address comments

doc/arkode/guide/source/Introduction.rst

@@ -224,10 +224,6 @@ Users now need to link to ``sundials_core`` in addition to the libraries already
 This will be picked up automatically in projects that use the SUNDIALS CMake target. The library ``sundials_generic`` has been superceded by ``sundials_core`` and is no longer available.
 This fixes some duplicate symbol errors on Windows when linking to multiple SUNDIALS libraries.
 
-**Breaking change**
-Users now need to link to ``sundials_core`` in addition to the libraries already linked to. 
-This will be picked up automatically in projects that use the SUNDIALS CMake target. The library ``sundials_generic`` has been superceded by ``sundials_core`` and is no longer available.
-
 
 Changes in v5.6.2
 -----------------

doc/arkode/guide/source/Usage/General.rst

@@ -35,11 +35,11 @@ modules, vectors and algebraic solvers, are found in
 
 .. code-block::
 
-  <libdir>/libsundials_nvec*.<so|a>
-  <libdir>/libsundials_sunmat*.<so|a>
-  <libdir>/libsundials_sunlinsol*.<so|a>
-  <libdir>/libsundials_sunnonlinsol*.<so|a>
-  <libdir>/libsundials_sunmem.<so|a>
+  <libdir>/libsundials_nvec*.lib
+  <libdir>/libsundials_sunmat*.lib
+  <libdir>/libsundials_sunlinsol*.lib
+  <libdir>/libsundials_sunnonlinsol*.lib
+  <libdir>/libsundials_sunmem*.lib
 
 The file extension ``.lib`` is typically ``.so`` for shared libraries 
 and ``.a`` for static libraries.  
@@ -63,24 +63,34 @@ prototypes, and include the shared ``arkode/arkode.h`` and
 included, but there are optional ones that can be included as necessary.
 Information on optional headers is given in the relevant documentation section.
 
+The calling program must also include an :c:type:`N_Vector` implementation header file,  
+of the form ``nvector/nvector_*.h``. See :numref:`NVectors` for the appropriate name.  
+
 If the user includes a non-trivial implicit component to their ODE system in
 ARKStep, or if the slow time scale for MRIStep should be treated implicitly,
 then each implicit stage will require a nonlinear solver for the resulting
 system of algebraic equations -- the default for this is a modified or inexact
 Newton iteration, depending on the user's choice of linear solver.  If choosing
 to set which nonlinear solver module, or when interacting with a
-:numref:`SUNNonlinSol` module directly, the calling program must also include a
-:numref:`SUNNonlinSol` header file, of the form ``sunnonlinsol/sunnonlinsol_***.h`` 
+:c:type:`SUNNonlinearSolver` module directly, the calling program must also include a
+:c:type:`SUNNonlinearSolver` header file, of the form ``sunnonlinsol/sunnonlinsol_***.h``
 where ``***`` is the name of the nonlinear solver module 
 (see :numref:`SUNNonlinSol` for more information). 
 
+
 If using a nonlinear solver that requires the solution of a linear system of the
 form :math:`\mathcal{A}x=b` (e.g., the default Newton iteration), then a linear
 solver module header file will also be required.  Similarly, if the ODE system
 in ARKStep involves a non-identity mass matrix :math:`M \ne I`, then each time
-step will require a linear solver for systems of the form :math:`Mx=b`. 
-In this case it will be necessary to include the header file for a SUNDIALS linear 
-solver, which is of the form ``sunlinsol/sunlinsol_***.h``. 
+step will require a linear solver for systems of the form :math:`Mx=b`. In this
+case it will be necessary to include the header file for a
+:c:type:`SUNLinearSolver` solver, which is of the form
+``sunlinsol/sunlinsol_***.h`` (see :numref:`SUNLinSol` for more information). 
+
+If the linear solver is matrix-based, the linear solver header will also include a  
+header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of the  
+matrix implementation compatible with the linear solver (see :numref:`SUNMatrix` for  
+more information). 
 
