GitLab

* wip: adds boilerplate fmi and fmu c interface

* adds working example FMU model import

* adds wrappers for doStep getReal and setReal

* fix issue with getting c++ obj pointer

* wip: debugging illegal fmu state after init

* wip: debugging illegal fmu state after init

* adds example FMU import

* adds calls to enter and exitInitilizationMode to setupExperiment and adds output to fmu step example

* adds verbosity flag for c/c++ interface fns

* remove extraneous module imports in fmu2_f_api

* example fmu step test now runs to endTime of 0.1s

* wraps clear get/setInteger and get/setBoolean

* parse the FMU XML modelDescription on init

* enables xml parser to handle FMU born XML files and adds getValueRef and getCausality methods to FMU wrapper

* wip: get and set FMU state for FMU setRestart and rewindToRestart functionality

* adds convinience method to get and set FMU variables

* wip: adds capability to setRestart and rewindToRestart an...

* Adding overloaded assignments for geometries, and 90 degree rotation.

Description:
These functions are needed to help speed up the geometry processing in
MPACT.

VERA-dev Issue # - ####

* Removing overloaded assignment.

Description:
Should be unnecessary for types with only intrinsics and no pointers.

VERA-dev Issue # - ####

* Addressing Pull Request comments.

Description:
Adding subroutine headers and explanations.

VERA-dev Issue # - ####

Description:
For this newer version of PETSc, a parallel run using SuperLU_dist needs to
specifically call that solver (not SuperLU, which only works for serial).  Older
versions of PETSc allowed the solver to be set to SuperLU whether it was serial
or parallel.

CASL Ticket # - 4661

* Mass rename and interface improvements to Geom_* files

* WIP Add failing BWR test to unit test

* WIP first pass at refactoring combine_GraphType

Everything compiles

* WIP All futility unit tests working

* WIP add generic for Geom_Plane

* WIP fix graphs: add theta filtering for circle-circle intersections

* WIP add comments, fix small bugs, delete old combine_graphtype routine

* Fix bugs in adding circular arcs

* Remove unused variable and debug statements

* Change == to .APPROXEQA. in unit test

* Add RECURSIVE attribute to subroutines

* Add more enumerations

* Initial base class implementation

* Adds picard and modified picard types

* Adds unit test for Relaxed and Modified Picard

* Updates to comments and fixes test failures

* Switch Anderson to use base Accelerator type

* Fixing unit test

* Removes unneeded DBC statement

* Addresses review comments

* Adds more DBC checking, updates comments

* Adds Gravitational Constant to constants module

* Added numbers up to 10

* Adds SOFTEQR interface for ASSERT

* Adds wide range of metric conversions

* Change existing conversions to use metric ones

* Adds mass, energy, and length conversions to constants

* Fix potential for bad ranks to be used in string gathers

In some cases, HUGE(...) was not being overwritten if there
were empty strings, which could then lead to errors in the
send/receive.  This was fixed by using -HUGE(...) instead,
and then only performing the send/receive for rank >= 0

* Forgot to add a check to the 1D gather routine

* Update comments

* Simplify string conversions

* Review comments additional testing

* Update testStrings.f90

Fix misspelled word.
Co-authored-by: Shane C. Henderson <hendersonsc@ornl.gov>

* Adds Gravitational Constant to constants module

* Added numbers up to 10

* Adds SOFTEQR interface for ASSERT

* Adds wide range of metric conversions

* Change existing conversions to use metric ones

Adds Gravitational Constant and numbers up to 10 to constants module

* Relaxed nnz requirement on serial banded matrices

* Updated set unit tests to cover un/assembled cases better

* Fix petsc issue for 8.3 TPLs

* Update interface for PETSc > 3.7

* Switch some checks to DBC

* Remove unused parameter

* Add gather collective for StringTypes

* Add pre-proc guards for non-MPI builds

* Modify collective interface

* Remove unused parameter

* Add 2D test for for string gather

* Add string collective to generic for other mpi_gather wrappers
Co-authored-by: Shane C. Henderson <hendersonsc@ornl.gov>

* Fix getUnique to always return allocated array

* Update headers for each getUnique routine

* Add BASIC label to testGenReqTables

* Set Futility_SRC_DIR configuration variable

* Adds pop_entry interface to ArrayUtils

* Add insertEntry interface

* Add mroe test cases for insertEntry

* Add constructor for string types

* Add unit tests and make constructor ELEMENTAL

* Add replace_entry interface to ArrayUtils

* Add replaceEntry unit test

* Fix potential bug in reaplceEntry

* Adding subroutines for Find interface for searching strings.

Description:
Fixing another issue with array utils assigning the first value as
unique, even if it is null.  Changing that to loop over all values
instead.

CASL Ticket # - PHI 6419

* Fixing doxygen documentation.

