*GSAS-II Utility Modules*
=========================

---------------------------------
*GSASIIpath: locations & updates*
---------------------------------

Routines for dealing with file locations, etc.

Determines the location of the compiled (.pyd or .so) libraries.

Interfaces with subversion (svn): 
Determine the subversion release number by determining the highest version number
where :func:`SetVersionNumber` is called (best done in every GSASII file).
Other routines will update GSASII from the subversion server if svn can be
found.

Accesses configuration options, as defined in config.py

GSASIIpath Classes & Routines
------------------------------------

.. automodule:: GSASIIpath
    :members: 

---------------------------------
*GSASIIlog: Logging of "Actions"*
---------------------------------

GSASIIlog Classes & Routines
------------------------------------

.. automodule:: GSASIIlog
    :members: 

-------------------------------------------
*config_example.py: Configuration options*
-------------------------------------------

Configuration variables
------------------------------------

.. automodule:: config_example
    :members: 

-----------------------------------------
*GSASIIElem: functions for element types*
-----------------------------------------

GSASIIElem Routines
------------------------------------

.. automodule:: GSASIIElem
    :members: 

-----------------------------------------
*GSASIIlattice: Unit Cell Computations*
-----------------------------------------

Performs lattice-related computations

Note that as used here 
*G* is the reciprocal lattice tensor, and *g* is its inverse,
:math:`G = g^{-1}`, where 

  .. math::

   g = \left( \begin{matrix}
   a^2 & a b\cos\gamma & a c\cos\beta \\
   a b\cos\gamma & b^2 & b c \cos\alpha \\
   a c\cos\beta &  b c \cos\alpha & c^2
   \end{matrix}\right)

The "*A* tensor" terms are defined as
:math:`A = (\begin{matrix} G_{11} & G_{22} & G_{33} & 2G_{12} & 2G_{13} & 2G_{23}\end{matrix})` and *A* can be used in this fashion:
:math:`d^* = \sqrt {A_0 h^2 + A_1 k^2 + A_2 l^2 + A_3 hk + A_4 hl + A_5 kl}`, where
*d* is the d-spacing, and :math:`d^*` is the reciprocal lattice spacing, 
:math:`Q = 2 \pi d^* = 2 \pi / d`. 
Note that GSAS-II variables ``p::Ai`` (i = 0, 1,... 5) and ``p`` is a phase number are 
used for the *Ai* values. See :func:`A2cell`, :func:`cell2A` for interconversion between A and 
unit cell parameters; :func:`cell2Gmat` :func:`Gmat2cell` for G and cell parameters. 

When the hydrostatic/elastic strain coefficients (*Dij*, :math:`D_{ij}`) are used, they are added to the 
*A* tensor terms (Ai, :math:`A_{i}`) so that A is redefined 
:math:`A = (\begin{matrix} A_{0} + D_{11} & A_{1} + D_{22} & A_{2} + D_{33} & A_{3} + D_{12} & A_{4} + D_{13} & A_{5} + D_{23}\end{matrix})`. See :func:`cellDijFill`. 
Note that GSAS-II variables ``p:h:Dij`` (i,j = 1, 2, 3) and ``p`` is a phase number 
and ``h`` a histogram number are used for the *Dij* values.

GSASIIlattice Classes & Routines
------------------------------------

.. automodule:: GSASIIlattice
    :members: 

       
-----------------------------------------
*GSASIIspc: Space Group Computations*
-----------------------------------------

Space group interpretation routines. Note that space group information is
stored in a :ref:`Space Group (SGData)<SGData_table>` object.

GSASIIspc Classes & Routines
------------------------------------

.. automodule:: GSASIIspc
    :members: 

---------------------------------------------
*GSASIIfiles: data (non-GUI) I/O routines*
---------------------------------------------

Module with miscellaneous routines for input and output from files.

GSASIIfiles Classes & Routines
------------------------------------

.. automodule:: GSASIIfiles
    :members: 

--------------------------------------------------
*GSASIImpsubs: routines used in multiprocessing*
--------------------------------------------------

GSASIImpsubs Classes & Routines
------------------------------------

.. automodule:: GSASIImpsubs
    :members: 

---------------------------------------------------
*Module nistlat: NIST*LATTICE cell computations*
---------------------------------------------------

nistlat Classes & Routines
------------------------------------

.. automodule:: nistlat
    :members: 

-----------------------------------------
*ReadMarCCDFrame: Read Mar Files*
-----------------------------------------

.. automodule:: ReadMarCCDFrame
    :members: 

-----------------------------------------
*G2shapes: Compute SAS particle shapes*
-----------------------------------------

Program SHAPES from
"A New Algroithm for the Reconstruction of Protein Molecular Envelopes
from X-ray Solution Scattering Data", 
John Badger, J. Appl. Cryst. (2019) 52, 937-944.
(DOI: 10.1107/S1600576719009774) modified to run inside GSAS-II.

.. automodule:: G2shapes
    :members:
       
--------------------------------------------
*tutorialIndex: index to GSAS-II tutorials*
--------------------------------------------

tutorialIndex Contents
------------------------------------

.. automodule:: tutorialIndex
    :members: