Description:
Add a method to the MPACT parameter list to convert to Teuchos parameter list,
using the ForTeuchos bindings. This is useful for specifying options to the
Trilinos solvers.

CASL Ticket # - 4169

Description:
To add capability to convert MPACT parameter lists  to Teuchos parameter lists,
Trilinos needs to be an optional dependency for Utils. This also adds the
HAVE_ForTeuchos preprocessor definition.

CASL Ticket # - 4169

Description:

CASL Ticket # - N/A

Description:

CASL Ticket # - N/A

Description:

CASL Ticket # - N/A

Description:
Previously, the containers used to by the Trilinos wrappers were stored as raw
pointers, necessitating an Init and Finalize routine. To avoid that, they are
instead stored in global reference counted pointers, which are initialized and
destroyed automatically

CASL Ticket # - N/A

Description:

CASL Ticket # - N/A

Description:

CASL Ticket # - N/A

Description:
This give Belos wrapper access to runtime options through parameters lists for
code that wishes to use it. This is done similarly to the Anasazi wrappers,
though unlike Anasazi, there is no client code yet where it makes sense to use
it

CASL Ticket # - N/A

Description:
This propagates the options from the anasazi options in the XML file through all
of the flaming hoops necessary to actually see them in the parameter list in
CMFD initialization.

CASL Ticket # - N/A

Description:
This adds a preprocessor branch to create and use a ForTeuchos parameter list to
configure the Anasazi solver in the EigenvalueSolverTypes. For now, it is just
manually setting some of the defailts that live in the Trilinos solver wrappers
already, but serves as a good place to customize later.

CASL Ticket # - 4169

Description:
Previously, the Anasazi_Init() function used hard-coded defaults to configure
the solver. This commit adds another function, Anasazi_Init_Params(), which
accepts a ForTeuchos parameter list, which can contain options determined on the
Fortran/MPACT side.

CASL Ticket # - 4169

Description:
Add a method to the MPACT parameter list to convert to Teuchos parameter list,
using the ForTeuchos bindings. This is useful for specifying options to the
Trilinos solvers.

CASL Ticket # - 4169

Description:
To add capability to convert MPACT parameter lists  to Teuchos parameter lists,
Trilinos needs to be an optional dependency for Utils. This also adds the
HAVE_ForTeuchos preprocessor definition.

CASL Ticket # - 4169

Description:
Added unit tests to test the INCL=0,1,2 options for findUp/LowBound and
by association findEleHtAbove/Below.  Tests pass and they exposed a
typo for one of the incl variables

CASL Ticket # - PHI #4485

Description:
This option was added to the findUp/LowBound routines but remained
commented out.  It is needed for control rod movement development and
has been uncommented and implemented.  Unit tests will be added shortly.

CASL Ticket # - PHI #4485

Description:
See title.

CASL Ticket # - PHI #3840

Description:
Some of the arrayutils routines did not use the tolerance input option.
That is fixed for findUpBound and findLowBound, and by association
findEleHtAbove and findEleHtBelow.

There was a range for valid tolerances in the findIndex routine.  The
upper bound check on this has been removed, so the tolerance can be as
coarse as needed.

Adding the tolerance value from parameter TOL_GEOM_cm to all of the
calls to findIndex, findEleHtAbove and findEleHtBelow.

CASL Ticket # - PHI #3840

Description:
Some optional arguments can be good, too many are a pain.  Reducing the
number of them, making some previous ones required, including the DELTA.
Removing the XI argument all together because it is possible to prepend
an array variable using the (/SRK, var/) notation.  This makes that
optional argument redundant.

Adding the TOL optional argmuent to more of the array utils routines
since it will likely be needed to resolve the control rod bug.

These changes are being made in preparation for the addition of the TOL
arguments in the control rod geom.

