more very minor updates of the docs

docs/source/using_kpp/04_input_for_kpp.rst

@@ -792,13 +792,13 @@ Inlined Code
 In order to offer maximum flexibility, KPP allows the user to include
 pieces of code in the kinetic description file. Inlined code begins on a
 new line with :command:`#INLINE` and the *inline_type*. Next, one or
-more lines of code follow, written in the target language (Fortran90,
-C, or Matlab) as specified by the *inline_type*. The inlined code ends
-with :command:`#ENDINLINE`. The code is inserted into the KPP output
-at a position which is also determined by *inline_type* as explained
-in :ref:`table-inl-type`. If two inline commands with the same inline
-type are declared, then the contents of the second is appended to the
-first one.
+more lines of code follow, written in the target language (Fortran90, C,
+or Matlab) as specified by the *inline_type*. The inlined code ends with
+:command:`#ENDINLINE`. The code is inserted into the KPP output at a
+position which is also determined by *inline_type* as shown in
+:ref:`table-inl-type`. If two inline commands with the same inline type
+are declared, then the contents of the second is appended to the first
+one.
 
 .. _list-of-inlined-types:
 
@@ -807,8 +807,7 @@ List of inlined types
 
 In this manual, we show the inline types for Fortran90. The inline
 types for the other languages are produced by replacing :code:`F90`
-by :code:`C`, or :code:`matlab`, respectively, as shown in
-:ref:`table-inl-type`:
+by :code:`C`, or :code:`matlab`, respectively.
 
 .. _table-inl-type:
 
@@ -863,11 +862,9 @@ Inlining code can be useful to introduce additional state variables
 (such as temperature, humidity, etc.) for use by KPP routines, such as
 for calculating rate coefficients.
 
-If a large number of state variables need to be held in inline code, or
+If a large number of state variables needs to be held in inline code, or
 require intermediate computation that may be repeated for many rate
-coefficients, a derived type object should be used for efficiency.
-
-An example of a derived-type object being included:
+coefficients, a derived type object should be used for efficiency, e.g.:
 
 .. code-block:: F90
 
@@ -877,21 +874,20 @@ An example of a derived-type object being included:
      END TYPE ObjGlobal_t
      TYPE(ObjGlobal_t), TARGET, PUBLIC :: ObjGlobal
      !$OMP THREADPRIVATE( ObjGlobal )
+   #ENDINLINE
 
 This global variable :code:`ObjGlobal` can then be used globally in KPP.
 
-Another way to avoid cluttering up the KPP input file is to add global
-variables into a header file that can be :code:`#include`-d:
+Another way to avoid cluttering up the KPP input file is to
+:code:`#include` a header file with global variables:
 
 .. code-block:: F90
 
    #INLINE F90_GLOBAL
-   ! Inline common variables into KPP_ROOT_Global.F90
-   #include "commonIncludeVars.H"
+   ! Inline common variables into KPP_ROOT_Global.f90
+   #include "commonIncludeVars.f90"
    #ENDINLINE
 
-where extra code is included in a separate file, :code:`commonIncludeVars.H`.
-
 In future versions of KPP, the global state will be reorganized into
 derived type objects as well.
 
@@ -901,7 +897,7 @@ F90_INIT
 --------
 
 This inline type can be used to define initial values before the start of the
-integartion, e.g.:
+integration, e.g.:
 
 .. code-block:: F90
 
@@ -975,15 +971,15 @@ This inline type can be used to define utility subroutines.
 Auxiliary files and the substitution preprocessor
 =================================================
 
-The `auxiliary files <auxiliary-files-for-fortran-90_>`_ are
-templates for integrators, drivers, and utilities. They are inserted
-into the KPP output after being run through the substitution
-preprocessor. This preprocessor replaces `several placeholder symbols
-<list-of-symbols-replaced_>`_ in the template files
-with their particular values in the model at hand. Usually, only
-:command:`KPP_ROOT` and :command:`KPP_REAL` are needed because the other
-values can also be obtained via the variables listed in
-:ref:`table-inl-type`.
+The `auxiliary files <auxiliary-files-for-fortran-90_>`_ in the
+:file:`$KPP_HOME/util` subdirectory are templates for integrators,
+drivers, and utilities. They are inserted into the KPP output after
+being run through the substitution preprocessor. This preprocessor
+replaces `several placeholder symbols <list-of-symbols-replaced_>`_ in
+the template files with their particular values in the model at hand.
+Usually, only :command:`KPP_ROOT` and :command:`KPP_REAL` are needed
+because the other values can also be obtained via the variables listed
+in :ref:`table-inl-type`.
 
