Markers <: CollectionContainer

Data structure containing parameter and array collections for markers.

Fields

• parameters::Parameters: Parameter groups for marker including distribution, advection, diffusion, and recycling settings
• arrays::Arrays: Array groups for marker arrays containing material properties, state variables, and location information

Parameters <: AbstractParameterCollection

Collection of marker parameters.

Fields

• distribution::Distribution: Marker distribution parameters
• advection::Advection: Marker advection parameters
• subgrid_diffusion::SubgridDiffusion: Subgrid diffusion parameters
• recycling::Recycling: Marker recycling parameters

Distribution <: AbstractParameterGroup

Parameter group for marker distribution configuration.

Fields

• iuse_random::ParameterInt: Randomize initial marker distribution: 0 off; 1 on
• dx_marker::ParameterFloat: Initial average marker spacing in horizontal direction in meters
• dy_marker::ParameterFloat: Initial average marker spacing in vertical direction in meters
• nmarkers_cell_x::ParameterFloat: Number of markers per cell in horizontal direction
• nmarkers_cell_y::ParameterFloat: Number of markers per cell in vertical direction
• mxnum::ParameterInt: Total number of markers in horizontal direction
• mynum::ParameterInt: Total number of markers in vertical direction
• marknum::ParameterInt: Number of markers
• mxstep::ParameterFloat: Distance between markers in horizontal direction in meters
• mystep::ParameterFloat: Distance between markers in vertical direction in meters
• obj_list::Vector{Union{ParameterFloat, ParameterInt}}: List of parameter objects.

Nested Dot Access

• iuse_random = model.markers.parameters.distribution.iuse_random.value
• dx_marker = model.markers.parameters.distribution.dx_marker.value
• dy_marker = model.markers.parameters.distribution.dy_marker.value
• nmarkers_cell_x = model.markers.parameters.distribution.nmarkers_cell_x.value
• nmarkers_cell_y = model.markers.parameters.distribution.nmarkers_cell_y.value
• mxnum = model.markers.parameters.distribution.mxnum.value
• mynum = model.markers.parameters.distribution.mynum.value
• marknum = model.markers.parameters.distribution.marknum.value
• mxstep = model.markers.parameters.distribution.mxstep.value
• mystep = model.markers.parameters.distribution.mystep.value

Constructor

Distribution(marker_parameters::NamedTuple)

Initializes marker distribution parameters from the provided named tuple.

Arguments

• marker_parameters::NamedTuple: Named tuple containing marker distribution parameters.

The named tuple marker_parameters must contain the following parameters:

• dx_marker: Initial average marker spacing in horizontal direction in meters.
• dy_marker: Initial average marker spacing in vertical direction in meters.
• nmarkers_cell_x: Number of markers per cell in horizontal direction.
• nmarkers_cell_y: Number of markers per cell in vertical direction.
• mynum: Total number of markers in vertical direction.
• mxnum: Total number of markers in horizontal direction.
• marknum: Total number of markers.
• mystep: Distance between markers in vertical direction in meters.
• mxstep: Distance between markers in horizontal direction in meters.

Returns

• A new Distribution struct with the given marker parameters.

Advection <: AbstractParameterGroup

Parameter group for marker advection configuration.

Fields

• marker_cell_displ_max::ParameterFloat: Maximum marker displacement as a fraction of cell size in meters
• itype_move_markers::ParameterInt: Displacement Options: 0 no motion 1 simp. advection; 4 4th-order Runge-Kutta
• stype_move_markers::ParameterStr: Displacement options name
• iuse_local_adaptive_time_stepping::ParameterInt: Activate local adaptive time stepping where displacement is calculated at staggered grid nodes. The default value is 0 (off). If deactivated then adaptive time stepping using average grid spacing. Note: when this flag is 1 the time step can vary significantly between steps, so iuse_fixed_output_counter is automatically forced to 0 during time-loop initialization so that output is triggered by total model time rather than by a fixed step counter.
• obj_list::Vector{Union{ParameterFloat, ParameterInt}}: List of parameter objects.

