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List functions ​

These are all the functions that are provided for the LaMEM Julia Setup interface

LaMEM.LaMEM_Model.BCBlock Type
julia
LaMEM boundary condition `BCBlock` object

  • npath::Int64: Number of path points of Bezier curve (path-points only!)

  • path_dim::Int64: Path dimension: 2 = x-y plane (default), 3 = full 3D (path then also moves bot/top z-coordinates)

  • theta::Vector{Float64}: # Orientation angles at path points (counter-clockwise positive)

  • time::Vector{Float64}: Times at path points

  • path::Vector{Float64}: Path points coordinates (x-y pairs if path_dim=2, x-y-z triplets if path_dim=3)

  • npoly::Int64: Number of polygon vertices

  • poly::Vector{Float64}: Polygon x-y coordinates at initial time

  • bot::Float64: Polygon bottom coordinate

  • top::Float64: Polygon top coordinate

source
LaMEM.LaMEM_Model.BoundaryConditions Type
julia
BoundaryConditions

Structure that contains the LaMEM boundary conditions information.

  • noslip::Vector{Int64}: No-slip boundary flag mask (left right front back bottom top)

  • open_top_bound::Int64: Stress-free (free surface/infinitely fast erosion) top boundary flag

  • temp_top::Float64: Constant temperature on the top boundary

  • temp_bot::Float64: Constant temperature on the bottom boundary

  • exx_num_periods::Int64: number intervals of constant background strain rate (x-axis)

  • exx_time_delims::Vector{Float64}: time delimiters (one less than number of intervals, not required for one interval)

  • exx_strain_rates::Vector{Float64}: strain rates for each interval

  • eyy_num_periods::Int64: number of intervals of constant background strain rate (y-axis)

  • eyy_time_delims::Vector{Float64}: time delimiters for eyy strain rate intervals (one less than number of intervals)

  • eyy_strain_rates::Vector{Float64}: background strain rates in yy-direction for each interval

  • exy_num_periods::Int64: number of intervals of constant background simple shear strain rate (xy-plane)

  • exy_time_delims::Vector{Float64}: time delimiters for exy strain rate intervals

  • exy_strain_rates::Vector{Float64}: background simple shear strain rates in xy-direction for each interval

  • exz_num_periods::Int64: number of intervals of constant background simple shear strain rate (xz-plane)

  • exz_time_delims::Vector{Float64}: time delimiters for exz strain rate intervals

  • exz_strain_rates::Vector{Float64}: background simple shear strain rates in xz-direction for each interval

  • eyz_num_periods::Int64: number of intervals of constant background simple shear strain rate (yz-plane)

  • eyz_time_delims::Vector{Float64}: time delimiters for eyz strain rate intervals

  • eyz_strain_rates::Vector{Float64}: background simple shear strain rates in yz-direction for each interval

  • bg_ref_point::Vector{Float64}: background strain rate reference point (fixed)

  • VelocityBoxes::Vector{VelocityBox}: List of added velocity boxes

  • BCBlocks::Vector{BCBlock}: List of added Bezier blocks

  • VelCylinders::Vector{VelCylinder}: List of added velocity cylinders

  • bvel_face::Union{Nothing, String}: Face identifier (Left; Right; Front; Back; CompensatingInflow)

  • bvel_face_out::Union{Nothing, Int64}: Velocity on opposite side: -1 for inverted velocity; 0 for no velocity; 1 for the same direction of velocity

  • bvel_bot::Union{Nothing, Float64}: Bottom coordinate of inflow window

  • bvel_top::Union{Nothing, Float64}: Top coordinate of inflow window

  • velin_num_periods::Union{Nothing, Int64}: Number of periods when velocity changes (Optional)

  • velin_time_delims::Union{Nothing, Vector}: Change velocity at 2 and 5 Myrs (one less than number of intervals, not required for one interval) (Optional)

  • bvel_velin::Union{Nothing, Vector}: inflow velocity for each time interval(Multiple values required if velin_num_periods>1)

  • bvel_velout::Union{Nothing, Float64}: outflow velocity (if not specified, computed from mass balance)

  • bvel_relax_d::Union{Nothing, Float64}: vert.distance from bvel_bot and bvel_top over which velocity is reduced linearly

  • bvel_velbot::Union{Nothing, Int64}: bottom inflow velocity for use with bvel_face=CompensatingInflow

  • bvel_veltop::Union{Nothing, Int64}: top inflow velocity for use with bvel_face=CompensatingInflow

  • bvel_temperature_inflow::Union{Nothing, String}: bvel_temperature_inflow: Thermal age of the plate, which can be constant if set to Fixed_thermal_age or Constant_T_inflow (Temperature of the inflow material is constant everywhere)

  • bvel_thermal_age::Union{Nothing, Float64}: In dimensional unit. If the user specify this value, he needs to specify the temperature of the mantle and top as well

  • bvel_temperature_mantle::Union{Nothing, Float64}: In dimensional unit. Temperature of the mantle

  • bvel_temperature_top::Union{Nothing, Float64}: In dimensional unit. temperature of the top

  • bvel_temperature_constant::Union{Nothing, Float64}: Constant temperature inflow.

  • bvel_num_phase::Union{Nothing, Int64}: Imposes a stratigraphy of phase injected in the inflow boundary [if undefined, it uses the phase close to the boundary]

  • bvel_phase::Union{Nothing, Vector{Int64}}: phase number of inflow material [if undefined, it uses the phase close to the boundary] from bottom to top

  • bvel_phase_interval::Union{Nothing, Vector{Float64}}: Depth interval of injection of the phase (the interval is defined by num_phase+1 coordinates). e.g. [-120 -100 -10 0 ]

  • open_bot_bound::Union{Nothing, Int64}: # Permeable lower boundary flag

  • permeable_phase_inflow::Union{Nothing, Int64}: Phase of the inflow material from the bottom (The temperature of the inflow phase it is the same of the bottom boundary) in case of open_bot_bound=1

  • fix_phase::Union{Nothing, Int64}: fixed phase (no-flow condition)

  • fix_cell::Union{Nothing, Int64}: fixed cells (no-flow condition)

  • fix_cell_file::Union{Nothing, String}: fixed cells input file (extension is .xxxxxxxx.dat)

  • temp_bot_num_periods::Union{Nothing, Int64}: How many periods with different temp_bot do we have?

  • temp_bot_time_delim::Union{Nothing, Vector{Float64}}: At which time do we switch from one to the next period?

  • Plume_InflowBoundary::Union{Nothing, Int64}: # have a plume-like inflow boundary @ bottom

  • Plume_Type::Union{Nothing, String}: Type of plume inflow boundary.

    • "Inflow_type" or

    • "Pressure_type" (circular) or

    • "Permeable_Type" which combines the open bot boundary with the plume boundary condition (the option herein listed overwrites open_bot, so do not activate that)

  • Plume_Dimension::Union{Nothing, String}: 2D or 3D (circular)

  • Plume_areaFrac::Union{Nothing, Float64}: how much of the plume is actually in the model. This usually 1 (default) but lower if the plume is in a corner of a symmetric setup and matters for the outflow

  • Plume_Phase::Union{Nothing, Int64}: phase of plume material

  • Plume_Depth::Union{Nothing, Float64}: # depth of provenience of the plume (i.e. how far from the bottom of the model the plume source is)

  • Plume_Mantle_Phase::Union{Nothing, Int64}: # Astenosphere phase (if the inflow occurs outside the plume radius)

  • Plume_Temperature::Union{Nothing, Float64}: # temperature of inflow plume

  • Plume_Inflow_Velocity::Union{Nothing, Float64}: # Inflow velocity (not required if Pressure_Type) in cm/year if using GEOunits

  • Plume_VelocityType::Union{Nothing, String}: "Gaussian" or "Poiseuille"

  • Plume_Center::Union{Nothing, Vector{Float64}}: # [X,Y] of center (2nd only in case of 3D plume)

  • Plume_Radius::Union{Nothing, Float64}: # Width/Radius of plume

  • Plume_Phase_Mantle::Union{Nothing, Int64}: # Inflow phase. If the velocity happens to be positive in the domain, the inflow material has a constant phase and the temperature of the bottom

  • pres_top::Union{Nothing, Float64}: Pressure on the top boundary

  • pres_bot::Union{Nothing, Float64}: Pressure on the bottom boundary

  • init_pres::Union{Nothing, Int64}: pressure initial guess flag; linear profile between pres_top and pres_bot in the unconstrained cells

  • init_temp::Union{Nothing, Int64}: temperature initial guess flag; linear profile between temp_top and temp_bot

source
LaMEM.LaMEM_Model.Dike Type
julia
Defines the properties related to inserting dikes

  • ID::Int64: Material phase ID

  • Mf::Float64: value for dike/magma- accommodated extension, between 0 and 1, in the front of the box, for phase dike

  • Mc::Float64: [optional] value for dike/magma- accommodate extension, between 0 and 1, for dike phase; M is linearly interpolated between Mf & Mc and Mc & Mb, if not set, Mc default is set to -1 so it is not used

  • y_Mc::Union{Nothing, Float64}: [optional], location for Mc, must be between front and back boundaries of dike box, if not set, default value to 0.0, but not used

  • Mb::Union{Nothing, Float64}: value for dike/magma-accommodated extension, between 0 and 1, in the back of the box, for phase dike

  • PhaseID::Union{Nothing, Int64}: Phase ID

  • PhaseTransID::Union{Nothing, Int64}: Phase transition ID

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LaMEM.LaMEM_Model.FreeSurface Type
julia
Structure that contains the LaMEM free surface information.

