diff --git a/.travis.yml b/.travis.yml
index faf5b90..5af78e2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,15 +1,15 @@
-language: python
-
-python:
- - "3.6"
-
-install:
- - pip install --upgrade pip
- - python -m pip install -r requirements.txt .
-
-branches:
- only:
- - /.*/
-
-script:
+language: python
+
+python:
+ - "3.6"
+
+install:
+ - pip install --upgrade pip
+ - python -m pip install -r requirements.txt .
+
+branches:
+ only:
+ - /.*/
+
+script:
- cd tests/ && python -m unittest
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
index fe6b903..f6798de 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,662 +1,662 @@
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-
- Copyright (C) 2007 Free Software Foundation, Inc.
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- END OF TERMS AND CONDITIONS
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- How to Apply These Terms to Your New Programs
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- If you develop a new program, and you want it to be of the greatest
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- To do so, attach the following notices to the program. It is safest
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-
-
- Copyright (C)
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- by the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
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- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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-Also add information on how to contact you by electronic and paper mail.
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-For more information on this, and how to apply and follow the GNU AGPL, see
-.
-
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc.
+ Everyone is permitted to copy and distribute verbatim copies
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+
+ Preamble
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+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published
+ by the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+.
+
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index 8b13789..d3f5a12 100644
--- a/docs/.nojekyll
+++ b/docs/.nojekyll
@@ -1 +1 @@
-
+
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index cd4c723..314af94 100644
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diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 15264bd..f72b76f 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -37,6 +37,7 @@
diff --git a/docs/_sources/contents.rst.txt b/docs/_sources/contents.rst.txt
index ac9d703..c934733 100644
--- a/docs/_sources/contents.rst.txt
+++ b/docs/_sources/contents.rst.txt
@@ -1,22 +1,22 @@
-.. ThermoPlotter documentation master file, created by
- sphinx-quickstart on Fri Dec 4 12:31:48 2020.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-ThermoPlotter
-=============
-
-.. toctree::
- :maxdepth: 3
-
- Gallery
- Tutorials
- Introduction
- Python Package
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+.. ThermoPlotter documentation master file, created by
+ sphinx-quickstart on Fri Dec 4 12:31:48 2020.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+ThermoPlotter
+=============
+
+.. toctree::
+ :maxdepth: 3
+
+ Gallery
+ Tutorials
+ Introduction
+ Python Package
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/_sources/gallery.rst.txt b/docs/_sources/gallery.rst.txt
index 2c43bb9..9756bc5 100644
--- a/docs/_sources/gallery.rst.txt
+++ b/docs/_sources/gallery.rst.txt
@@ -1,109 +1,146 @@
--------
-Gallery
--------
-
-.. hint::
- Click on the images to see the script which generated them.
-
-At its simplest, ``ThermoPlotter`` is a way to quickly plot useful data
-from either a python script or the command line.
-
-.. image:: figures/ztmap.png
- :alt: A heatmap of ZT against carrier concentration and temperature
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/ztmap/plot-zt.py
-
-Click on the plot to see the script, or one could use
-
-.. code-block:: bash
-
- tp-ztmap boltztrap.hdf5 -k kappa-m.hdf5 -c #800080 -d x
-
-A related plot we hope people find useful is the kappa-target plot,
-which calculates the lattice thermal conductivity required to reach a
-ZT, in this case 2.
-
-.. image:: figures/kappa-target.png
- :alt: A heatmap of target lattice thermal conductivity against carrier concentration and temperature
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/kappa-target/plot-kappa-target.py
-
-.. code-block:: bash
-
- tp-kappa-target boltztrap.hdf5 -c #008080 -d x
-
-Slightly more complex plots also with command line scripts are the
-phonon dispersions:
-
-.. image:: figures/multiphon.png
- :alt: A plot converging phonon dispersions against supercell size
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/multiphon/plot-multiphon.py
-
-.. code-block:: bash
-
- tp-converge-phonons -l 111 222 333 444 555 -t Supercell\ Size
-
-.. image:: figures/phonons.png
- :alt: A phonon dispersion and DoS
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/phonons/plot-phonons.py
-
-.. code-block:: bash
-
- tp-phonons band.yaml -c #ff8000 -d projected_dos.dat --doscolour #ffff00 #00ffff
-
-This is where some of the more useful functions of ``ThermoPlotter``
-come in, e.g. the rescaling of the x axis in the former plot, and the
-simplicity of compund plots in the latter.
-
-There are other `command-line scripts`_, but the main functionality is
-intended as a python package, which enables much more customisable
-plotting, to enable nicely formatted multi-axes plots
-
-.. _command-line scripts: https://github.com/SMTG-UCL/ThermoPlotter/tree/master/scripts
-
-.. image:: figures/cumkappa.png
- :alt: Cumulative kappa against frequency and mean free path, broken down by direction
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/cumkappa/plot-cumkappa.py
-
-and ones where multiple plots are on the same axes, to highlight
-particular interactions.
-
-.. image:: figures/waterfall.png
- :alt: A plot of mean free path and lattice thermal conductivity against frequency overlaid on a DoS
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/waterfall/plot-waterfall.py
-
-As well as projecting third-order phonon properties onto each other as
-above, so below we see there are also a number of functions for
-projecting these properties onto phonon dispersions. The former is an
-oft plotted widening of the bands due to scattering,\ :sup:`1` and the
-latter shows the same data, but in a more quantitative way.
