List functions
These are all the functions that are provided for the LaMEM Julia Setup interface
LaMEM.LaMEM_Model.BCBlock — TypeLaMEM boundary condition `BCBlock` objectnpath::Int64: Number of path points of Bezier curve (path-points only!)theta::Vector{Float64}: # Orientation angles at path points (counter-clockwise positive)time::Vector{Float64}: Times at path pointspath::Vector{Float64}: Path points x-y coordinatesnpoly::Int64: Number of polygon verticespoly::Vector{Float64}: Polygon x-y coordinates at initial timebot::Float64: Polygon bottom coordinatetop::Float64: Polygon top coordinate
LaMEM.LaMEM_Model.BoundaryConditions — TypeStructure 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 flagtemp_top::Float64: Constant temperature on the top boundarytemp_bot::Float64: Constant temperature on the bottom boundaryexx_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 intervaleyy_num_periods::Int64: eyynumperiodseyy_time_delims::Vector{Float64}: eyytimedelimseyy_strain_rates::Vector{Float64}: eyystrainratesexy_num_periods::Int64: exynumperiodsexy_time_delims::Vector{Float64}: exytimedelimsexy_strain_rates::Vector{Float64}: exystrainratesexz_num_periods::Int64: exznumperiodsexz_time_delims::Vector{Float64}: exztimedelimsexz_strain_rates::Vector{Float64}: exzstrainrateseyz_num_periods::Int64: eyznumperiodseyz_time_delims::Vector{Float64}: eyztimedelimseyz_strain_rates::Vector{Float64}: eyzstrainratesbg_ref_point::Vector{Float64}: background strain rate reference point (fixed)VelocityBoxes::Vector{VelocityBox}: List of added velocity boxesBCBlocks::Vector{BCBlock}: List of added Bezier blocksVelCylinders::Vector{VelCylinder}: List of added velocity cylindersbvel_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 velocitybvel_bot::Union{Nothing, Float64}: Bottom coordinate of inflow windowbvel_top::Union{Nothing, Float64}: Top coordinate of inflow windowvelin_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 velinnumperiods>1)bvel_velout::Union{Nothing, Float64}: outflow velocity (if not specified, computed from mass balance)bvel_relax_d::Union{Nothing, Float64}: vert.distance from bvelbot and bveltop over which velocity is reduced linearlybvel_velbot::Union{Nothing, Int64}: bottom inflow velocity for use with bvel_face=CompensatingInflowbvel_veltop::Union{Nothing, Int64}: top inflow velocity for use with bvel_face=CompensatingInflowbvel_temperature_inflow::Union{Nothing, String}: bveltemperatureinflow: Thermal age of the plate, which can be constant if set to Fixedthermalage or ConstantTinflow (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 wellbvel_temperature_mantle::Union{Nothing, Float64}: In dimensional unit. Temperature of the mantlebvel_temperature_top::Union{Nothing, Float64}: In dimensional unit. temperature of the topbvel_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 topbvel_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 flagpermeable_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 openbotbound=1fix_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 @ bottomPlume_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 outflowPlume_Phase::Union{Nothing, Int64}: phase of plume materialPlume_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 plumePlume_Inflow_Velocity::Union{Nothing, Float64}: # Inflow velocity (not required if Pressure_Type) in cm/year if using GEOunitsPlume_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 plumePlume_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 bottompres_top::Union{Nothing, Float64}: Pressure on the top boundarypres_bot::Union{Nothing, Float64}: Pressure on the bottom boundaryinit_pres::Union{Nothing, Int64}: pressure initial guess flag; linear profile between prestop and presbot in the unconstrained cellsinit_temp::Union{Nothing, Int64}: temperature initial guess flag; linear profile between temptop and tempbot
LaMEM.LaMEM_Model.Dike — TypeDefines the properties related to inserting dikesID::Int64: Material phase IDMf::Float64: value for dike/magma- accommodated extension, between 0 and 1, in the front of the box, for phase dikeMc::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 usedy_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 usedMb::Union{Nothing, Float64}: value for dike/magma-accommodated extension, between 0 and 1, in the back of the box, for phase dikePhaseID::Union{Nothing, Int64}: Phase IDPhaseTransID::Union{Nothing, Int64}: Phase transition ID