CASL Ticket # - PHI #3840

CASL Ticket # - 4579

Description:
Previous implementation had an extremely simplistic method to prime the BDF solver.
This commit updates that implementation to use smaller time-steps to account for the
accuracy difference in the different levels of solve.  This resulted in 2nd order
convergence at best but now, BDF-n is able to obtain nth order accuracy.

CASL Ticket # - 4579

Description:

CASL Ticket # - #4314

Description:
The unit test file readtest.h5 is now written from the test itself and
then deleted.  No more need to carry it around in the repo.

The new readtest.h5 also has the correct scalar/simple data types for
logicals and strings that were changed in the filetype_hdf5.f90.

Added testing for the read_pList routine.

CASL Ticket # - PHI #4314

Description:
Adding functionality to read in an arbitrary data set object and put it
onto our internal parameter list object, which is encapsulated by
read_parameter.

The read_pList routine loops over all sub-objects of a
specified path and adds each data set to the parameter list with the
given full path.

CASL Ticket # - PHI #4314

Description:
The logic for the read_st0_helper was duplicated from the
read_st1_helper routine.  In it, there is logic to determine whether the
dataset to be read is a character array or a string.  This necessitated
the creation of read_ca0.  It was patterened after read_ca1.

This effort was primarily done to support the reading of logicals into
the parameter list object.

CASL Ticket # - PHI #4314

Description:
See above.

CASL Ticket # - PHI #4314

Description:
It seems this was not the case before as it was using the
write_st1_helper routine.  Fixed it.

CASL Ticket # - PHI #4314

Description:
It would seem that the root path was not registered as existing when
using the h5lexists_f routine.  This affected the isgrp not thinking it
was a group, which in turn affected the ls function not returned the
list of objects.

The fix was to check if the path passed in is in fact length 1 and the
first character equals '/'.

CASL Ticket # - PHI #4314

Description:
Was running into issues where this function would be called on a dataset
and not a group.  Added a check to the routine so that it returns an
allocated array of the sub-objects if the path entered is a group.  It
will return a deallocated array if the path is not a group.

CASL Ticket # - PHI #4314

Description:

CASL Ticket # - N/A

The settings in the OMP parallel environment were getting squashed by the call
to omp_set_num_threads(1) in the initialization of the Trilinos solvers. This
call was there because in the absence of a defined OMP_NUM_THREADS environment
variable, the Trilinos solvers would use all cores on a system. Manually setting
OpenMP to use on thread in the Trilinos initialization affected the result of
omp_get_max_threads, which was being treated as the maximum allowable number of
threads, effectively limiting the number of threads to 1 for all cases.

This commit changes the thread setting logic to:
 - Make sure that the requested number of threads is <= to the number of
   physical cores, otherwise raise a warning.
 - Call omp_set_num_threads() to the maximum number of threads requested over
   all instances of the OMP_EnvType
 - If the requested number of threads is zero, use omp_get_max_threads() to as
   the number of threads. This is not the same as omp_get_num_procs(); read the
   specification for details. Essentially this sets the number of threads to the
   OpenMP default value, which is usually the value of OMP_NUM_THREADS, if
   defined, or the result of omp_get_num_procs().

Description:

CASL Ticket # - N/A

Description:
Implemented tests for convergence rates for bdf methods 1-5 for both the
exponential ODE set and the nonlinear ODE set.  Strangly, BDF methods 2-5
all give second order accuracy.  I can't find documentation that that is
reality but I confirmed with a hand calculation (ok, Excel calc) than
bdf 3-5 all give 2nd order convergence.

CASL Ticket # - 4579

Description:
BDF orders 1-5 are under unit test for the linear solution and all are passing.
Next step is to add order of convergence tests for each level of BDF.

CASL Ticket # - 4579

CASL Ticket # - 4579

CASL Ticket # - 4579

Description:
Previous design was causing issues with Intel, having an abstract interface
with a function pointer passed as an argument.  There was also an unresolved
issue with getting data (constants) passed into the function which is resolved
by having an extended class.  Overall, the design is considerably better.

CASL Ticket # - 4579

CASL Ticket # - 4579