 :command:`KPP_REAL` is replaced by the appropriate single or double
 precision declaration  type. Depending on the target language KPP will
@@ -995,14 +991,15 @@ must be used:
 
    KPP_REAL :: BIG(1000)
 
-When used with the option :code:`DOUBLE on`, the above line will be
+When used with the command :command:`#DOUBLE ON`, the above line will be
 automatically translated into:
 
 .. code-block:: F90
 
    REAL(kind=dp) :: BIG(1000)
 
-and when used with the option :code:`DOUBLE off`, the same line will become:
+and when used with the command :command:`#DOUBLE OFF`, the same line will
+become:
 
 .. code-block:: F90
 
@@ -1031,9 +1028,6 @@ in the generated Fortran90 output file.
 List of auxiliary files for Fortran90
 --------------------------------------
 
-KPP inline codes or other instructions contained in the following
-files, as shown in :ref:`table-aux-files`.
-
 .. _table-aux-files:
 
 .. table:: Table 2: Auxiliary files for Fortran90
@@ -1074,9 +1068,6 @@ files, as shown in :ref:`table-aux-files`.
 List of symbols replaced by the substitution preprocessor
 ---------------------------------------------------------
 
-The following symbols in KPP-generated source code will be replaced
-with corresponding values, as highlighted in :ref:`table-sym-repl`.
-
 .. _table-sym-repl:
 
 .. table:: Table 3: Symbols and their replacements
@@ -1119,10 +1110,8 @@ In order to offer more control over the integrator, KPP provides the
 arrays :code:`ICNTRL` (integer) and :code:`RCNTRL` (real). Each of them
 is an array of 20 elements that allow the fine-tuning of the integrator.
 All integrators (except for :code:`tau_leap` and :code:`gillespie`) use
-:code:`ICNTRL` and :code:`RCNTRL`. Array elements not listed here are
-either not used or are integrator-specific options. Details can be found
-in the comment lines of the individual integrator files in
-:code:`$KPP_HOME/int/`.
+:code:`ICNTRL` and :code:`RCNTRL`. Details can be found in the comment
+lines of the individual integrator files in :code:`$KPP_HOME/int/`.
 
 ICNTRL
 ------

docs/source/using_kpp/05_output_from_kpp.rst

@@ -169,8 +169,8 @@ The code to update the rate constants is in :file:`ROOT_Rates.f90` (or
 ROOT_Parameters
 ---------------
 
-The global parameters listed in :ref:`table-par` are defined and
-initialized in :file:`ROOT_Parameters.f90` (or :file:`.F90`).
+Global parameters are defined and initialized in
+:file:`ROOT_Parameters.f90` (or :file:`.F90`):
 
 .. _table-par:
 
@@ -231,8 +231,8 @@ Hessian, etc.
 ROOT_Global
 -----------
 
-The global variables listed in :ref:`table-glob` are declared in
-:file:`ROOT_Global.f90` (or :file:`.F90`).
+Several global variables are declared in :file:`ROOT_Global.f90` (or
+:file:`.F90`):
 
 .. _table-glob:
 
