.. highlight:: rst

Tutorials
=========

Slides and notebooks used in the course "Symmetry & Shape in Structural Chemistry"
given by P. Alemany at the Universidad de Santiago de Chile (USACH) from 5-9 June 2023.

The notebooks and the associated data files give an overview of the main uses of
the *cosymlib*. They can be run directly on *Google colab* without the need of installing
locally the *cosymlib* in the user's computer. If the *cosymlib* is installed in the user's computer,
the notebooks can be also run locally or, alternatively, the commands included in them may
be directly executed, without the need of the notebook. For a routine calculation of CSMs & CShMs
we recommend to download and install the *cosymlib* in your computer and run the scripts
directly, without the need of using notebooks.

Slides
------

:download:`Introduction <tutorials/S1_Intro_red.pdf>`

:download:`Molecular Shapes <tutorials/S2_Mol_shape_red.pdf>`

:download:`Molecular Symmetry <tutorials/S3_Mol_sym_red.pdf>`

:download:`Polyhedra in Chemistry <tutorials/S4_Polyh_red.pdf>`

:download:`Continuous Symmetry Measures <tutorials/S5_CSM_red.pdf>`

:download:`Group Theory <tutorials/S6_GT.pdf>`

:download:`Representation Theory <tutorials/S7_RepT.pdf>`

:download:`Irreducible Representations <tutorials/S8_IReps.pdf>`

Notebooks & data files
----------------------

You can execute directly the notebooks in Google Colab just by clicking at the links
below or you may download the notebooks to your computer and run them there. To do this
you will need to install the *cosymlib* in your computer and download also the data files
associated to each notebook. If you run the notebooks in your computer you don't need
to execute the first cells loading the *cosymlib* and loading the data files, just make
sure that the data files are in the same folder where you have the .ipynb files.

Point Group Determinaton:
-------------------------

.. figure:: https://colab.research.google.com/assets/colab-badge.svg
    :target: http://colab.research.google.com/github/GrupEstructuraElectronicaSimetria/cosymlib/blob/pere_tutorial/docs/tutorials/Pointgroup.ipynb

:download:`Download notebook <tutorials/Pointgroup.ipynb>`
:download:`Download datafile 1 <tutorials/h2o.xyz>`
:download:`Download datafile 2 <tutorials/square.xyz>`
:download:`Download datafile 3 <tutorials/h2o2_path.xyz>`


Continuous Symmetry Measures:
-----------------------------

.. figure:: https://colab.research.google.com/assets/colab-badge.svg
    :target: http://colab.research.google.com/github/GrupEstructuraElectronicaSimetria/cosymlib/blob/pere_tutorial/docs/tutorials/CSM.ipynb

:download:`Download notebook <tutorials/CSM.ipynb>`
:download:`Download datafile 1 <tutorials/h2o2_path.xyz>`
:download:`Download datafile 2 <tutorials/equilateral_triang.xyz>`
:download:`Download datafile 3 <tutorials/isosceles_triang.xyz>`


Shape Measures:
---------------

.. figure:: https://colab.research.google.com/assets/colab-badge.svg
    :target: http://colab.research.google.com/github/GrupEstructuraElectronicaSimetria/cosymlib/blob/pere_tutorial/docs/tutorials/Shape.ipynb

:download:`Download notebook <tutorials/CSM.ipynb>`
:download:`Download datafile 1 <tutorials/sqplanar.xyz>`
:download:`Download datafile 2 <tutorials/cent_sqplanar.xyz>`
:download:`Download datafile 3 <tutorials/crn6.xyz>`
:download:`Download datafile 4 <tutorials/S_coord_9.xyz>`
:download:`Download datafile 5 <tutorials/S_coord_8.xyz>`


Symmetry Measures for the Electronic Structure:
-----------------------------------------------

.. figure:: https://colab.research.google.com/assets/colab-badge.svg
    :target: http://colab.research.google.com/github/GrupEstructuraElectronicaSimetria/cosymlib/blob/pere_tutorial/docs/tutorials/eCSM.ipynb


Data files with additional molecular structures:
------------------------------------------------

:download:`adamantane <tutorials/adamantane.xyz>`
:download:`allene <tutorials/allene.xyz>`
:download:`ammonia <tutorials/ammonia.xyz>`
:download:`benzenetriol <tutorials/benzenetriol.xyz>`
:download:`c5_cp <tutorials/c5_cp.xyz>`
:download:`C60 <tutorials/c60.xyz>`
:download:`C70 <tutorials/c70.xyz>`
:download:`Co_complex <tutorials/co_c2_compl.xyz>`
:download:`18-crown-6 <tutorials/crown_18_6.xyz>`
:download:`cubane <tutorials/cubane.xyz>`
:download:`cyclobutane <tutorials/cyclobutane.xyz>`
:download:`cyclohex_chair <tutorials/cyclohex_chair.xyz>`
:download:`diborane <tutorials/diborane.xyz>`
:download:`difluoroethene <tutorials/difluoethene.xyz>`
:download:`dodecaborate <tutorials/dodecaborate.xyz>`
:download:`dodecahedrane <tutorials/dodecahedrane.xyz>`
:download:`ethane <tutorials/ethane.xyz>`
:download:`ethylene <tutorials/ethylene.xyz>`
:download:`ferrocene_ec <tutorials/ferrocene_ec.xyz>`
:download:`ferrocene_st <tutorials/ferrocene_st.xyz>`
:download:`Ge9 <tutorials/ge9.xyz>`
:download:`H2O <tutorials/h2o.xyz>`
:download:`H2O2 <tutorials/h2o2.xyz>`
:download:`methane <tutorials/methane.xyz>`
:download:`Os2Cl8 <tutorials/os2cl8.xyz>`
:download:`SF6 <tutorials/sf6.xyz>`
:download:`snub_dodecahedron <tutorials/snub_dode.xyz>`
:download:`trisen_co <tutorials/trisen_co.xyz>`
:download:`twistane <tutorials/twistane.xyz>`
:download:`vanadate <tutorials/vanadate.xyz>`
:download:`h2o2_path <tutorials/h2o2_path.xyz>`
:download:`CrN6 <tutorials/crn6.xyz>`
:download:`Eu_coord_9 <tutorials/S_coord_9.xyz>`