 Other headers may be needed, according to the choice of preconditioner, etc.
 For example, if preconditioning for an iterative linear solver were performed

doc/cvode/guide/source/Usage/index.rst

@@ -70,11 +70,11 @@ modules, vectors and algebraic solvers, are found in
 
 .. code-block::
 
-  <libdir>/libsundials_nvec*.<so|a>
-  <libdir>/libsundials_sunmat*.<so|a>
-  <libdir>/libsundials_sunlinsol*.<so|a>
-  <libdir>/libsundials_sunnonlinsol*.<so|a>
-  <libdir>/libsundials_sunmem.<so|a>
+  <libdir>/libsundials_nvec*.lib
+  <libdir>/libsundials_sunmat*.lib
+  <libdir>/libsundials_sunlinsol*.lib
+  <libdir>/libsundials_sunnonlinsol*.lib
+  <libdir>/libsundials_sunmem*.lib
 
 The file extension ``.lib`` is typically ``.so`` for shared libraries 
 and ``.a`` for static libraries.  
@@ -88,23 +88,32 @@ the header file for CVODE in addition to the SUNDIALS core header file:
   #include <sundials/sundials_core.h> // Provides core SUNDIALS types
   #include <cvode/cvode.h>            // CVODE provides linear multistep methods 
 
-The calling program must also include an ``N_Vector`` implementation header file, of the form
+The calling program must also include an :c:type:`N_Vector` implementation header file, of the form  
 ``nvector/nvector_*.h``. See :numref:`NVectors` for the appropriate name.
 
-If using a non-default nonlinear solver module, or when interacting with a ``SUNNonlinearSolver``
-module directly, the calling program must also include a ``SUNNonlinearSolver`` implementation
-header file, of the form ``sunnonlinsol/sunnonlinsol_*.h`` where is the name of the nonlinear solver
-module (see :numref:`SUNNonlinSol` for more information). This file in turn includes the header file
-which defines the abstract data type.
+If using a non-default nonlinear solver module, or when interacting with a  
+:c:type:`SUNNonlinearSolver` module directly, the calling program must  
+also include a :c:type:`SUNNonlinearSolver` implementation header file,  
+of the form ``sunnonlinsol/sunnonlinsol_*.h`` where ``*`` is the name of  
+the nonlinear solver module (see :numref:`SUNNonlinSol` for more  
+information).  
 
 If using a nonlinear solver that requires the solution of a linear system of the form
 :eq:`CVODE_Newton` (e.g., the default Newton iteration), then a linear solver module header file
-will be required.
+will be required. In this case it will be necessary to include the header file for a  
+:c:type:`SUNLinearSolver` solver, which is of the form ``sunlinsol/sunlinsol_***.h``  
+(see :numref:`SUNLinSol` for more information). 
+
+If the linear solver is matrix-based, the linear solver header will also include a  
+header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of the  
+matrix implementation compatible with the linear solver (see :numref:`SUNMatrix` for  
+more information). 
 
 Other headers may be needed, according to the choice of preconditioner, etc. For example, in the
 example (see :cite:p:`cvode_ex`), preconditioning is done with a block-diagonal matrix. For this,
-even though the ``SUNLINSOL_SPGMR`` linear solver is used, the header is included for access to the
-underlying generic dense matrix arithmetic routines.
+even though the ``SUNLINSOL_SPGMR`` linear solver is used, the header  
+``sundials dense.h`` is included for access to the underlying generic dense matrix  
+arithmetic routines.  
 
 .. _CVODE.Usage.CC.skeleton_sim:
 

doc/cvodes/guide/source/Usage/SIM.rst

@@ -69,11 +69,11 @@ modules, vectors and algebraic solvers, are found in
 
 .. code-block::
 
-  <libdir>/libsundials_nvec*.<so|a>
-  <libdir>/libsundials_sunmat*.<so|a>
-  <libdir>/libsundials_sunlinsol*.<so|a>
-  <libdir>/libsundials_sunnonlinsol*.<so|a>
-  <libdir>/libsundials_sunmem.<so|a>
+  <libdir>/libsundials_nvec*.lib
+  <libdir>/libsundials_sunmat*.lib
+  <libdir>/libsundials_sunlinsol*.lib
+  <libdir>/libsundials_sunnonlinsol*.lib
+  <libdir>/libsundials_sunmem*.lib
 
