.. sas_calculator_help.rst

.. This is a port of the original SasView html help file to ReSTructured text
.. by S King, ISIS, during SasView CodeCamp-III in Feb 2015.

.. _SANS_Calculator_Tool:

Generic SANS Calculator Tool
============================

Description
-----------

This tool attempts to simulate the SANS expected from a specified
shape/structure or scattering length density profile. The tool can
handle both nuclear and magnetic contributions to the scattering.

Theory
------

In general, a particle with a volume $V$ can be described by an ensemble
containing $N$ 3-dimensional rectangular pixels where each pixel is much
smaller than $V$.

Assuming that all the pixel sizes are the same, the elastic scattering
intensity from the particle is defined as

.. image:: gen_i.png

Equation 1.

where $\beta_j$ and $r_j$ are the scattering length density and
the position of the $j^\text{th}$ pixel respectively.

The total volume $V$ is equal to

.. math::

    V = \sum_j^N v_j

for $\beta_j \ne 0$ where $v_j$ is the volume of the $j^\text{th}$
pixel (or the $j^\text{th}$ natural atomic volume (= atomic mass / (natural molar
density * Avogadro number) for the atomic structures).

$V$ can be corrected by users (input parameter `Total volume`). This correction
is useful especially for an atomic structure (such as taken from a PDB file)
to get the right normalization.

*NOTE! $\beta_j$ displayed in the GUI may be incorrect (input parameter
`solvent_SLD`) but this will not affect the scattering computation if the
correction of the total volume V is made.*

The scattering length density (SLD) of each pixel, where the SLD is uniform, is
a combination of the nuclear and magnetic SLDs and depends on the spin states
of the neutrons as follows.

Magnetic Scattering
^^^^^^^^^^^^^^^^^^^

For magnetic scattering, only the magnetization component, $M_\perp$,
perpendicular to the scattering vector $Q$ contributes to the magnetic
scattering length.

.. image:: mag_vector.png

The magnetic scattering length density is then

.. image:: dm_eq.png

where the gyromagnetic ratio is $\gamma = -1.913$, $\mu_B$ is the Bohr
magneton, $r_0$ is the classical radius of electron, and $\sigma$ is the
Pauli spin.

For a polarized neutron, the magnetic scattering is depending on the spin states.

Let us consider that the incident neutrons are polarised both parallel (+) and
anti-parallel (-) to the x' axis (see below). The possible states after
scattering from the sample are then

*  Non-spin flips: (+ +) and (- -)
*  Spin flips:     (+ -) and (- +)

.. image:: gen_mag_pic.png

Now let us assume that the angles of the *Q* vector and the spin-axis (x')
to the x-axis are $\phi$ and $\theta_\text{up}$ respectively (see above). Then,
depending upon the polarization (spin) state of neutrons, the scattering
length densities, including the nuclear scattering length density ($\beta_N$)
are given as

*  for non-spin-flips

   .. image:: sld1.png

*  for spin-flips

   .. image:: sld2.png

where

.. image:: mxp.png



.. image:: myp.png



.. image:: mzp.png



.. image:: mqx.png



.. image:: mqy.png

Here the $M_{0x}$, $M_{0y}$ and $M_{0z}$ are the $x$, $y$ and $z$
components of the magnetisation vector in the laboratory $xyz$ frame.


.. .. image:: Mxyzp.png


.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

Using the tool
--------------

.. figure:: gen_gui_help.png

   ..

   1) Load .sld, .txt, or .omf datafile
   2) Select default shape of sample
   3) Draw magnetization with arrows (not recommended for a large number of
      pixels).
   4) Ratio of (+/total) neutrons after analyser
   5) Ratio of (+/total) neutrons before sample
   6) Polarization angle in degrees
   7) Default volume calculated from the pixel info
      (or natural density of pdf file)
   8) Compute the scattering pattern
   9) Reset GUI to initial state
   10) Display mean values or enter a new value if enabled
   11) Save the sld data as sld format

.. After computation the result will appear in the *Theory* box in the SasView *Data Explorer* panel.

*Up_frac_in* and *Up_frac_out* are the ratio

   (spin up) / (spin up + spin down)

of neutrons before the sample and at the analyzer, respectively.

*NOTE 1. The values of Up_frac_in and Up_frac_out must be in the range
0.0 to 1.0. Both values are 0.5 for unpolarized neutrons.*

*NOTE 2. This computation is totally based on the pixel (or atomic) data fixed
in xyz coordinates. No angular orientational averaging is considered.*

*NOTE 3. For the nuclear scattering length density, only the real component
is taken into account.*

.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

Using PDB/OMF or SLD files
--------------------------

The SANS Calculator tool can read some PDB, OMF or SLD files but ignores
polarized/magnetic scattering when doing so, thus related parameters such as
*Up_frac_in*, etc, will be ignored.

The calculation for fixed orientation uses Equation 1 above resulting in a 2D
output, whereas the scattering calculation averaged over all the orientations
uses the Debye equation below providing a 1D output

.. image:: gen_debye_eq.png

where $v_j \beta_j \equiv b_j$ is the scattering
length of the $j^\text{th}$ atom.
.. The calculation output is passed to the *Data Explorer*
for further use.

.. figure:: pdb_combo.png

   ..

   1) PDB file loaded
   2) disabled input for *Up_frac_in*, *Up_frac_oupt*, *Up_theta*
   3) option to perform the calculations using "Fixed orientations" (2D output)
      or "Averaging over all orientations using Debye equation" (1D output).
      This choice is only available for PDB files.



.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ

.. note::  This help document was last changed by Steve King, 01May2015
