Commit 93453947 authored by Alan O'Cais's avatar Alan O'Cais

Merge branch 'W90_non_orthogonal_cube' into 'master'

Module for plotting volumetric data in GAUSSIAN CUBE format with non-orthogonal cells

See merge request e-cam/E-CAM-Library!129
parents 0820dab2 fccd459c
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W90_cube_format_non-orthogonal
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.. sidebar:: Software Technical Information
Name
Cube format files for non-orthogonal cells
Language
Fortran90
Licence
`GPL <https://opensource.org/licenses/gpl-license>`_
Documentation Tool
`Ford <http://fortranwiki.org/fortran/show/FORD>`_ online link to different Wannier90 source files `<http://www.wannier.org/ford/>`_
Application Documentation
Wannier90 `User guide pdf <https://github.com/wannier-developers/wannier90/raw/v3.0.0/doc/compiled_docs/user_guide.pdf>`_ and `Tutorial pdf <https://github.com/wannier-developers/wannier90/raw/v3.0.0/doc/compiled_docs/tutorial.pdf>`_ and `Solution booklet pdf <https://github.com/wannier-developers/wannier90/raw/v3.0.0/doc/compiled_docs/solution_booklet.pdf>`_
Relevant Training Material
Training material is accessible via tests and examples as well as a tutorial and its solutions.
Software Module Developed by
Valerio Vitale
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _Cube_format_files_for_cells_with_non-orthogonal_lattice_vectors:
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
For many applications that rely on the detail of the electronic structure of solids, it is crucial to inspect the symmetries, centres and shapes of the Wannier functions. To this end, one needs to use a visualisation program such as VESTA [1]_ or VMD [2]_. One of the most popular format to encode volumetric data is the GAUSSIAN CUBE format, which is supported by almost all molecular visualization programs. This module extends the cability of Wannier90 in generating output files in the CUBE format for periodic calculations with non-orthogonal unit cells.
.. [1] J. Appl. Crystallogr **44**, 1272-1276 (2011)
.. [2] J. Molec. Graphics **14**, 33-38 (1996)
Purpose of Module
_________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
.. Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
.. figure:: ./images/gaas_00003_cellsize3_vesta.png
:scale: 25 %
:align: left
This modules allows the User to output volumetric data, e.g. the Wannier functions on a real space grid, in the GAUSSIAN CUBE format even when the unit cell lattice vectors of the periodic calculation are non-orthogonal. The User can activate this feature by inserting the following two lines in the input file:
`wannier_plot = .true.`
`wannier_plot_format = cube`
In addition, one can also specify the cut-off radius for the Wannier functions, i.e. the radius of the sphere that must fit inside the parallelepiped in which the Wannier function is plotted, via the `wannier_plot_radius` keyword. The number of atoms to plot with the volumetric data can be implicitly defined by the `wannier_plot_scale` keyword.
This module is part of the Wannier90 code [3]_. The name of the subroutine that implements it is `internal_cube_format` and can be found in the `plot.F90` file within the `src` folder.
.. [3] Comput. Phys. Commun. **185**, 2309 (2014)
Background Information
______________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
Wannier90 source code is available from the official repository on Git-hub `<http://github.com/wannier-developers/wannier90>`_. Documentation of the source code is done via the FORD program, an online version of this documentation is available `online <http://www.wannier.org/ford/>`_. Instructions on how to install Wannier90 on a variety of architectures may be found in the `user guide <https://github.com/wannier-developers/wannier90/raw/v3.0.0/doc/compiled_docs/user_guide.pdf>`_.
Building and Testing
____________________
.. Keep the helper text below around in your module by just adding ".. " in front of it, which turns it into a comment
For building the module one "simply" has to compile the Wannier90 code as explained in the online documentation. This will produce the executable ``wannier90.x``, which contains the module. The source code can be found in the src folder within the plot.F90 module.
Source Code
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.. Notice the syntax of a URL reference below `Text <URL>`_ the backticks matter!
* `Link to a merge request containing my source code changes
<https://github.com/wannier-developers/wannier90/pull/162>`_
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