 The file extension ``.lib`` is typically ``.so`` for shared libraries 
 and ``.a`` for static libraries.  
@@ -87,24 +87,32 @@ the header file for CVODES in addition to the SUNDIALS core header file:
   #include <sundials/sundials_core.h> // Provides core SUNDIALS types
   #include <cvodes/cvodes.h>          // CVODES provides linear multistep methods with sensitivity analysis
 
-The calling program must also include an ``N_Vector`` implementation header file, of the form
+The calling program must also include an :c:type`N_Vector` implementation header file, of the form  
 ``nvector/nvector_*.h``. See :numref:`NVectors` for the appropriate name.
 
-If using a non-default nonlinear solver module, or when interacting with a ``SUNNonlinearSolver``
-module directly, the calling program must also include a ``SUNNonlinearSolver`` implementation
-header file, of the form ``sunnonlinsol/sunnonlinsol_*.h`` where is the name of the nonlinear solver
-module (see :numref:`SUNNonlinSol` for more information). This file in turn includes the header file
-which defines the abstract data type.
+If using a non-default nonlinear solver module, or when interacting with a  
+:c:type:`SUNNonlinearSolver` module directly, the calling program must  
+also include a :c:type:`SUNNonlinearSolver` implementation header file,  
+of the form ``sunnonlinsol/sunnonlinsol_*.h`` where ``*`` is the name of  
+the nonlinear solver module (see :numref:`SUNNonlinSol` for more  
+information).  
 
 If using a nonlinear solver that requires the solution of a linear system of the form
 :eq:`CVODES_Newton` (e.g., the default Newton iteration), then a linear solver module header file
-will be required.
+will be required. In this case it will be necessary to include the header file for a  
+:c:type:`SUNLinearSolver` solver, which is of the form ``sunlinsol/sunlinsol_***.h``  
+(see :numref:`SUNLinSol` for more information). 
+
+If the linear solver is matrix-based, the linear solver header will also include a  
+header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of the  
+matrix implementation compatible with the linear solver (see :numref:`SUNMatrix` for  
+more information). 
 
 Other headers may be needed, according to the choice of preconditioner, etc. For example, in the
 example (see :cite:p:`cvodes_ex`), preconditioning is done with a block-diagonal matrix. For this,
-even though the ``SUNLINSOL_SPGMR`` linear solver is used, the header is included for access to the
-underlying generic dense matrix arithmetic routines.
-
+even though the ``SUNLINSOL_SPGMR`` linear solver is used, the header  
+``sundials dense.h`` is included for access to the underlying generic dense matrix  
+arithmetic routines.
 
 .. warning::
 

doc/ida/guide/source/Usage/index.rst

@@ -63,11 +63,11 @@ modules, vectors and algebraic solvers, are found in
 
 .. code-block::
 
-  <libdir>/libsundials_nvec*.<so|a>
-  <libdir>/libsundials_sunmat*.<so|a>
-  <libdir>/libsundials_sunlinsol*.<so|a>
-  <libdir>/libsundials_sunnonlinsol*.<so|a>
-  <libdir>/libsundials_sunmem.<so|a>
+  <libdir>/libsundials_nvec*.lib
+  <libdir>/libsundials_sunmat*.lib
+  <libdir>/libsundials_sunlinsol*.lib
+  <libdir>/libsundials_sunnonlinsol*.lib
+  <libdir>/libsundials_sunmem*.lib
 
 The file extension ``.lib`` is typically ``.so`` for shared libraries 
 and ``.a`` for static libraries.  
@@ -81,27 +81,25 @@ the header file for IDA in addition to the SUNDIALS core header file:
   #include <sundials/sundials_core.h> // Provides core SUNDIALS types
   #include <ida/ida.h>                // IDA provides methods for DAEs
 
-The calling program must also include an ``N_Vector`` implementation header file, of the form
+The calling program must also include an :c:type:`N_Vector` implementation header file, of the form  
 ``nvector/nvector_*.h``. See :numref:`NVectors` for the appropriate name.
-The calling program must also include an ``N_Vector`` implementation
-header file, of the form ``nvector/nvector_*.h`` (see Chapter :numref:`NVectors`
-for more information). 
 