  • surf_use::Int64: Free surface activation flag

  • surf_corr_phase::Int64: air phase ratio correction flag (phases in an element that contains are modified based on the surface position)

  • surf_level::Union{Nothing, Float64}: initial level of the free surface

  • surf_air_phase::Union{Nothing, Int64}: phase ID of sticky air layer

  • surf_max_angle::Float64: maximum angle with horizon (smoothed if larger)

  • surf_topo_file::String: initial topography file (redundant)

  • erosion_model::Int64: erosion model [0-none (default), 1-infinitely fast, 2-prescribed rate with given level]

  • er_num_phases::Int64: number of erosion phases

  • er_time_delims::Vector{Float64}: erosion time delimiters (one less than number)

  • er_rates::Vector{Float64}: constant erosion rates in different time periods

  • er_levels::Vector{Int64}: levels above which we apply constant erosion rates in different time periods

  • er_x_min::Union{Nothing, Vector{Float64}}: [only used if erosion_model=3] minimum x-coordinates of the spatially limited erosion zone, per erosion phase

  • er_x_max::Union{Nothing, Vector{Float64}}: [only used if erosion_model=3] maximum x-coordinates of the spatially limited erosion zone, per erosion phase

  • topo_diff::Int64: activate topographic diffusion of the free surface [0-none (default), 1-active]

  • topo_diffusivity::Float64: topographic diffusivity used if topo_diff=1

  • sediment_model::Int64: sedimentation model [0-none (dafault), 1-prescribed rate with given level, 2-cont. margin]

  • sed_num_layers::Int64: number of sediment layers

  • sed_time_delims::Vector{Float64}: sediment layers time delimiters (one less than number)

  • sed_rates::Vector{Float64}: sediment rates in different time periods

  • sed_levels::Vector{Float64}: levels below which we apply constant sediment rates in different time periods

  • sed_phases::Vector{Int64}: sediment layers phase numbers in different time periods

  • marginO::Vector{Float64}: lateral coordinates of continental margin - origin

  • marginE::Vector{Float64}: lateral coordinates of continental margin - 2nd point

  • hUp::Float64: up dip thickness of sediment cover (onshore)

  • hDown::Float64: down dip thickness of sediment cover (off shore)

  • dTrans::Float64: half of transition zone

  • Topography::Union{Nothing, GeophysicalModelGenerator.CartData}: Topography grid

source
LaMEM.LaMEM_Model.GeomBox Type
julia
LaMEM geometric primitive `Box` object

  • phase::Int64: phase

  • bounds::Vector{Float64}: box bound coordinates: left, right, front, back, bottom, top

  • Temperature::Union{Nothing, String}: optional: Temperature structure. possibilities: [constant, linear, halfspace]

  • cstTemp::Union{Nothing, Float64}: required in case of [constant]: temperature value [in Celcius in case of GEO units]

  • topTemp::Union{Nothing, Float64}: required in case of [linear,halfspace]: temperature @ top [in Celcius in case of GEO units]

  • botTemp::Union{Nothing, Float64}: required in case of [linear,halfspace]: temperature @ top [in Celcius in case of GEO units]

  • thermalAge::Union{Nothing, Float64}: required in case of [halfspace]: thermal age of lithosphere [in Myrs if GEO units are used]

source
LaMEM.LaMEM_Model.GeomCylinder Type
julia
LaMEM geometric primitive `Cylinder` object

  • phase::Int64: phase

  • radius::Float64: radius of cylinder

  • base::Vector{Float64}: center of base of cylinder

  • cap::Vector{Float64}: center of cap of cylinder

  • Temperature::Union{Nothing, String}: optional: Temperature structure. possibilities: [constant]

  • cstTemp::Union{Nothing, Float64}: required in case of [constant]: temperature value [in Celcius in case of GEO units]

source
LaMEM.LaMEM_Model.GeomEllipsoid Type
julia
LaMEM geometric primitive `Ellipsoid` object

  • phase::Int64: phase

  • axes::Vector{Float64}: semi-axes of ellipsoid in x, y and z

  • center::Vector{Float64}: center of sphere

  • Temperature::Union{Nothing, String}: optional: Temperature of the sphere. possibilities: [constant, or nothing]

  • cstTemp::Union{Nothing, Float64}: required in case of [constant]: temperature value [in Celcius in case of GEO units]

source
LaMEM.LaMEM_Model.GeomHex Type
julia
LaMEM geometric primitive `Hex` object to define hexahedral elements

  • phase::Int64: phase

  • coord::Vector{Float64}: x-y-z coordinates for each of 8 nodes (24 parameters) (counter)-clockwise for an arbitrary face, followed by the opposite face

source
LaMEM.LaMEM_Model.GeomLayer Type
julia
LaMEM geometric primitive `Layer` object

  • phase::Int64: phase

  • top::Float64: top of layer

  • bottom::Float64: bottom of layer

  • cosine::Union{Nothing, Int64}: optional: add a cosine perturbation on top of the interface (if 1)

  • wavelength::Union{Nothing, Float64}: required if cosine: wavelength in x-direction

  • amplitude::Union{Nothing, Float64}: required if cosine: amplitude of perturbation

  • Temperature::Union{Nothing, String}: optional: Temperature structure. possibilities: [constant, linear, halfspace]

  • cstTemp::Union{Nothing, Float64}: required in case of [constant]: temperature value [in Celcius in case of GEO units]

  • topTemp::Union{Nothing, Float64}: required in case of [linear,halfspace]: temperature @ top [in Celcius in case of GEO units]

  • botTemp::Union{Nothing, Float64}: required in case of [linear,halfspace]: temperature @ top [in Celcius in case of GEO units]

  • thermalAge::Union{Nothing, Float64}: required in case of [halfspace]: thermal age of lithosphere [in Myrs if GEO units are used]

source
LaMEM.LaMEM_Model.GeomRidgeSeg Type
julia
LaMEM geometric primitive `RidgeSeg` object

  • phase::Int64: phase

  • bounds::Vector{Float64}: box bound coordinates: left, right, front, back, bottom, top

  • ridgeseg_x::Vector{Float64}: coordinate order: left, right [can be different for oblique ridge]

  • ridgeseg_y::Vector{Float64}: coordinate order: front, back [can be different for oblique ridge]

  • Temperature::String: initial temperature structure [ridge must be set to halfspace_age –> setTemp=4]

  • topTemp::Float64: required in case of [linear,halfspace]: temperature @ top [in Celcius in case of GEO units]

  • botTemp::Float64: required in case of [linear,halfspace]: temperature @ top [in Celcius in case of GEO units]

  • age0::Float64: minimum age of seafloor at ridge [in Myr in case of GEO units]

  • maxAge::Union{Nothing, Float64}: [optional] parameter that indicates the maximum thermal age of a plate

  • v_spread::Union{Nothing, Float64}: [optional] parameter that indicates the spreading velocity of the plate; if not defined it uses bvel_velin specified elsewhere

source
LaMEM.LaMEM_Model.GeomSphere Type
julia
LaMEM geometric primitive `sphere` object

  • phase::Int64: phase

  • radius::Float64: radius of sphere

  • center::Vector{Float64}: center of sphere

  • Temperature::Union{Nothing, String}: optional: Temperature of the sphere. possibilities: [constant, or nothing]