-
-.. image:: figures/wideband.png
- :alt: A phonon dispersion where widened bands show phonon scattering
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/wideband/plot-wideband.py
-
-.. code-block:: bash
-
- tp-wideband band.yaml kappa-m.hdf5 -c #000000 #ff0000 -s dark_background
-
-.. image:: figures/prophon.png
- :alt: A phonon dispersion where dark colours show phonn scattering
- :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/projected-phonons/plot-projected-phonons.py
-
-Through the python interface it is also possible to use individual parts
-of the code in ones own packages, for example the custom colourmaps,
-outside the scope of the package at large.
-
-Reference
----------
-
-.. code-block:: bibtex
-
- @article{Maradudin1962,
- title={Scattering of neutrons by an anharmonic crystal},
- author={Maradudin, AA and Fein, AE},
- journal={Physical Review},
- volume={128},
- number={6},
- pages={2589},
- year={1962},
- publisher={APS}
- }
+-------
+Gallery
+-------
+
+This is a gallery of some things you can do in ThermoPlotter with brief
+explanations. More details on each of the plots, including the scripts
+and specific commands used are available in the `examples`_, and we
+also have `tutorials`_!
+
+.. _examples: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/
+.. _tutorials: https://smtg-ucl.github.io/ThermoPlotter/tutorials.html
+
+.. hint::
+ Click on the images to see the script which generated them.
+
+At its simplest, ``ThermoPlotter`` is a way to quickly plot useful data
+from either a python script or the command line, such as the classic
+``ztmap`` heatmap (the power factor ``pfmap`` is also available):
+
+.. image:: figures/ztmap.png
+ :alt: A heatmap of ZT against carrier concentration and temperature
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/heatmaps/plot-zt.py
+
+Click on the plot to see the script, or one could use
+
+.. code-block:: bash
+
+ tp plot ztmap boltztrap.hdf5 -k kappa-m.hdf5 -c '#800080' -d x
+
+A related plot we hope people find useful for screening materials to
+run three+ phonon calculations on is the ``kappa-target`` plot, which
+calculates the lattice thermal conductivity required to reach a given
+ZT, in this case 2.
+
+.. image:: figures/kappa-target.png
+ :alt: A heatmap of target lattice thermal conductivity against carrier concentration and temperature
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/heatmaps/plot-kappa-target.py
+
+.. code-block:: bash
+
+ tp plot kappa-target boltztrap.hdf5 -c '#008080' -d x
+
+Or on the analytical end of the process, ``zdiff`` and ``pfdiff`` allow
+comparison among different datasets.
+
+.. image:: figures/ztdiff.png
+ :alt: A heatmap of differentce in ZT against carrier concentration and temperature
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/heatmaps/plot-ztdiff.py
+
+.. code-block:: bash
+
+ tp plot ztdiff /boltztrap.hdf5 /boltztrap.hdf5 -k /kappa-m.hdf5 /kappa-m.hdf5 -l
+
+Slightly more complex plots also with command line scripts are the
+phonon dispersions, which can be overlayed and plotted with DoSs.
+
+.. image:: figures/multiphon.png
+ :alt: A plot converging phonon dispersions against supercell size
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/phonons/plot-multiphon.py
+
+.. code-block:: bash
+
+ tp plot phonons -l -t 'Supercell\ Size'
+
+.. image:: figures/phonons.png
+ :alt: A phonon dispersion and DoS
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/phonons/plot-phonons.py
+
+.. code-block:: bash
+
+ tp plot phonons band.yaml -c '#ff8000' -d projected_dos.dat --doscolour '#ffff00' '#00ffff'
+
+This is where some of the more useful functions of ``ThermoPlotter``
+come in, e.g. the rescaling of the x axis in the former plot, and the
+simplicity of compound axes in the latter.
+
+There are command-line script, but the main functionality is
+intended as a python package, which enables much more customisable
+plotting, to enable nicely formatted multi-axes plots...
+
+.. image:: figures/cumkappa.png
+ :alt: Cumulative kappa against frequency and mean free path, broken down by direction
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/cumkappa/plot-cumkappa.py
+
+\...and multi-plot axes, to highlight particular interactions.
+
+.. image:: figures/waterfall.png
+ :alt: A plot of mean free path and lattice thermal conductivity against frequency overlaid on a DoS
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/waterfall/plot-waterfall.py
+
+As well as projecting third-order phonon properties onto each other as
+above, so below we see there are also a number of functions for
+projecting these properties onto phonon dispersions. The former is an
+oft plotted widening of the bands due to scattering,\ :sup:`1` and the
+latter shows the same data, but in a more quantitative way.
+
+.. image:: figures/wideband.png
+ :alt: A phonon dispersion where widened bands show phonon scattering
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/projected-phonons/plot-wideband.py
+
+.. code-block:: bash
+
+ tp plot wideband band.yaml kappa-m.hdf5 -c '#000000' '#ff0000' -s dark_background
+
+.. image:: figures/prophon.png
+ :alt: A phonon dispersion where dark colours show phonn scattering
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/projected-phonons/plot-projected-phonons.py
+
+Besides plotting, ThermoPlotter offers a number of ways to streamline
+trnasport property workflows, from generating more efficent input files
+(``tp gen``) to data consolidation (``tp.utilities.merge``) and
+retrieval (``tp.utilities.resolve`` and ``tp get``), many of which are
+outlined in the `tutorials`_. Most of these don't lend themselves to a
+gallery, except the ability to add gaussian smearing to a DoS plot
+during plotting, removing the need to rerun e.g. Phonopy or maintain
+multiple data files.