Nested Dot Access

• marker_cell_displ_max = model.markers.parameters.advection.marker_cell_displ_max.value
• itype_move_markers = model.markers.parameters.advection.itype_move_markers.value
• stype_move_markers = model.markers.parameters.advection.stype_move_markers.value
• iuse_local_adaptive_time_stepping = model.markers.parameters.advection.iuse_local_adaptive_time_stepping.value

Constructor

Advection()

Returns

• A new Advection struct with the given marker parameters.

SubgridDiffusion <: AbstractParameterGroup

Parameter group for subgrid diffusion coefficients.

Fields

• subgrid_diff_coef_stress::ParameterFloat: Numerical subgrid stress diffusion coefficient
• subgrid_diff_coef_temp::ParameterFloat: Numerical subgrid temperature diffusion coefficient
• obj_list::Vector{ParameterFloat}: List of parameter objects.

Nested Dot Access

• subgrid_diff_coef_stress = model.markers.parameters.subgrid_diffusion.subgrid_diff_coef_stress.value
• subgrid_diff_coef_temp = model.markers.parameters.subgrid_diffusion.subgrid_diff_coef_temp.value

Constructor

SubgridDiffusion()

Returns

• A new SubgridDiffusion struct with the given marker parameters.

Recycling <: AbstractParameterGroup

Parameter group for marker recycling configuration.

Fields

• imantle::ParameterInt: Material ID of the mantle. This is no longer used and will be removed in the future
• obj_list::Vector{ParameterInt}: List of numerical parameter objects

Nested Dot Access

• imantle = model.markers.parameters.recycling.imantle.value

Constructor

Recycling()

Returns

• A new Recycling struct with the given marker parameters.

Arrays <: AbstractArrayCollection

Collection of marker arrays.

Fields

• strat::Stratigraphy: Stratigraphy marker arrays
• rheology::Rheology: Rheology marker arrays
• thermal::Thermal: Thermal marker arrays
• material::Material: Material marker arrays
• stress::Stress: Stress marker arrays
• strain::Strain: Strain marker arrays
• pressure::Pressure: Pressure marker arrays
• location::Location: Location marker arrays
• grid_marker_relationship::GridMarkerRelationship: Grid-marker relationship arrays
• melt::Melt: Melt marker arrays
• advection::Advection: Marker advection velocity/spin arrays
• compaction::Compaction: Marker compaction scratch buffers
• solidification::Solidification: Marker solidification scratch buffer
• recycle::Recycle: Marker recycling scratch buffer
• serpentinization::Serpentinization: Serpentinization scratch buffer
• subgrid_heat::SubgridHeat: Subgrid heat-diffusion scratch buffer
• sediment_transport::SedimentTransport: Sediment-transport marker advection scratch buffers
• lithostatic::Lithostatic: Lithostatic-pressure column-filter scratch buffers

Stratigraphy <: AbstractArrayGroup

Array group for marker stratigraphic properties.

Fields

• marker_age::MarkerArrayFloat1DState Float64: (marknum) : Age of marker in million years.

Nested Dot Access

• marker_age = model.markers.arrays.stratigraphy.marker_age.array

Constructor

Stratigraphy(marknum::Int)

Initializes marker age array with zero values.

Arguments

• marknum::Int: Number of markers

Returns

• A new Stratigraphy struct with the given marker parameters.

Rheology <: AbstractArrayGroup

Array group for marker rheological properties.

Fields

• marker_eta::MarkerArrayFloat1DState Float64: (marknum) : Marker viscoplastic viscosity in Pa.s.
• marker_fric_ini::MarkerArrayFloat1DState Float64: (marknum) : Initial friction coefficient (sine of friction angle) of marker.
• marker_fric::MarkerArrayFloat1DState Float64: (marknum) : Friction coefficient (sine of friction angle) of marker.
• marker_cohesion::MarkerArrayFloat1DState Float64: (marknum) : Cohesion of marker in Pa.
• marker_preexp::MarkerArrayFloat1DState Float64: (marknum) : Pre-exponential factor for dislocation creep of marker in 1/s/MPa^n.
• marker_pfailure::MarkerArrayFloat1DState Float32: (marknum) : Flag indicating plastic failure of marker.
• marker_eta_flow::MarkerArrayFloat1DState Float64: (marknum) : Marker viscosity from flow law in Pa.s.
• marker_dilatation_angle::MarkerArrayFloat1DState Float32: (marknum) : Marker dilatation angle in Degrees.