LaMEM.LaMEM_Model.FreeSurface — TypeStructure that contains the LaMEM free surface information.surf_use::Int64: Free surface activation flagsurf_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 surfacesurf_air_phase::Union{Nothing, Int64}: phase ID of sticky air layersurf_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 phaseser_time_delims::Vector{Float64}: erosion time delimiters (one less than number)er_rates::Vector{Float64}: constant erosion rates in different time periodser_levels::Vector{Int64}: levels above which we apply constant erosion rates in different time periodssediment_model::Int64: sedimentation model [0-none (dafault), 1-prescribed rate with given level, 2-cont. margin]sed_num_layers::Int64: number of sediment layerssed_time_delims::Vector{Float64}: sediment layers time delimiters (one less than number)sed_rates::Vector{Float64}: sediment rates in different time periodssed_levels::Vector{Float64}: levels below which we apply constant sediment rates in different time periodssed_phases::Vector{Int64}: sediment layers phase numbers in different time periodsmarginO::Vector{Float64}: lateral coordinates of continental margin - originmarginE::Vector{Float64}: lateral coordinates of continental margin - 2nd pointhUp::Float64: up dip thickness of sediment cover (onshore)hDown::Float64: down dip thickness of sediment cover (off shore)dTrans::Float64: half of transition zoneTopography::Union{Nothing, GeophysicalModelGenerator.CartData}: Topography grid
LaMEM.LaMEM_Model.GeomBox — TypeLaMEM geometric primitive `Box` objectphase::Int64: phasebounds::Vector{Float64}: box bound coordinates:left,right,front,back,bottom,topTemperature::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]
LaMEM.LaMEM_Model.GeomCylinder — TypeLaMEM geometric primitive `Cylinder` objectphase::Int64: phaseradius::Float64: radius of cylinderbase::Vector{Float64}: center of base of cylindercap::Vector{Float64}: center of cap of cylinderTemperature::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]
LaMEM.LaMEM_Model.GeomEllipsoid — TypeLaMEM geometric primitive `Ellipsoid` objectphase::Int64: phaseaxes::Vector{Float64}: semi-axes of ellipsoid inx,yandzcenter::Vector{Float64}: center of sphereTemperature::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]
LaMEM.LaMEM_Model.GeomHex — TypeLaMEM geometric primitive `Hex` object to define hexahedral elementsphase::Int64: phasecoord::Vector{Float64}:x-y-zcoordinates for each of 8 nodes (24 parameters) (counter)-clockwise for an arbitrary face, followed by the opposite face
LaMEM.LaMEM_Model.GeomLayer — TypeLaMEM geometric primitive `Layer` objectphase::Int64: phasetop::Float64: top of layerbottom::Float64: bottom of layercosine::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-directionamplitude::Union{Nothing, Float64}: required if cosine: amplitude of perturbationTemperature::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]
LaMEM.LaMEM_Model.GeomRidgeSeg — TypeLaMEM geometric primitive `RidgeSeg` objectphase::Int64: phasebounds::Vector{Float64}: box bound coordinates:left,right,front,back,bottom,topridgeseg_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 tohalfspace_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 [inMyrin case of GEO units]maxAge::Union{Nothing, Float64}: [optional] parameter that indicates the maximum thermal age of a platev_spread::Union{Nothing, Float64}: [optional] parameter that indicates the spreading velocity of the plate; if not defined it uses bvel_velin specified elsewhere
LaMEM.LaMEM_Model.GeomSphere — TypeLaMEM geometric primitive `sphere` objectphase::Int64: phaseradius::Float64: radius of spherecenter::Vector{Float64}: center of sphereTemperature::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]
LaMEM.LaMEM_Model.Grid — TypeStructure that contains the LaMEM grid informationnmark_x::Int64: number of markers/element in x-directionnmark_y::Int64: number of markers/element in y-directionnmark_z::Int64: number of markers/element in x-directionnel_x::Vector{Int64}: number of elements in x-directionnel_y::Vector{Int64}: number of elements in y-directionnel_z::Vector{Int64}: number of elements in z-directioncoord_x::Vector{Float64}: coordinates in x-directioncoord_y::Vector{Float64}: coordinates in y-directioncoord_z::Vector{Float64}: coordinates in z-directionnseg_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 objectPhases::Array{Int32}: Phases; 3D phase informationTemp::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])
+Available functions · LaMEM.jl List functions
These are all the functions that are provided for the LaMEM Julia Setup interface
LaMEM.LaMEM_Model.BCBlock — TypeLaMEM boundary condition `BCBlock` object
npath::Int64: Number of path points of Bezier curve (path-points only!)