+
+.. image:: figures/dos.png
+ :alt: A DoS plot without and with gaussian smearing (sigma=0.2)
+ :target: https://github.com/SMTG-UCL/ThermoPlotter/blob/master/examples/dos/plot-dos.py
+
+The right-hand plot can be plotted with:
+
+.. code-block:: bash
+
+ tp plot dos projected_dos.dat --atoms "Ba Sn O O_2 2" --sigma 0.2 --location 1 -c magenta -c cyan -c red -c orange
+
+There are also a number of cosmetic options in the python interface,
+which may be of interest outside the main scope of ThermoPlotter, e.g.
+the custom colourmaps, legend formatting tools and axes labels.
+
+Reference
+---------
+
+.. code-block:: bibtex
+
+ @article{Maradudin1962,
+ title={Scattering of neutrons by an anharmonic crystal},
+ author={Maradudin, AA and Fein, AE},
+ journal={Physical Review},
+ volume={128},
+ number={6},
+ pages={2589},
+ year={1962},
+ publisher={APS}
+ }
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
index a6210d3..0517a6b 100644
--- a/docs/_sources/index.rst.txt
+++ b/docs/_sources/index.rst.txt
@@ -1 +1 @@
-.. include:: ../../README.rst
+.. include:: ../../README.rst
diff --git a/docs/_sources/introduction.rst.txt b/docs/_sources/introduction.rst.txt
index a6210d3..0517a6b 100644
--- a/docs/_sources/introduction.rst.txt
+++ b/docs/_sources/introduction.rst.txt
@@ -1 +1 @@
-.. include:: ../../README.rst
+.. include:: ../../README.rst
diff --git a/docs/_sources/modules.rst.txt b/docs/_sources/modules.rst.txt
index e45e504..a4a0061 100644
--- a/docs/_sources/modules.rst.txt
+++ b/docs/_sources/modules.rst.txt
@@ -1,7 +1,7 @@
-tp
-==
-
-.. toctree::
- :maxdepth: 4
-
- tp
+tp
+==
+
+.. toctree::
+ :maxdepth: 4
+
+ tp
diff --git a/docs/_sources/tp.axes.rst.txt b/docs/_sources/tp.axes.rst.txt
index 8f41fea..48f1d3b 100644
--- a/docs/_sources/tp.axes.rst.txt
+++ b/docs/_sources/tp.axes.rst.txt
@@ -1,37 +1,37 @@
-tp.axes package
-===============
-
-Submodules
-----------
-
-tp.axes.small module
---------------------
-
-.. automodule:: tp.axes.small
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.axes.large module
---------------------
-
-.. automodule:: tp.axes.large
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.axes.legend module
----------------------
-
-.. automodule:: tp.axes.legend
- :members:
- :undoc-members:
- :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: tp.axes
- :members:
- :undoc-members:
- :show-inheritance:
+tp.axes package
+===============
+
+Submodules
+----------
+
+tp.axes.small module
+--------------------
+
+.. automodule:: tp.axes.small
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.axes.large module
+--------------------
+
+.. automodule:: tp.axes.large
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.axes.legend module
+---------------------
+
+.. automodule:: tp.axes.legend
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tp.axes
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_sources/tp.cli.rst.txt b/docs/_sources/tp.cli.rst.txt
index 7f0a438..886347f 100644
--- a/docs/_sources/tp.cli.rst.txt
+++ b/docs/_sources/tp.cli.rst.txt
@@ -1,29 +1,29 @@
-tp.cli package
-==============
-
-Submodules
-----------
-
-tp.cli.cli module
------------------
-
-.. automodule:: tp.cli.cli
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.cli.options module
----------------------
-
-.. automodule:: tp.cli.options
- :members:
- :undoc-members:
- :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: tp.cli
- :members:
- :undoc-members:
- :show-inheritance:
+tp.cli package
+==============
+
+Submodules
+----------
+
+tp.cli.cli module
+-----------------
+
+.. automodule:: tp.cli.cli
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.cli.options module
+---------------------
+
+.. automodule:: tp.cli.options
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tp.cli
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_sources/tp.data.rst.txt b/docs/_sources/tp.data.rst.txt
index 6436dde..a5f2b5c 100644
--- a/docs/_sources/tp.data.rst.txt
+++ b/docs/_sources/tp.data.rst.txt
@@ -1,45 +1,45 @@
-tp.data package
-===============
-
-Submodules
-----------
-
-tp.data.load module
--------------------
-
-.. automodule:: tp.data.load
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.data.utilities module
-------------------------
-
-.. automodule:: tp.data.utilities
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.data.run module
-------------------
-
-.. automodule:: tp.data.run
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.data.save module
--------------------
-
-.. automodule:: tp.data.save
- :members:
- :undoc-members:
- :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: tp.data
- :members:
- :undoc-members:
- :show-inheritance:
+tp.data package
+===============
+
+Submodules
+----------
+
+tp.data.load module
+-------------------
+
+.. automodule:: tp.data.load
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.data.utilities module
+------------------------
+
+.. automodule:: tp.data.utilities
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.data.run module
+------------------
+
+.. automodule:: tp.data.run
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.data.save module
+-------------------
+
+.. automodule:: tp.data.save
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tp.data
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_sources/tp.plot.rst.txt b/docs/_sources/tp.plot.rst.txt
index cf4e0b9..06aa56e 100644
--- a/docs/_sources/tp.plot.rst.txt
+++ b/docs/_sources/tp.plot.rst.txt
@@ -1,61 +1,61 @@
-tp.plot package
-===============
-
-Submodules
-----------
-
-tp.plot.colour module
