This is an example of setting up a 2D SlabBurner Simulation using the gMsh python api with a series of derived slab burner points.

Mesh Generation Script

  1. Open the slabBurner2DMeshGen.py python
  2. Update the geometry if necessary
  3. To preview the resulting mesh run with the --preview argument
  4. Generate the slabBurner2DMesh.msh mesh file by running without the preview argument.

slabBurner2D/slabBurner2D_zerork.yaml

---
test:
  # a unique test name for this integration tests
  name: slabBurner2DZerork
  # run on multiple mpi ranks
  ranks: 2
  # create a list of asserts to compare
  assert:
    # create a default assert that compares the log file
    "inputs/slabBurner2D/expectedOutput.txt"

# metadata for the simulation
environment:
  title: _slabBurner2DZerork
  tagDirectory: false
# global arguments that can be used by petsc
arguments:
  # The gmsh arguments must be global because they are used before the mesh options are parsed
  dm_plex_gmsh_use_regions: true
# set up the time stepper responsible for marching in time
timestepper:
  # time stepper specific input arguments
  arguments:
    ts_type: rk
    ts_max_time: 100000
    ts_max_steps: 100
    ts_dt: 1.0E-10
    ts_adapt_safety: 0.9
    ts_adapt_type: physicsConstrained
  # io controls how often the results are saved to a file for visualization and restart
  io: !ablate::io::Hdf5MultiFileSerializer
    interval: 10 # results are saved at every 5 steps.  In real simulations this should be much larger.
  # load in the gmsh produced mesh file
  domain: !ablate::domain::MeshFile
    path: slabBurner2DMesh.msh
    options:
      dm_plex_check_all: true # check to make sure the mesh if valid from gMsh
      dm_distribute: false # turn off default dm_distribute so that we can extrude label first
      dm_plex_hash_location: true # enable the fast look up particle locations
    # specify any modifications to be performed to the mesh/domain
    modifiers:
      - # GMsh/dm_plex_gmsh_use_regions creates individual labels with their separate values. By collapsing the labels to the default values
        # this input file does not need to individually specify each one for boundary conditions
        !ablate::domain::modifiers::CollapseLabels
        regions:
          - name: inlet
          - name: wall
          - name: outlet
          - name: slab
          - name: main
      - # use the newly collapsed labels to extrude the boundary.  Do not extrude the main mesh
        !ablate::domain::modifiers::ExtrudeLabel
        regions:
          - name: inlet
          - name: wall
          - name: outlet
          - name: slab
        # mark all the resulting boundary faces with boundaryFaces label
        boundaryRegion:
          name: boundaryFaces
        # tag the original mesh as the flow region
        originalRegion:
          name: flowRegion
        # tag the new boundary cells for easy boundary condition specifications
        extrudedRegion:
          name: boundaryCells

      # if using mpi, this modifier distributes cells
      - !ablate::domain::modifiers::DistributeWithGhostCells
        ghostCellDepth: 2

      # remove the slabBurnerFace from the flowRegion so that the ablate::boundarySolver::physics::Sublimation can handle the boundary condition
      - !ablate::domain::modifiers::SubtractLabel
        differenceRegion:
          name: interiorFlowRegion
        minuendRegion:
          name: flowRegion
        subtrahendRegions:
          - name: slab
        incompleteLabel: true # allow the faces to be removed the flowRegion

      # this can be enabled to print a domain summary
      # - !ablate::domain::modifiers::PrintDomainSummary

    fields:
      # all fields must be defined before solvers.  The ablate::finiteVolume::CompressibleFlowFields is a helper
      # class that creates the required fields for the compressible flow solver (rho, rhoE, rhoU, ...)
      - !ablate::finiteVolume::CompressibleFlowFields
        # The soot equation of state is an extension of the tChem eos with support for a simple soot model
        eos: &eos !ablate::eos::zerorkEOS # the tchem eos uses tChem to parse the mechanisms and determine what species are needed to be tracked
          reactionFile: MMAReduced.soot.inp
          thermoFile: MMAReduced.soot.dat
          options:
            reactorType: ConstantPressure #zerork deafult is constant volume
            # set a minimum temperature for the chemical kinetics ode integration
            thresholdTemperature: 560
        # use a higher order field for the conserved field transport options
        conservedFieldOptions:
          petscfv_type: leastsquares
          petsclimiter_type: vanleer

      # create a conserved field to track ndd
      - !ablate::finiteVolume::ExtraVariable
        name: "Progress"
        components: [ "NDD" ]