 If using a non-default nonlinear solver object, or when interacting with a
-``SUNNonlinearSolver`` object directly, the calling program must also include a
-``SUNNonlinearSolver`` implementation header file, of the form
+:c:type:`SUNNonlinearSolver` object directly, the calling program must also include a  
+:c:type:`SUNNonlinearSolver` implementation header file, of the form  
 ``sunnonlinsol/sunnonlinsol_*.h`` where ``*`` is the name of the nonlinear
 solver (see Chapter :numref:`SUNNonlinSol` for more information).
 
 If using a nonlinear solver that requires the solution of a linear system of the
 form :eq:`IDA_DAE_nls` (e.g., the default Newton iteration), the calling program
-must also include a ``SUNLinearSolver`` implementation header file, of the from
+must also include a :c:type:`SUNLinearSolver` implementation header file, of the from  
 ``sunlinsol/sunlinsol_*.h`` where ``*`` is the name of the linear solver
 (see Chapter :numref:`SUNLinSol` for more information). 
 
 If the linear solver is matrix-based, the linear solver header will also include
 a header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of
-the matrix implementation compatible with the linear solver. 
+the matrix implementation compatible with the linear solver (see Chapter  
+:numref:`SUNMatrix` for more information). 
 
 Other headers may be needed, according to the choice of preconditioner, etc. For
 example, in the example ``idaFoodWeb_kry_p`` (see :cite:p:`ida_ex`),

doc/idas/guide/source/Usage/SIM.rst

@@ -55,18 +55,18 @@ where ``instdir`` is the directory where SUNDIALS was installed.
 Regardless of where the user's application program resides, its
 associated compilation and load commands must make reference to the
 appropriate locations for the library and header files required by
-IDAS. IDAS symbols are found in ``libdir/libsundials_ida.lib``. 
+IDAS. IDAS symbols are found in ``libdir/libsundials_idas.lib``. 
 Thus, in addition to linking to ``libdir/libsundials_core.lib``, IDAS
 users need to link to the IDAS library. Symbols for additional SUNDIALS
 modules, vectors and algebraic solvers, are found in
 
 .. code-block::
 
-  <libdir>/libsundials_nvec*.<so|a>
-  <libdir>/libsundials_sunmat*.<so|a>
-  <libdir>/libsundials_sunlinsol*.<so|a>
-  <libdir>/libsundials_sunnonlinsol*.<so|a>
-  <libdir>/libsundials_sunmem.<so|a>
+  <libdir>/libsundials_nvec*.lib
+  <libdir>/libsundials_sunmat*.lib
+  <libdir>/libsundials_sunlinsol*.lib
+  <libdir>/libsundials_sunnonlinsol*.lib
+  <libdir>/libsundials_sunmem*.lib
 
 The file extension ``.lib`` is typically ``.so`` for shared libraries 
 and ``.a`` for static libraries.  
@@ -80,27 +80,25 @@ the header file for IDAS in addition to the SUNDIALS core header file:
   #include <sundials/sundials_core.h> // Provides core SUNDIALS types
   #include <idas/idas.h>              // IDAS provides methods for DAEs with sensitivity analysis
 
-The calling program must also include an ``N_Vector`` implementation header file, of the form
+The calling program must also include an :c:type:`N_Vector` implementation header file, of the form  
 ``nvector/nvector_*.h``. See :numref:`NVectors` for the appropriate name.
-The calling program must also include an ``N_Vector`` implementation
-header file, of the form ``nvector/nvector_*.h`` (see Chapter :numref:`NVectors`
-for more information). 
 
 If using a non-default nonlinear solver object, or when interacting with a
-``SUNNonlinearSolver`` object directly, the calling program must also include a
-``SUNNonlinearSolver`` implementation header file, of the form
+:c:type:`SUNNonlinearSolver` object directly, the calling program must also include a  
+:c:type:`SUNNonlinearSolver` implementation header file, of the form 
 ``sunnonlinsol/sunnonlinsol_*.h`` where ``*`` is the name of the nonlinear
 solver (see Chapter :numref:`SUNNonlinSol` for more information).
 