  • cstTemp::Union{Nothing, Float64}: required in case of [constant]: temperature value [in Celcius in case of GEO units]

source
LaMEM.LaMEM_Model.Grid Type
julia
Structure that contains the LaMEM grid information

  • nmark_x::Int64: number of markers/element in x-direction

  • nmark_y::Int64: number of markers/element in y-direction

  • nmark_z::Int64: number of markers/element in x-direction

  • nel_x::Vector{Int64}: number of elements in x-direction

  • nel_y::Vector{Int64}: number of elements in y-direction

  • nel_z::Vector{Int64}: number of elements in z-direction

  • coord_x::Vector{Float64}: coordinates in x-direction

  • coord_y::Vector{Float64}: coordinates in y-direction

  • coord_z::Vector{Float64}: coordinates in z-direction

  • nseg_x::Int64: number of segments in x-direction (if we employ variable grid spacing in x-direction)

  • nseg_y::Int64: number of segments in y-direction (if we employ variable grid spacing in y-direction)

  • nseg_z::Int64: number of segments in z-direction (if we employ variable grid spacing in z-direction)

  • bias_x::Vector{Float64}: bias in x-direction (if we employ variable grid spacing in x-direction)

  • bias_y::Vector{Float64}: bias in y-direction (if we employ variable grid spacing in y-direction)

  • bias_z::Vector{Float64}: bias in z-direction (if we employ variable grid spacing in z-direction)

  • Grid::GeophysicalModelGenerator.LaMEM_grid: Contains the LaMEM Grid object

  • Phases::Array{Int32}: Phases; 3D phase information

  • Temp::Array{Float64}: Temp; 3D phase information

  • APS::Array{Float64}: APS; accumulated plastic strain

Example 1

julia
julia> d=LaMEM.Grid(coord_x=[0.0, 0.7, 0.8, 1.0], bias_x=[0.3,1.0,3.0], nel_x=[10,4,2])
LaMEM grid with 1D refinement: 
  nel         : ([10, 4, 2], [16], [16])
  marker/cell : (3, 3, 3)
  x           ϵ [0.0, 0.7, 0.8, 1.0], bias=[0.3, 1.0, 3.0], nseg=3, Δmin=0.025000000000000022, Δmax=0.1499999999999999
  y           ϵ [-10.0 : 0.0]
  z           ϵ [-10.0 : 0.0]

Example 2

julia
julia> d=LaMEM.Grid(nel=(10,20))
LaMEM grid with constant Δ: 
  nel         : ([10], [1], [20])
  marker/cell : (3, 3, 3)
  x           ϵ [-10.0 : 10.0]
  y           ϵ [-10.0 : 0.0]
  z           ϵ [-10.0 : 0.0]
source
LaMEM.LaMEM_Model.Materials Type
julia
Structure that contains the material properties in the current simulation

  • Phases::Vector{Phase}: Different Materials implemented

  • SofteningLaws::Vector{Softening}: Softening laws implemented

  • PhaseTransitions::Vector{PhaseTransition}: Internal Phase Transitions (that change the ID of markers) implemented

  • Dikes::Vector{Dike}: Dikes implemented (mostly for MOR simulations)

  • PhaseAggregates::Vector{PhaseAggregate}: Phase aggregates (combines different phases such as upper_lower crust into one for visualization purposes)

source
LaMEM.LaMEM_Model.Model Type
julia
Model

Structure that holds all the information to create a LaMEM input file

  • Scaling::Scaling: Scaling parameters

  • Grid::Grid: LaMEM Grid

  • Time::Any: Time options

  • FreeSurface::Any: Free surface options

  • BoundaryConditions::Any: Boundary conditions

  • SolutionParams::Any: Global solution parameters

  • Solver::Any: Solver options and optional PETSc options

  • ModelSetup::Any: Model setup

  • Output::Any: Output options

  • PassiveTracers::Any: Passive tracers

  • Materials::Any: Material parameters for each of the phases

source
LaMEM.LaMEM_Model.Model Method
julia
Model(args...)

Allow to define a model setup by specifying some of the basic objects

Example

julia
julia> d = Model(Grid(nel=(10,1,20)), Scaling(NO_units()))
LaMEM Model setup
|
|-- Scaling             :  GeoParams.Units.GeoUnits{GeoParams.Units.NONE}
|-- Grid                :  nel=(10, 1, 20); xϵ(-10.0, 10.0), yϵ(-10.0, 0.0), zϵ(-10.0, 0.0) 
|-- Time                :  nstep_max=50; nstep_out=1; time_end=1.0; dt=0.05
|-- Boundary conditions :  noslip=[0, 0, 0, 0, 0, 0]
|-- Solution parameters :  
|-- Solver options      :  direct solver; superlu_dist; penalty term=10000.0
|-- Model setup options :  Type=geom; 
|-- Output options      :  filename=output; pvd=1; avd=0; surf=0
|-- Materials           :  1 phases;
source
LaMEM.LaMEM_Model.Model Method
julia
Model(;
    Scaling=Scaling(GEO_units()),
    Grid=Grid(), 
    Time=Time(),
    FreeSurface=FreeSurface(),
    BoundaryConditions=BoundaryConditions(),
    SolutionParams=SolutionParams(),
    Solver=Solver(),
    ModelSetup=ModelSetup(),
    Output=Output(),
    PassiveTracers=PassiveTracers(),
    Materials=Materials()
    )

Creates a LaMEM Model setup.

  • Scaling::Scaling

  • Grid::Grid

  • Time::Any

  • FreeSurface::Any

  • BoundaryConditions::Any

  • SolutionParams::Any

  • Solver::Any

  • ModelSetup::Any

  • Output::Any

  • PassiveTracers::Any

  • Materials::Any

source
LaMEM.LaMEM_Model.ModelSetup Type
julia
Structure that contains the LaMEM Model Setup and Advection options

  • msetup::String: Setup type - can be geom (phases are assigned from geometric primitives, using add_geom!(model, ...)), files (from julia input), polygons (from geomIO input, which requires poly_file to be specified)

  • rand_noise::Int64: add random noise to the particle location

  • rand_noiseGP::Int64: random noise flag, subsequently applied to geometric primitives

  • bg_phase::Int64: background phase ID

  • save_mark::Int64: save marker to disk flag

  • mark_load_file::String: marker input file (extension is .xxxxxxxx.dat), if using msetup=files

  • mark_save_file::String: marker output file (extension is .xxxxxxxx.dat)

  • poly_file::String: polygon geometry file (redundant), if using msetup=polygons

  • temp_file::String: initial temperature file (redundant), if not set on markers

  • advect::String: advection scheme; options=none (no advection); basic (Euler classical implementation [default]); Euler (Euler explicit in time); rk2 (Runge-Kutta 2nd order in space)

  • interp::String: velocity interpolation scheme; options = stag (trilinear interpolation from FDSTAG points), minmod ( MINMOD interpolation to nodes, trilinear interpolation to markers + correction), stagp ( STAG_P empirical approach by T. Gerya)

  • stagp_a::Float64: STAG_P velocity interpolation parameter

  • mark_ctrl::String: marker control type; options are subgrid (default; marker control enforced over fine scale grid), none (none), basic (AVD for cells + corner insertion), and avd (pure AVD for all control volumes)

  • nmark_lim::Vector{Int64}: min/max number per cell (marker control)

  • nmark_avd::Vector{Int64}: x-y-z AVD refinement factors (avd marker control)

  • nmark_sub::Int64: max number of same phase markers per subcell (subgrid marker control)

  • geom_primitives::Vector: Different geometric primitives that can be selected if we msetup``=geom; seeGeomSphere`

source
LaMEM.LaMEM_Model.Multigrid Type
julia
Structure that has info about setting up multigrid for LaMEM

  • nel::Tuple{Int64, Int64, Int64}: Number of elements at the fine level

  • levels::Int64: Number of levels

  • smooth::Int64: number of smoothening steps per level

  • smooth_jacobi_factor::Float64: factor for jacbi smoothener oer level

  • smoother::String: smoother used at every level

  • coarse_ksp::String: coarse grid ksp type preonly or fgmres

  • coarse_pc::String: coarse grid pc type ["superlu_dist", "mumps", "gamg", "telescope","redundant"]

  • coarse_coarse_pc::String: coarse coarse grid solver in case we use redundant or telescope coarse grid solves

  • coarse_coarse_ksp::String: coarse coarse grid solver in case we use redundant or telescope coarse grid solves