      # by adding a pressure field the code will compute and output pressure
      - !ablate::domain::FieldDescription
        name: pressure
        type: FV
        location: aux
  # set the initial conditions of the flow field
  initialization:
    # initialize the flow the entire domain with the default values using the flow state.  The flow state can be used to compute
    # both ablate::finiteVolume::fieldFunctions::Euler and ablate::finiteVolume::fieldFunctions::DensityMassFractions consistently
    - !ablate::finiteVolume::fieldFunctions::Euler
      # the ablate::finiteVolume::fieldFunctions::CompressibleFlowState defines a field given T, P, vel, and Yi
      state: &flowFieldState
        eos: *eos
        # use a sphere geometry to set up an ignition kernel
        temperature: !ablate::mathFunctions::geom::Sphere
          center: [ 0.0182024,  0.007 ]
          radius: 0.005
          insideValues: 1673.15
          outsideValues: 300
        # set the entire domain to atmospheric pressure
        pressure: 101325.0
        # set the velocity everywhere to zero
        velocity: "0.0, 0.0"
        # the eos requires mass fractions to compute initial conditions
        other: !ablate::finiteVolume::fieldFunctions::MassFractions
          &oxMassFrac
          eos: *eos
          values:
            - fieldName: O2
              field: 1.0
    # using the same CompressibleFlowState set the initial conserved mass fractions
    - !ablate::finiteVolume::fieldFunctions::DensityMassFractions
      state: *flowFieldState

    # Set the soot number density to zero
    - fieldName: densityProgress
      field: "0.0"

    # Set the boundary cells for the slab to a different initial condition
    - !ablate::finiteVolume::fieldFunctions::Euler
      # slab Burner
      region:
        name: slab
      state: &fuelFieldState
        eos: *eos
        # the fuel is assumed to be at 653.0K
        temperature: 653.0 #fuel temperature
        pressure: 101325.0
        velocity: "0.0, 0.0"
        # set the mass fractions in the fuel boundary cells to 100% mma
        other: !ablate::finiteVolume::fieldFunctions::MassFractions
          &fuelMassFrac
          eos: *eos
          values:
            - fieldName: MMETHAC_C5H8O2 # The fuel boundary condition
              field: 1.0

    # using the fuelFieldState set the initial conserved mass fractions in the boundary slab region
    - !ablate::finiteVolume::fieldFunctions::DensityMassFractions
      region:
        name: slab
      state: *fuelFieldState

# list the solvers that apply over the main mesh and the boundary cells
solvers:
  # The compressible flow solver will solve the compressible flow equations over the interiorCells
  - !ablate::finiteVolume::CompressibleFlowSolver
    id: flowField
    # the flow solver should only operate over the interiorFlowRegion.  This does not include boundary cells or slab boundary faces
    region:
      name: interiorFlowRegion
    # set the cfl constraint to be used by the physicsConstrained time stepper
    parameters:
      cfl: 0.45

    # the flow solver requires access to the eos
    eos: *eos
    # the primary transport model applies to everything but the extra variables.
    transport: !ablate::eos::tChemSoot::SootSpeciesTransportModel
      # the SootSpeciesTransportModel adjusts the diffusion coefficient to carbon appropriately
      transport: !ablate::eos::transport::Sutherland
        eos: *eos
    # if specified, the evTransport is used for the ndd transport
    evTransport: !ablate::eos::tChemSoot::SootProgressTransportModel
      transport: !ablate::eos::transport::Sutherland
        eos: *eos
    # additional monitors can be added to the flow solver.
    monitors:
      # The time step monitor outputs the current timestep and dt every 10 steps
      - !ablate::monitors::TimeStepMonitor
        interval: 10
      # The TurbFlowStats monitor starts to take statistics after 0.01 seconds every 25 time steps
      - !ablate::monitors::TurbFlowStats
        fields: [ velocity, temperature ]
        eos: *eos
        interval: !ablate::io::interval::DelayInterval
          interval: 25
          minimumSimulationTime: .01 #about 1 flow
      # The mixture fraction calculator outputs zMix and Yi everytime the serializer saves
      - !ablate::monitors::MixtureFractionMonitor
        mixtureFractionCalculator: !ablate::monitors::MixtureFractionCalculator
          eos: *eos
          massFractionsFuel: *fuelMassFrac
          massFractionsOxidizer: *oxMassFrac
    # additional processes can be added to the flow solver
    additionalProcesses:
      # in addition to the default process PressureGradientScaling can be used to speed up the simulation.
      # the pgs must be supplied to other components to keep consistent calculations
      - !ablate::finiteVolume::processes::PressureGradientScaling
        &pgs
        eos: *eos
        alphaInit: 5.0
        maxAlphaAllowed: 100.0
        domainLength: 0.165354
      # the chemistry process is used to compute the species and energy source terms from the reactions
      - !ablate::finiteVolume::processes::Chemistry
        eos: *eos
      # ThermophoreticDiffusion diffusion controls the diffusion of solid carbon and ndd
      - !ablate::finiteVolume::processes::ThermophoreticDiffusion
        transport: !ablate::eos::transport::Sutherland
          eos: *eos
      # use ablate::finiteVolume::processes::Soot to compute ndd and carbon source terms
      - !ablate::finiteVolume::processes::Soot
        eos: *eos
        # set a minimum temperature for the chemical kinetics ode integration
        thresholdTemperature: 560
    # a flux calculator must be specified to so solver for advection
    fluxCalculator: !ablate::finiteVolume::fluxCalculator::AusmpUp
      pgs: *pgs