 If using a nonlinear solver that requires the solution of a linear system of the
 form :eq:`IDAS_DAE_nls` (e.g., the default Newton iteration), the calling program
-must also include a ``SUNLinearSolver`` implementation header file, of the from
+must also include a :c:type:`SUNLinearSolver` implementation header file, of the from  
 ``sunlinsol/sunlinsol_*.h`` where ``*`` is the name of the linear solver
 (see Chapter :numref:`SUNLinSol` for more information). 
 
 If the linear solver is matrix-based, the linear solver header will also include
 a header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of
-the matrix implementation compatible with the linear solver. 
+the matrix implementation compatible with the linear solver. (see Chapter  
+:numref:`SUNMatrix` for more information). 
 
 Other headers may be needed, according to the choice of preconditioner, etc. For
 example, in the example ``idasFoodWeb_kry_p`` (see :cite:p:`ida_ex`),

doc/kinsol/guide/source/Usage/index.rst

@@ -57,18 +57,18 @@ where ``instdir`` is the directory where SUNDIALS was installed.
 Regardless of where the user's application program resides, its
 associated compilation and load commands must make reference to the
 appropriate locations for the library and header files required by
-KINSOL. KINSOL symbols are found in ``libdir/libsundials_ida.lib``. 
+KINSOL. KINSOL symbols are found in ``libdir/libsundials_kinsol.lib``. 
 Thus, in addition to linking to ``libdir/libsundials_core.lib``, KINSOL
 users need to link to the KINSOL library. Symbols for additional SUNDIALS
 modules, vectors and algebraic solvers, are found in
 
 .. code-block::
 
-  <libdir>/libsundials_nvec*.<so|a>
-  <libdir>/libsundials_sunmat*.<so|a>
-  <libdir>/libsundials_sunlinsol*.<so|a>
-  <libdir>/libsundials_sunnonlinsol*.<so|a>
-  <libdir>/libsundials_sunmem.<so|a>
+  <libdir>/libsundials_nvec*.lib
+  <libdir>/libsundials_sunmat*.lib
+  <libdir>/libsundials_sunlinsol*.lib
+  <libdir>/libsundials_sunnonlinsol*.lib
+  <libdir>/libsundials_sunmem*.lib
 
 The file extension ``.lib`` is typically ``.so`` for shared libraries 
 and ``.a`` for static libraries.  
@@ -82,20 +82,19 @@ the header file for KINSOL in addition to the SUNDIALS core header file:
   #include <sundials/sundials_core.h> // Provides core SUNDIALS types
   #include <kinsol/kinsol.h>          // KINSOL provides methods for solving nonlinear systems
 
-The calling program must also include an ``N_Vector`` implementation header file, of the form
+The calling program must also include an :c:type:`N_Vector` implementation header file, of the form  
 ``nvector/nvector_*.h``. See :numref:`NVectors` for the appropriate name.
-The calling program must also include an ``N_Vector`` implementation
-header file, of the form ``nvector/nvector_*.h`` (see Chapter :numref:`NVectors`
-for more information). 
 
 If using a Newton or Picard nonlinear solver that requires the solution of a
-linear system, then a linear solver module header file will be required. If the
-linear solver is matrix-based, the linear solver header will also include a
-header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of
-the matrix implementation compatible with the linear solver. The matrix header
-file provides access to the relevant matrix functions/macros and in turn
-includes the header file ``sundials_matrix.h`` which defines the abstract matrix
-data type.
+linear system, the calling program must also include a ``SUNLinearSolver``
+implementation header file, of the from ``sunlinsol/sunlinsol_*.h`` where ``*``
+is the name of the linear solver (see Chapter :numref:`SUNLinSol` for more
+information). 
+
+If the linear solver is matrix-based, the linear solver header will also include
+a header file of the from ``sunmatrix/sunmatrix_*.h`` where ``*`` is the name of
+the matrix implementation compatible with the linear solver. (see Chapter  
+:numref:`SUNMatrix` for more information). 
 
 Other headers may be needed, according to the choice of preconditioner, etc. For
 example, in the example ``kinFoodWeb_kry_p`` (see :cite:p:`kinsol_ex`),