Nested Dot Access

• marker_eta = model.markers.arrays.rheology.marker_eta.array
• marker_fric_ini = model.markers.arrays.rheology.marker_fric_ini.array
• marker_fric = model.markers.arrays.rheology.marker_fric.array
• marker_cohesion = model.markers.arrays.rheology.marker_cohesion.array
• marker_preexp = model.markers.arrays.rheology.marker_preexp.array
• marker_pfailure = model.markers.arrays.rheology.marker_pfailure.array
• marker_eta_flow = model.markers.arrays.rheology.marker_eta_flow.array
• marker_dilatation_angle = model.markers.arrays.rheology.marker_dilatation_angle.array

Constructor

Rheology(marknum::Int)

Arguments

• marknum::Int: Number of markers

Returns

• A new Rheology struct with the given marker parameters.

Thermal <: AbstractArrayGroup

Array group for marker thermal properties.

Fields

• marker_TK::MarkerArrayFloat1DState Float64: (marknum) : Temperature of marker in Kelvin.
• marker_rhocp::MarkerArrayFloat1DState Float64: (marknum) : Marker density multiplied by heat capacity in J/K/m^3.
• marker_kt::MarkerArrayFloat1DState Float64: (marknum) : Marker thermal conductivity in W/m/K.
• marker_ha::MarkerArrayFloat1DState Float64: (marknum) : Marker adiabatic heating term (expansivity x temperature).

Nested Dot Access

• marker_TK = model.markers.arrays.thermal.marker_TK.array
• marker_rhocp = model.markers.arrays.thermal.marker_rhocp.array
• marker_kt = model.markers.arrays.thermal.marker_kt.array
• marker_ha = model.markers.arrays.thermal.marker_ha.array

Constructor

Thermal(marknum::Int)

Arguments

• marknum::Int: Number of markers

Returns

• A new Thermal struct with the given marker parameters.

Material <: AbstractArrayGroup

Array group for marker material properties.

Fields

• marker_matid::MarkerArrayInt1DState Int16: (marknum) : Material ID of marker.
• marker_rho::MarkerArrayFloat1DState Float64: (marknum) : Marker density in kg/m^3.
• marker_porosity_initial::MarkerArrayFloat1DState Float32: (marknum) : Initial porosity at sediment-water interface used in Athy's law in fraction.
• marker_decay_depth::MarkerArrayFloat1DState Float32: (marknum) : Porosity decay depth used in Athy's law in meters.
• marker_max_burial_depth::MarkerArrayFloat1DState Float32: (marknum) : Maximum burial depth of marker in meters.
• marker_serpentinization::MarkerArrayFloat1DState Float32: (marknum) : Serpentinization fraction of marker in fraction.
• marker_serpentinization_heat_production::MarkerArrayFloat1DState Float32: (marknum) : Serpentinization heat production of marker in W/m^3.

Nested Dot Access

• marker_matid = model.markers.arrays.material.marker_matid.array
• marker_rho = model.markers.arrays.material.marker_rho.array
• marker_porosity_initial = model.markers.arrays.material.marker_porosity_initial.array
• marker_decay_depth = model.markers.arrays.material.marker_decay_depth.array
• marker_max_burial_depth = model.markers.arrays.material.marker_max_burial_depth.array
• marker_serpentinization = model.markers.arrays.material.marker_serpentinization.array
• marker_serpentinization_heat_production = model.markers.arrays.material.marker_serpentinization_heat_production.array

Constructor

Material(marknum::Int)

Arguments

• marknum::Int: Number of markers

Returns

• A new Material struct with the given marker parameters.

Stress <: AbstractArrayGroup

Array group for marker stress components.

Fields

• marker_sxx::MarkerArrayFloat1DState Float64: (marknum) : Deviatoric normal stress of marker in Pa.
• marker_sxy::MarkerArrayFloat1DState Float64: (marknum) : Deviatoric shear stress of marker in Pa.

