ExaDEM & ExaNBody Documentation

ExaDEM Variant

• 1. ExaDEM Software
  • 1.1. Overview of ExaDEM
  • 1.2. ExaDEM Capabilities
  • 1.3. Default Execution Graph With ExaDEM
• 2. Installing ExaDEM
  • 2.1. Installation With CMake
    • 2.1.1. Minimal Requirements
    • 2.1.2. Optional Dependencies
    • 2.1.3. ExaDEM Installation
    • 2.1.4. Launch examples / ctest
  • 2.2. Installation With Spack
    • 2.2.1. Installing Spack
    • 2.2.2. Installing ExaDEM
  • 2.3. Running your simulation
    • 2.3.1. CMake
    • 2.3.2. Spack
  • 2.4. Adding Optional Packages:
    • 2.4.1. RSA
    • 2.4.2. Rockable
• 3. Test cases
  • 3.1. Example Using Spheres
    • 3.1.1. Example 1: Rotating drum
    • 3.1.2. Example 2: Rigid surface
    • 3.1.3. Example 3: Impose Velocity
    • 3.1.4. Example 4: Movable wall
    • 3.1.5. Example 5: Using a RShape Driver (STL)
    • 3.1.6. Example 6: Particle Generation With RSA Algorithm
    • 3.1.7. Example 7: Jet
    • 3.1.8. Example 8: Mirror Boundary Conditions
  • 3.2. Examples Using Polyhedra
    • 3.2.1. Example 1: Polyhedra Generation Frequency
    • 3.2.2. Example 2: Octahedra in a Rotating Drum
    • 3.2.3. Example 3: Hexapods in a Ball
    • 3.2.4. Example 4: Polyhedra With a RShape Driver (Box)
    • 3.2.5. Example 5: Funnel
    • 3.2.6. Example 6: Rescale shape
    • 3.2.7. Example 7: Fragmentation with two fragments
    • 3.2.8. Example 8: Impact of a Sphere
  • 3.3. Show-cases
    • 3.3.1. On a laptop or single node
      • 3.3.1.1. Rotating drum simulation
    • 3.3.2. On a supercomputer
      • 3.3.2.1. Mixer simulation
• 4. User Guide
  • 4.1. Spherical Particle
    • 4.1.1. Interaction / Contact
  • 4.2. R-Shape / Polyhedron
    • 4.2.1. Overview
    • 4.2.2. Shape
    • 4.2.3. Basic Shapes
    • 4.2.4. Interaction / Contact
    • 4.2.5. Fragmentation Feature
    • 4.2.6. Data layout: Particle Vertices
  • 4.3. Particle Fields
    • 4.3.1. Unified Field Operators
    • 4.3.2. Field Operators For All Particles
    • 4.3.3. Field Operators For Polyhedra
  • 4.4. Force Field
    • 4.4.1. Contact Force Laws
      • 4.4.1.1. Elastic linear force with friction tangent force (hooke)
      • 4.4.1.2. cohesive normal law
      • 4.4.1.3. dmt adhesive normal law
    • 4.4.2. Contact Law Operators
    • 4.4.3. Multi-Material
    • 4.4.4. External Forces
    • 4.4.5. Inner Bond Forces
  • 4.5. Numerical Scheme
    • 4.5.1. Velocity Verlet Scheme
    • 4.5.2. Operators
      • 4.5.2.1. Reset Forces and Moments
      • 4.5.2.2. Update Particle Acceleration
      • 4.5.2.3. Update Particle Orientation
      • 4.5.2.4. Update Angular Velocity
      • 4.5.2.5. Update Angular Acceleration
      • 4.5.2.6. Combined Prolog
      • 4.5.2.7. Combined Epilog
  • 4.6. Drivers
    • 4.6.1. Quick Overview of Drivers
      • 4.6.1.1. What is a driver in ExaDEM
      • 4.6.1.2. Common Driver Parameters
      • 4.6.1.3. Add a Driver To Your Simulation
    • 4.6.2. Rotating Drum / Cylinder
    • 4.6.3. Wall / Surface
      • 4.6.3.1. STATIONARY mode
      • 4.6.3.2. LINEAR_MOTION mode
      • 4.6.3.3. LINEAR_COMPRESSIVE_MOTION mode
      • 4.6.3.4. SHAKER mode
      • 4.6.3.5. PENDULUM_MOTION mode
    • 4.6.4. Ball / Sphere
      • 4.6.4.1. STATIONARY mode
      • 4.6.4.2. LINEAR MOTION mode
      • 4.6.4.3. COMPRESSIVE_FORCE mode
      • 4.6.4.4. TABULATED mode
    • 4.6.5. RShape / Polyhedron
      • 4.6.5.1. STATIONARY mode
      • 4.6.5.2. LINEAR_MOTION mode
      • 4.6.5.3. TABULATED mode
      • 4.6.5.4. LINEAR_FORCE_MOTION mode
      • 4.6.5.5. LINEAR_COMPRESSIVE_MOTION mode
      • 4.6.5.6. SHAKER mode
      • 4.6.5.7. EXPRESSION mode
      • 4.6.5.8. Applying a Constant Moment with Sample Retroaction
    • 4.6.6. Modification of a Driver’s Motion Type
    • 4.6.7. I/O Drivers
    • 4.6.8. Advanced Operators
      • 4.6.8.1. Update Grid For RShape Driver
      • 4.6.8.2. Compute Driver Vertices
      • 4.6.8.3. Check Driver Displacement
  • 4.7. Input/Output
    • 4.7.1. Configuration
      • 4.7.1.1. IO Configuration
    • 4.7.2. Checkpoint/Restart Operators
      • 4.7.2.1. Reader Of xyz File
      • 4.7.2.2. Reader Of MPIIO File
      • 4.7.2.3. Restart file script
      • 4.7.2.4. Reader Of Rockable Files
      • 4.7.2.5. Read Shape File
      • 4.7.2.6. Writer Of MPIIO Files
      • 4.7.2.7. Writer Of Rockable Files
      • 4.7.2.8. Writer Of XYZ Files
  • 4.8. Post Processings
    • 4.8.1. Paraview For Polyhedra
    • 4.8.2. Paraview With OBB
    • 4.8.3. Contact Network
    • 4.8.4. Project Field Quantities onto Cartesian Grid
    • 4.8.5. Dump Interaction Data
    • 4.8.6. Interaction Summary
    • 4.8.7. Global Stress Tensor
    • 4.8.8. Particle Counter
    • 4.8.9. Barycenter
  • 4.9. External Packages
    • 4.9.1. RSA_MPI package
• 5. Developer Guide
  • 5.1. ExaDEM Changelog
    • 5.1.1. Release Note
      • 5.1.1.1. Release Notes v1.1.0 (03/25)
      • 5.1.1.2. Release Notes v1.0.2 (11/24)
      • 5.1.1.3. Release Notes for Version 1.0.1 (06/24):
  • 5.2. Parallelization
    • 5.2.1. MPI Parallelization
      • 5.2.1.1. Domain Decomposition
      • 5.2.1.2. Cost Model
    • 5.2.2. Thread Parallelization
    • 5.2.3. GPU Support
    • 5.2.4. Benchmarks
      • 5.2.4.1. Balde - CPU (Polyhedron)
      • 5.2.4.2. Rotating Drum - GPU (Polyhedron)
      • 5.2.4.3. Rotating Drum - CPU (Sphere)
  • 5.3. Contributing Guide
    • 5.3.1. Using the issue tracker
    • 5.3.2. Bug reports
      • 5.3.2.1. Guidelines for bug reports:
    • 5.3.3. Pull requests
      • 5.3.3.1. Style
      • 5.3.3.2. Tests
    • 5.3.4. Pull request process
  • 5.4. Contributors
    • 5.4.1. Main developers
    • 5.4.2. Developers
• 6. Tutorials
  • 6.1. Polyhedra tutorials
    • 6.1.1. Build Your Rotating Drum Simulation With Hexapods And A Particle Generator
    • 6.1.2. Tutorial: Blade simulation
  • 6.2. Developers Tutorials
    • 6.2.1. Add Your Own mutator_field Operator
• 7. Public Examples
  • 7.1. Example 1
  • 7.2. Example 2
  • 7.3. Example 3