Description:

CASL Ticket # - PHI 6419

* Add str_SBK to str interface

* Add str_sbk test

* Adding array routines to round reals and query for remainders.

Description:
These routines are needed for checking input value tolerances during the
input processing.

CASL Ticket # - PHI 5989

* Removing ApplyTol.

Description:
Not needed at this time.

CASL Ticket # - PHI 5989

* Changing the DBC tolerance bounds and adding tests.

Description:
The previous lower bound tolerance needed to be raised.  Adding tests to
check the full range of the tolerances.

CASL Ticket # - PHI 5989

* Enable editing pvtu files for serial cases

* Adds least common multiple routine

* Add some tests, refine logic
Co-authored-by: Shane C. Henderson <hendersonsc@ornl.gov>

* Fix testTimes to work with virtual systems and WSL

* Add space in error message for HDF5 file

* Address review comments

Co-authored-by: Shane C. Henderson <hendersonsc@ornl.gov>

* Add support to ParameterLists for 4D SNK, SLK, SSK, and SDK arrays

* Add PLPtr wrapper class to ParameterLists

* Consolidate reallocation statements in ParameterLists

* Add support to HDF5 for reading rank 4 arrays into a PL

* Add capability to HDF5 to get data type and shape

* Add some protection for unneeded / in HDF5

* Remove spurious write statement

* Add missing preproc symbols

* Address unused variables

* Changes to code to reflect changes in Parallel Datatypes review

* Initial solver commit

* Added options to speed up MPACT

* Moved some communication outside of gmres restart loop

* Fixed bug in VectorResemble

* Made VectorResemble more useful/unified getResidual

* WIP commit including updates of various utilities

* cleaned up unit tests of linear solver

* Updated parallel tests and briefs

* Formatting in changes for #5855

* Addressed performance issues relative to PETSc

* Updated parameter names and brought in residual calculation changes

* Adjusted residual calculation

* Adjusted default preconditioner and allowed distributed vectors with one entry

* Updated native LS conventions

* Changes to orthogonalization in native solver

* adds checks for newton iteration convergence in bdf ode step

* adds maxIter arg to ODE solver paramlist and update doxygen for new maxIter_in and keepSolving_in optional args

* fix indentation on continuation lines

* removes maxIter parameter

Please enter the commit message for your changes. Lines starting

This reverts commit aac36b20.

* Adding coding to create a LaTeX output file with the requirements tables.

Description:

CASL Ticket # - N/A

* Modifying ConvertToLatex to make tables pretty

Description:
Uses predefined colors caslcolor1, caslcolor2, and caslheader.

CASL Ticket # - 5690

* Adding tracing to CDash test name for Requirements Table

Description:
Added a new input option to GenerateRequirementsTable.py for
specifying an additional file that relates the CDash test name
to the test input.

This info is now incorporated on the requirement object and printed
to the LaTeX table.

CASL Ticket # - 5690

* Addressing review comments for updates to GenerateRequirementsTable

Description:
-Added documentation for testName on the __init__ routine for the Requirement Class
-Fixed runtime error when --cdash-test-name-name-file option is not given
-Added escaping of "&" in requirements decsription
-Removed "MPACT" from requirement LaTeX table header
-Fixing bug with parsing test name depending on whether path arg ends with "/".

CASL Ticket # - 5690

* Adding unit tests to GenerateRequirementsTable

Description:
-subtest01: nominal behavior. One path argument, that has one file with
            one extension, and one requirement correctly documented.
-subtest02: extension of nominal behavior where multiple files are present
            with same extension all with a correct requirement block.
            Also an output file name is specified.
-subtest03: test for two file extensions (e.g. f90 and inp) all files
            have correct requirements.
-subtest04: another extension of nominal behavior, include 3 extensions
            and for the new one without requirements blocks.
-subtest05: rerun 4 with the --skip--no-require option.
-subtest06: test a requirement without a ticket entry.
-subtest07: test a requirement block with a multiline description.
-subtest08: test a requirement block that is defined but empty.
-subtest09: test a requirement block with too many dashes.
-subtest10: test a requirement block missing the end keyword (or a typo).

CASL Ticket # - 5690

* Getting back to reality (from Mars).

Description:
  Replace requirement statements with what's being test in that subtest.

CASL Ticket # - 5690

* Comment out the dependence of IPython package since the HTML table was deactivated (#184)
  * This package is probably another missing one on travis CI.
  * Command line helper messages about "HTML" are also updated to 'latex'.

* Temporarily make the failing test verbose in travis CI (#184).

* Sort the file pathes to avoid ambiguity of file orders in the requirement table (#184).

* Restore travis CI ctesting (#184).)
Co-authored-by: Dan Jabaay <djabaay@umich.edu>
Co-authored-by: Yuxuan Liu <yuxuanl@umich.edu>