From jmwille at software.sandia.gov  Thu Apr 20 20:06:56 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:06:58 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos Makefile.in aclocal.m4
	configure
Message-ID: <200604210206.k3L26u6G027327@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos
In directory software.sandia.gov:/tmp/cvs-serv27187

Modified Files:
	Makefile.in aclocal.m4 configure 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:06:57 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:06:59 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example Makefile.in
Message-ID: <200604210206.k3L26vEa027361@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example
In directory software.sandia.gov:/tmp/cvs-serv27187/example

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:06:57 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:06:59 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/config acx_blas.m4
	acx_lapack.m4
Message-ID: <200604210206.k3L26vot027343@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/config
In directory software.sandia.gov:/tmp/cvs-serv27187/config

Modified Files:
	acx_blas.m4 acx_lapack.m4 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:06:58 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:01 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example/constExample
	Makefile.in
Message-ID: <200604210206.k3L26weF027421@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/constExample
In directory software.sandia.gov:/tmp/cvs-serv27187/example/constExample

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:06:58 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:01 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example/basicExample
	Makefile.in
Message-ID: <200604210206.k3L26vQ9027380@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/basicExample
In directory software.sandia.gov:/tmp/cvs-serv27187/example/basicExample

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:06:58 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:01 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example/classExample
	Makefile.in
Message-ID: <200604210206.k3L26wv2027395@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/classExample
In directory software.sandia.gov:/tmp/cvs-serv27187/example/classExample

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:06:59 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:02 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example/epetra
	Makefile.in
Message-ID: <200604210206.k3L26xss027438@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/epetra
In directory software.sandia.gov:/tmp/cvs-serv27187/example/epetra

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:00 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:02 2006
Subject: [Rythmos-checkins] 
	Trilinos/packages/rythmos/example/refCountPtrExample Makefile.in
Message-ID: <200604210207.k3L270uT027471@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/refCountPtrExample
In directory software.sandia.gov:/tmp/cvs-serv27187/example/refCountPtrExample

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:00 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:02 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example/epetra/1Dfem
	Makefile.in
Message-ID: <200604210207.k3L27043027454@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/epetra/1Dfem
In directory software.sandia.gov:/tmp/cvs-serv27187/example/epetra/1Dfem

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:00 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:02 2006
Subject: [Rythmos-checkins] 
	Trilinos/packages/rythmos/example/refCountPtrExample2 Makefile.in
Message-ID: <200604210207.k3L2707C027495@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/refCountPtrExample2
In directory software.sandia.gov:/tmp/cvs-serv27187/example/refCountPtrExample2

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:02 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:04 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/example/verySimple
	Makefile.in
Message-ID: <200604210207.k3L2721V027520@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/example/verySimple
In directory software.sandia.gov:/tmp/cvs-serv27187/example/verySimple

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:02 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:06 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/src Makefile.in
Message-ID: <200604210207.k3L272ve027537@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/src
In directory software.sandia.gov:/tmp/cvs-serv27187/src

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:03 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:06 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/test Makefile.in
Message-ID: <200604210207.k3L273eF027554@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/test
In directory software.sandia.gov:/tmp/cvs-serv27187/test

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From jmwille at software.sandia.gov  Thu Apr 20 20:07:03 2006
From: jmwille at software.sandia.gov (James M. Willenbring)
Date: Thu Apr 20 20:07:10 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/test/unitTests
	Makefile.in
Message-ID: <200604210207.k3L2732G027580@software.sandia.gov>

Update of /space/CVS/Trilinos/packages/rythmos/test/unitTests
In directory software.sandia.gov:/tmp/cvs-serv27187/test/unitTests

Modified Files:
	Makefile.in 
Log Message:

Bug 1409.

Modified the blas and lapack search .m4 files to stop searching if a user
specified blas or lapack library cannot be found.

This only applies to blas or lapack libraries specified via --with-blas and
--with-lapack.  It is not reasonable to apply this to other options such as
--with-libs and --with-ldflags.

In the past if a user specified blas or lapack library was not found, the .m4
would continue to try to find blas or lapack in different places.
This was confusing for users because they might have been trying to use an
optimized blas library, but ended up with a different blas library.
Unless a person looked through all of the configure output, this was not
noticable.

I tested this modification by checking it into Epetra for a few days before
applying the change to other packages.

The most recent bootstrap was done with the wrong version of automake so all
Makefile.in's were modified by my bootstrap.