----------------------
-
-.. automodule:: tp.plot.colour
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.plot.frequency module
-------------------------
-
-.. automodule:: tp.plot.frequency
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.plot.heatmap module
-----------------------
-
-.. automodule:: tp.plot.heatmap
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.plot.mfp module
-------------------
-
-.. automodule:: tp.plot.mfp
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.plot.phonons module
-----------------------
-
-.. automodule:: tp.plot.phonons
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.plot.utilities module
-------------------------
-
-.. automodule:: tp.plot.utilities
- :members:
- :undoc-members:
- :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: tp.plot
- :members:
- :undoc-members:
- :show-inheritance:
+tp.plot package
+===============
+
+Submodules
+----------
+
+tp.plot.colour module
+---------------------
+
+.. automodule:: tp.plot.colour
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.plot.frequency module
+------------------------
+
+.. automodule:: tp.plot.frequency
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.plot.heatmap module
+----------------------
+
+.. automodule:: tp.plot.heatmap
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.plot.mfp module
+------------------
+
+.. automodule:: tp.plot.mfp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.plot.phonons module
+----------------------
+
+.. automodule:: tp.plot.phonons
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.plot.utilities module
+------------------------
+
+.. automodule:: tp.plot.utilities
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tp.plot
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_sources/tp.rst.txt b/docs/_sources/tp.rst.txt
index 7d7024c..b4b2166 100644
--- a/docs/_sources/tp.rst.txt
+++ b/docs/_sources/tp.rst.txt
@@ -1,41 +1,41 @@
-tp package
-==========
-
-Subpackages
------------
-
-.. toctree::
- :maxdepth: 4
-
- tp.axes
- tp.data
- tp.plot
- tp.cli
- tp.setup
-
-Submodules
-----------
-
-tp.calculate module
--------------------
-
-.. automodule:: tp.calculate
- :members:
- :undoc-members:
- :show-inheritance:
-
-tp.settings module
-------------------
-
-.. automodule:: tp.settings
- :members:
- :undoc-members:
- :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: tp
- :members:
- :undoc-members:
- :show-inheritance:
+tp package
+==========
+
+Subpackages
+-----------
+
+.. toctree::
+ :maxdepth: 4
+
+ tp.axes
+ tp.data
+ tp.plot
+ tp.cli
+ tp.setup
+
+Submodules
+----------
+
+tp.calculate module
+-------------------
+
+.. automodule:: tp.calculate
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+tp.settings module
+------------------
+
+.. automodule:: tp.settings
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tp
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_sources/tp.setup.rst.txt b/docs/_sources/tp.setup.rst.txt
index 985ba5f..7924a53 100644
--- a/docs/_sources/tp.setup.rst.txt
+++ b/docs/_sources/tp.setup.rst.txt
@@ -1,21 +1,21 @@
-tp.setup package
-================
-
-Submodules
-----------
-
-tp.setup.vasp module
---------------------
-
-.. automodule:: tp.setup.vasp
- :members:
- :undoc-members:
- :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: tp.setup
- :members:
- :undoc-members:
- :show-inheritance:
+tp.setup package
+================
+
+Submodules
+----------
+
+tp.setup.vasp module
+--------------------
+
+.. automodule:: tp.setup.vasp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tp.setup
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_sources/tutorials.rst.txt b/docs/_sources/tutorials.rst.txt
index dacb328..e8bd2c3 100644
--- a/docs/_sources/tutorials.rst.txt
+++ b/docs/_sources/tutorials.rst.txt
@@ -6,10 +6,16 @@ Tutorials
At some point these could be replaced by a Jupyter binder
.. toctree::
- :glob:
:hidden:
- tutorial-??
+ Tutorial-00: CLI Fundamentals
+ Tutorial-01: Python Foundations
+ Tutorial-02: Individual Customisation
+ Tutorial-03: Compound Axes
+ Tutorial-04: Layered Plots
+ Tutorial-05: Helper Functions
+ Tutorial-06: Package Customaisation
+ Tutorial-0X: VASP Assists
Here we have compiled a series of tutorials hoping to introduce the
structure of tp (particularly tutorials 01-04), as well as more
diff --git a/docs/contents.html b/docs/contents.html
index 9dba462..675f50e 100644
--- a/docs/contents.html
+++ b/docs/contents.html
@@ -38,6 +38,7 @@
This is a gallery of some things you can do in ThermoPlotter with brief
+explanations. More details on each of the plots, including the scripts
+and specific commands used are available in the examples, and we
+also have tutorials!
Hint
Click on the images to see the script which generated them.
At its simplest, ThermoPlotter is a way to quickly plot useful data
-from either a python script or the command line.
-
+from either a python script or the command line, such as the classic
+ztmap heatmap (the power factor pfmap is also available):
+
Click on the plot to see the script, or one could use
-
tp-ztmap boltztrap.hdf5 -k kappa-m<xxx>.hdf5 -c #800080 -d x
+
tp plot ztmap boltztrap.hdf5 -k kappa-m<xxx>.hdf5 -c '#800080' -d x
-
A related plot we hope people find useful is the kappa-target plot,
-which calculates the lattice thermal conductivity required to reach a
+
A related plot we hope people find useful for screening materials to
+run three+ phonon calculations on is the kappa-target plot, which
+calculates the lattice thermal conductivity required to reach a given
ZT, in this case 2.
