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diffpy.Structure
Package diffpy :: Package Structure :: Module atom :: Class Atom
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Class Atom

source code

object --+
         |
        Atom

Atom --> class for storing atom information

Data members:
    element     -- type of the atom
    xyz         -- fractional coordinates
    name        -- atom label
    occupancy   -- fractional occupancy
    xyz_cartn   -- absolute Cartesian coordinates, property synced with xyz
    anisotropy  -- flag for anisotropic thermal displacements, property
    U           -- anisotropic thermal displacement tensor, property
    Uij         -- elements of U tensor, where i, j are from (1, 2, 3),
                   property
    Uisoequiv   -- isotropic thermal displacement or equivalent value,
                   property
    Bisoequiv   -- Debye-Waler isotropic temperature factor or equivalent
                   value, property
    lattice     -- coordinate system for fractional coordinates,
                   an instance of Lattice or None for Cartesian system

Private data:
    _U          -- storage of U property, 3x3 numpy matrix
    _Uisoequiv  -- storage of Uisoequiv property, float
    _anisotropy -- storage of anisotropy property, bool or
                   None when not determined
    _Uijsynced  -- flag for consistency of _U with _Uisoequiv,
                   it is meaningful only for isotropic atoms

Class data:
    tol_anisotropy -- tolerated U matrix deviation for isotropic atom


Instance Methods [hide private]
 
__init__(self, atype=None, xyz=None, name=None, occupancy=None, anisotropy=None, U=None, Uisoequiv=None, lattice=None)
Create atom of a specified type at given lattice coordinates.		 source code
 
msdLat(self, vl)
mean square displacement of an atom along lattice vector...		 source code
 
msdCart(self, vc)
mean square displacement of an atom along cartesian vector...		 source code
 
__repr__(self)
simple string representation		 source code
 
__copy__(self)
Return a copy of this instance.		 source code
 
_get_xyz_cartn(self) source code
 
_set_xyz_cartn(self, value) source code
 
_get_anisotropy(self) source code
 
_set_anisotropy(self, value) source code
 
_get_U(self) source code
 
_set_U(self, value) source code
 
_get_Uij(self, i, j) source code
 
_set_Uij(self, i, j, value) source code
 
_get_Uisoequiv(self) source code
 
_set_Uisoequiv(self, value) source code
 
_get_Bisoequiv(self) source code
 
_set_Bisoequiv(self, value) source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __str__

Class Variables [hide private]
  tol_anisotropy = 1e-06
Properties [hide private]
  xyz_cartn
absolute Cartesian coordinates of an atom...
  anisotropy
flag for anisotropic thermal displacements.
  U
anisotropic thermal displacement tensor.
  U11
U11 element of anisotropic displacement tensor
  U22
U22 element of anisotropic displacement tensor
  U33
U33 element of anisotropic displacement tensor
  U12
U12 element of anisotropic displacement tensor
  U13
U13 element of anisotropic displacement tensor
  U23
U23 element of anisotropic displacement tensor
  Uisoequiv
isotropic thermal displacement or equivalent value
  B11
B11 element of Debye-Waler displacement tensor
  B22
B22 element of Debye-Waler displacement tensor
  B33
B33 element of Debye-Waler displacement tensor
  B12
B12 element of Debye-Waler displacement tensor
  B13
B13 element of Debye-Waler displacement tensor
  B23
B23 element of Debye-Waler displacement tensor
  Bisoequiv
Debye-Waler isotropic thermal displacement or equivalent value

Inherited from object: __class__

Method Details [hide private]

__init__(self, atype=None, xyz=None, name=None, occupancy=None, anisotropy=None, U=None, Uisoequiv=None, lattice=None)
(Constructor)

source code  
Create atom of a specified type at given lattice coordinates.
Atom(a) creates a copy of Atom instance a.

atype       -- element symbol string or Atom instance
xyz         -- fractional coordinates
name        -- atom label
occupancy   -- fractional occupancy
anisotropy  -- flag for anisotropic thermal displacements
U           -- anisotropic thermal displacement tensor, property
Uisoequiv   -- isotropic thermal displacement or equivalent value,
               property
lattice     -- coordinate system for fractional coordinates
Overrides: object.__init__

msdLat(self, vl)

source code  
mean square displacement of an atom along lattice vector

vl -- vector in lattice coordinates

return mean square displacement

msdCart(self, vc)

source code  
mean square displacement of an atom along cartesian vector

vc -- vector in absolute cartesian coordinates

return mean square displacement

__repr__(self)
(Representation operator)

source code  
simple string representation
Overrides: object.__repr__

Property Details [hide private]

xyz_cartn

absolute Cartesian coordinates of an atom
Get Method:
diffpy.Structure.atom.Atom._get_xyz_cartn(self)
Set Method:
diffpy.Structure.atom.Atom._set_xyz_cartn(self, value)

anisotropy

flag for anisotropic thermal displacements.
Get Method:
diffpy.Structure.atom.Atom._get_anisotropy(self)
Set Method:
diffpy.Structure.atom.Atom._set_anisotropy(self, value)

U

anisotropic thermal displacement tensor.
Get Method:
diffpy.Structure.atom.Atom._get_U(self)
Set Method:
diffpy.Structure.atom.Atom._set_U(self, value)

U11

U11 element of anisotropic displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

U22

U22 element of anisotropic displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

U33

U33 element of anisotropic displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

U12

U12 element of anisotropic displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

U13

U13 element of anisotropic displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

U23

U23 element of anisotropic displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

Uisoequiv

isotropic thermal displacement or equivalent value
Get Method:
diffpy.Structure.atom.Atom._get_Uisoequiv(self)
Set Method:
diffpy.Structure.atom.Atom._set_Uisoequiv(self, value)

B11

B11 element of Debye-Waler displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

B22

B22 element of Debye-Waler displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

B33

B33 element of Debye-Waler displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

B12

B12 element of Debye-Waler displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

B13

B13 element of Debye-Waler displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

B23

B23 element of Debye-Waler displacement tensor
Get Method:
unreachable.<lambda>(self)
Set Method:
unreachable.<lambda>(self, value)

Bisoequiv

Debye-Waler isotropic thermal displacement or equivalent value
Get Method:
diffpy.Structure.atom.Atom._get_Bisoequiv(self)
Set Method:
diffpy.Structure.atom.Atom._set_Bisoequiv(self, value)

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diffpy.Structure
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