theta::Vector{Float64}: # Orientation angles at path points (counter-clockwise positive)
time::Vector{Float64}: Times at path points
path::Vector{Float64}: Path points x-y coordinates
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
sourceLaMEM.LaMEM_Model.BoundaryConditions — TypeStructure 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: eyynumperiods
eyy_time_delims::Vector{Float64}: eyytimedelims
eyy_strain_rates::Vector{Float64}: eyystrainrates
exy_num_periods::Int64: exynumperiods
exy_time_delims::Vector{Float64}: exytimedelims
exy_strain_rates::Vector{Float64}: exystrainrates
exz_num_periods::Int64: exznumperiods
exz_time_delims::Vector{Float64}: exztimedelims
exz_strain_rates::Vector{Float64}: exzstrainrates
eyz_num_periods::Int64: eyznumperiods
eyz_time_delims::Vector{Float64}: eyztimedelims
eyz_strain_rates::Vector{Float64}: eyzstrainrates
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 velinnumperiods>1)
bvel_velout::Union{Nothing, Float64}: outflow velocity (if not specified, computed from mass balance)
bvel_relax_d::Union{Nothing, Float64}: vert.distance from bvelbot and bveltop 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}: bveltemperatureinflow: Thermal age of the plate, which can be constant if set to Fixedthermalage or ConstantTinflow (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 openbotbound=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 prestop and presbot in the unconstrained cells
init_temp::Union{Nothing, Int64}: temperature initial guess flag; linear profile between temptop and tempbot
sourceLaMEM.LaMEM_Model.Dike — TypeDefines 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
sourceLaMEM.LaMEM_Model.FreeSurface — TypeStructure 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
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
sourceLaMEM.LaMEM_Model.GeomBox — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.GeomCylinder — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.GeomEllipsoid — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.GeomHex — TypeLaMEM 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
sourceLaMEM.LaMEM_Model.GeomLayer — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.GeomRidgeSeg — TypeLaMEM 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
sourceLaMEM.LaMEM_Model.GeomSphere — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.Grid — TypeStructure 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)
@@ -11,7 +11,7 @@
marker/cell : (3, 3, 3)
x ϵ [-10.0 : 10.0]
y ϵ [-10.0 : 0.0]
- z ϵ [-10.0 : 0.0]
sourceLaMEM.LaMEM_Model.Materials — TypeStructure 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)
sourceLaMEM.LaMEM_Model.Model — TypeModel
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
sourceLaMEM.LaMEM_Model.Model — MethodModel(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()))
+ z ϵ [-10.0 : 0.0]
sourceLaMEM.LaMEM_Model.Materials — TypeStructure 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)
sourceLaMEM.LaMEM_Model.Model — TypeModel
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
sourceLaMEM.LaMEM_Model.Model — MethodModel(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}
@@ -23,7 +23,7 @@
|-- Model setup options : Type=geom;
|-- Output options : filename=output; pvd=1; avd=0; surf=0
|-- Materials : 1 phases;
-
sourceLaMEM.LaMEM_Model.Model — MethodModel(;
+
sourceLaMEM.LaMEM_Model.Model — MethodModel(;
Scaling=Scaling(GEO_units()),
Grid=Grid(),
Time=Time(),
@@ -35,29 +35,29 @@
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
sourceLaMEM.LaMEM_Model.ModelSetup — TypeStructure 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`
sourceLaMEM.LaMEM_Model.Multigrid — TypeStructure 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)
sourceLaMEM.LaMEM_Model.Output — TypeStructure 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: outoverpress
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_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
sourceLaMEM.LaMEM_Model.PassiveTracers — TypeStructure 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
sourceLaMEM.LaMEM_Model.Phase — TypeDefines 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:
- 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"
- 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:
- 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"