Nested Dot Access

• marker_sxx = model.markers.arrays.stress.marker_sxx.array
• marker_sxy = model.markers.arrays.stress.marker_sxy.array

Constructor

Stress(marknum::Int)

Initializes marker stress arrays with zero values.

Arguments

• marknum::Int: Number of markers

Returns

• A new Stress struct with the given marker parameters.

Strain <: AbstractArrayGroup

Array group for marker strain and strain rate.

Fields

• marker_GII::MarkerArrayFloat1DState Float64: (marknum) : Accumulated strain of marker.
• marker_strain_plastic::MarkerArrayFloat1DState Float64: (marknum) : Accumulated plastic strain of marker.
• marker_exx::MarkerArrayFloat1DState Float64: (marknum) : Normal strain rate of marker in 1/s.
• marker_exy::MarkerArrayFloat1DState Float64: (marknum) : Shear strain rate of marker in 1/s.
• marker_sr_ratio::MarkerArrayFloat1DState Float64: (marknum) : Ratio of nodal-stress-based to nodal-velocity-based strain rate invariant for each marker.
• marker_strain_rate_plastic::MarkerArrayFloat1DState Float64: (marknum) : Plastic strain rate of marker in 1/s.
• marker_melt_damage::MarkerArrayFloat1DState Float32: (marknum) : Damage factor of marker associated with melt intrusion.

Nested Dot Access

• marker_GII = model.markers.arrays.strain.marker_GII.array
• marker_strain_plastic = model.markers.arrays.strain.marker_strain_plastic.array
• marker_exx = model.markers.arrays.strain.marker_exx.array
• marker_exy = model.markers.arrays.strain.marker_exy.array
• marker_sr_ratio = model.markers.arrays.strain.marker_sr_ratio.array
• marker_strain_rate_plastic = model.markers.arrays.strain.marker_strain_rate_plastic.array
• marker_melt_damage = model.markers.arrays.strain.marker_melt_damage.array

Constructor

Strain(marknum::Int)

Arguments

• marknum::Int: Number of markers

Returns

• A new Strain struct with the given marker parameters.

Pressure <: AbstractArrayGroup

Array group for marker pressure values.

Fields

• marker_pr::MarkerArrayFloat1DState Float64: (marknum) : Pressure of marker in Pa.

Nested Dot Access

• marker_pr = model.markers.arrays.pressure.marker_pr.array

Constructor

Pressure(marknum::Int)

Initializes marker pressure array with zero values.

Arguments

• marknum::Int: Number of markers

Location <: AbstractArrayGroup

Array group for marker spatial coordinates.

Fields

• marker_x::MarkerArrayFloat1DState Float64: (marknum) : x-coordinate of marker in meters.
• marker_y::MarkerArrayFloat1DState Float64: (marknum) : y-coordinate of marker in meters.

Nested Dot Access

• marker_x = model.markers.arrays.location.marker_x.array
• marker_y = model.markers.arrays.location.marker_y.array

Constructor

Location(marknum::Int)

Initializes marker location arrays with zero values.

Arguments

• marknum::Int: Number of markers

GridMarkerRelationship <: AbstractArrayGroup

Array group for grid-marker spatial relationships.

Fields

• marker_xn::MarkerArrayInt1DState Int32: (marknum) : Horizontal index of upper left node of basic grid cell containing marker.
• marker_yn::MarkerArrayInt1DState Int32: (marknum) : Vertical index of upper left node of basic grid cell containing marker.
• marker_dx::MarkerArrayFloat1DState Float64: (marknum) : Normalized x-distance between marker and upper-left basic grid node in meters.
• marker_dy::MarkerArrayFloat1DState Float64: (marknum) : Normalized y-distance between marker and upper-left basic grid node in meters.
• marker_xn_vy::MarkerArrayInt1DState Int32: (marknum) : Horizontal index of upper left node of staggered vy grid cell containing marker.
• marker_yn_vy::MarkerArrayInt1DState Int32: (marknum) : Vertical index of upper left node of staggered vy grid cell containing marker.
• marker_dx_vy::MarkerArrayFloat1DState Float64: (marknum) : Normalized x-distance between marker and upper-left grid node of staggered vy grid in meters.
• marker_dy_vy::MarkerArrayFloat1DState Float64: (marknum) : Normalized y-distance between marker and upper-left grid node of staggered vy grid in meters.