-
-
tp-kappa-target boltztrap.hdf5 -c #008080 -d x
+
+
tp plot kappa-target boltztrap.hdf5 -c '#008080' -d x
+
+
+
Or on the analytical end of the process, zdiff and pfdiff allow
+comparison among different datasets.
This is where some of the more useful functions of ThermoPlotter
come in, e.g. the rescaling of the x axis in the former plot, and the
-simplicity of compund plots in the latter.
-
There are other command-line scripts, but the main functionality is
+simplicity of compound axes in the latter.
+
There are command-line script, but the main functionality is
intended as a python package, which enables much more customisable
-plotting, to enable nicely formatted multi-axes plots
+plotting, to enable nicely formatted multi-axes plots…
-
and ones where multiple plots are on the same axes, to highlight
-particular interactions.
+
...and multi-plot axes, to highlight particular interactions.
As well as projecting third-order phonon properties onto each other as
above, so below we see there are also a number of functions for
projecting these properties onto phonon dispersions. The former is an
oft plotted widening of the bands due to scattering,1 and the
latter shows the same data, but in a more quantitative way.
Through the python interface it is also possible to use individual parts
-of the code in ones own packages, for example the custom colourmaps,
-outside the scope of the package at large.
+
Besides plotting, ThermoPlotter offers a number of ways to streamline
+trnasport property workflows, from generating more efficent input files
+(tpgen) to data consolidation (tp.utilities.merge) and
+retrieval (tp.utilities.resolve and tpget), many of which are
+outlined in the tutorials. Most of these don’t lend themselves to a
+gallery, except the ability to add gaussian smearing to a DoS plot
+during plotting, removing the need to rerun e.g. Phonopy or maintain
+multiple data files.
+
+
The right-hand plot can be plotted with:
+
tp plot dos projected_dos.dat --atoms "Ba Sn O O_2 2" --sigma 0.2 --location 1 -c magenta -c cyan -c red -c orange
+
+
+
There are also a number of cosmetic options in the python interface,
+which may be of interest outside the main scope of ThermoPlotter, e.g.
+the custom colourmaps, legend formatting tools and axes labels.
Contributingexamples, further documentation and tests are greatly
appreciated. Documentation uses the sphinx package, and can be built from
-the docs directory with sphinx-build-bhtmlsrc/..
+the docs directory with sphinx-build-bhtmlsrc/..
ThermoPlotter is a toolkit for quickly, easily and prettily plotting the
-outputs of specialised analytical codes. It is focused on computational
-materials science and particularly thermoelectrics materials. It
-essentially wraps around matplotlib functions, and is intended to be
-used as a python package, to build easily customisable plotting scripts.
-There are also several basic command-line scripts.
The -e or editable option is encouraged so you can add your own
-defaults in tp.settings and elsewhere. For the same reason, when
-upgrading you may want to preserve your changes:
ThermoPlotter is designed to have four main stages:
-
-
Axes:
-Pick an axis layout from tp.axes.
-
-
Load:
Use the functions is tp.data.load to load the relevant data.
-
-
-
-
-
Add:
Use functions in modules in tp.plot to add graphs to the axes.
-
-
-
-
-
Save:
Use plt.savefig or equivalent to produce the figure.
-
-
-
-
-
As ThermoPlotter is simply a scripting code, each option can be
-substituted with bespoke code (i.e. using matplotlib.pyplot.subplots
-or matplotlib.axes.Axes.scatter); but these can still be
-supplemented with helper functions, such as default labels in
-tp.settings or colourmap generators in tp.plot.colour.
tp.plot.phonons contains plots along a high-symmetry path,
-including phonon dispersions and plots which project other quantities
-onto these paths in various ways.
-
tp.plot.frequency plots frequency on the x-axis, including density
-of states (DoS), cumulative kappa and “waterfall” plots.
-Each function has a main argument, which can be useful when
-plotting multiple quantities on the same set of axes; and an
-invert argument, which swaps the x and y axes to let you plot
-DoS-style next to a tp.plot.phonons plot.
-
tp.plot.mfp contains a cumulative kappa against mean free path
-plot.
-
tp.plot.heatmap contains a heatmap plotter, and wrappers which
-format appropriately for ZT against temperature and doping
-concentration; and one which plots the lattice thermal conductivity
-required to reach a target ZT, again against temperature and doping.
-
-
A set of example scripts is provided in the tp/examples folder, and
-there is documentation.
We welcome any contributions, whether they be a feature request or a new
-piece of code (or anything else). Adding options is inteded to be
-straightforward, as each step is mostly independent of the others, so
-only one new function should be required. We would of course be happy to
-discuss, if desired.
-
Bugs and feature requests can be submitted to the issue tracker,
-while contributions can be made using the fork and pull approach.
-Contributions should have comprehensive docstrings, and where
-appropriate examples, documentation and tests are greatly
-appreciated.
ThermoPlotter is a toolkit for quickly, easily and prettily plotting the
+outputs of specialised analytical codes. It is focused on computational
+materials science and particularly thermoelectrics materials. It
+essentially wraps around matplotlib functions, and is intended to be
+used as a python package, to build easily customisable plotting scripts.
