Merge branch 'jeremy/short-names' into 'main'

- Add support of user setting any 2 of the 5 neo-Hookean model parameters: Poisson's ratio, Young's modulus, shear modulus, Lame's first parameter, and bulk modulus.

- Add flexible flux boundary conditions with time variance during a quasistatic or dynamic simulation.

- Add command line option `-view_models` to display list of all Ratel material models.

### Breaking changes

	$(info ENZYME_LIB    = $(or $(ENZYME_LIB),(not found)))

	$(info ADOLC_LIB     = $(or $(ADOLC_LIB),(not found)))

	$(info ADOLC_INCLUDE = $(or $(ADOLC_INCLUDE),(not found)))

	$(info FC (UHyper)   = $(or $(FC),(not found)))

	$(info )

	$(info -----------------------------------------)

	$(info )

	$(info ENZYME_LIB     = $(or $(ENZYME_LIB),(not found)))

	$(info ADOLC_LIB      = $(or $(ADOLC_LIB),(not found)))

	$(info ADOLC_INCLUDE  = $(or $(ADOLC_INCLUDE),(not found)))

	$(info FC (UHyper)   = $(or $(FC),(not found)))

	$(info )

	$(info -----------------------------------------)

	$(info )

# Source files

# ------------------------------------------------------------

libratel.c := $(sort $(filter-out $(SRCDIR)/internal/ratel-jit-source-root-$(if $(for_install),default,install).c %-ad-enzyme.c %-ad-adolc.c %-uhyper.c, $(shell find $(SRCDIR) -type f -name "*.c")))

libratel.c := $(sort $(filter-out $(SRCDIR)/internal/ratel-jit-source-root-$(if $(for_install),default,install).c %-ad-enzyme.c %-ad-adolc.c %uhyper.c, $(shell find $(SRCDIR) -type f -name "*.c")))

# Enzyme-AD

ifneq ($(ENZYME_LIB),)

	CFLAGS     += $(ENZYMEFLAGS)

	libratel.c += $(sort $(wildcard $(SRCDIR)/materials/*-ad-enzyme.c))

	libratel.c += $(sort $(wildcard $(SRCDIR)/materials/**/**/*-ad-enzyme.c))

endif

# ADOL-C

ifneq ($(WITH_ADOLC),)

    LDLIBS       += -ladolc

    CXXFLAGS     += -fPIC

	libratel.c   += $(sort $(wildcard $(SRCDIR)/materials/*-ad-adolc.c))

	libratel.cpp += $(sort $(wildcard $(SRCDIR)/materials/*-ad-adolc-cpp.cpp))

	libratel.c   += $(sort $(wildcard $(SRCDIR)/materials/**/**/*-ad-adolc.c))

	libratel.cpp += $(sort $(wildcard $(SRCDIR)/materials/**/**/*-ad-adolc-cpp.cpp))

endif

# UHyper

ifneq ($(FC),)

  libratel.c   += $(sort $(wildcard $(SRCDIR)/materials/*-uhyper.c))

  libratel.for := $(sort $(wildcard $(SRCDIR)/materials/*_uhyper.for))

  libratel.c   += $(sort $(wildcard $(SRCDIR)/materials/**/**/*uhyper*.c))

  libratel.for := $(sort $(wildcard $(SRCDIR)/materials/**/**/*uhyper*.for))

endif

# Tests

# Developer Notes

## Style Guide

Please check your code for style issues by running

Also, documentation files should have one sentence per line to help make git diffs clearer and less disruptive.

## Function Conventions

### Naming

    All other functions should have their *declarations* prefixed with `RATEL_INTERN`.

    Function *definitions* should have neither.

## Logging

Ratel supports logging at four levels: trace, debug, info, and warn.

Previously, Ratel used macros `RatelDebug` and `RatelDebug256` for plain and colored debug output.

These macros are now deprecated.

