Fierro

Fierro (LANL code number C21030) is a modern C++ code designed to simulate quasi-static solid mechanics problems and transient, compressible material dynamic problems with Lagrangian methods, which have meshes with constant mass elements that move with the material, or with Eulerian methods, which have stationary meshes. Fierro is designed to aid a) material model research that has historically been done using commercial implicit and explicit finite element codes, b) numerical methods research, and c) computer science research. The linear Lagrangian finite element methods in Fierro supports user developed material models. Fierro is built on the ELEMENTS library that supports a diverse suite of element types, including high-order elements, and quadrature rules. The mesh class within the ELEMENTS library is designed for efficient calculations on unstructured meshes and to minimize memory usage. Fierro is designed to readily accommodate a range of numerical methods including continuous finite element, finite volume, and discontinuous Galerkin methods. Fierro is designed to support explicit and implicit time integration methods as well as implicit optimization methods.

Computer implementation

Fierro is implemented in C++ following modern programming practices. Fierro leverages the unique features of the ELEMENTS library, as such, this code serves as an example for solving a system of partial differential equations using the mesh class and geometric functions within the ELEMENTS library. Fierro registers state at material points within the element, registers polynomial fields in the element, and registers kinematic variables at element vertices. The routines for the state are designed for highly efficient computations and to minimize memory usage. The loops are written to aid fine-grained parallelization and to allow vectorization. Fierro is a light-weight software application, and cleanly written following modern programming practices, so it useful for researching computer science based technologies for software performances portability.

Spatial discretization methods

Fierro has an established conservative low-order Lagrangian finite element method, a low-order Lagrangian cell-centered finite volume method, and an arbitrary-order Lagrangian Discontinuous Galerkin method for solving the governing equations (e.g., mass, momentum, and energy evolution equations) for compressible material dynamics using unstructured hexahedral meshes. These methods are combined with a multidirectional approximate Riemann solver (MARS) for improved accuracy on smooth flows and stable solutions near velocity discontinuities and large gradients in a flow. Fierro is designed for both low and high-order Lagrangian methods research and development but other types of numerical methods can be readily added to the code. Likewise, other high-order methods can be studied within the code because it is built upon the ELEMENTS library that supports high-order elements and high-order quadrature rules. Numerical methods are being added to Fierro to simulate quasi-static solid mechanics problems. Likewise, direct Eulerian hydrodynamic methods can be investigated using Fierro.

Temporal discretization methods

Fierro supports a range of published multi-step time integration methods. The code has an explicit multi-step Runge Kutta time integration method. Implicit time integration methods can be implemented in Fierro.

Usage

Anaconda

The recommended way to use Fierro is through the provided Anaconda package. To use the anaconda package, follow the steps for your platform to install anaconda/miniconda/mamba.

Open a terminal on your machine and go to a folder where you want to run the Fierro code. Then create and activate an Anaconda environment by typing:

conda create -n FierroCode
conda activate FierroCode  

In this example, the enviroment is called FierroCode, but any name can be used. In some cases, the text to activate an enviroment is source activate FierroCode. Likewise, if an enviroment already exists, then just activate the desired environment.

To install the finite element physics solvers in Fierro, please type within the activated Anaconda environment:

conda install -c conda-forge -c fierromechanics fierro-fe-cpu

The EVPFFT physics solver in Fierro can be installed by typing:

conda install -c conda-forge -c fierromechanics fierro-evpfft-cpu

A GUI is offered, it can be installed by typing:

conda install -c conda-forge -c fierromechanics fierro-gui

After installing the finite element solvers, it gives you access to fierro-mesh-builder,fierro-parallel-explicit,fierro-parallel-implicit, and the fierro-voxelizer executables. These can be run by calling the appropriate executable with the desired input. For example, to call the parallel explicit hydrodynamics solver, use the following command:

fierro-parallel-explicit input.yaml

Sample yaml input files for the explicit finite element solver can be found at: ./src/Parallel-Solvers/Parallel-Explicit/Example_Yaml_Scripts

The implicit solver and topology optimization modules can be called using:

fierro-parallel-implicit input.yaml

Sample yaml input files for the implicit finite element solver and topology optimization problem setups can be found at: ./src/Parallel-Solvers/Implicit-Lagrange/Example_Yaml_Scripts

The GUI can be run in the anaconda enviroment by typing:

fierro-gui

The anaconda distributions of Fierro are located here.

Material models

The classical ideal gas model is the only material model implemented in the code, and it is useful for verification tests of the software and simple gas dynamic simulations. The linear Lagrangian finite element methods for explicit material dynamics have an interface to user developed material models. The interface is to enable Fierro to be used for model research and development that has historically been done with commercial explicit finite element codes.

