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Added static DOI to README.md, updated text in ROOT_Model section
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README.md
- Now points to static DOI https://doi.org/10.5281/zenodo.6563908,
  which will always point to the latest KPP version

docs/source/using_kpp/05_output_from_kpp.rst
- Reworded paragraph about how ROOT_Model unifies all modules
  for easy inclusion into F90 programs

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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yantosca committed May 19, 2022
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5 changes: 4 additions & 1 deletion README.md
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[![Latest Release](https://img.shields.io/github/v/release/KineticPreProcessor/KPP?label=Latest%20Release)](https://kpp.readthedocs.io) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/KineticPreProcessor/KPP/blob/main/LICENSE.txt) [![C-I tests](https://img.shields.io/azure-devops/build/KineticPreProcessor/KPP/1/main?label=C-I%20Tests)](https://dev.azure.com/KineticPreProcessor/KPP/_build) [![ReadTheDocs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://kpp.readthedocs.io/en/latest)
[![Latest
Release](https://img.shields.io/github/v/release/KineticPreProcessor/KPP?label=Latest%20Release)](https://kpp.readthedocs.io) [![License: GPL
v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/KineticPreProcessor/KPP/blob/main/LICENSE.txt) [![C-I
tests](https://img.shields.io/azure-devops/build/KineticPreProcessor/KPP/1/main?label=C-I%20Tests)](https://dev.azure.com/KineticPreProcessor/KPP/_build) [![ReadTheDocs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://kpp.readthedocs.io/en/latest) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6563908.svg)](https://doi.org/10.5281/zenodo.6563908)

# The Kinetic PreProcessor: KPP
This is the repository for the The Kinetic PreProcessor (KPP) source code.
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13 changes: 8 additions & 5 deletions docs/source/using_kpp/05_output_from_kpp.rst
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Expand Up @@ -64,8 +64,9 @@ Using :command:`#DRIVER none` will skip generating this file.
ROOT_Model
----------

The file :file:`ROOT_Model.f90` (or :file:`.F90`) completely
defines the model by using all the associated modules.
The file :file:`ROOT_Model.f90` (or :file:`.F90`) unifies all model
definitions in a single module. This simplifies inclusion into
external Fortran programs.

.. _Initialize:

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The global parameters listed in :ref:`table-par` are defined and
initialized in :file:`ROOT_Parameters.f90` (or
:file:`.F90`). The values listed in the third column
of Table 4 are taken from the :command:`small_strato` example mechanism,
which is described in :ref:`running-kpp-with-an-example-mechanism`.
:file:`.F90`).

.. _table-par:

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| :code:`indf_spc` | Index of fixed species *spc* in :code:`FIX` | |
+--------------------+---------------------------------------------+--------+

NOTE: Values listed the 3rd column of Table 5 are from the
:command:`small_strato` mechanism
(cf. :ref:`running-kpp-with-an-example-mechanism`).

KPP orders the variable species such that the sparsity pattern of the
Jacobian is maintained after an LU decomposition. For our example there
are five variable species (:code:`NVAR = 5`) ordered as
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