From rabartl at software.sandia.gov  Fri Apr 28 08:32:05 2006
From: rabartl at software.sandia.gov (Roscoe A. Bartlett)
Date: Fri Apr 28 08:32:07 2006
Subject: [Rythmos-checkins] Trilinos/packages/rythmos/src
	Rythmos_Stepper_BackwardEuler.hpp Rythmos_Stepper_ExplicitRK.hpp
	Rythmos_Stepper_ExplicitTaylorPolynomial.hpp
	Rythmos_Stepper_ForwardEuler.hpp Rythmos_Stepper_ImplicitBDF.hpp
Message-ID: <200604281432.k3SEW58i022765@software.sandia.gov>

Update of /cvsroot/Trilinos/packages/rythmos/src
In directory software.sandia.gov:/tmp/cvs-serv22505/packages/rythmos/src

Modified Files:
	Rythmos_Stepper_BackwardEuler.hpp 
	Rythmos_Stepper_ExplicitRK.hpp 
	Rythmos_Stepper_ExplicitTaylorPolynomial.hpp 
	Rythmos_Stepper_ForwardEuler.hpp 
	Rythmos_Stepper_ImplicitBDF.hpp 
Log Message:
I have done several things here:

Changes to Thyra::ModelEvaluator and related software.

1) I Broke up the file Thyra_ModelEvaluator.hpp into two files Thyra_ModelEvaluatorBase.hpp (containing the non-templated base base class Thyra::ModelEvaluatorBase) and Thyra_ModelEvaluator.hpp (containing the templated base class Thyra::ModelEvaluator).

2) I removed all of the default function implementations from Thyra::ModelEvaluator and put them into a new base class (derived from Thyra::ModelEvaluator) called Thyra::StateFuncModelEvaluatorBase in thyra/src/support/nonlinear/model_evaluator/client_support/Thyra_StateFuncModelEvaluatorBase.hpp.  I also moved all of the wrapper functions like calc_f() and calc_f_W() to a new file thyra/src/support/nonlinear/model_evaluator/client_support/Thyra_ModelEvaluatorHelpers.hpp.  Now I think that the interface files Thyra_ModelEvaluator.hpp and Thyra_ModelEvaluatorBase.hpp are much cleaner and all extraneous non-interoperability code has been moved to support code directories.

3) From Thyra::ModelEvaluator I have replaced get_x_init(), get_p_init(l), and get_t_init() with a single function called getNominalValues() that returns an InArgs object.  I did the same thing for upper and lower bounds.  This significantly reduced the number of virtual functions in Thyra::ModelEvaluator, makes it easier to override the initial guess (or nominal values depending on how they are used), and make it easier to use in general (in my opinion).

4) From Thyra::ModelEvaluator I removed the create_DfDp_mv(), create_DgDx_mv() and create_DgDp_mv() functions and have replacement them with non-member helper functions in Thyra_ModelEvaluatorHelpers.hpp.  The reason that 
the create_DfDp_mv(), create_DgDx_mv() and create_DgDp_mv() where part of the interface was to allow the ModelEvaluator subclass to attach a non-Euclidean scalar product to the domain (or range) space for these multi-vectors.  However, this is not the right way to do this.  What Thyra needs is to replace the createMembers(space,numMembers) with createMembers(space,domain).  Our ANAs don't really handle non-Euclidean spaces well yet and this is up in the air somewhat.

5) I create a base class called Thyra::ModelEvaluatorDelegatorBase that makes it very easy to create and maintain Thyra::ModelEvaluator decorator classes.  Now it is much easier to create a whole host of different types of decorators as described below.

6) I added several new concrete Decorator subclasses:

- Thyra:::DefaultStateEliminationModelEvaluator: Given a Thyra::NonlinearSolverBase object, eliminates state variables x and the state equations f(x,) and computes the reduced functions g_j(x(),). I am using this to implement a black-box optimization approach.

- Thyra::DefaultFiniteDifferenceModelEvaluator:  Computes derivatives using finite differences.  This is very simple right now just computing DgDp but it will become more sophisticated very quickly.

- Thyra::DefaultNominalBoundsOverideModelEvaluator:  Overrides the nominal values (initial guess) and/or the upper or lower bounds.

I did not make any changes whatsoever to EpetraExt::ModelEvaluator and I do not think any such changes are needed.  Thyra::ModelEvaluator and EpetraExt::ModelEvaluator have completely different purposes and it is appropriate that they be different.

This checkin also includes the beginnings of a black-box finite-difference mode for the MOOCHO AdvDiffReact problem.  There is still lots to do however.

There are also other small changes but I do not want to list them all.