add docs for the generic classes from other branch and update

doc/arkode/guide/source/Usage/ARKStep/ASA.rst

@@ -3,20 +3,53 @@
 Adjoint Sensitivity Analysis
 ============================
 
+The previous sections discuss using ARKStep for the intergation of forward ODE models.
+This section discusses how to use ARKStep for adjoint sensitivity analysis as introduced
+in :numref:`ARKODE.Mathematics.ASA`. To use ARKStep for ASA, users simply setup the forward
+integration as usual (following :numref:`ARKODE.Usage.Skeleton`) with one exception:
+a :c:type:`SUNAdjointCheckpointScheme` object must be provided to the forward ARKStep stepper
+creating a :c:type:`SUNAdjointCheckpointScheme` object and then calling
+:c:func:`ARKodeSetAdjointCheckpointScheme` before the call to the :c:func:`ARKodeEvolve`
+function. After the forward model integration code, a :c:type:`SUNAdjointStepper` object
+can be created for the adjoint model integration by calling :c:func:`ARKStepCreateAdjointStepper`.
+The code snippet below demonstrates these steps in brief and the example code
+``examples/arkode/C_serial/ark_lotka_volterra_asa.c`` demonstrates these steps in detail.
+
+.. code-block:: C
+
+   // 1. Create a SUNAdjointCheckpointScheme object
+
+   // 2. Setup ARKStep for forward integration
+
+   // 3. Attach the SUNAdjointCheckpointScheme
+
+   // 4. Evolve the forward model
+
+   // 5. Create the SUNAdjointStepper
+
+   // 6. Setup the adjoint model
+
+   // 7. Evolve the adjoint model
+
+   // 8. Cleanup
+
+
+
+User Callable Functions
+-----------------------
+
 This section describes ARKStep-specific user-callable functions for performing
 adjoint sensitivity analysis with methods with ARKStep.
 
-
 .. c:function:: int ARKStepCreateAdjointStepper(void* arkode_mem, N_Vector sf, SUNAdjointStepper* adj_stepper_ptr)
 
-   Creates a :c:type:`SUNAdjointStepper` object compatible with the provided ARKStep instance for 
+   Creates a :c:type:`SUNAdjointStepper` object compatible with the provided ARKStep instance for
    integrating the adjoint sensitivity system :eq:`ARKODE_ADJOINT_ODE`.
 
    :param arkode_mem: a pointer to the ARKStep memory block.
    :param sf: the sensitivity vector holding the adjoint system terminal condition.
-      This must be an instance of the ManyVector ``N_Vector`` implementation with two subvectors. 
-      The first subvector must hold :math:`\partial g/\partial y |_{t=t_f} \in \mathbb{R}^N` and the second subvector must
-      hold  :math:`\partial g / \partial p |_{t=t_f} \in \mathbb{R}^d`.
+      This must be an instance of the ManyVector ``N_Vector`` implementation with two subvectors.
+      The first subvector must hold :math:`\partial g/\partial y |_{t=t_f} \in \mathbb{R}^N` and the second subvector must hold  :math:`\partial g / \partial p |_{t=t_f} \in \mathbb{R}^d`.
    :param adj_stepper_ptr: the newly created :c:type:`SUNAdjointStepper` object.
 
    :return:

doc/arkode/guide/source/sunadjoint/index.rst

@@ -11,7 +11,7 @@
    SUNDIALS Copyright End
    ----------------------------------------------------------------
 
-.. _SUNAdaptController:
+.. _SUNAdjoint:
 
 ###########################
 Adjoint Sensitivty Analysis
@@ -24,6 +24,7 @@ sensitivity analysis (ASA). The API itself does not implement ASA, but it provid
 interface for ASA capabilties implemented in the SUNDIALS packages. Right now it supports :ref:`the
 ASA capabilties in ARKODE <ARKODE.Mathematics.ASA>`, while the ASA capabilities in :ref:`CVODES
 <CVODES.Mathematics.ASA>` and :ref:`IDAS <IDAS.Mathematics.ASA>` must be used directly.
+*Users should read the package specific sections on ASA capabiltiies before this section.*
 
 .. toctree::
    :maxdepth: 1