### Logging Complex Data

Ratel also supports logging data which cannot be natively passed to `printf`.

```

## Clang-tidy

Please check your code for common issues by running

This tool is much slower than actual compilation (`make -j` parallelism helps).

All issues reported by `make tidy` should be fixed.

## Header Files

Header inclusion for source files should follow the principal of 'include what you use' rather than relying upon transitive `#include` to define all symbols.

Header guard macros should be done using `#pragma once`. This must be the very first non-comment line of the file.

## `restrict` Semantics

QFunction arguments can be assumed to have `restrict` semantics.

That is, each input and output array must reside in distinct memory without overlap.

## Continuous Integration (CI) and Testing

Whenever a merge request is created, the Ratel test suite is run against a variety of hardware and software configurations.

You can also see the CGNS or CSV output of a failed run, if applicable, by selecting "Download" on the Job Artifacts (to the right of the log).

Artifacts from failed runs will be contained in the `test_failure_artifacts` folder inside the artifacts archive.

## Adding New Material Models

Each material model (`elasticity-neo-hookean-damage-current`, etc.) requires files in several places.

- Any new typedefs for structs required by the material model go in `include/ratel/models/`. For example, the struct typedefs for neo-Hookean models are located in `include/ratel/models/neo-hookean.h`.

- The functions for creating these parameter structs from command line options goes in `src/materials/[model group]/params`, where `[model group]` is a broad category, such as `elasticity` or `poromechanics`. For example, the functions for creating the parameter structs for neo-Hookean damage are located in `src/materials/elasticity/params/neo-hookean.c` and `src/materials/elasticity/params/damage.c`.

- The QFunction source for the material model goes in `include/ratel/qfunctions/models/...`. Select the correct folder and file name based upon the material model. For example, the QFunction source file for neo-Hookean elasticity in the current configuration with damage is `include/ratel/qfunctions/models/elasticity/neo-hookean/damage-current.h`. Additional files in the folders under `include/ratel/qfunctions/...` may contain common code, such as `include/ratel/qfunctions/models/elasticity/neo-hookean/damage-common.h` or `include/ratel/qfunctions/utils.h`.

- The associated model data structs, creation function, and registration function for the material model goes in `src/materials/[model group]`, where `[model group]` is a broad category, such as `elasticity` or `poromechanics`. This folder may be further subdivided. For example, the file for neo-Hookean elasticity in the current configuration with damage is `src/materials/elasticity/neo-hookean/damage-current.h`. All of the functions in this file should have a common, unique suffix, such as `_ElasticityNeoHookeanDamageCurrent`.

- Finally, the command line option string for the material model and its unique function suffix should be added to `src/materials/ratel-model-list.h`, wrapped in the `RATEL_MODEL` macro. This macro is used in `src/materials/ratel-model.c` to register the full list of material models available to users.

- If the material model requires special dependencies, such as Enzyme or ADOL-C, then do not list this material model in `src/materials/ratel-model-list.h`. Instead, place the command line option string and unique function suffix in a separate header, such as `src/materials/ratel-model-list-enzyme.h` and include this header in `src/materials/ratel-model-list.h`. Also create a corresponding file in `src/materials/weak`, such as `src/materials/weak/ratel-model-enzyme-weak.c`, to register a weak symbol for this material model if the required dependencies are not available at compile time. Corresponding logic will also need to be added to `Makefile`.

## Adding New Boundary Conditions

Each boundary condition (e.g. pressure, slip, traction, flux, etc.) gets its own folder `include/ratel/boundary/[bc-name]` containing:

                                                        &RatelBoundarySetupMultigridLevel_CellToFace));

```

## Adding New Initial Conditions

Ratel supports non-zero initial condition for linear poromechanincs MMS and as a constant value for other cases. If user needs to add non-zero initial condition as function of coordinate, a function with the same structure as `RatelSetupInitialConditionMMS` needs to be added with its own QFunction expressing the initial condition of each active field.

  -

* - `-model`

  - Material model to use (`elasticity-linear`, `elasticity-neo-hookean-current`, `elasticity-mooney-rivlin-initial`, etc.)

  - Material model to use (`elasticity-linear`, `elasticity-neo-hookean-current`, `elasticity-mooney-rivlin-initial`, etc.). Note: The option `-view_models` will display all valid values for this option.

  - `elasticity-linear`

* - `-forcing`

* - `-help`

  - View comprehensive information about run-time options

  -

* - `-view_models`

  - View full list of material model command line options

  -

:::

To verify the convergence of the linear elasticity formulation on a given mesh with the method of manufactured solutions, run:

#include "contact-common.h"

#include "friction.h"

#include "ratel/qfunctions/models/elasticity-common.h"

#include "ratel/qfunctions/models/elasticity/common.h"

#include "ratel/qfunctions/utils.h"

// Shapes