ExaNB Framework

• 1. ExaNBody: Framework for N-Body Simulations on HPC Platforms
  • 1.1. ExaDEM Variant
  • 1.2. ExaSPH Variant
  • 1.3. ExaSTAMP Variant
• 2. Installing ExaNB
• 3. N-Body Background
  • 3.1. N-body methods
  • 3.2. N-body simulation codes
• 4. Software stack of ExaNBody
  • 4.1. Software Stack Layers:
  • 4.2. Guidelines for operators:
• 5. Performance and portability
  • 5.1. Application level specialization
  • 5.2. Spatial domain decomposition and inter-process communications
  • 5.3. Intra-node parallelization API
  • 5.4. Particle data layout and auxiliary data structures
  • 5.5. Flexible and user friendly construction of N-Body simulations
• 6. Algorithm Patterns
  • 6.1. Block Parallel For
  • 6.2. Compute Cell Particles
  • 6.3. Reduce Cell Particles
  • 6.4. Compute Pair Interaction
• 7. List of Plugins
  • 7.1. DefBox
  • 7.2. Core features
  • 7.3. Logic
  • 7.4. AMR
  • 7.5. ParticleNeighbors
  • 7.6. GridCellParticles
  • 7.7. IO
  • 7.8. Extra Storage
  • 7.9. MPI
• 8. ExaNBody Command Lines
  • 8.1. Command line and input file interaction
  • 8.2. Commands ‘Help’ for your application
  • 8.3. Index of command line options to customize configuration block
  • 8.4. Tune your run with OpenMP
  • 8.5. Tune GPU execution options
  • 8.6. Profiling tools available in exaNBody
  • 8.7. Using Timers with MPI and GPU
  • 8.8. Debug features in exaNBody
• 9. Tutorials
  • 9.1. Add a new plugin
  • 9.2. Add a new operator
• 10. ExaNBody Publications
• 11. Example for rst usage (math, code etc)
  • 11.1. Example of math citatiion :
  • 11.2. Example of math with latex as equation :
  • 11.3. Example of math with latex as inline text :
  • 11.4. Example of bash code :
  • 11.5. Example of cpp code :
  • 11.6. Example of yaml code :
  • 11.7. Example of simple figure :

