Documentation for alamo

Getting Started

Initial step-by-step instructions for downloading, building, and running Alamo. Basic instructions on troubleshooting.

Start here if you’re brand new

Running Tests

Explore the set of examples and regression tests that demonstrate Alamo functionality.

Next steps after compiling Alamo

SimBA

Use the Alamo Simulation Browser Analysis system to manage Alamo simulations for regression tests or your own projects.

Optional but useful for regular users

API and Inputs

Browse the auto-generated documentation for Alamo classes and input file input specifications.

For those using existing code to run new siulations.

Developer Instructions

Basics of Alamo design philosophy and practice. How to create branches, implement new models, run tests, and avoid breaking the repository.

Starting point for all new alamo developers

Alamo’s autodoc system

Alamo’s custom auto-documentation and test system designed to enforce documentation and testing standards, while preventing stagnant/depricated content.

Required reading for all developers

References

• Vinamra Agrawal and Brandon Runnels. Block structured adaptive mesh refinement and strong form elasticity approach to phase field fracture with applications to delamination, crack branching and crack deflection. Computer Methods in Applied Mechanics and Engineering, 385:114011, 2021.

• Vinamra Agrawal and Brandon Runnels. Robust, strong form mechanics on an adaptive structured grid: efficiently solving variable-geometry near-singular problems with diffuse interfaces. Computational Mechanics, 2023.

• Asha-Dee N Celestine, Vinamra Agrawal, and Brandon Runnels. Experimental and numerical investigation into mechanical degradation of polymers. Composites Part B: Engineering, 201:108369, 2020.

• Erdem Eren, Brandon Runnels, and Jeremy Mason. Comparison of evolving interfaces, triple points, and quadruple points for discrete and diffuse interface methods. Computational Materials Science, 213:111632, 2022.

• Mahi Gokuli and Brandon Runnels. Multiphase field modeling of grain boundary migration mediated by emergent disconnections. Acta Materialia, 217:117149, 2021.

• Yang Hu, Dennis M Kochmann, and Brandon Runnels. Atomistic-informed phase field modeling of magnesium twin growth by disconnections. arXiv preprint, 2024.

• Baburaj Kanagarajan, J Matt Quinlan, and Brandon Runnels. A diffuse interface method for solid-phase modeling of regression behavior in solid composite propellants. Combustion and Flame, 2022.

• Maycon Meier and Brandon Runnels. Finite kinematics diffuse interface mechanics coupled to solid composite propellant deflagration. Computer Methods in Applied Mechanics and Engineering, 427:117040, 2024.

• Maycon Meier, Emma Schmidt, Patrick Martinez, J Matt Quinlan, and Brandon Runnels. Diffuse interface method for solid composite propellant ignition and regression. Combustion and Flame, 259:113120, 2024.

• Josep Gras Ribot, Vinamra Agrawal, and Brandon Runnels. A new approach for phase field modeling of grain boundaries with strongly nonconvex energy. Modelling and Simulation in Materials Science and Engineering, 27(8):084007, 2019.

• Brandon Runnels and Vinamra Agrawal. Phase field disconnections: a continuum method for disconnection-mediated grain boundary motion. Scripta Materialia, 186:6–10, 2020.

• Brandon Runnels, Vinamra Agrawal, Weiqun Zhang, and Ann Almgren. Massively parallel finite difference elasticity using block-structured adaptive mesh refinement with a geometric multigrid solver. Journal of Computational Physics, 427:110065, 2021.

• Jared W Strutton, Newell H Moser, Edward J Garboczi, Abby R Jennings, Brandon Runnels, and Jena M McCollum. Interface history on strain field evolution in epoxy resins. ACS Applied Polymer Materials, 2022.

Sponsors

The development team gratefully acknowledges the funding sources that enable the development and extension of Alamo.

Office of Naval Research

Mesoscale and continuum modeling of solid-phase propellant coupled to gas-phase to determine continuum burn rates in AP/HTPB

National Science Foundation

CAREER: A multichannel convolutional neural network framework for prediction of damage nucleation sites in microstructure

National Science Foundation

MRI: Acquisition of a high performance computing cluster for next-generation computational science in Southern Colorado

Berkeley Lab

Extending the capability of the AMReX MLMG nodal solver

Table of contents

Contents:

• Getting Started
  • Downloading Alamo
  • Installing dependencies
  • Setting MPICH as default MPI
  • Configuring
  • Compiling
  • Testing
  • Common Error Messages
  • Generating this documentation
  • Compiling on STAMPEDE2
  • System Install Scripts
    • Ubuntu
      • 20.04 and 22.04
    • Mac OS
    • Windows
• SimBA
  • Running SimBA
  • Updating SimBA Records
  • Sharing results on the network
• Autodoc and Autotest
  • Autodoc system
    • Parser comments
    • Header comments
    • ReStructuredText
    • Documentation generation
  • Autotest system
    • Test requirements
    • Creating a test
    • Input file directives
    • Test verification
• Tests
• Inputs
  • BC
    • BC::Constant
    • BC::Expression
    • BC::Operator
      • BC::Operator::Elastic
  • IC
    • IC::BMP
    • IC::Cuboid
    • IC::Constant
    • IC::Ellipse
    • IC::Expression
    • IC::Laminate
    • IC::PS
    • IC::PSRead
    • IC::PerturbedInterface
    • IC::PNG
    • IC::Random
    • IC::Sphere
    • IC::Trig
    • IC::TabulatedInterface
    • IC::Voronoi
  • IO
    • IO::FileNameParse
    • IO::ParmParse
    • IO::WriteMetaData
  • Integrator
    • Integrator::AllenCahn
    • Integrator::CahnHilliard
    • Integrator::Dendrite
    • Integrator::Flame
    • Integrator::Fracture
    • Integrator::HeatConduction
    • Integrator::Mechanics
    • Integrator::PhaseFieldMicrostructure
    • Integrator::SutureCrack
    • Integrator::ThermoElastic
    • Integrator::TopOp
    • Integrator::Base
      • Integrator::Base::Mechanics
  • Model
    • Model::Interface
      • Model::Interface::Crack
      • Model::Interface::GB
    • Model::Solid
      • Model::Solid::Affine
      • Model::Solid::Finite
      • Model::Solid::Linear
  • Numeric
    • Numeric::Interpolator
      • Numeric::Interpolator::Linear
      • Numeric::Interpolator::NodeBilinear
  • Operator
    • Operator::Elastic
  • Set
    • Set::Matrix4_Isotropic
  • Solver
    • Solver::Nonlocal
      • Solver::Nonlocal::Linear
      • Solver::Nonlocal::Newton
  • Util
• Inputs Search
• Developer Guide
  • Step-by-step development guide
  • Tutorial: A new Integrator
  • Conventions
    • Namespaces
      • Regular and Pure Virtual classes
    • Include Guards
    • Member and Argument Variable Names
  • Python (In development)
    • Compiling Alamo Python interface
    • Extending the Alamo Python interface
  • Restart files
• Questions
  • Where to ask for help
  • Submitting a help request
• Builder (alpha)