  • cores::Int64: number of cores used in the simulation

  • cores_coarse::Int64: number of cores used for coarse grid solver (in case we use pctelescope)

  • gamg_threshold::Float64: GAMG threshold

  • gamg_coarse_eq_limit::Int64: GAMG coarse grid equation limit

  • gamg_repartition::Bool: GAMG repartition coarse grids? (default=false)

  • gamg_parallel_coarse::Bool: GAMG parallel coarse grid solver? (default=false)

source
LaMEM.LaMEM_Model.Output Type
julia
Structure that contains the LaMEM output options

  • out_file_name::Any: output file name

  • out_dir::Any: output directory

  • param_file_name::Any: parameter filename

  • write_VTK_setup::Any: write VTK initial model setup

  • out_pvd::Any: activate writing .pvd file

  • out_phase::Any: dominant phase

  • out_density::Any: density

  • out_visc_total::Any: total (viscoelastoplastic) viscosity

  • out_visc_creep::Any: creep viscosity

  • out_velocity::Any: velocity

  • out_pressure::Any: (dynamic) pressure

  • out_tot_press::Any: total pressure

  • out_eff_press::Any: effective pressure

  • out_over_press::Any: out_over_press

  • out_litho_press::Any: lithospheric pressure

  • out_pore_press::Any: pore pressure

  • out_temperature::Any: temperature

  • out_dev_stress::Any: deviatoric strain rate tensor

  • out_j2_dev_stress::Any: second invariant of deviatoric stress tensor

  • out_strain_rate::Any: deviatoric strain rate tensor

  • out_j2_strain_rate::Any: second invariant of strain rate tensor

  • out_shmax::Any: sh max

  • out_ehmax::Any: eh max

  • out_yield::Any: yield stress

  • out_rel_dif_rate::Any: relative proportion of diffusion creep strainrate

  • out_rel_dis_rate::Any: relative proportion of dislocation creep strainrate

  • out_rel_prl_rate::Any: relative proportion of peierls creep strainrate

  • out_rel_pl_rate::Any: relative proportion of plastic strainrate

  • out_plast_strain::Any: accumulated plastic strain

  • out_plast_dissip::Any: plastic dissipation

  • out_tot_displ::Any: total displacement

  • out_moment_res::Any: momentum residual

  • out_cont_res::Any: continuity residual

  • out_energ_res::Any: energy residual

  • out_melt_fraction::Any: Melt fraction

  • out_fluid_density::Any: fluid density

  • out_conductivity::Any: conductivity

  • out_vel_gr_tensor::Any: velocity gradient tensor

  • out_surf::Any: activate surface output

  • out_surf_pvd::Any: activate writing .pvd file

  • out_surf_velocity::Any: surface velocity

  • out_surf_topography::Any: surface topography

  • out_surf_amplitude::Any: amplitude of topography (=topo-average(topo))

  • out_mark::Any: activate marker output

  • out_mark_pvd::Any: activate writing .pvd file

  • out_avd::Any: activate AVD phase output

  • out_avd_pvd::Any: activate writing .pvd file

  • out_avd_ref::Any: AVD grid refinement factor

  • out_ptr::Any: activate

  • out_ptr_ID::Any: ID of the passive tracers

  • out_ptr_phase::Any: phase of the passive tracers

  • out_ptr_Pressure::Any: interpolated pressure

  • out_ptr_Temperature::Any: temperature

  • out_ptr_APS::Any: accumulated plastic strain

  • out_ptr_MeltFraction::Any: melt fraction computed using P-T of the marker

  • out_ptr_Active::Any: option that highlight the marker that are currently active

  • out_ptr_Grid_Mf::Any: option that allow to store the melt fraction seen within the cell

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LaMEM.LaMEM_Model.PassiveTracers Type
julia
Structure that contains the LaMEM passive tracers parameters.

  • Passive_Tracer::Int64: activate passive tracers?"

  • PassiveTracer_Box::Union{Nothing, Vector{Float64}}: Dimensions of box in which we distribute passive tracers [Left, Right, Front, Back, Bottom, Top]

  • PassiveTracer_Resolution::Vector{Int64}: The number of passive tracers in every direction

  • PassiveTracer_ActiveType::Union{Nothing, String}: Under which condition are they activated? ["Always"], "Melt_Fraction", "Temperature", "Pressure", "Time"

  • PassiveTracer_ActiveValue::Union{Nothing, Float64}: The value to activate them

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LaMEM.LaMEM_Model.Phase Type
julia
Defines the material properties for each of the phases

  • ID::Union{Nothing, Int64}: Material phase ID

  • Name::Union{Nothing, String}: Description of the phase

  • rho::Union{Nothing, Float64}: Density [kg/m^3]

  • eta::Union{Nothing, Float64}: Linear viscosity [Pas]

  • visID::Union{Nothing, Int64}: material ID for phase visualization (default is ID)

  • diff_prof::Union{Nothing, String}: Build-in DIFFUSION creep profiles: Example: "Dry__Olivine_diff_creep-Hirth_Kohlstedt_2003" Available build-in diffusion creep rheologies are:

    1. From [Hirth, G. and Kohlstedt D. (2003), Rheology of the upper mantle and the mantle wedge: A view from the experimentalists]:

    • "Dry_Olivine_diff_creep-Hirth_Kohlstedt_2003"

    • "Wet_Olivine_diff_creep-Hirth_Kohlstedt_2003_constant_C_OH"

    • "Wet_Olivine_diff_creep-Hirth_Kohlstedt_2003"

    1. From [Rybacki and Dresen, 2000, JGR]:

    • "Dry_Plagioclase_RybackiDresen_2000"

    • "Wet_Plagioclase_RybackiDresen_2000"

    Note that you can always specify your own, by setting Bd, Ed, Vd accordingly.

  • disl_prof::Union{Nothing, String}: Build-in DISLOCATION creep profiles: Example: "Granite-Tirel_et_al_2008" Available build-in dislocation creep rheologies are:

    1. From [Ranalli 1995]:

    • "Dry_Olivine-Ranalli_1995"

    • "Wet_Olivine-Ranalli_1995"

    • "Wet_Quarzite-Ranalli_1995"

    • "Quarzite-Ranalli_1995"

    • "Mafic_Granulite-Ranalli_1995"

    • "Plagioclase_An75-Ranalli_1995"

    1. From [Carter and Tsenn (1986). Flow properties of continental lithosphere - page 18]:
    • "Quartz_Diorite-Hansen_Carter_1982"
    1. From [J. de Bremond d'Ars et al. Tectonophysics (1999). Hydrothermalism and Diapirism in the Archaean: gravitational instability constrains. - page 5]

    • "Diabase-Caristan_1982"

    • "Tumut_Pond_Serpentinite-Raleigh_Paterson_1965"

    1. From [Mackwell, Zimmerman & Kohlstedt (1998). High-temperature deformation]:
    • "Maryland_strong_diabase-Mackwell_et_al_1998"
    1. From [Ueda et al (PEPI 2008)]:
    • "Wet_Quarzite-Ueda_et_al_2008"
    1. From [Huismans et al 2001]:

    • "Diabase-Huismans_et_al_2001"

    • "Granite-Huismans_et_al_2001"

    1. From [Burg And Podladchikov (1999)]:

    • "Dry_Upper_Crust-Schmalholz_Kaus_Burg_2009"

    • "Weak_Lower_Crust-Schmalholz_Kaus_Burg_2009"

    • "Olivine-Burg_Podladchikov_1999"

    1. From [Rybacki and Dresen, 2000, JGR]:

    • "Dry_Plagioclase_RybackiDresen_2000"

    • "Wet_Plagioclase_RybackiDresen_2000"

    1. From [Hirth, G. & Kohlstedt (2003), D. Rheology of the upper mantle and the mantle wedge: A view from the experimentalists]:

    • "Wet_Olivine_disl_creep-Hirth_Kohlstedt_2003"

    • "Wet_Olivine_disl_creep-Hirth_Kohlstedt_2003_constant_C_OH"

    • "Dry_Olivine_disl_creep-Hirth_Kohlstedt_2003"

    1. From [SchmalholzKausBurg(2009), Geology (wet olivine)]:

    • "Wet_Upper_Mantle-Burg_Schmalholz_2008"

    • "Granite-Tirel_et_al_2008"

    1. From [Urai et al.(2008)]:
    • "Ara_rocksalt-Urai_et_al.(2008)"
    1. From [Bräuer et al. (2011) Description of the Gorleben site (PART 4): Geotechnical exploration of the Gorleben salt dome - page 126]:
    • "RockSaltReference_BGRa_class3-Braeumer_et_al_2011"
    1. From [Mueller and Briegel (1978)]:
    • "Polycrystalline_Anhydrite-Mueller_and_Briegel(1978)"

    Note that you can always specify your own, by setting Bn, En, Vn, and n accordingly.

