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CellSizer Transform Library
Documentation for the CellSizer transform library, which includes the following classes: CellSizer, Vector, BravaisLattice, and Atom.
Transform Library: CellSizer
| Author: | Karl Norby <knorby at uchicago dot edu> |
|---|---|
| Date: | Fri, 1 Sept 2006 |
| Category: | Computational Materials Science |
| Description: | Library containing functions to change the size and shape of a crystal lattice structure |
| Copyright: | pyXSD License |
Other Information
CellSizer is part of the pyXSD standard release
Functions
CellSizer methods
cellSizerInit()
Args: No Args
Description: Adds on Init function for use with any class dependent on CellSizer
getBravaisVectors()
Args: No Args
Description: Gets the vectors from the tree, makes them instances of Vector, stores them in self.bravaisVectors, and returns self.bravaisVectors. self.bravaisVector is a dictionary with a1, a2, and a3 as keys. Stores order in self.vectorOrder.
getVectorList()
Args: No Args
Description: Returns the vectors that getBravaisVectors() produces in an ordered list.
getAtoms()
Args: No Args
Description: Gets the atoms from the tree, and creates instances of these atoms with the class Atom. In the instance, the variable position is a list containing the components of the position in terms of the vectors, and the variable atomType is a string containg the atom type. Stores the instances in the list self.atoms, and returns that list.
makeNewXml(bravaisLattice)
Args:
- bravaisLattice : Instance of BravaisLattice
- An instance of the class BravaisLattice, which contains the vectors and atoms
Description: Replaces the old vectors and atoms with the new ones in the tree. Works only for xml documents following the ORNL CMS schema. Returns root.
makeNewXmlAtomElements(atom)
Args:
- atom : Instance of atom
- An instance of the class atom
Description: formats an atom correctly for the xml tree.
makeAtom(position, atomType)
Args:
- position : list
- A list that has the component of the atom position in terms of the vectors
- atomType : string
- A string that states the atom type
Description: Makes an instance of the Atom class with the given information. Use this function to avoid importing Atom in a transform class.
makeBravaisLattice(newVectors, newAtoms)
Args:
- newVectors : list
- A list of the Bravais vectors to use in the Bravais Lattice
- newAtoms : list
- A list of atoms to include in the Bravais Lattice
Description: Makes an instance of the BravaisLattice class with the given information. Use this function to avoid importing BravaisLattice in a transform class.
getCartesianCoords(vectors, position)
Args:
- vectors : list
- A list of the Bravais vectors
- position : list
- A list that has the component of the atom position in terms of the vectors
Description: returns a list of the cartesian coords for an atom
findCenter(vectors)
Args:
- vectors : list
- A list of the Bravais vectors
Description: returns a the center of a cell in cartesian coords
Vector Class Methods
Vector is a subclass of tuple
__init__(val)
Args:
- val : Sequence
- The i, j, k values that define a vector
Description: Initializes the vector as a tuple, so self is a tuple of the values NOTE: self will not be mention in the list of arguments, but will be stated as an argument for for other vector methods.
__mul__(self, scalar)
Args:
- scalar : Number
- The scalar to use
Description: defines scalar multiplication. lets the user use the * for multiplication. The scalar must be the second term.
__add__(self, vector)
Args:
- vector : instance of the Vector class
- The vector to use
Description: Defines vector addition. Allows one to use the + for vector additon. Returns a new vector.
__sub__(self, vector)
Args:
- vector : instance of the Vector class
- The vector to use
Description: Defines vector subtraction. Allows one to use the - for vector subtraction. Returns a new vector.
findDotProduct(self, vector)
Args:
- vector : instance of the Vector class
- The vector to use
Description: Returns the dot product.
distance(self, vector)
Args:
- vector : instance of the Vector class
- The vector to use
Description: Returns the distance between two vectors.
findLength(self, vector)
Args:
- vector : instance of the Vector class
- The vector to use
Description: returns the length of a vector