@@ -246,27 +246,27 @@ The global variables listed in :ref:`table-glob` are declared in
    +-------------------------+---------------------------------------------+
    | :code:`VAR(:)`          | Concentrations, variable species (pointer)  |
    +-------------------------+---------------------------------------------+
-   | :code:`FIX(:)`          | Concentrations, fixed species (pointer)	   |
+   | :code:`FIX(:)`          | Concentrations, fixed species (pointer)     |
    +-------------------------+---------------------------------------------+
-   | :code:`RCONST(NREACT)`  | Rate coefficient values			   |
+   | :code:`RCONST(NREACT)`  | Rate coefficient values                     |
    +-------------------------+---------------------------------------------+
-   | :code:`TIME`            | Current integration time			   |
+   | :code:`TIME`            | Current integration time                    |
    +-------------------------+---------------------------------------------+
-   | :code:`SUN`             | Sun intensity between 0 and 1		   |
+   | :code:`SUN`             | Sun intensity between 0 and 1               |
    +-------------------------+---------------------------------------------+
-   | :code:`TEMP`            | Temperature				   |
+   | :code:`TEMP`            | Temperature                                 |
    +-------------------------+---------------------------------------------+
-   | :code:`TSTART, TEND`    | Simulation start/end time		   |
+   | :code:`TSTART, TEND`    | Simulation start/end time                   |
    +-------------------------+---------------------------------------------+
-   | :code:`DT`              | Simulation step				   |
+   | :code:`DT`              | Simulation time step                        |
    +-------------------------+---------------------------------------------+
-   | :code:`ATOL(NSPEC)`     | Absolute tolerances			   |
+   | :code:`ATOL(NSPEC)`     | Absolute tolerances                         |
    +-------------------------+---------------------------------------------+
-   | :code:`RTOL(NSPEC)`     | Relative tolerances			   |
+   | :code:`RTOL(NSPEC)`     | Relative tolerances                         |
    +-------------------------+---------------------------------------------+
-   | :code:`STEPMIN`         | Lower bound for time step		   |
+   | :code:`STEPMIN`         | Lower bound for time step                   |
    +-------------------------+---------------------------------------------+
-   | :code:`STEPMAX`         | Upper bound for time step		   |
+   | :code:`STEPMAX`         | Upper bound for time step                   |
    +-------------------------+---------------------------------------------+
    | :code:`CFACTOR`         | Conversion factor                           |
    +-------------------------+---------------------------------------------+
@@ -420,7 +420,7 @@ The Jacobian matrix for our example contains 18 non-zero elements:
 It defines how the temporal change of each chemical species depends on
 all other species. For example, :math:`\mathbf{J}(5,2)` shows that :math:`NO_2`
 (species number 5) is affected by :math:`O` (species number 2) via
-reaction number R9. The sparse data structures for the Jacobian are
+reaction R9. The sparse data structures for the Jacobian are
 declared and initialized in :file:`ROOT_JacobianSP.f90` (or
 :file:`.F90`). The code for the ODE Jacobian and
 sparse multiplications is in :file:`ROOT_Jacobian.f90` (or
@@ -432,15 +432,14 @@ sparse multiplications is in :file:`ROOT_Jacobian.f90` (or
    :command:`#JACOBIAN SPARSE_LU_ROW` to the KPP definition file will
    create the file :file:`ROOT_JacobianSP.f90` (or :file:`.F90`).
 
-The Jacobian of the ODE function is automatically constructed by
-KPP. KPP generates the Jacobian subroutine :code:`Jac` or
-:code:`JacSP`  where the latter is generated when the sparse format is
-required. Using the variable species :code:`V`, the fixed
-species :code:`F`, and the rate coefficients :code:`RCT` as input, the
-subroutine calculates the Jacobian :code:`JVS`. The default data
-structures for the sparse compressed on rows Jacobian
-representation are shown in :ref:`table-jac` (for the case where the LU fill-in
-is accounted for).
+The Jacobian of the ODE function is automatically constructed by KPP.
+KPP generates the Jacobian subroutine :code:`Jac` or :code:`JacSP` where
+the latter is generated when the sparse format is required. Using the
+variable species :code:`V`, the fixed species :code:`F`, and the rate
+coefficients :code:`RCT` as input, the subroutine calculates the
+Jacobian :code:`JVS`. The default data structures for the sparse
+compressed on rows Jacobian representation (for the case where the LU
+fill-in is accounted for) are:
 
 .. _table-jac:
 
@@ -530,16 +529,6 @@ in :file:`ROOT_Hessian.f90` (or :file:`.F90`). The Hessian
 function and associated sparse multiplications are in
 :code:`ROOT_HessianSP.f90` (or :code:`.F90`).
 
-.. tip::
-
-   Adding :command:`#HESSIAN ON` to the KPP definition file will
-   create the file :file:`ROOT_Hessian.f90` (or :file:`.F90`)
-
-   Additionally, if either :command:`#JACOBIAN SPARSE ROW` or
-   :command:`#JACOBIAN SPARSE_LU_ROW` are also added to the KPP
-   definition file, the file :file:`ROOT_HessianSP.f90` (or
-   :file:`.F90`) will also be created.
-
 The Hessian contains the second order derivatives of the time derivative
 functions. More exactly, the Hessian is a 3-tensor such that
 
@@ -549,7 +538,7 @@ functions. More exactly, the Hessian is a 3-tensor such that
      \qquad 1 \le i,j,k \le N_{\rm var}~.
    \label{eqn:Hessian1}
 
-KPP generates the routine :code:`Hessian` (see :ref:`table-hess-fun`) below:
+KPP generates the routine :code:`Hessian`:
 
 .. _table-hess-fun: