List functions

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

• eyy_time_delims::Vector{Float64}

• eyy_strain_rates::Vector{Float64}

• exy_num_periods::Int64

• exy_time_delims::Vector{Float64}

• exy_strain_rates::Vector{Float64}

• exz_num_periods::Int64

• exz_time_delims::Vector{Float64}

• exz_strain_rates::Vector{Float64}

• eyz_num_periods::Int64

• eyz_time_delims::Vector{Float64}

• eyz_strain_rates::Vector{Float64}

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

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

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::Float64: initial level of the free surface

• surf_air_phase::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

• 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

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

Example 1

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> 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]

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)

; 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

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

Model(args...)

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

Example

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;  

Model(;
    Scaling=Scaling(GEO_units()),
    Grid=Grid(), 
    Time=Time(),
    FreeSurface=FreeSurface(),
    BoundaryConditions=BoundaryConditions(),
    SolutionParams=SolutionParams(),
    Solver=Solver(),
    ModelSetup=ModelSetup(),
    Output=Output(),
    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

• Materials::Any

Structure that contains the LaMEM Model Setup and Advection options

• msetup::String: Setup type - can be geom (phases are assigned from geometric primitives), 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; seegeom_Sphere`

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_litho_press::Any

• out_pore_press::Any

• 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

• out_ehmax::Any

• out_yield::Any

• 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

• out_moment_res::Any

• out_cont_res::Any

• out_energ_res::Any

• out_melt_fraction::Any

• out_fluid_density::Any

• out_conductivity::Any

• out_vel_gr_tensor::Any

• 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_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

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}: DIFFUSION creep profile; example: "DryOlivinediffcreep-HirthKohlstedt_2003"

• disl_prof::Union{Nothing, String}: DISLOCATION creep profile; example: "Granite-Tireletal_2008"

• peir_prof::Union{Nothing, String}: PEIERLS creep profile; example: "OlivinePeierls-Kameyama1999"

• 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)

• 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)

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, Int64}: Type of predefined Clapeyron slope, such as MantleTransition660km

• 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::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}}

• 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::String: [BothWays=default; BelowToAbove; AboveToBelow] Direction in which transition works

• ResetParam::String: [APS] Parameter to reset on particles below PT or within box

• PTBox_TempType::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

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()

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::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

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

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

• Adiabatic_Heat::Float64: Adiabatic Heating activation flag and efficiency. 0.0 - 1.0

• 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

• 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

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

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: timeend/dtmax)

• 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

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]

AddBox!(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

AddCylinder!(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

AddEllipsoid!(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

AddSphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)

See the documentation of the GMG routine

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.

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

Check_LaMEM_Model(m::Model)

Checks the LaMEM Setup Model m for errors

This creates a LaMEM grid

Write_LaMEM_InputFile(d::Model,fname::String; dir=pwd())

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

Write_LaMEM_InputFile(io, d::BoundaryConditions)

Writes the boundary conditions related parameters to file

Write_LaMEM_InputFile(io, d::FreeSurface)

Writes the free surface related parameters to file

Write_LaMEM_InputFile(io, d::Grid)

This writes grid info to a LaMEM input file

Example

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)

Write_LaMEM_InputFile(io, d::Output)

Writes the free surface related parameters to file

Write_LaMEM_InputFile(io, d::ModelSetup)

Writes options related to the Model Setup to disk

Write_LaMEM_InputFile(io, d::Output)

Writes the free surface related parameters to file

Write_LaMEM_InputFile(io, d::SolutionParams)

Writes the boundary conditions related parameters to file

Write_LaMEM_InputFile(io, d::Solver)

Writes the free surface related parameters to file

Writes the Time related parameters to file

Write_LaMEM_InputFile(io, d::geom_Sphere)

Write_LaMEM_InputFile_PETSc(io, d::Solver)

Writes the (optional) PETSc options to file

add_dike!(model::Model, dike::Dike)

This adds a phase transition phase_trans to model

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:

• geom_Sphere

add_petsc!(model::Model, option::String)

Adds one or more PETSc options to the model

Example

julia> d = Model()
julia> add_petsc!(d,"-snes_npicard 3")

add_phase!(model::Model, phase::Phase)

This adds a phase (with material properties) to model

add_phase!(model::Model, phases...)

Add several phases @ once.

add_phasetransition!(model::Model, phase_trans::PhaseTransition)

This adds a phase transition phase_trans to model

add_softening!(model::Model, soft::Softening)

This adds a plastic softening law soft to model

create_initialsetup(model::Model, cores::Int64=1, args::String="")

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

• Writing the LaMEM (*.dat) input file
• Write the VTK file (if requested when model.Output.write_VTK_setup=true)
• Write the marker files to disk (if model.ModelSetup.msetup="files")

help_info::String = get_doc(structure, field::Symbol)

This returns a string with the documentation for a parameter field that is within the structure. Note that this structure must be a help structure of the current one.

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.

rm_last_phase!(model::Model, phase::Phase)

This removes the last added phase from model

rm_phase!(model::Model, ID::Int64)

This removes a phase with ID from model

This sets the geometry

run_lamem(model::Model, cores::Int64=1, args:String=""; wait=true)

Performs a LaMEM run for the parameters that are specified in model