- From [Carter and Tsenn (1986). Flow properties of continental lithosphere - page 18]:
"Quartz_Diorite-Hansen_Carter_1982"
- 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"
- From [Mackwell, Zimmerman & Kohlstedt (1998). High-temperature deformation]:
"Maryland_strong_diabase-Mackwell_et_al_1998"
- From [Ueda et al (PEPI 2008)]:
"Wet_Quarzite-Ueda_et_al_2008"
- From [Huismans et al 2001]:
"Diabase-Huismans_et_al_2001""Granite-Huismans_et_al_2001"
- From [Burg And Podladchikov (1999)]:
"Dry_Upper_Crust-Schmalholz_Kaus_Burg_2009""Weak_Lower_Crust-Schmalholz_Kaus_Burg_2009""Olivine-Burg_Podladchikov_1999"
- From [Rybacki and Dresen, 2000, JGR]:
"Dry_Plagioclase_RybackiDresen_2000""Wet_Plagioclase_RybackiDresen_2000"
- 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"
- From [SchmalholzKausBurg(2009), Geology (wet olivine)]:
"Wet_Upper_Mantle-Burg_Schmalholz_2008""Granite-Tirel_et_al_2008"
- From [Urai et al.(2008)]:
"Ara_rocksalt-Urai_et_al.(2008)"
- 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"
- 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> using GeoParams
+ )
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
sourceLaMEM.LaMEM_Model.ModelSetup — TypeStructure 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`
sourceLaMEM.LaMEM_Model.Multigrid — TypeStructure 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)
sourceLaMEM.LaMEM_Model.Output — TypeStructure 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: outoverpress
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_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
sourceLaMEM.LaMEM_Model.PassiveTracers — TypeStructure 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
sourceLaMEM.LaMEM_Model.Phase — TypeDefines 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:
- 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"
- 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:
- 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"
- From [Carter and Tsenn (1986). Flow properties of continental lithosphere - page 18]:
"Quartz_Diorite-Hansen_Carter_1982"
- 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"
- From [Mackwell, Zimmerman & Kohlstedt (1998). High-temperature deformation]:
"Maryland_strong_diabase-Mackwell_et_al_1998"
- From [Ueda et al (PEPI 2008)]:
"Wet_Quarzite-Ueda_et_al_2008"
- From [Huismans et al 2001]:
"Diabase-Huismans_et_al_2001""Granite-Huismans_et_al_2001"
- From [Burg And Podladchikov (1999)]:
"Dry_Upper_Crust-Schmalholz_Kaus_Burg_2009""Weak_Lower_Crust-Schmalholz_Kaus_Burg_2009""Olivine-Burg_Podladchikov_1999"
- From [Rybacki and Dresen, 2000, JGR]:
"Dry_Plagioclase_RybackiDresen_2000""Wet_Plagioclase_RybackiDresen_2000"
- 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"
- From [SchmalholzKausBurg(2009), Geology (wet olivine)]:
"Wet_Upper_Mantle-Burg_Schmalholz_2008""Granite-Tirel_et_al_2008"
- From [Urai et al.(2008)]:
"Ara_rocksalt-Urai_et_al.(2008)"
- 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"
- 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> 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 This is not actually used in LaMEM, but is required when setting diffusion creep parameters by using GeoParams
sourceLaMEM.LaMEM_Model.PhaseAggregate — TypeDefines 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
sourceLaMEM.LaMEM_Model.PhaseTransition — TypeDefines 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 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::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]
sourceLaMEM.LaMEM_Model.Scaling — TypeScaling{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()
sourceLaMEM.LaMEM_Model.Softening — TypeDefines 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
sourceLaMEM.LaMEM_Model.SolutionParams — TypeStructure 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
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?
sourceLaMEM.LaMEM_Model.Solver — TypeStructure 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
sourceLaMEM.LaMEM_Model.Time — TypeStructure 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
sourceLaMEM.LaMEM_Model.VelCylinder — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.VelocityBox — TypeDefine velocity regions within the modelling region, by specifying its center point and width along the three axis.
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
sourceGeophysicalModelGenerator.above_surface — Methodabove_surface(model::Model, DataSurface_Cart::CartData)
Returns a boolean grid that is true if the Phases/Temp grid are above the surface
sourceGeophysicalModelGenerator.add_box! — Methodadd_box!(model::Model; xlim=Tuple{2}, [ylim=Tuple{2}], zlim=Tuple{2},
+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 This is not actually used in LaMEM, but is required when setting diffusion creep parameters by using GeoParams
sourceLaMEM.LaMEM_Model.PhaseAggregate — TypeDefines 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
sourceLaMEM.LaMEM_Model.PhaseTransition — TypeDefines 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 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::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]
sourceLaMEM.LaMEM_Model.Scaling — TypeScaling{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()
sourceLaMEM.LaMEM_Model.Softening — TypeDefines 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
sourceLaMEM.LaMEM_Model.SolutionParams — TypeStructure 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
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?
sourceLaMEM.LaMEM_Model.Solver — TypeStructure 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
sourceLaMEM.LaMEM_Model.Time — TypeStructure 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
sourceLaMEM.LaMEM_Model.VelCylinder — TypeLaMEM 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]
sourceLaMEM.LaMEM_Model.VelocityBox — TypeDefine velocity regions within the modelling region, by specifying its center point and width along the three axis.
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
sourceGeophysicalModelGenerator.above_surface — Methodabove_surface(model::Model, DataSurface_Cart::CartData)
Returns a boolean grid that is true if the Phases/Temp grid are above the surface
sourceGeophysicalModelGenerator.add_box! — Methodadd_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.
sourceGeophysicalModelGenerator.add_cylinder! — Methodadd_cylinder!(model::Model; # required input
+ 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.
sourceGeophysicalModelGenerator.add_cylinder! — Methodadd_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
sourceGeophysicalModelGenerator.add_ellipsoid! — Methodadd_ellipsoid!(model::Model; # required input
+ T=nothing ) # Sets the thermal structure (various fucntions are available)
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.add_ellipsoid! — Methodadd_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
sourceGeophysicalModelGenerator.add_layer! — Methodadd_layer!(model::Model; xlim, ylim, zlim=Tuple{2},
+ T=nothing )
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.add_layer! — Methodadd_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.
sourceGeophysicalModelGenerator.add_polygon! — Methodadd_polygon!(model::Model; # required input
+ 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.
sourceGeophysicalModelGenerator.add_polygon! — Methodadd_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
sourceGeophysicalModelGenerator.add_slab! — Methodadd_slab!(model::Model; # required input
+ T=nothing)
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.add_slab! — Methodadd_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
sourceGeophysicalModelGenerator.add_sphere! — Methodadd_sphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.add_stripes! — Methodadd_stripes!(Phase, Grid::AbstractGeneralGrid;
+ T=nothing)
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.add_sphere! — Methodadd_sphere!(model::Model; cen=Tuple{3}, radius=Tuple{1}, phase = ConstantPhase(1), T=nothing)
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.add_stripes! — Methodadd_stripes!(Phase, Grid::AbstractGeneralGrid;
stripAxes = (1,1,0),
stripeWidth = 0.2,
stripeSpacing = 1,
@@ -65,10 +65,10 @@
StrikeAngle = 0,
DipAngle = 10,
phase = ConstantPhase(3),
- stripePhase = ConstantPhase(4))
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.below_surface — Methodbelow_surface(model::Model, DataSurface_Cart::CartData)
Returns a boolean grid that is true if the Phases/Temp grid are below the surface
sourceLaMEM.IO_functions.passivetracer_time — Functionsource LaMEM.IO_functions.passivetracer_time — MethodPT = 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.
sourceLaMEM.IO_functions.read_LaMEM_simulation — MethodTimestep, 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.
sourceLaMEM.IO_functions.read_LaMEM_timestep — Functiondata, 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
sourceLaMEM.LaMEM_Model.Check_LaMEM_Model — MethodCheck_LaMEM_Model(m::Model)
Checks the LaMEM Setup Model m for errors
sourceLaMEM.LaMEM_Model.Create_Grid — MethodThis creates a LaMEM grid
sourceLaMEM.LaMEM_Model.UpdateDefaultParameters — Methodmodel = 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
sourceLaMEM.LaMEM_Model.above_surface! — Methodabove_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.
sourceLaMEM.LaMEM_Model.add_dike! — Methodadd_dike!(model::Model, dike::Dike)
This adds a phase transition phase_trans to model
sourceLaMEM.LaMEM_Model.add_geom! — Methodadd_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:
GeomSphereGeomEllipsoidGeomBoxGeomLayerGeomCylinderGeomRidgeSegGeomHex
sourceLaMEM.LaMEM_Model.add_geom! — Methodadd_geom!(model::Model, geom_object)
Add several geometric objects @ once.
sourceLaMEM.LaMEM_Model.add_petsc! — Methodadd_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")
sourceLaMEM.LaMEM_Model.add_phase! — Methodadd_phase!(model::Model, phase::Phase)
This adds a phase (with material properties) to model
sourceLaMEM.LaMEM_Model.add_phase! — Methodadd_phase!(model::Model, phases...)
Add several phases @ once.
sourceLaMEM.LaMEM_Model.add_phaseaggregate! — Methodadd_phaseaggregate!(model::Model, phaseagg::PhaseAggregate)
This adds a phase aggregate law phaseagg to model
sourceLaMEM.LaMEM_Model.add_phasetransition! — Methodadd_phasetransition!(model::Model, phase_trans::PhaseTransition)
This adds a phase transition phase_trans to model
sourceLaMEM.LaMEM_Model.add_softening! — Methodadd_softening!(model::Model, soft::Softening)
This adds a plastic softening law soft to model
sourceLaMEM.LaMEM_Model.add_topography! — Methodadd_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
sourceLaMEM.LaMEM_Model.add_vbox! — Methodadd_vbox!(model::Model, vboxes...)
Add several phases @ once.
sourceLaMEM.LaMEM_Model.add_vbox! — Methodadd_vbox!(model::Model, vbox::VelocityBox) This adds a vbox (with its properties) to model
sourceLaMEM.LaMEM_Model.adjust_for_platforms — Methodmodel, 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)
sourceLaMEM.LaMEM_Model.below_surface! — Methodbelow_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.
sourceLaMEM.LaMEM_Model.compute_dof — MethodReturns the total degrees of freedom for a LaMEM simulation
sourceLaMEM.LaMEM_Model.copy_phase — Methodcopy_phase(phase::Phase; kwargs...)
This copies a phase with material properties, while allowing to change some parameters
sourceLaMEM.LaMEM_Model.create_initialsetup — Functioncreate_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 employt 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")
sourceLaMEM.LaMEM_Model.cross_section — FunctionCross = 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
sourceLaMEM.LaMEM_Model.cross_section — Functiondata_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
sourceLaMEM.LaMEM_Model.digitsep — Methoddigitsep(value::Integer; separator=",", per_separator=3)
Convert an integer to a string, separating each per_separator digits by separator.
digitsep(12345678) # "12,345,678"
+ stripePhase = ConstantPhase(4))
See the documentation of the GMG routine
sourceGeophysicalModelGenerator.below_surface — Methodbelow_surface(model::Model, DataSurface_Cart::CartData)
Returns a boolean grid that is true if the Phases/Temp grid are below the surface
sourceLaMEM.IO_functions.passivetracer_time — Functionsource LaMEM.IO_functions.passivetracer_time — MethodPT = 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.
sourceLaMEM.IO_functions.read_LaMEM_simulation — MethodTimestep, 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.
sourceLaMEM.IO_functions.read_LaMEM_timestep — Functiondata, 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
sourceLaMEM.LaMEM_Model.Check_LaMEM_Model — MethodCheck_LaMEM_Model(m::Model)
Checks the LaMEM Setup Model m for errors
sourceLaMEM.LaMEM_Model.Create_Grid — MethodThis creates a LaMEM grid
sourceLaMEM.LaMEM_Model.UpdateDefaultParameters — Methodmodel = 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
sourceLaMEM.LaMEM_Model.above_surface! — Methodabove_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.
sourceLaMEM.LaMEM_Model.add_dike! — Methodadd_dike!(model::Model, dike::Dike)
This adds a phase transition phase_trans to model
sourceLaMEM.LaMEM_Model.add_geom! — Methodadd_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:
GeomSphereGeomEllipsoidGeomBoxGeomLayerGeomCylinderGeomRidgeSegGeomHex
sourceLaMEM.LaMEM_Model.add_geom! — Methodadd_geom!(model::Model, geom_object)
Add several geometric objects @ once.
sourceLaMEM.LaMEM_Model.add_petsc! — Methodadd_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")
sourceLaMEM.LaMEM_Model.add_phase! — Methodadd_phase!(model::Model, phase::Phase)
This adds a phase (with material properties) to model
sourceLaMEM.LaMEM_Model.add_phase! — Methodadd_phase!(model::Model, phases...)