Using exaNBody applications on Adastra

• 1. Installing ExaNB and Your application on Adastra
  • 1.1. Download sources
  • 1.2. Load your Environment:
  • 1.3. Configuration File Example
  • 1.4. Compilation:
  • 1.5. Compile And Run Your Application On Adastra
  • 1.6. Profiling tools:

[1]

Thierry Carrard, Raphaël Prat, Guillaume Latu, Killian Babilotte, Paul Lafourcade, Lhassan Amarsid, and Laurent Soulard. ExaNBody: a HPC framework for N-Body applications. In Euro-Par 2023: Parallel Processing Workshops, 342–354. Cham, 2024. Springer Nature Switzerland. doi:10.1007/978-3-031-50684-0_27.

[2]

Emmanuel Cieren, Laurent Colombet, Samuel Pitoiset, and Raymond Namyst. Exastamp: a parallel framework for molecular dynamics on heterogeneous clusters. In Euro-Par 2014: Parallel Processing Workshops: Euro-Par 2014 International Workshops, Porto, Portugal, August 25-26, 2014, Revised Selected Papers, Part II 20, 121–132. Springer, 2014. doi:10.1007/978-3-319-14313-2_11.

[3]

Estelle Dirand, Laurent Colombet, and Bruno Raffin. Tins: a task-based dynamic helper core strategy for in situ analytics. In Supercomputing Frontiers: 4th Asian Conference, SCFA 2018, Singapore, March 26-29, 2018, Proceedings 4, 159–178. Springer, 2018. doi:10.1007/978-3-319-69953-0_10.

[4]

O Durand, L Soulard, L Colombet, and R Prat. Influence of the phase transitions of shock-loaded tin on microjetting and ejecta production using molecular dynamics simulations. Journal of Applied Physics, 2020. doi:10.1063/5.0003744.

[5]

Olivier Durand, S Jaouen, L Soulard, Olivier Heuze, and Laurent Colombet. Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension. Journal of Applied Physics, 2017. doi:10.1063/1.4994789.

[6]

Luning Fang, Ruochun Zhang, Colin Vanden Heuvel, Radu Serban, and Dan Negrut. Chrono:: gpu: an open-source simulation package for granular dynamics using the discrete element method. Processes, 9(10):1813, 2021.

[7]

Marc Josien and Raphaël Prat. Parallel and bias-free rsa algorithm for maximal poisson-sphere sampling. Computer Physics Communications, 305:109354, 2024. doi:https://doi.org/10.1016/j.cpc.2024.109354.

[8]

Raphaël Prat, Thierry Carrard, Laurent Soulard, Olivier Durand, Raymond Namyst, and Laurent Colombet. Amr-based molecular dynamics for non-uniform, highly dynamic particle simulations. Computer Physics Communications, 253:107177, 2020. doi:10.1016/j.cpc.2020.107177.

[9]

Raphaël Prat, Laurent Colombet, and Raymond Namyst. Combining task-based parallelism and adaptive mesh refinement techniques in molecular dynamics simulations. In Proceedings of the 47th International Conference on Parallel Processing, 1–10. 2018. doi:10.1145/3225058.3225085.

[10]

L Soulard. Micro-jetting: a semi-analytical model to calculate the velocity and density of the jet from a triangular groove. Journal of Applied Physics, 2023. doi:10.1063/5.0142057.

[11]

L Soulard, Th Carrard, and O Durand. Molecular dynamics study of the impact of a solid drop on a solid target. Journal of Applied Physics, 2022. doi:10.1063/5.0083266.

[12]

Laurent Soulard and O Durand. Observation of phase transitions in shocked tin by molecular dynamics. Journal of Applied Physics, 2020.

[13]

Laurent Soulard, Olivier Durand, Jean-René Burie, and Killian Babilotte. Micro-jetting: areal density calculation from a triangular groove. Journal of Applied Physics, 2024. doi:10.1063/5.0209692.