+There are also several basic command-line scripts.
The -e or editable option is encouraged so you can add your own
+defaults in tp.settings and elsewhere. For the same reason, when
+upgrading you may want to preserve your changes:
ThermoPlotter is designed to have four main stages:
+
+
Axes:
+Pick an axis layout from tp.axes.
+
+
Load:
Use the functions is tp.data.load to load the relevant data.
+
+
+
+
+
Add:
Use functions in modules in tp.plot to add graphs to the axes.
+
+
+
+
+
Save:
Use plt.savefig or equivalent to produce the figure.
+
+
+
+
+
As ThermoPlotter is simply a scripting code, each option can be
+substituted with bespoke code (i.e. using matplotlib.pyplot.subplots
+or matplotlib.axes.Axes.scatter); but these can still be
+supplemented with helper functions, such as default labels in
+tp.settings or colourmap generators in tp.plot.colour.
tp.plot.phonons contains plots along a high-symmetry path,
+including phonon dispersions and plots which project other quantities
+onto these paths in various ways.
+
tp.plot.frequency plots frequency on the x-axis, including density
+of states (DoS), cumulative kappa and “waterfall” plots.
+Each function has a main argument, which can be useful when
+plotting multiple quantities on the same set of axes; and an
+invert argument, which swaps the x and y axes to let you plot
+DoS-style next to a tp.plot.phonons plot.
+
tp.plot.mfp contains a cumulative kappa against mean free path
+plot.
+
tp.plot.heatmap contains a heatmap plotter, and wrappers which
+format appropriately for ZT against temperature and doping
+concentration; and one which plots the lattice thermal conductivity
+required to reach a target ZT, again against temperature and doping.
+
+
A set of example scripts is provided in the tp/examples folder, and
+there is documentation.
We welcome any contributions, whether they be a feature request or a new
+piece of code (or anything else). Adding options is inteded to be
+straightforward, as each step is mostly independent of the others, so
+only one new function should be required. We would of course be happy to
+discuss, if desired.
+
Bugs and feature requests can be submitted to the issue tracker,
+while contributions can be made using the fork and pull approach.
+Contributions should have comprehensive docstrings, and where
+appropriate examples, documentation and tests are greatly
+appreciated.
diff --git a/docs/searchindex.js b/docs/searchindex.js
index b53cf61..6435f35 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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[1,8],script:[1,2,8,12,14,15,18],scs:14,sdata:8,sean:2,search:0,second:[8,13,17],section:8,see:[1,2,7],seebeck:[4,7,8,15],seem:17,select:[6,7,8,13,18],self:[4,8],semi:8,separ:[7,13,16],sequenc:5,seri:18,set:[0,2,3,5,7,8,9,11,13,14,15,16,17],set_loc:[8,14,15],set_xlabel:[14,15],set_ylabel:[14,15],set_ylim:13,setup:[3,4,17],sever:[11,12,13,15],shade:8,shape:[5,7,8,11,15],share:[7,13,18],sheet:[2,4,5,12,16],short_label:[4,15,16],shorten:14,shorthand:12,should:[2,7,8,9,11,14,15,16,17],show:[1,13,17],shown:13,shrink:4,shrunk:4,side:5,sidewai:8,sigma:[1,4,8],significantli:5,similar:[7,10],simplest:[1,10],simpli:[10,11],simplic:1,simplifi:2,singh:7,singl:[2,5,7,8,13],singular:6,six:16,size:[1,4,5,11,14,16],skelton:8,slash:10,slightli:[1,4],slower:5,small:[3,4,11,13,14,15,16],smallest:4,smear:1,smooth:8,smtg:2,snyder:7,soc:7,solid:8,solv:14,some:[1,5,11,14,15,17,18],someth:[8,10,14],sometim:8,somewhat:5,sort:[4,8],sourc:[2,4,5,6,7,8,9,11,15],space:[5,12,13,14],specialis:18,specialist:2,specif:[1,2,7,8],specifi:[7,8,13,15,16,17],sphinx:2,spin:7,split:[2,14],spooner:2,squar:[5,10],src:2,stage:[2,11],stand:[12,14],standard:[4,7,12,13,16],standardis:7,start:[5,8,10,14],state:[2,7,8],stdout:7,step:[2,7,11,12],still:[2,8],stitch:9,stop:[12,14],str:[4,5,7,8,9],straightforward:2,streamlin:[1,6,13],string:[7,8,12,13],strong:14,structur:[2,7,8,10,18],stuff:[4,12],style:[2,4,5,12,14,15,16,18],stylelib:12,stype:7,sub:14,subdictionari:[7,15],subfig:11,submit:2,submodul:[0,3],subpackag:[0,3],subplot:2,subsequ:5,subset:8,substitut:[2,10],suffix:[5,15],suggest:[9,17],suit:[2,5],suitabl:17,sum:7,sumo:7,sup:[],supercel:[1,14],supplement:2,suppli:9,support:[2,14],sure:[8,15],swap:[2,7],symmetri:[2,8,9],symmop:8,symop:8,symprec:9,tab10:8,tag:10,take:[2,5,7,8,10,11,12,13,15],taken:[8,11],target:[1,2,4,7,8],tell:12,temperatur:[2,4,6,7,8,12,14,15