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Table of parameters in ROOT_Parameter
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RolfSander committed May 21, 2022
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Expand Up @@ -174,38 +174,38 @@ initialized in :file:`ROOT_Parameters.f90` (or :file:`.F90`).

.. _table-par:

.. table:: Table 5: Parameters Declared in ROOT_Parameter
.. table:: Table 5: Parameters Declared in ROOT_Parameters
:align: center

+----------------+---------------------------------------------+--------+
| Parameter | Represents | Value |
+================+=============================================+========+
| ``NSPEC`` | No. chemical species (``NVAR`` + ``NFIX``) | 7 |
+----------------+---------------------------------------------+--------+
| ``NVAR`` | No. variable species | 5 |
+----------------+---------------------------------------------+--------+
| ``NFIX`` | No. fixed species | 2 |
+----------------+---------------------------------------------+--------+
| ``NREACT`` | No. reactions | 10 |
+----------------+---------------------------------------------+--------+
| ``NONZERO`` | No. nonzero entries Jacobian | 18 |
+----------------+---------------------------------------------+--------+
| ``LU_NONZERO`` | As above, after LU factorization | 19 |
+----------------+---------------------------------------------+--------+
| ``NHESS`` | Length, sparse Hessian | 10 |
+----------------+---------------------------------------------+--------+
| ``NJVRP`` | Length, sparse Jacobian JVRP | 13 |
+----------------+---------------------------------------------+--------+
| ``NSTOICM`` | Length, stoichiometric matrix | 22 |
+----------------+---------------------------------------------+--------+
| ``ind_spc`` | Index of species *spc* in :code:`C` | |
+----------------+---------------------------------------------+--------+
| ``indf_spc`` | Index of fixed species *spc* in :code:`FIX` | |
+----------------+---------------------------------------------+--------+

Values listed the 3rd column of Table 5 are from the
:command:`small_strato` mechanism
(cf. :ref:`running-kpp-with-an-example-mechanism`).
+----------------+---------------------------------------------+---------+
| Parameter | Represents | Example |
+================+=============================================+=========+
| ``NSPEC`` | No. chemical species (``NVAR`` + ``NFIX``) | 7 |
+----------------+---------------------------------------------+---------+
| ``NVAR`` | No. variable species | 5 |
+----------------+---------------------------------------------+---------+
| ``NFIX`` | No. fixed species | 2 |
+----------------+---------------------------------------------+---------+
| ``NREACT`` | No. reactions | 10 |
+----------------+---------------------------------------------+---------+
| ``NONZERO`` | No. nonzero entries Jacobian | 18 |
+----------------+---------------------------------------------+---------+
| ``LU_NONZERO`` | As above, after LU factorization | 19 |
+----------------+---------------------------------------------+---------+
| ``NHESS`` | Length, sparse Hessian | 10 |
+----------------+---------------------------------------------+---------+
| ``NJVRP`` | Length, sparse Jacobian JVRP | 13 |
+----------------+---------------------------------------------+---------+
| ``NSTOICM`` | Length, stoichiometric matrix | 22 |
+----------------+---------------------------------------------+---------+
| ``ind_spc`` | Index of species *spc* in :code:`C` | |
+----------------+---------------------------------------------+---------+
| ``indf_spc`` | Index of fixed species *spc* in :code:`FIX` | |
+----------------+---------------------------------------------+---------+

Example values listed in the 3rd column are taken 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
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