Index: docs/sphinx-docs/source/user/sasgui/perspectives/calculator/sas_calculator_help.copy
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--- docs/sphinx-docs/source/user/sasgui/perspectives/calculator/sas_calculator_help.copy	(revision 49148bbc34832e06f4f05e8e4c4c32c0da92d133)
+++ docs/sphinx-docs/source/user/sasgui/perspectives/calculator/sas_calculator_help.copy	(revision 49148bbc34832e06f4f05e8e4c4c32c0da92d133)
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+.. 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.
+
+.. |beta| unicode:: U+03B2
+.. |gamma| unicode:: U+03B3
+.. |theta| unicode:: U+03B8
+.. |mu| unicode:: U+03BC
+.. |sigma| unicode:: U+03C3
+.. |phi| unicode:: U+03C6
+
+.. |equiv| unicode:: U+2261
+.. |noteql| unicode:: U+2260
+
+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
+
+.. image:: gen_i.gif
+
+Equation 1.
+
+where |beta|\ :sub:`j` and *r*\ :sub:`j` are the scattering length density and 
+the position of the j'th pixel respectively.
+
+The total volume *V*
+
+.. image:: v_j.gif
+
+for |beta|\ :sub:`j` |noteql|\0 where *v*\ :sub:`j` is the volume of the j'th 
+pixel (or the j'th natural atomic volume (= atomic mass / (natural molar 
+density * Avogadro number) for the atomic structures).
+
+*V* can be corrected by users. This correction is useful especially for an 
+atomic structure (such as taken from a PDB file) to get the right normalization. 
+
+*NOTE!* |beta|\ :sub:`j` *displayed in the GUI may be incorrect 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*\ :sub:`perp`\ , 
+perpendicular to the scattering vector *Q* contributes to the magnetic 
+scattering length.
+
+.. image:: mag_vector.bmp
+
+The magnetic scattering length density is then
+
+.. image:: dm_eq.gif
+
+where the gyromagnetic ratio |gamma| = -1.913, |mu|\ :sub:`B` is the Bohr 
+magneton, *r*\ :sub:`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.bmp
+
+Now let us assume that the angles of the *Q* vector and the spin-axis (x') 
+to the x-axis are |phi| and |theta|\ :sub:`up` respectively (see above). Then, 
+depending upon the polarization (spin) state of neutrons, the scattering 
+length densities, including the nuclear scattering length density (|beta|\ :sub:`N`\ ) 
+are given as
+
+*  for non-spin-flips
+
+   .. image:: sld1.gif
+
+*  for spin-flips
+
+   .. image:: sld2.gif
+
+where
+
+.. image:: mxp.gif
+
+.. image:: myp.gif
+
+.. image:: mzp.gif
+
+.. image:: mqx.gif
+
+.. image:: mqy.gif
+
+Here the *M0*\ :sub:`x`\ , *M0*\ :sub:`y` and *M0*\ :sub:`z` are the x, y and z 
+components of the magnetisation vector in the laboratory xyz frame. 
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+Using the tool
+--------------
+
+.. image:: gen_gui_help.bmp
+
+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 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.gif
+
+where *v*\ :sub:`j` |beta|\ :sub:`j` |equiv| *b*\ :sub:`j` is the scattering 
+length of the j'th atom. The calculation output is passed to the *Data Explorer* 
+for further use.
+
+.. image:: pdb_combo.jpg
+
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
+
+.. note::  This help document was last changed by Steve King, 01May2015