Nested Dot Access

• marker_xn = model.markers.arrays.grid_marker_relationship.marker_xn.array
• marker_yn = model.markers.arrays.grid_marker_relationship.marker_yn.array
• marker_dx = model.markers.arrays.grid_marker_relationship.marker_dx.array
• marker_dy = model.markers.arrays.grid_marker_relationship.marker_dy.array
• marker_xn_vy = model.markers.arrays.grid_marker_relationship.marker_xn_vy.array
• marker_yn_vy = model.markers.arrays.grid_marker_relationship.marker_yn_vy.array
• marker_dx_vy = model.markers.arrays.grid_marker_relationship.marker_dx_vy.array
• marker_dy_vy = model.markers.arrays.grid_marker_relationship.marker_dy_vy.array

Constructor

GridMarkerRelationship(marknum::Int)

Arguments

• marknum::Int: Number of markers

Melt <: AbstractArrayGroup

Array group for marker melt fractions.

Fields

• marker_meltfrac::MarkerArrayFloat1DState Float64: (marknum) : Melt fraction of marker in fraction.
• marker_extracted_meltfrac::MarkerArrayFloat1DState Float64: (marknum) : Extracted melt fraction of marker in fraction.
• marker_extractable_meltfrac::MarkerArrayFloat1DState Float64: (marknum) : Extractable melt fraction of marker in fraction.

Nested Dot Access

• marker_meltfrac = model.markers.arrays.melt.marker_meltfrac.array
• marker_extracted_meltfrac = model.markers.arrays.melt.marker_extracted_meltfrac.array
• marker_extractable_meltfrac = model.markers.arrays.melt.marker_extractable_meltfrac.array

Constructor

Melt(marknum::Int)

Arguments

• marknum::Int: Number of markers

Returns

• A new Melt struct with the given marker parameters.

Advection <: AbstractArrayGroup

Array group for per-marker Runge-Kutta-interpolated velocity and spin. The arrays are pre-allocated and re-written every advection step; consumers must gate reads by the same inside_flags used by the producer.

Fields

• marker_vx::MarkerArrayFloat1DState Float64: (marknum) : Runge-Kutta-interpolated x-velocity at marker (m/s). Re-computed every advection step; zero for markers outside the domain.
• marker_vy::MarkerArrayFloat1DState Float64: (marknum) : Runge-Kutta-interpolated y-velocity at marker (m/s). Re-computed every advection step; zero for markers outside the domain.
• marker_spin::MarkerArrayFloat1DState Float64: (marknum) : Runge-Kutta-interpolated spin rate at marker (1/s). Re-computed every advection step; zero for markers outside the domain.

Nested Dot Access

• marker_vx = model.markers.arrays.advection.marker_vx.array
• marker_vy = model.markers.arrays.advection.marker_vy.array
• marker_spin = model.markers.arrays.advection.marker_spin.array

Constructor

Advection(marknum::Int)

Arguments

• marknum::Int: Number of markers.

Compaction <: AbstractArrayGroup

Array group holding scratch buffers used by marker compaction.

Fields

• markers_topo_xindex_buffer::MarkerArrayInt1DState Int64
• markers_compaction_yindex_buffer::MarkerArrayInt1DState Int64
• markers_unit_distance_from_cell_top_buffer::MarkerArrayFloat1DState Float64
• total_marker_compaction_displacement_buffer::MarkerArrayFloat1DState Float64
• sticky_displacement_factors_buffer::MarkerArrayFloat1DState Float64
• sticky_marker_displacement_buffer::MarkerArrayFloat1DState Float64
• marker_swarm_index_scratch::MarkerArrayInt1DState Int64
• marker_swarm_x_gather_scratch::MarkerArrayFloat1DState Float64
• marker_swarm_sortperm_scratch::MarkerArrayInt1DState Int64

Constructor

Compaction()

The marker-length buffers start empty and are sized on first use by ensure_compaction_buffers!.

ensure_compaction_buffers!(compaction::Compaction, marknum::Int)

Idempotently size all nine marker-length compaction scratch buffers to marknum. Safe to call repeatedly — does nothing when sizes already match. Called at the top of:

• ApplyCompaction.apply_compaction_model!
• The variable_property branch in SedimentTransportSolverManager.run_sediment_transport_time_steps!