  # each boundary can be updated with a separate boundary solver
  - !ablate::boundarySolver::BoundarySolver
    id: inlet
    # works over the extruded cells that were labeled inlet in gMsh
    region:
      name: inlet
    fieldBoundary:
      name: boundaryFaces
    mergeFaces: true
    processes:
      # The LODI inlet boundary can adjust velocity over time
      - !ablate::boundarySolver::lodi::Inlet
        eos: *eos
        pgs: *pgs
        # The velocity is specified with a nested, nested formula to simplify specifying a radius based function
        velocity: !ablate::mathFunctions::Formula
          formula: "max(0.0, min(vel, t*vel/.001)), 0.0"
          nested:
            vel: !ablate::mathFunctions::Formula
              formula: velFac*(1 - r/(dia/2.0))^(1/7)
              constants:
                dia: 0.0254
                velFac: 6.16223189034601  # .153 m3/min
              nested:
                r: !ablate::mathFunctions::Formula
                  formula: sqrt((x-xc)^2 + (y-yc)^2)
                  constants:
                    yc: 0.0127
                    xc: 0.0

  # the outlet boundary uses a reference pressure and maxAcousticsLength
  - !ablate::boundarySolver::BoundarySolver
    id: outlet
    region:
      name: outlet
    fieldBoundary:
      name: boundaryFaces
    mergeFaces: true
    processes:
      - !ablate::boundarySolver::lodi::OpenBoundary
        referencePressure: 101325.0
        maxAcousticsLength: 0.165354
        reflectFactor: 1.5
        pgs: *pgs
        eos: *eos

  # The no slip/isothermal walls are applied everywhere except the slab
  - !ablate::boundarySolver::BoundarySolver
    id: walls
    region:
      name: wall
    fieldBoundary:
      name: boundaryFaces
    mergeFaces: true
    processes:
      - !ablate::boundarySolver::lodi::IsothermalWall
        eos: *eos
        pgs: *pgs

  # The slab boundary id used to couple the flow and heat/mass transfer from the fuel
  - !ablate::boundarySolver::BoundarySolver
    id: slabboundary
    region:
      name: slab
    fieldBoundary:
      name: boundaryFaces
    processes:
      # the sublimation boundary solver is responsible for predicting mass release and flow source terms
      - !ablate::boundarySolver::physics::Sublimation

        # the transport model is enforce to update the zero slip wall condition
        transportModel: !ablate::eos::transport::Sutherland
          eos: *eos
        # the eos/pgs is used tor pressure boundary condition
        pgs: *pgs
        eos: *eos
        # the specified mass fractions are assumed off-gassed by the fuel
        massFractions: *fuelMassFrac
        # the radiviative heat flux to the surface is updated every 10 flow time steps
        radiationInterval: 10
        # The sublimation model is used to compute mass flux rate from the surface, the default is complete sublimation
        sublimationModel:
          # the latent heat of fusion of PMMA is used to predict the mass release from heating
          latentHeatOfFusion: 840890
          #density of pmma used to output reg rate
          solidDensity: 1190.0
        # a surface radiation solver is used to compute heat flux to the surface
        radiation: !ablate::radiation::SurfaceRadiation
          id: surfaceflux
          # the region is used to describe the area in which the flow solver is valid
          region:
            name: flowRegion
          rays: 25
          # the properties are a function of both gas and soot
          properties: !ablate::eos::radiationProperties::Sum
            - !ablate::eos::radiationProperties::Zimmer
              eos: *eos
            - !ablate::eos::radiationProperties::SootMeanProperties
              eos: *eos
        emissivity: 0.9

    monitors:
      # the boundary solver monitor is used to record regression rate and heat flux to the surface
      - !ablate::monitors::BoundarySolverMonitor

      # the volume radiation solver compute the gas/gas energy transfer within the gas phase
  - !ablate::radiation::VolumeRadiation
    id: radiationSolver
    # this is the region for which the solver operates (no boundary cells)
    region:
      name: flowRegion
    # update the entire radiation solver every 10 flow steps
    interval: 10
    # The radiation solver and the associated region
    radiation: !ablate::radiation::Radiation
      id: volRad
      region:
        name: flowRegion
      rays: 5
      properties: !ablate::eos::radiationProperties::Sum
        - !ablate::eos::radiationProperties::Zimmer
          eos: *eos
        - !ablate::eos::radiationProperties::SootMeanProperties
          eos: *eos