To include your own custom material models, you need to implement them under Fierro/Parallel-Solvers/User-Material-Interface and re-build the project. Steps:

1. Create an anaconda environment for your build
2. Install Fierro anaconda dependencies with conda install elements fierro-trilinos-cpu elements -c fierromechanics
3. Clone the code
4. Build the code

Now, if all went correctly, you should be able to run your custom Fierro build by calling the executable located at Fierro/build/bin/fierro. The executables can be installed into your system directories with the make install command as well.

Cloning the code

If the user has set up ssh keys with GitHub, type

git clone --recursive ssh://git@github.com/lanl/Fierro.git

The code can also be cloned using

git clone --recursive https://github.com/lanl/Fierro.git

Building the code

Building the code from source allows you to compile with more targeted hardware optimizations that could offer a potentially faster executable. To build it yourself, run the following from the root directory. The native CPU architecture will automatically be taken into account.

GPU hardware will be leveraged according to the distribution of Trilinos that Fierro is built against. You are welcome to only compile the desired solver, or all of the currently available ones.

Building dependencies

Fierro depends on both ELEMENTS and Trilinos. If you are building Fierro for hardware optimizations, you should also build ELEMENTS from source. ELEMENTS is included in the Fierro source distribution and building ELEMENTS is enabled by default when building Fierro.

As for Trilinos, we recommend installing the Anaconda package for the desired build into a new Anaconda environment to satisfy Fierro's dependency rather than building it from source. If you do wish to build it from source, however, sample build scripts for Trilinos can be found in Fierro/Trilinos-Build-Scripts. Build scripts for all Anaconda packages can be found in Fierro/Anaconda-Packages/.

Alternative Build Workflows

In addition to the primary build workflow described above, there are build scripts for a variety of alternative workflows. These scripts can be found under Fierro/scripts. Although there are multiple scripts shown in this directory, the only one that will be run directly by the user is build-fierro.sh

Building the explicit and implicit Lagrangian methods with Trilinos+Kokkos

Explicit Lagrangian codes are being added to the repository that are written using MATAR+Kokkos and run with fine-grained parallellism on multi-core CPUs and GPUs. Build scripts are provided for each Lagrangian code, and those scripts follow those used in the MATAR GitHub repository. The scripts to build the Lagrangian codes (that use MATAR+Kokkos) are in the scripts folder. The user must update the modules loaded by the build scripts (for the compiler etc.), and then type Immediate help with all scripts can be had running

source {path-to-repo}/build-fierro.sh --help

The default run will build the full-app settting up the Explicit* solver with serial Kokkos for a linux computer (non-HPC machine) Running with --help option will list all parameters and their accepted arguments If the scripts fail to build a Lagrangian code, then carefully review the modules used and the computer architecture settings.
For building on a Mac, please see the extra info in the BUILD.md #A more lenghtly discussion of the build scripts is provided in the MATAR GitHub repository.

For help with Trilinos For help with Kokkos compilation

Updating submodules

The ELEMENTS library and MATAR library can be updated to the newest release using

git submodule update --remote --merge

Contributing to Fierro

As an open source software team, we greatly appreciate any and all community involvement. There are many ways to contribute to Fierro, from tidying up code sections to implementing novel solvers. To streamline the integration of community contributions, we follow the following guidelines.

Writing commit messages

Write your commit messages using these standard prefixes:

• BUG: Fix for runtime crash or incorrect result
• COMP: Compiler error or warning fix
• DOC: Documentation change
• ENH: New functionality
• PERF: Performance improvement
• STYLE: No logic impact (indentation, comments)
• WIP: Work In Progress not ready for merge

The commit message should assist in the review process and allow future developers to understand the change. To that end, please follow these few rules:

1. Try to keep the subject line below 72 characters, ideally 50.
2. Be concise, but honor the change.
3. If the change is uncharacteristically large (or diverse), consider breaking the change into multiple distinct commits.
4. If the commit references a specific issue, link it in the message

This is a great post on how to write a good commit message.

The PR Process

If you are new to Fierro development and don't have push access to the repository, here are the steps:

1. Fork and clone the repository.
2. Create a branch for your work.
3. Push the branch to your GitHub fork.
4. Build and test your changes.
5. Update any necessary documentation.
6. Synchronize your branch with changes made to the upstream repository since the last merge/fork.
7. Create a Pull Request.

This corresponds to the Fork & Pull Model described in the GitHub collaborative development documentation.

Integrating a PR

Integrating your contributions to Fierro is relatively straightforward; here is the checklist:

• All tests pass
• The changes build with no new compiler warnings/errors
• All feedback has been addressed
• Consensus is reached. This usually means that at least two reviewers approved the changes (or added a LGTM comment) and at least one business day passed without anyone objecting. LGTM is an acronym for Looks Good to Me.
• If you do NOT have push access, a Fierro core developer will integrate your PR.

Benevolent dictators for life

The benevolent dictators can integrate changes to keep the platform healthy and help interpret or address conflict related to the contribution guidelines and the platform as a whole.

These currently include:

• Nathaniel Morgan