  • peir_prof::Union{Nothing, String}: Build-in PEIERLS creep profiles: example: "Olivine_Peierls-Kameyama_1999" Available profiles:

    • "Olivine_Peierls-Kameyama_1999"

  • rho_n::Union{Nothing, Float64}: depth-dependent density model parameter

  • rho_c::Union{Nothing, Float64}: depth-dependent density model parameter

  • beta::Union{Nothing, Float64}: pressure-dependent density model parameter

  • G::Union{Nothing, Float64}: shear modulus

  • Kb::Union{Nothing, Float64}: bulk modulus

  • E::Union{Nothing, Float64}: Young's modulus

  • nu::Union{Nothing, Float64}: Poisson's ratio

  • Kp::Union{Nothing, Float64}: pressure dependence parameter

  • Bd::Union{Nothing, Float64}: DIFFUSION creep pre-exponential constant

  • Ed::Union{Nothing, Float64}: activation energy

  • Vd::Union{Nothing, Float64}: activation volume

  • eta0::Union{Nothing, Float64}: POWER LAW reference viscosity

  • e0::Union{Nothing, Float64}: reference strain rate

  • Bn::Union{Nothing, Float64}: DISLOCATION creep pre-exponential constant

  • En::Union{Nothing, Float64}: activation energy

  • Vn::Union{Nothing, Float64}: activation volume

  • n::Union{Nothing, Float64}: power law exponent

  • Bp::Union{Nothing, Float64}: PEIERLS creep pre-exponential constant

  • Ep::Union{Nothing, Float64}: activation energy

  • Vp::Union{Nothing, Float64}: activation volume

  • taup::Union{Nothing, Float64}: scaling stress

  • gamma::Union{Nothing, Float64}: approximation parameter

  • q::Union{Nothing, Float64}: stress-dependence parameter

  • eta_fk::Union{Nothing, Float64}: reference viscosity for Frank-Kamenetzky viscosity

  • gamma_fk::Union{Nothing, Float64}: gamma parameter for Frank-Kamenetzky viscosity

  • TRef_fk::Union{Nothing, Float64}: reference Temperature for Frank-Kamenetzky viscosity (if not set it is 0°C)

  • ch::Union{Nothing, Float64}: cohesion

  • fr::Union{Nothing, Float64}: friction angle

  • eta_st::Union{Nothing, Float64}: stabilization viscosity (default is eta_min)

  • eta_vp::Union{Nothing, Float64}: viscoplastic plasticity regularisation viscosity

  • rp::Union{Nothing, Float64}: pore-pressure ratio

  • chSoftID::Union{Nothing, Int64}: friction softening law ID

  • frSoftID::Union{Nothing, Int64}: cohesion softening law ID

  • healID::Union{Nothing, Int64}: healing ID, points to healTau in Softening

  • alpha::Union{Nothing, Float64}: thermal expansivity

  • Cp::Union{Nothing, Float64}: specific heat (capacity), J⋅K−1⋅kg−1

  • k::Union{Nothing, Float64}: thermal conductivity

  • A::Union{Nothing, Float64}: radiogenic heat production

  • T::Union{Nothing, Float64}: optional temperature to set within the phase

  • Latent_hx::Union{Nothing, Float64}: optional, used for dike heating, J/kg

  • T_liq::Union{Nothing, Float64}: optional, used for dike heating, liquidus temperature of material, celsius

  • T_sol::Union{Nothing, Float64}: optional, used for dike heating, solidus temperature of material, celsius

  • T_Nu::Union{Nothing, Float64}: default value for thermal conductivity boundary

  • nu_k::Union{Nothing, Float64}: optional parameter, Nusselt number for use with conductivity

  • rho_ph::Union{Nothing, String}: name of the phase diagram you want to use (still needs rho to be defined for the initial guess of pressure)

  • rho_ph_dir::Union{Nothing, String}: in case the phase diagram has a different path provide the path (without the name of the actual PD) here

  • mfc::Union{Nothing, Float64}: melt fraction viscosity correction factor (positive scalar)

  • GeoParams::Union{Nothing, Vector{GeoParams.MaterialParameters.ConstitutiveRelationships.AbstractCreepLaw}}: GeoParams creeplaws Set diffusion or dislocation creeplaws as provided by the GeoParams package:

    julia
    julia> using GeoParams
julia> a = SetDiffusionCreep(GeoParams.Diffusion.dry_anorthite_Rybacki_2006);
julia> p = Phase(ID=1,Name="test", GeoParams=[a]);

    Note that GeoParams should be a vector, as you could, for example, have diffusion and dislocation creep parameters Note also that this will overwrite any other creeplaws provided in the Phase struct.

  • grainsize::Union{Nothing, Float64}: grainsize [m] (not used in LaMEM) This is not actually used in LaMEM, but is required when setting diffusion creep parameters by using GeoParams

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LaMEM.LaMEM_Model.PhaseAggregate Type
julia
Defines phase aggregates, which can be useful for visualization purposes

  • name::String: Name of the phase aggregate

  • phaseID::Union{Nothing, Vector{Int64}}: Phases to be combined

  • numPhase::Union{Nothing, Int64}: number of aggregated phases

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LaMEM.LaMEM_Model.PhaseTransition Type
julia
Defines phase transitions on markers (that change the Phase ID of a marker depending on some conditions)

  • ID::Int64: Phase_transition law ID

  • Type::String: [Constant, Clapeyron, Box]: Constant - the phase transition occurs only at a fixed value of the parameter; Clapeyron - clapeyron slope

  • Name_Clapeyron::Union{Nothing, String}: Type of predefined Clapeyron slope, such as Mantle_Transition_660km

  • PTBox_Bounds::Union{Nothing, Vector{Float64}}: box bound coordinates: [left, right, front, back, bottom, top]

  • BoxVicinity::Union{Nothing, Int64}: 1: only check particles in the vicinity of the box boundaries (2: in all directions)

  • Parameter_transition::Union{Nothing, String}: [T = Temperature, P = Pressure, Depth = z-coord, X=x-coord, Y=y-coord, APS = accumulated plastic strain, MeltFraction, t = time] parameter that triggers the phase transition

  • ConstantValue::Union{Nothing, Float64}: Value of the parameter [unit of T,P,z, APS]

  • number_phases::Union{Nothing, Int64}: The number of involved phases [default=1]

  • PhaseAbove::Union{Nothing, Vector{Int64}}: Above the chosen value the phase is 1, below it, the value is PhaseBelow

  • PhaseBelow::Union{Nothing, Vector{Int64}}: Below the chosen value the phase is PhaseBelow, above it, the value is 1

  • PhaseInside::Union{Nothing, Vector{Int64}}: Phase within the box [use -1 if you don't want to change the phase inside the box]

  • PhaseOutside::Union{Nothing, Vector{Int64}}: Phase outside the box [use -1 if you don't want to change the phase outside the box. If combined with OutsideToInside, all phases that come in are set to PhaseInside]

  • PhaseDirection::Union{Nothing, String}: [BothWays=default; BelowToAbove; AboveToBelow] Direction in which transition works

  • ResetParam::Union{Nothing, String}: [APS] Parameter to reset on particles below PT or within box

  • PTBox_TempType::Union{Nothing, String}: # Temperature condition witin the box [none, constant, linear, halfspace]

  • PTBox_topTemp::Union{Nothing, Float64}: Temp @ top of box [for linear & halfspace]

  • PTBox_botTemp::Union{Nothing, Float64}: Temp @ bottom of box [for linear & halfspace]

  • PTBox_thermalAge::Union{Nothing, Float64}: Thermal age, usually in geo-units [Myrs] [only in case of halfspace]

  • PTBox_cstTemp::Union{Nothing, Float64}: Temp within box [only for constant T]

  • v_box::Union{Nothing, Float64}: [optional] only for NotInAirBox, velocity with which box moves in cm/yr

  • t0_box::Union{Nothing, Float64}: [optional] beginning time of movemen in Myr

  • t1_box::Union{Nothing, Float64}: [optional] end time of movement in Myr

  • clapeyron_slope::Union{Nothing, Float64}: [optional] clapeyron slope of phase transition [in K/MPa]; P = ( T - T0_clapeyron ) * clapeyron_slope + P0_clapeyron

