List of all Atoms of the cluster including the name, position and type and name of the valence orbitals
  
 ===== Example ===== ===== Example =====
  
 ### ###
-description text+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 ==== ==== Input ====
 <code Quanty Example.Quanty> <code Quanty Example.Quanty>
--- some example code+ 
 +-- 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> </code>
  
 ==== Result ==== ==== Result ====
 <file Quanty_Output> <file Quanty_Output>
-text produced as 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> </file>
  

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