],temperature_opt:6,templat:16,test:0,text:[5,7,10],than:[5,7,12,13,14,16],thank:2,thei:[2,7,8,11,13,14],them:[1,11,12,13,14],themselv:[1,10],therefor:14,thermal:[1,2,4,7,8],thermal_conduct:4,thermoelectr:2,thermoplott:[1,2,4,10,11,12,13,15,18],thi:[1,2,4,7,8,9,10,11,12,13,14,15,18],thing:[1,5,8,10,11,15],third:[1,17],those:[2,8,16],three:[1,5,7,10,11],three_h:5,three_h_colourbar:5,three_squar:5,three_square_colourbar:5,through:15,throughout:11,thrown:11,thz:4,tick:[4,7,8,14,16],tick_label:8,tick_posit:8,ticklabel:8,tidi:12,tile:8,tile_properti:8,time:[7,15,17],tinterp:7,titl:[1,13,15],tmax:7,tmin:[7,15],to_amset:4,to_boltztrap:4,to_phono3pi:4,to_tp:4,to_xxx:16,togeth:[9,13],toggl:[6,10],tol:8,toler:8,too:[8,11,16,17],tool:[1,2,4,7,8,9,17],toolkit:2,top:[5,12,13,16],total:[4,7,8,10],totalcolour:8,totallabel:8,tprc:[2,4,8,18],tracker:2,tradit:8,translat:4,transpar:12,transport:[2,6,7,15],transport_75x75x75:15,transverse_1:8,transverse_2:8,treat:8,trivial:11,trnasport:1,tstep:7,tupl:8,turn:[7,8,14],tutori:[0,1,2],twice:8,two:[2,5,8,9,11,12,15,17],two_h:[5,14],two_h_colourbar:5,two_v:[5,14],two_v_colourbar:5,type:[4,5,6,7,8,9,10,11,12,18],typic:10,ucl:2,unalik:13,under:[2,8],undercolour:8,underli:[11,16],uniform:8,unit:[2,4,7,11,15,16,18],unittest:2,unless:8,unoccupi:8,unweight:17,unweighted_kpoint:17,updat:[4,16],usag:0,use:[1,2,4,10,11,12,14,15,16,18],use_tprc:4,used:[1,2,4,5,8,10,11,13,14,15,18],useful:[1,2,5,8,13,15],user:[2,12,16,18],uses:[2,5,13,17],using:[2,4,7,8,11,13,15],usr:[11,12,13,14],usual:13,util:[1,3,4,14,15,17],valu:[4,7,8,10,15,17],vari:7,variabl:[4,7,8,15],variable_nam:15,variat:15,variou:[2,8],vasp:[3,4,7,8,18],vasprun:7,veloc:4,verbos:[6,8],verbose_opt:6,veri:17,version:[7,11,12,13,14],vertic:[5,14],via:[10,15],viridi:[8,14],viridis_r:8,visibl:[8,14],volum:1,wai:[1,2,8,10,11,12,13],want:[2,8,12,13,16,17],warda:2,waterfal:[2,6,8,14],weight:[7,9],weighted_kpoint:17,weighted_r:7,welcom:[2,16],well:[1,4,8,14,18],what:[9,12,15,17],when:[2,4,15,17,18],where:[1,2,5,8,11,12,14,15],wherea:8,whether:2,which:[1,2,5,7,8,9,10,11,12,13,14,15,16,17,18],whilst:5,white:8,who:2,whole:[7,8,11],wide:[2,12],wideband:[1,6,12],widen:1,width:[4,5,8],wiedemann:7,willi:2,wink:[],winter_r:[8,14],within:[8,11],without:[7,9,14,16,17],work:[5,7,8,14,15],worker:8,workflow:1,worri:16,worth:[7,14],would:[7,8,9,14,16,17],wrapper:[2,4,7,8],write:[7,8,9,16],written:[10,12],wrt:[4,7],x_tick:8,xdata:7,xinterp:8,xmarker:8,xmarkkwarg:8,xmax:8,xmin:8,xml:7,xquantiti:8,xscale:8,xxx:1,xxx_name:16,xy_limit_opt:6,y_tick:8,yaml:[1,2,4,7,8,11,12,13,14,18],yamldata:7,year:1,yet:14,yinterp:8,ymarker:8,ymax:8,ymin:8,you:[1,2,5,7,8,9,10,11,12,13,14,15,16,17,18],your:[2,5,11,12,13,16],your_hdf5_path:2,yourself:8,yourstyl:16,yquantiti:8,yscale:8,yyi:1,zdiff:1,zero:[7,8,9],zero_weight:9,zhu:2,zno:[11,12,13],zt_fromdict:4,ztdiff:[1,6],ztmap:[1,6]},titles:["ThermoPlotter","Gallery","Installation","tp","tp package","tp.axes package","tp.cli package","tp.data package","tp.plot package","tp.setup package","Tutorial-00: CLI Fundamentals","Tutorial-01: Python Foundations","Tutorial-02: Individual Customisation","Tutorial-03: Compound Axes","Tutorial-04: Layered Plots","Tutorial-05: Helper Functions","Tutorial-06: Package Customisation","Tutorial-0X: VASP Assists","Tutorials"],titleterms:{"function":[4,5,6,7,8,9,15],Axes:[11,12,13,14,15],assist:17,axes:5,calcul:4,cli:[6,10],colour:8,command:2,compound:13,conducit:17,content:[4,5,6,7,8,9],contribut:2,contributor:2,customis:[12,16],data:7,extend:16,format:14,foundat:11,frequenc:8,fundament:10,galleri:1,heatmap:8,help:11,helper:15,indic:0,individu:12,instal:2,label:15,larg:5,lattic:17,layer:14,legend:[5,13,15],licens:2,line:[2,11,12,13,14,15],load:[7,11,12,14],locat:15,mac:2,merg:17,mfp:8,modul:[4,5,6,7,8,9],more:11,option:6,packag:[4,5,6,7,8,9,16],phonon:8,plot:[8,11,12,13,14],point:17,python:[2,11],refer:1,requir:2,resolv:15,run:7,save:[7,11],set:4,setup:9,small:5,submodul:[4,5,6,7,8,9],subpackag:4,tabl:0,target:17,test:2,thermal:17,thermoplott:[0,16],tick:15,tprc:16,tutori:[10,11,12,13,14,15,16,17,18],usag:2,util:[7,8],variabl:12,vasp:[9,17],weight:17,yaml:16,zero:17}})
\ No newline at end of file
diff --git a/docs/src/Makefile b/docs/src/Makefile
index d4bb2cb..73a28c7 100644
--- a/docs/src/Makefile
+++ b/docs/src/Makefile
@@ -1,20 +1,20 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS ?=
-SPHINXBUILD ?= sphinx-build
-SOURCEDIR = .
