.. _diagram_structure_page:

========================
Diagram Structure
========================

.. contents:: Table of Contents
    :depth: 3
    :local:
    

Reminder about data structure
-----------------------------

Please see the MT structure page to be aware of how the analysis are stored in ||frog|. 

In short, an MT contains all the information regarding a set of molecule at a given MD frame. There are as many MT object as time step and molecule type declared. 

It contains all the parameters needed to performed the analysis, which does not depend on the time step, in the :ref:`Molecule Type Parameter object<autodoc_mt_mtparameter>`.

It contains a :ref:`list of all the molecule<autodoc_mt_L_molecule>`: every molecule is described using a singlemolecule object. In this :ref:`Single Molecule object<single_molecule_object_page>`, all the individual property which should be computed are stored: the mean position, the number of H-bond, the hyperpolarizability... In :ref:`the analysis available page<diagram_list_page>`, is presented what singlemolecule attribute is generated for each analysis required. For instance, asking for a 'beta' analysis will create for each singlemolecule object an attribute 'beta' where the individual beta value will be stored for each time step. 

Finaly, the MT object contains the diagram corresponding to the analysis done for this molecule set. There are at least as many diagram as analysis performed. 


The diagram structure
---------------------

Every analysis declared refers to a class, which inherite from the Diagram class. This diagram class defines the attributes presented bellow as well as basic function. Every analysis defines how to deal with the user-input, how to compute the individual quantity, how to add an individual quantity to the distribution... These informations relative to the analysis are presented in :ref:`this page<diagram_list_page>`.


Every diagram are attached to a Single Diagram Parameter object, contained in the :ref:`myMT.mtparameter.dparamter.L_diagram<autodoc_diagramparameter_L_diagram>` list. This object contains the parameter needed for the analysis and the discretization. This idea is that the sdparameter contains most of the time-invariant parameters for the diagram, while the diagram itself contains the time-dependant values -- *i.e.* the results for every time step. 

.. note:: The diagram are directly stored in the MT object. Therefore, to call a diagram, you may want to look at the sdparamter first. To call the diagram relative to the sdparameter, use: `getattr(myMT, sdparameter.name)`

Here is what contains every diagram, due to the Diagram class inheritance:

.. _autodoc_diagram_name:
.. autoattribute:: Frog.class_Diagrams.Diagram.name
    :noindex:

|

.. _autodoc_diagram_size:
.. autoattribute:: Frog.class_Diagrams.Diagram.size
   :noindex:

|

.. _autodoc_diagram_population:
.. autoattribute:: Frog.class_Diagrams.Diagram.population
    :noindex:

|

.. _autodoc_diagram_value:
.. autoattribute:: Frog.class_Diagrams.Diagram.value
    :noindex:

|

.. _autodoc_diagram_valuesquare:
.. autoattribute:: Frog.class_Diagrams.Diagram.valuesquare
    :noindex:

|

.. _autodoc_diagram_mean:
.. autoattribute:: Frog.class_Diagrams.Diagram.mean
    :noindex:

|

.. _autodoc_diagram_sd:
.. autoattribute:: Frog.class_Diagrams.Diagram.sd
    :noindex:

|

.. _autodoc_diagram_axis_population:
.. autoattribute:: Frog.class_Diagrams.Diagram.axis_population
    :noindex:

|

.. _autodoc_diagram_unit:
.. autoattribute:: Frog.class_Diagrams.Diagram.unit
    :noindex:

|

.. _autodoc_diagram_axis_observable:
.. autoattribute:: Frog.class_Diagrams.Diagram.axis_observable
    :noindex:

|

.. _autodoc_diagram_axis_space:
.. autoattribute:: Frog.class_Diagrams.Diagram.axis_space
    :noindex:




Diagram Parameter
---------------------
.. _diagram_parameter_page:


The :ref:`dparameter<autodoc_mtparameter_dparameter>` attribute is a Diagram Parameter object. It is contained in the mtparameter (which is a :ref:`Molecule Type Parameter object<autodoc_mt_mtparameter>`) attribute of the Molecule Type Object. In Short: `myMT.mtparameter.dparameter`. 

It is built when the diagram input are set by the user using the function `myMT.read_diagram_input`, see :ref:`this page<how_to_creat_diagram_page>` for pratical examples. It contains information about the analysis and diagram required for this MT. 

.. note:: If 'optical' analysis are required, the parameters relative to these analysis are completed by the one provided in the Optcial Parameter object: :ref:`myMT.mtparameter.optparameter<autodoc_mtparameter_optparameter>`.

Here are the available attribute of this object. Please note that you have no use to call or add them manually for a standard use of |frog|. This part is intented for advance user. 

.. _autodoc_diagramparameter_L_possible_diagram:
.. autoattribute:: Frog.class_DiagramParameter.DiagramParameter.L_possible_diagram
    :noindex:

|

.. _autodoc_diagramparameter_L_diagram:
.. autoattribute:: Frog.class_DiagramParameter.DiagramParameter.L_diagram
    :noindex:

|

.. _autodoc_diagramparameter_IS_rot_mat:
.. autoattribute:: Frog.class_DiagramParameter.DiagramParameter.IS_rot_mat
    :noindex:

|

.. _autodoc_diagramparameter_IS_density:
.. autoattribute:: Frog.class_DiagramParameter.DiagramParameter.IS_density
    :noindex:

|

.. _autodoc_diagramparameter_special_selection:
.. autoattribute:: Frog.class_DiagramParameter.DiagramParameter.special_selection
    :noindex:

|

.. _autodoc_diagramparameter_L_allowed_molecule:
.. autoattribute:: Frog.class_DiagramParameter.DiagramParameter.L_allowed_molecule
    :noindex:



Single Diagram Parameter
-------------------------
.. _single_diagram_parameter_page:

All the single parameter object are contained in the :ref:`myMT.mtparameter.dparameter.L_diagram <autodoc_diagramparameter_L_diagram>` list. See above for the dparameter object. 

They are built when the diagram input are set by the user using the function `myMT.read_diagram_input`, see :ref:`this page<how_to_creat_diagram_page>` for pratical examples. Each sdparameter objects are attached to a diagram. The attributes of these sdparameter depend on the analysis required. In the :ref:`list of the available analysis<diagram_list_page>` is details which sdparameter attributed are added for each analysis.  

.. note:: If 'optical' analysis are required, the parameters relative to these analysis are completed by the one provided in the Optcial Parameter object: :ref:`myMT.mtparameter.optparameter<autodoc_mtparameter_optparameter>`.

Here are the available attribute of this object. Please note that you have no use to call or add them manually for a standard use of |frog|. This part is intented for advance user. 


.. _autodoc_singlediagramparameter_name:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.name
    :noindex:

|

.. _autodoc_singlediagramparameter_analysis_type:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.analysis_type
    :noindex:

|

.. _autodoc_singlediagramparameter_discretization_type:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.discretization_type
    :noindex:

.. Note:: See :ref:`this page<diagram_geometry_selection_page>` for more informations about the geometrical discretization of diagram.

|

.. _autodoc_singlediagramparameter_bin_size:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.bin_size
    :noindex:

|

.. _autodoc_singlediagramparameter_mean_size:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.mean_size
    :noindex:

|

.. _autodoc_singlediagramparameter_L_reassignation_selection:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.L_reassignation_selection
    :noindex:

|

.. _autodoc_singlediagramparameter_real_space_discretization_bin_number:
.. autoattribute:: Frog.class_DiagramParameter.SingleDiagramParameter.real_space_discretization_bin_number
    :noindex: