Skip to content

Commit

Permalink
doc agin
Browse files Browse the repository at this point in the history
  • Loading branch information
@bonfus
bonfus committed May 20, 2016
1 parent cb17f04 commit a7238f0
Showing 1 changed file with 150 additions and 7 deletions.
157 changes: 150 additions & 7 deletions docs/Usage.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,13 +50,17 @@ In :mod:`muesr` the magnetic structure is defined by the propagation
vector `k`, the Fouerier components and the phases
(see :ref:`intro_description_of_magnetic_structures`)

The propagation vector

There are `many <http://magcryst.org/resources/magnetic-coordinates/>`_
conventions to specify the Fourier components of a magnetic structures:
Propagation vector
++++++++++++++++++

In :mod:`muesr`, the propagation vector is always specified
in **reciprocal lattice units**.

Fourier components
++++++++++++++++++

There are `many <http://magcryst.org/resources/magnetic-coordinates/>`_
conventions to specify the Fourier components of a magnetic structures.
At the current stage :mod:`muesr` supports the following coordinate
systems:

Expand All @@ -66,7 +70,7 @@ systems:

1. Bohr Magneton/Angstrom units, with x||a, y||b and z||c
This is the reduced lattice coordinate system, where the magnetic
metric tensor (M) is the same metric used for interatomic distances
metric tensor (M) is the same metric used for inter-atomic distances
(G).

2. Bohr Magneton units, with x||a, y||b and z||c
Expand All @@ -76,7 +80,143 @@ systems:
If we define L = {{a,0,0},{0,b,0},{0,0,c}}, then the magnetic metric
tensor is M = L.G.L^(-1), which is unitless.

In practice
+++++++++++

To define a new magnetic structure just do ::

>>> from muesr.core.sample import Sample
>>> from muesr.core.magmodel import MM
>>> smp = Sample()
>>>
>>> # load a lattice structure!
>>>
>>> smp.new_mm()

The newly created magnetic structure is automatically selected as the
current magnetic model and can be obtained with the
:py:attr:`~muesr.core.sample.Sample.mm` property.
From that you can access and define all the properties of the magnetic definition ::

>>> smp.mm.k
... array([0, 0, 0])

Plese see the :py:mod:`~muesr.core.magmodel.MM` documentation for the
details.

To simplify the definition of the magnetic structure, the
:py:func:`~muesr.utilities.ms.mago_add` helper function is available.

It prompts an interactive interface like the one shown below
(for a Ti2O3 structure): ::

>>> mago_add(smp,coordinates='bohr-lattice')
... Propagation vector (w.r.t. conv. rec. cell): 0 0 0
... Magnetic moments in bohr magnetons and lattice coordinates.
... Which atom? (enter for all)Ti
... Lattice vectors:
... a 5.149000000000000 0.000000000000000 0.000000000000000
... b -2.574499999999999 4.459164804086075 0.000000000000000
... c 0.000000000000001 0.000000000000001 13.641999999999999
... Atomic positions (fractional):
... 1 Ti 0.00000000000000 0.00000000000000 0.34500000000000 47.867
... 2 Ti 0.66666666666667 0.33333333333333 0.67833333333333 47.867
... 3 Ti 0.33333333333333 0.66666666666667 0.01166666666667 47.867
... 4 Ti 0.00000000000000 0.00000000000000 0.84500000000000 47.867
... 5 Ti 0.66666666666667 0.33333333333333 0.17833333333333 47.867
... 6 Ti 0.33333333333333 0.66666666666667 0.51166666666667 47.867
... 7 Ti 0.00000000000000 0.00000000000000 0.15500000000000 47.867
... 8 Ti 0.66666666666667 0.33333333333333 0.48833333333333 47.867
... 9 Ti 0.33333333333333 0.66666666666667 0.82166666666667 47.867
... 10 Ti 0.00000000000000 0.00000000000000 0.65500000000000 47.867
... 11 Ti 0.66666666666667 0.33333333333333 0.98833333333333 47.867
... 12 Ti 0.33333333333333 0.66666666666667 0.32166666666667 47.867
... FC for atom 1 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 2 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 3 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 4 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 5 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 6 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 7 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 8 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 9 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 10 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 11 Ti (3 real, [3 imag]): 0 1 0
... FC for atom 12 Ti (3 real, [3 imag]): 0 1 0
...
This produces the following Fouerier components in Cartesian coordinates ::

>>> smp.mm.fc
... array([[-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [-0.5000000+0.j, 0.8660254+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j],
... [ 0.0000000+0.j, 0.0000000+0.j, 0.0000000+0.j]])

Which are indeed: ::

>>> smp.mm.fcLattBM
... array([[ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 1.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j],
... [ 0.+0.j, 0.+0.j, 0.+0.j]])


The zeros in the Fourier components are from the atoms different from
`Ti`.


Useful readings
Expand Down Expand Up @@ -134,9 +274,12 @@ Understanding errors
:mod:`muesr` raises the conventional python exceptions (mainly ValueError and
TypeError) or other 4 specific Exceptions:

- CellError
- :py:class:`~muesr.core.sampleErrors.CellError`
- :py:class:`~muesr.core.sampleErrors.MuonError`
- :py:class:`~muesr.core.sampleErrors.MagDefError`
- :py:class:`~muesr.core.sampleErrors.SymmetryError`

To see their meaning follow the links.

The utility functions are mainly intented for interactive usage and report
problems
problems by printing messages on the screen.

0 comments on commit a7238f0

Please sign in to comment.