Add data assimilation capabilities to the app

[stvdwtt]

This PR adds data assimilation capabilities to the adamantine app.

Main changes:

• Adds the option for the initial temperature to be different for different ensemble members
• Adds a section of code before the time stepping loop to read experimental data (if directed by the input file)
• Fix how the experiment data size is set in DataAssimilator
• Add data assimilation to the main time stepping loop
• Add an integration test for data assimilation

Other changes:

• Fix parsing of the experimental log file (previously the first line was discarded)
• Add section break comments in run_ensemble to make it easier to read through (at least for me)
• Add some output to screen about the progress of experimental data parsing and data assimilation

Notes:

• Data assimilation still only works in serial
• Data assimilation still uses some dense linear algebra

[stvdwtt]

@Rombur -- I just realized I didn't merge the current master into this so the thermal conductivity input files are wrong. I'll fix that early this afternoon.

[stvdwtt]

Do you know what we should do about the cuda failures in set_with_experimental_data? For now should I only have that test run on the host?

[Rombur]

There is a bug with rank, you need to get it before using it (dealii::Utilities::MPI::this_mpi_process(comm) will give to you). It also look like clang-sanitizer is not happy.

[Rombur]

Clang-tidy and CUDA fails on the same error inside deal.II https://cloud.cees.ornl.gov/jenkins-ci/blue/organizations/jenkins/adamantine/detail/adamantine/136/tests/

An error occurred in line <2241> of file </scratch/source/dealii/source/dofs/dof_tools.cc> in function
    void dealii::DoFTools::internal::{anonymous}::map_dofs_to_support_points(const dealii::hp::MappingCollection<dim, spacedim>&, const dealii::DoFHandler<dim, spacedim>&, std::map<long unsigned int, dealii::Point<spacedim> >&, const dealii::ComponentMask&) [with int dim = 3; int spacedim = 3]
The violated condition was: 
    fe_collection[fe_index].has_support_points()
Additional information: 
    You are trying to access the support points of a finite element that
    either has no support points at all, or for which the corresponding
    tables have not been implemented.

[Rombur]

The reason it passes on the CPU is because we use the Release version and so we skip, deal.II's assert. You should be able to reproduce the error using the Debug version.

[stvdwtt]

@Rombur, I just want to confirm -- since the deal.II PR removed the assert (instead of moving it inside the masked off loop), the code is in this PR is good as it is and doesn't need the mask?

[Rombur]

That's right. The mask is actually for the vector component not the fe index, so there is no point in using it.