Solidification <: AbstractArrayGroup

Array group holding scratch buffers reused by melt-solidification routines.

Fields

• marker_random_buffer::MarkerArrayFloat1DState Float64: (marknum) : Pre-allocated scratch for per-marker random numbers. Used by Solidification.solidify! during friction-coefficient randomization, and by MarkerRecycle.RandomMarkerArray.getrandommarker_array for subsurface-marker reset. Each consumer refills via Random.rand! before reading, so values do not leak between consumers.

Nested Dot Access

• model.markers.arrays.solidification.marker_random_buffer.array

Constructor

Solidification(marknum::Int)

Arguments

• marknum::Int: Number of markers (buffer is sized to this length).

Recycle <: AbstractArrayGroup

Array group holding scratch buffers reused by marker-recycling routines.

Fields

• marker_outside_indices_scratch::MarkerArrayInt1DState Int64: (marknum) : Pre-allocated scratch for the marknum-sized intermediate inside GridFuncs.getindicesofmarkersoutside_domain. Filled in marker-index order, then packed in place before the function returns a length-nrecycle copy.
• marker_inside_flags_buffer::MarkerArrayInt1DState Int8: (marknum) : Pre-allocated Vector{Int8} of length marknum filled by GridFuncs.get_marker_inside_flags with 1 for in-domain markers and -1 for out-of-domain markers. The function returns this buffer directly; downstream consumers in the time loop treat it as read-only. Two call sites per timestep (pre-solver setup and post-solver re-evaluation) overwrite the buffer in sequence — the second call's values supersede the first; nothing in between persists a reference to the prior values past the second call.

Nested Dot Access

• model.markers.arrays.recycle.marker_outside_indices_scratch.array
• model.markers.arrays.recycle.marker_inside_flags_buffer.array

Constructor

Recycle(marknum::Int)

Arguments

• marknum::Int: Number of markers (buffers are sized to this length).

Serpentinization <: AbstractArrayGroup

Array group holding scratch buffers reused by serpentinization routines.

Fields

• marker_serpentinization_increment_buffer::MarkerArrayFloat1DState Float64

Constructor

Serpentinization(marknum::Int)

SubgridHeat <: AbstractArrayGroup

Array group holding scratch buffers reused by subgrid heat-diffusion routines.

Fields

• marker_subgrid_temp_delta_buffer::MarkerArrayFloat1DState Float64

Constructor

SubgridHeat(marknum::Int)

SedimentTransport <: AbstractArrayGroup

Array group holding scratch buffers reused by sediment-transport marker advection routines.

Fields

• marker_displacement_factors_buffer::MarkerArrayFloat1DState Float64
• marker_displacement_buffer::MarkerArrayFloat1DState Float64

Constructor

SedimentTransport()

The marker-length buffers start empty and are sized on first use by ensure_sediment_transport_buffers!.

ensure_sediment_transport_buffers!(st::SedimentTransport, marknum::Int)

Idempotently size the marker-length advection scratch buffers to marknum. Safe to call every advect — does nothing when sizes already match. Called at the top of MarkerAdvection.advect_markers_using_compaction.

Lithostatic <: AbstractArrayGroup

Array group holding the three marker-sized scratch buffers used by LithostaticPressure.filter_markers_for_column.

Fields

• marker_x_filter_scratch::MarkerArrayFloat1DState Float64
• marker_y_filter_scratch::MarkerArrayFloat1DState Float64
• marker_rho_filter_scratch::MarkerArrayFloat1DState Float64

Constructor

Lithostatic(marknum::Int)

Arguments

• marknum::Int: Number of markers (each buffer is sized to this length).