  • P0_clapeyron::Union{Nothing, Float64}: [optional] P0_clapeyron [Pa]

  • T0_clapeyron::Union{Nothing, Float64}: [optional] T0_clapeyron [C]

  • numberofequation::Union{Nothing, Int64}: Number of phase transition equations. Must be 1 or 2 for Clapeyron phase transitions

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LaMEM.LaMEM_Model.Scaling Type
julia
Scaling{T} is a structure that contains the scaling info, employed in the current simulation
  • Scaling::Any: Scaling object (as in GeoParams), which can be GEO_units(), NO_units(), or SI_units()
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LaMEM.LaMEM_Model.Softening Type
julia
Defines strain softening parameters

  • ID::Int64: softening law ID

  • APS1::Float64: Begin of softening, in units of accumulated plastic strain (APS)

  • APS2::Float64: End of softening, in units of accumulated plastic strain (APS)

  • A::Float64: Reduction ratio

  • Lm::Union{Nothing, Float64}: Material length scale (in selected units, e.g. km in geo)

  • APSheal2::Union{Nothing, Float64}: APS when healTau2 activates

  • healTau::Union{Nothing, Float64}: healing timescale parameter [Myr]

  • healTau2::Union{Nothing, Float64}: healing timescale parameter [Myr] starting at APS=APSheal2

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LaMEM.LaMEM_Model.SolutionParams Type
julia
Structure that contains the LaMEM global solution parameters.

  • gravity::Vector{Float64}: gravitational acceleration vector

  • FSSA::Float64: free surface stabilization parameter [0 - 1]; The value has to be between 0 and 1

  • FSSA_allVel::Int64: free surface stabilization parameter applied to all velocity components? Default is yes; if not it is only applied to the z-component

  • shear_heat_eff::Float64: shear heating efficiency parameter [0 - 1]

  • Adiabatic_Heat::Float64: Adiabatic Heating activation flag and efficiency. [0.0 - 1.0] (e.g., 0.5 means that only 50 percent of the potential adiabatic heating affects the energy equation)

  • act_temp_diff::Int64: temperature diffusion activation flag

  • act_therm_exp::Int64: thermal expansion activation flag

  • act_steady_temp::Int64: steady-state temperature initial guess activation flag

  • steady_temp_t::Float64: time for (quasi-)steady-state temperature initial guess

  • nstep_steady::Int64: number of steps for (quasi-)steady-state temperature initial guess (default = 1)

  • act_heat_rech::Int64: recharge heat in anomalous bodies after (quasi-)steady-state temperature initial guess (=2: recharge after every diffusion step of initial guess)

  • init_lith_pres::Int64: sets initial pressure to be the lithostatic pressure (stabilizes compressible setups in the first steps)

  • init_guess::Int64: create an initial guess step (using constant viscosity eta_ref before starting the simulation

  • p_litho_visc::Int64: use lithostatic instead of dynamic pressure for creep laws

  • p_litho_plast::Int64: use lithostatic pressure for plasticity

  • p_lim_plast::Int64: limit pressure at first iteration for plasticity

  • p_shift::Int64: add a constant value [MPa] to the total pressure field, before evaluating plasticity (e.g., when the domain is located @ some depth within the crust)

  • act_p_shift::Int64: pressure shift activation flag (enforce zero pressure on average in the top cell layer); note: this overwrites p_shift above!

  • eta_min::Float64: viscosity lower bound [Pas]

  • eta_max::Float64: viscosity upper limit [Pas]

  • eta_ref::Float64: Reference viscosity (used for the initial guess) [Pas]

  • T_ref::Float64: Reference temperature [C]

  • RUGC::Float64: universal gas constant (you need to change this only for non-dimensional setups)

  • min_cohes::Float64: cohesion lower bound [Pa]

  • min_fric::Float64: friction lower bound [degree]

  • tau_ult::Float64: ultimate yield stress [Pa]

  • rho_fluid::Float64: fluid density for depth-dependent density model

  • gw_level_type::String: ground water level type for pore pressure computation (see below)

  • gw_level::Float64: ground water level at the free surface (if defined)

  • biot::Float64: Biot pressure parameter

  • get_permea::Float64: effective permeability computation activation flag

  • rescal::Float64: stencil rescaling flag (for internal constraints, for example while computing permeability)

  • mfmax::Float64: maximum melt fraction affecting viscosity reduction

  • lmaxit::Int64: maximum number of local rheology iterations

  • lrtol::Float64: local rheology iterations relative tolerance

  • act_dike::Int64: dike activation flag (additonal term in divergence)

  • useTk::Int64: switch to use T-dependent conductivity, 0: not active

  • dikeHeat::Int64: switch to use Behn & Ito heat source in the dike

  • adiabatic_gradient::Float64: Adiabatic gradient in combination with Behn & Ito dike

  • Compute_velocity_gradient::Int64: compute the velocity gradient tensor 1: active, 0: not active. If active, it automatically activates the output in the .pvd file

  • Phasetrans::Int64: Activate Phase Transitions on Particles or not, 0: not.

  • Passive_Tracer::Int64: Activate Passive Tracers or not?

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LaMEM.LaMEM_Model.Solver Type
julia
Structure that contains the LaMEM solver options

  • SolverType::String: solver employed ["direct" or "multigrid"]

  • DirectSolver::String: mumps/superlu_dist/pastix/umfpack (requires these external PETSc packages to be installed!)

  • DirectPenalty::Float64: penalty parameter [employed if we use a direct solver]

  • MGLevels::Int64: number of MG levels [default=3]

  • MGSweeps::Int64: number of MG smoothening steps per level [default=10]

  • MGSmoother::String: type of smoothener used [chebyshev or jacobi]

  • MGJacobiDamp::Float64: Dampening parameter [only employed for Jacobi smoothener; default=0.6]

  • MGCoarseSolver::String: coarse grid solver if using multigrid ["direct" / "mumps" / "superlu_dist" or "redundant" - more options specifiable through the command-line options -crs_ksp_type & -crs_pc_type]

  • MGRedundantNum::Int64: How many times do we copy the coarse grid? [only employed for redundant solver; default is 4]

  • MGRedundantSolver::String: The coarse grid solver for each of the redundant solves [only employed for redundant; options are "mumps"/"superlu_dist" with default "superlu_dist"]

  • PETSc_options::Vector{String}: List with (optional) PETSc options

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LaMEM.LaMEM_Model.Time Type
julia
Structure that contains the LaMEM timestepping information. An explanation of the paramneters is given in the struct `Time_info`

  • time_end::Float64: simulation end time

  • dt::Float64: initial time step

  • dt_min::Float64: minimum time step (declare divergence if lower value is attempted)

  • dt_max::Float64: maximum time step

  • dt_out::Float64: output step (output at least at fixed time intervals)

  • inc_dt::Float64: time step increment per time step (fraction of unit)

  • CFL::Float64: CFL (Courant-Friedrichs-Lewy) criterion

  • CFLMAX::Float64: CFL criterion for elasticity

  • nstep_max::Int64: maximum allowed number of steps (lower bound: time_end/dt_max)

  • nstep_out::Int64: save output every n steps; Set this to -1 to deactivate saving output

  • nstep_rdb::Int64: save restart database every n steps

  • num_dt_periods::Int64: number of time stepping periods

  • time_dt_periods::Vector{Int64}: timestamps where timestep should be fixed (first entry has to 0)

  • step_dt_periods::Vector{Float64}: target timesteps ar timestamps above

  • nstep_ini::Int64: save output for n initial steps

  • time_tol::Float64: relative tolerance for time comparisons

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LaMEM.LaMEM_Model.VelCylinder Type
julia
LaMEM boundary condition internal velocty cylinder `VelCylinder` object

  • baseX::Float64: X-coordinate of base of cylinder

  • baseY::Float64: Y-coordinate of base of cylinder

  • baseZ::Float64: Z-coordinate of base of cylinder

  • capX::Float64: X-coordinate of cap of cylinder

  • capY::Float64: Y-coordinate of cap of cylinder

  • capZ::Float64: Z-coordinate of cap of cylinder

  • radius::Float64: radius of cylinder

  • vx::Union{Nothing, Float64}: Vx velocity of cylinder (default is unconstrained)

  • vy::Union{Nothing, Float64}: Vy velocity of cylinder (default is unconstrained)

  • vz::Union{Nothing, Float64}: Vz velocity of cylinder (default is unconstrained)

  • advect::Int64: cylinder advection flag

  • vmag::Float64: magnitude of velocity applied along the cylinder's axis of orientation

  • type::String: velocity profile [uniform or parabolic]

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LaMEM.LaMEM_Model.VelocityBox Type
julia
VelocityBox

Defines a velocity region within the modelling domain by specifying its center point and width along the three axes.

  • cenX::Float64: X-coordinate of center of box

  • cenY::Float64: Y-coordinate of center of box

  • cenZ::Float64: Z-coordinate of center of box

  • widthX::Float64: Width of box in x-direction

  • widthY::Float64: Width of box in y-direction

  • widthZ::Float64: Width of box in Z-direction

  • vx::Union{Nothing, Float64}: Vx velocity of box (default is unconstrained)

  • vy::Union{Nothing, Float64}: Vx velocity of box (default is unconstrained)

  • vz::Union{Nothing, Float64}: Vx velocity of box (default is unconstrained)

  • advect::Int64: box advection flag

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GeophysicalModelGenerator.above_surface Method
julia
above_surface(model::Model, DataSurface_Cart::CartData)

Returns a boolean grid that is true if the Phases/Temp grid are above the surface

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GeophysicalModelGenerator.add_box! Method
julia
add_box!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},
        Origin=nothing, StrikeAngle=0, DipAngle=0,
        phase = ConstantPhase(1),
        T=nothing )

Adds a box with phase & temperature structure to a 3D model setup. This simplifies creating model geometries in geodynamic models See the documentation of the GMG routine for the full options.

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GeophysicalModelGenerator.add_cylinder! Method
julia
add_cylinder!(model::Model;                                      # required input
                base=Tuple{3}, cap=Tuple{3}, radius=Tuple{1},   # center and radius of the sphere
                phase = ConstantPhase(1),                       # Sets the phase number(s) in the sphere
                T=nothing )                                     # Sets the thermal structure (various fucntions are available)

See the documentation of the GMG routine

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GeophysicalModelGenerator.add_ellipsoid! Method
julia
add_ellipsoid!(model::Model;                                 # required input
                cen=Tuple{3}, axes=Tuple{3},                # center and semi-axes of the ellpsoid
                Origin=nothing, StrikeAngle=0, DipAngle=0,  # origin & dip/strike
                phase = ConstantPhase(1),                   # Sets the phase number(s) in the box
                T=nothing )

See the documentation of the GMG routine

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GeophysicalModelGenerator.add_layer! Method
julia
add_layer!(model::Model; xlim, ylim, zlim=Tuple{2},
        phase = ConstantPhase(1),
        T=nothing )

Adds a layer with phase & temperature structure to a 3D model setup. This simplifies creating model geometries in geodynamic models See the documentation of the GMG routine for the full options.

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GeophysicalModelGenerator.add_polygon! Method
julia
add_polygon!(model::Model;                                 # required input
                xlim::Vector, 
                ylim=Vector,
                zlim=Vector(), 
                phase = ConstantPhase(1),                 # Sets the phase number(s) in the box
                T=nothing)

See the documentation of the GMG routine

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GeophysicalModelGenerator.add_slab! Method
julia
add_slab!(model::Model;                                 # required input
                trench::Trench; 
                phase = ConstantPhase(1),                 # Sets the phase number(s) in the box
                T=nothing)

See the documentation of the GMG routine

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GeophysicalModelGenerator.add_sphere! Method
julia
add_sphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)

See the documentation of the GMG routine

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GeophysicalModelGenerator.add_stripes! Method
julia
add_stripes!(Phase, Grid::AbstractGeneralGrid;
            stripAxes       = (1,1,0),
            stripeWidth     =  0.2,
            stripeSpacing   =  1,
            Origin          =  nothing,
            StrikeAngle     =  0,
            DipAngle        =  10,
            phase           =  ConstantPhase(3),
            stripePhase     =  ConstantPhase(4))

See the documentation of the GMG routine

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GeophysicalModelGenerator.below_surface Method
julia
below_surface(model::Model, DataSurface_Cart::CartData)

Returns a boolean grid that is true if the Phases/Temp grid are below the surface

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LaMEM.IO_functions.passivetracer_time Function
julia
passivetracer_time(model::Model, cores::Int64=1, args::String=""; wait=true)

Placeholder for passive tracer time evolution using the configuration in model. See the passivetracer_time(ID, model::Model) method to retrieve tracer data by particle ID.

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LaMEM.IO_functions.passivetracer_time Method
julia
PT = passivetracer_time(ID::Union{Vector{Int64},Int64}, model::Model)

This reads passive tracers with ID from a LaMEM simulation specified by model, and returns a named tuple with the temporal evolution of these passive tracers. We return x,y,z coordinates and all fields specified in FileName for particles number ID.

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LaMEM.IO_functions.project_onto_crosssection Method
julia
project_onto_crosssection(model::Model, Cross::CartData)

Reads the output of a LaMEM simulation and projects it onto a 2D cross-section Cross

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LaMEM.IO_functions.read_LaMEM_simulation Method
julia
Timestep, FileNames, Time = read_LaMEM_simulation(model::Model; phase=false, surf=false, passive_tracers=false)

Reads a LaMEM simulation as specified in model and returns the timesteps, times and filenames of that simulation once it is finished.

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LaMEM.IO_functions.read_LaMEM_timestep Function
julia
data, time = read_LaMEM_timestep(model::Model, TimeStep::Int64=0; fields=nothing, phase=false, surf=false, last=true)

Reads a specific Timestep from a simulation specified in model

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LaMEM.LaMEM_Model.Check_LaMEM_Model Method
julia
Check_LaMEM_Model(m::Model; warn_constant_grid=true)

Checks the LaMEM Setup Model m for errors.

warn_constant_grid toggles the warning that is emitted when both the initial Phases and Temp grids are constant. Set it to false for intentionally uniform setups (e.g. the 0D rheology benchmark in stress_strainrate_0D).

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LaMEM.LaMEM_Model.Create_Grid Method

This creates a LaMEM grid

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LaMEM.LaMEM_Model.UpdateDefaultParameters Method
julia
model = UpdateDefaultParameters(model::Model)

This updates the default parameters depending on some of the input parameters. If you activate passive tracers, for example, it will also activate output for that

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LaMEM.LaMEM_Model.above_surface! Method
julia
above_surface!(model::Model, DataSurface_Cart::CartData; phase::Int64=nothing, T::Number=nothing)

Sets the Temp or Phases above the surface DataSurface_Cart to a constant value.

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LaMEM.LaMEM_Model.add_dike! Method
julia
add_dike!(model::Model, dike::Dike)

This adds a phase transition phase_trans to model

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LaMEM.LaMEM_Model.add_geom! Method
julia
add_geom!(model::Model, geom_object)

This adds an internal geometric primitive object geom_object to the LaMEM Model Setup model.

Currently available primitive geom objects are:

  • GeomSphere

  • GeomEllipsoid

  • GeomBox

  • GeomLayer

  • GeomCylinder

  • GeomRidgeSeg

  • GeomHex

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LaMEM.LaMEM_Model.add_geom! Method
julia
add_geom!(model::Model, geom_object)

Add several geometric objects @ once.

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LaMEM.LaMEM_Model.add_petsc! Method
julia
add_petsc!(model::Model, option::String)

Adds one or more PETSc options to the model

Example

julia
julia> d = Model()
julia> add_petsc!(d,"-snes_npicard 3")
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LaMEM.LaMEM_Model.add_phase! Method
julia
add_phase!(model::Model, phase::Phase)

This adds a phase (with material properties) to model

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LaMEM.LaMEM_Model.add_phase! Method
julia
add_phase!(model::Model, phases...)

Add several phases @ once.

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LaMEM.LaMEM_Model.add_phaseaggregate! Method
julia
add_phaseaggregate!(model::Model, phaseagg::PhaseAggregate)

This adds a phase aggregate law phaseagg to model

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LaMEM.LaMEM_Model.add_phasetransition! Method
julia
add_phasetransition!(model::Model, phase_trans::PhaseTransition)

This adds a phase transition phase_trans to model

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LaMEM.LaMEM_Model.add_softening! Method
julia
add_softening!(model::Model, soft::Softening)

This adds a plastic softening law soft to model

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LaMEM.LaMEM_Model.add_topography! Method
julia
add_topography!(model::Model, topography::CartData; surf_air_phase=0, surf_topo_file="topography.txt", open_top_bound=1,  surf_level=0.0)

Adds the topography surface to the model

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LaMEM.LaMEM_Model.add_vbox! Method
julia
add_vbox!(model::Model, vboxes...)

Add several phases @ once.

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LaMEM.LaMEM_Model.add_vbox! Method
julia
add_vbox!(model::Model, vbox::VelocityBox)

This adds a vbox (with its properties) to model

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LaMEM.LaMEM_Model.adjust_for_platforms Method
julia
model, cores =  adjust_for_platforms(model, cores::Int64)

On certain platforms we have restrictions (MPI is broken on windows currently, so we need to adjust things accordingly)

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LaMEM.LaMEM_Model.below_surface! Method
julia
below_surface!(model::Model, DataSurface_Cart::CartData; phase::Union{Int64,Nothing}=nothing, T::Union{Number,Nothing}=nothing)

Sets the Temp or Phases below the surface DataSurface_Cart to a constant value.

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LaMEM.LaMEM_Model.compute_dof Method

Returns the total degrees of freedom for a LaMEM simulation

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LaMEM.LaMEM_Model.copy_phase Method
julia
copy_phase(phase::Phase; kwargs...)

This copies a phase with material properties, while allowing to change some parameters

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LaMEM.LaMEM_Model.create_initialsetup Function
julia
create_initialsetup(model::Model, cores::Int64=1, args::String=""; verbose=verbose)

Creates the initial model setup of LaMEM from model, which includes:

  • Writing the LaMEM (*.dat) input file

and in case we do not employ geometric primitives to create the setup:

  • Write the VTK file (if requested when model.Output.write_VTK_setup=true)

  • Write the marker files to disk (if model.ModelSetup.msetup="files")

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LaMEM.LaMEM_Model.cross_section Function
julia
Cross = cross_section(cart::CartData, field::Symbol =:phase; x=nothing, y=nothing, z=nothing)

Creates a cross-section through the data and returns x,z coordinates

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LaMEM.LaMEM_Model.cross_section Function
julia
data_tuple, axes_str = cross_section(model::LaMEM.Model, field=:phases; x=nothing, y=nothing, z=nothing)

This creates a cross-section through the initial model setup & returns a 2D array

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LaMEM.LaMEM_Model.digitsep Method
julia
digitsep(value::Integer; separator=",", per_separator=3)

Convert an integer to a string, separating each per_separator digits by separator.

julia
digitsep(12345678)  # "12,345,678"
digitsep(12345678, seperator= "'")  # "12'345'678"
digitsep(12345678, seperator= "-", per_separator=4)  # "1234-5678"
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LaMEM.LaMEM_Model.flatten Method
julia
data_tuple, axes_str = flatten(cross::CartData, field::Symbol, x, y, z)

Creates a 2D array out of a cross-section cross for the specified data field. Returns a named tuple (x, z, data) and axis/title strings.

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LaMEM.LaMEM_Model.hasplasticity Method
julia
hasplasticity(p::Phase)

true if p contains plastic parameters (cohesion or friction angle)

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LaMEM.LaMEM_Model.is_rectilinear Method
julia
is_rectilinear(topography::CartData)

Checks whether topography is rectilinear

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LaMEM.LaMEM_Model.isdefault Method
julia
isdefault(s1::S, s_default::S)

Checks whether a struct s1 has default parameters s_default

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LaMEM.LaMEM_Model.prepare_lamem Function
julia
prepare_lamem(model::Model, cores::Int64=1, args::String=""; verbose=false, add_APS=false)

Prepares a LaMEM run for the parameters specified in model, without running the simulation: 1) Create the *.dat file 2) Write markers to disk in case we use a "files" setup

This is useful if you want to prepare a model on one machine but run it on another one (e.g. a cluster).

  • add_APS: if true, write accumulated plastic strain (APS) to marker files (requires LaMEM ≥ 2.2.1)

Set model.Output.write_VTK_setup to true if you want to write a VTK file of the model setup.

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LaMEM.LaMEM_Model.print_short Method

This creates a single string, so we can use it in the command line

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LaMEM.LaMEM_Model.replace_phase! Method
julia
replace_phase!(model::Model, phase_new::Phase; ID::Int64=nothing, Name::String=nothing)

This replaces a phase within a LaMEM Model Setup model with phase_new either based on its Name or ID. Note that it is expected that only one such phase is present in the current setup.

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LaMEM.LaMEM_Model.rm_geom! Method
julia
rm_geom!(model::Model)

This removes all existing geometric objects from model

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LaMEM.LaMEM_Model.rm_last_phase! Method
julia
rm_last_phase!(model::Model, phase::Phase)

This removes the last added phase from model

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LaMEM.LaMEM_Model.rm_last_vbox! Method
julia
rm_last_vbox!(model::Model)

This removes the last added vbox from model

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LaMEM.LaMEM_Model.rm_phase! Method
julia
rm_phase!(model::Model, ID::Int64)

This removes a phase with ID from model

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LaMEM.LaMEM_Model.rm_phase! Method
julia
rm_phase!(model::Model)

This removes all existing phases from model

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LaMEM.LaMEM_Model.rm_vbox! Method
julia
rm_vbox!(model::Model)

This removes all existing velocity boxes from model

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LaMEM.LaMEM_Model.set_air Method
julia
set_air(; Name="air", ID=0, rho=1, alpha=nothing, eta=1e17, G=nothing, nu=nothing, fr=nothing, ch=nothing, k=30,Cp=1000)

Sets an air phase, with high conductivity

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LaMEM.LaMEM_Model.set_geom! Method
julia
set_geom!(model::Model, d::GeomSphere)

Sets the geometry of the model using the GeomSphere geometric primitive d. This populates model.Grid.Phases and model.Grid.Temp using the GMG sphere primitive.

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LaMEM.LaMEM_Model.stress_strainrate_0D Method
julia
τ = stress_strainrate_0D(rheology, ε_vec::Vector; n=8, T=700, nstep_max=2, clean=true)

Computes the stress for a given strain rate and 0D rheology setup, for viscous creep rheologies. n is the resolution in x,z, T the temperature, nstep_max the number of time steps, ε_vec the strainrate vector (in 1/s).

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LaMEM.LaMEM_Model.within_bounds Method
julia
within_bounds(model::Model, topography::CartData)

Verifies that the bounds of the topography grid are larger than that of the model

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Function
julia
write_LaMEM_inputFile(d::Model,fname::String; dir=pwd())

Writes a LaMEM input file based on the data stored in Model

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::BoundaryConditions)

Writes the boundary conditions related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::FreeSurface)

Writes the free surface related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomBox)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomCylinder)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomEllipsoid)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomHex)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomLayer)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomRidgeSeg)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomSphere)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::Grid)

This writes grid info to a LaMEM input file

Example

julia
julia> d=LaMEM.Grid(coord_x=[0.0, 0.7, 0.8, 1.0], bias_x=[0.3,1.0,3.0], nel_x=[10,4,2])
julia> io = open("test.dat","w")
julia> LaMEM.write_LaMEM_inputFile(io, d)
julia> close(io)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::Output)

Writes the free surface related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::ModelSetup)

Writes options related to the Model Setup to disk

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::Output)

Writes the free surface related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::PassiveTracers)

Writes the boundary conditions related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::Scaling)

Writes the scaling/units section to the LaMEM input file io.

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::SolutionParams)

Writes the boundary conditions related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::Solver)

Writes the free surface related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method

Writes the Time related parameters to file

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LaMEM.LaMEM_Model.write_LaMEM_inputFile Method
julia
write_LaMEM_inputFile(io, d::GeomSphere)
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LaMEM.LaMEM_Model.write_LaMEM_inputFile_PETSc Method
julia
write_LaMEM_inputFile_PETSc(io, d::Solver)

Writes the (optional) PETSc options to file

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LaMEM.Run.run_lamem Function
julia
run_lamem(model::Model, cores::Int64=1, args::String=""; wait=true, add_APS=false)

Performs a LaMEM run for the parameters specified in model.

  • cores: number of MPI cores to use

  • args: additional command-line arguments passed to LaMEM

  • wait: if true, wait for the simulation to finish before returning

  • add_APS: if true, write accumulated plastic strain (APS) to marker files. Requires LaMEM ≥ 2.2.1 (header 1211215). Default is false (LaMEM ≥ 2.2.0).

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