-BUILDDIR = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
- @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
- @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/src/_build/doctrees/environment.pickle b/docs/src/_build/doctrees/environment.pickle
index 87c58b2..0f7becf 100644
Binary files a/docs/src/_build/doctrees/environment.pickle and b/docs/src/_build/doctrees/environment.pickle differ
diff --git a/docs/src/_build/doctrees/index.doctree b/docs/src/_build/doctrees/index.doctree
index 692394b..1476ea2 100644
Binary files a/docs/src/_build/doctrees/index.doctree and b/docs/src/_build/doctrees/index.doctree differ
diff --git a/docs/src/_build/doctrees/tutorials.doctree b/docs/src/_build/doctrees/tutorials.doctree
index 96bc81a..3594c00 100644
Binary files a/docs/src/_build/doctrees/tutorials.doctree and b/docs/src/_build/doctrees/tutorials.doctree differ
diff --git a/docs/src/_build/html/.buildinfo b/docs/src/_build/html/.buildinfo
index 05405d8..97296a3 100644
--- a/docs/src/_build/html/.buildinfo
+++ b/docs/src/_build/html/.buildinfo
@@ -1,4 +1,4 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fad783a679d791275e1ea075c3ba0d6e
-tags: 645f666f9bcd5a90fca523b33c5a78b7
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: fad783a679d791275e1ea075c3ba0d6e
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/src/_build/html/_modules/index.html b/docs/src/_build/html/_modules/index.html
index 6184b84..43f4d25 100644
--- a/docs/src/_build/html/_modules/index.html
+++ b/docs/src/_build/html/_modules/index.html
@@ -1,106 +1,106 @@
-
-
-
-
-
- Overview: module code — ThermoPlotter 2.0.0 documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-defconversions():
- """Get dictionary of custom unit conversions from tprc.yaml."""
-
- conversions={}
-
- ifconfisnotNoneand'conversions'inconfand \
- conf['conversions']isnotNone:
- conversions=conf['conversions']
-
- returnconversions
-
-
[docs]defamset_conversions():
- """Get dictionary of unit conversions for amset to tp."""
-
- conversions={}
-
- returnconversions
-
-
[docs]defboltztrap_conversions():
- """Get dictionary of unit conversions for boltztrap to tp."""
-
- conversions={}
-
- returnconversions
-
-
[docs]defphonopy_conversions():
- """Get dictionary of unit conversions for phonopy to tp."""
-
- conversions={}
-
- returnconversions
-
-
[docs]defphono3py_conversions():
- """Get dictionary of unit conversions for phono3py to tp."""
-
- conversions={'group_velocity':1e2,# THz AA to m s-1
- 'gv_by_gv':1e4,# THz2 AA2 to m2 s-2
- 'heat_capacity':1.60218e-19,# eV K-1 to J K-1
- 'lifetime':1e-12,# THz-1 to s
- 'mean_free_path':1e-10}# AA to m
-
- returnconversions
+
+defconversions():
+ """Get dictionary of custom unit conversions from tprc.yaml."""
+
+ conversions={}
+
+ ifconfisnotNoneand'conversions'inconfand \
+ conf['conversions']isnotNone:
+ conversions=conf['conversions']
+
+ returnconversions
+
+
[docs]defamset_conversions():
+ """Get dictionary of unit conversions for amset to tp."""
+
+ conversions={}
+
+ returnconversions
+
+
[docs]defboltztrap_conversions():
+ """Get dictionary of unit conversions for boltztrap to tp."""
+
+ conversions={}
+
+ returnconversions
+
+
[docs]defphonopy_conversions():
+ """Get dictionary of unit conversions for phonopy to tp."""
+
+ conversions={}
+
+ returnconversions
+
+
[docs]defphono3py_conversions():
+ """Get dictionary of unit conversions for phono3py to tp."""
+
+ conversions={'group_velocity':1e2,# THz AA to m s-1
+ 'gv_by_gv':1e4,# THz2 AA2 to m2 s-2
+ 'heat_capacity':1.60218e-19,# eV K-1 to J K-1
+ 'lifetime':1e-12,# THz-1 to s
+ 'mean_free_path':1e-10}# AA to m
+
+ returnconversions
-