Add several phases @ once.
sourceLaMEM.LaMEM_Model.add_phaseaggregate! — Methodadd_phaseaggregate!(model::Model, phaseagg::PhaseAggregate)
This adds a phase aggregate law phaseagg to model
sourceLaMEM.LaMEM_Model.add_phasetransition! — Methodadd_phasetransition!(model::Model, phase_trans::PhaseTransition)
This adds a phase transition phase_trans to model
sourceLaMEM.LaMEM_Model.add_softening! — Methodadd_softening!(model::Model, soft::Softening)
This adds a plastic softening law soft to model
sourceLaMEM.LaMEM_Model.add_topography! — Methodadd_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
sourceLaMEM.LaMEM_Model.add_vbox! — Methodadd_vbox!(model::Model, vboxes...)
Add several phases @ once.
sourceLaMEM.LaMEM_Model.add_vbox! — Methodadd_vbox!(model::Model, vbox::VelocityBox) This adds a vbox (with its properties) to model
sourceLaMEM.LaMEM_Model.adjust_for_platforms — Methodmodel, 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)
sourceLaMEM.LaMEM_Model.below_surface! — Methodbelow_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.
sourceLaMEM.LaMEM_Model.compute_dof — MethodReturns the total degrees of freedom for a LaMEM simulation
sourceLaMEM.LaMEM_Model.copy_phase — Methodcopy_phase(phase::Phase; kwargs...)
This copies a phase with material properties, while allowing to change some parameters
sourceLaMEM.LaMEM_Model.create_initialsetup — Functioncreate_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 employt 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")
sourceLaMEM.LaMEM_Model.cross_section — Functiondata_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
sourceLaMEM.LaMEM_Model.cross_section — FunctionCross = 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
sourceLaMEM.LaMEM_Model.digitsep — Methoddigitsep(value::Integer; separator=",", per_separator=3)
Convert an integer to a string, separating each per_separator digits by separator.
digitsep(12345678) # "12,345,678"
digitsep(12345678, seperator= "'") # "12'345'678"
-digitsep(12345678, seperator= "-", per_separator=4) # "1234-5678"
sourceLaMEM.LaMEM_Model.flatten — MethodCreates a 2D array out of a cross-section and a specified data field
sourceLaMEM.LaMEM_Model.hasplasticity — Methodhasplasticity(p::Phase)
true if p contains plastic parameters (cohesion or friction angle)
sourceLaMEM.LaMEM_Model.is_rectilinear — Methodis_rectilinear(topography::CartData)
Checks whether topography is rectilinear
sourceLaMEM.LaMEM_Model.isdefault — Methodisdefault(s1::S, s_default::S)
Checks whether a struct s1 has default parameters s_default
sourceLaMEM.LaMEM_Model.prepare_lamem — Functionprepare_lamem(model::Model, cores::Int64=1, args:String=""; verbose=false)
Prepares a LaMEM run for the parameters that are 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)
Set model.Output.write_VTK_setup to true if you want to write a VTK file of the model setup
sourceLaMEM.LaMEM_Model.print_short — MethodThis creates a single string, so we can use it in the command line
sourceLaMEM.LaMEM_Model.replace_phase! — Methodreplace_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.
sourceLaMEM.LaMEM_Model.rm_geom! — Methodrm_geom!(model::Model)
This removes all existing geometric objects from model
sourceLaMEM.LaMEM_Model.rm_last_phase! — Methodrm_last_phase!(model::Model, phase::Phase)
This removes the last added phase from model
sourceLaMEM.LaMEM_Model.rm_last_vbox! — Methodrmlastvbox!(model::Model) This removes the last added vbox from model
sourceLaMEM.LaMEM_Model.rm_phase! — Methodrm_phase!(model::Model, ID::Int64)
This removes a phase with ID from model
sourceLaMEM.LaMEM_Model.rm_phase! — Methodrm_phase!(model::Model)
This removes all existing phases from model
sourceLaMEM.LaMEM_Model.rm_vbox! — Methodrm_vbox!(model::Model)
This removes all existing velocity boxes from model
sourceLaMEM.LaMEM_Model.set_air — Methodset_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
sourceLaMEM.LaMEM_Model.set_geom! — MethodThis sets the geometry
sourceLaMEM.LaMEM_Model.stress_strainrate_0D — Methodτ = 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).
sourceLaMEM.LaMEM_Model.within_bounds — Methodwithin_bounds(model::Model, topography::CartData)
Verifies that the bounds of the topography grid are larger than that of the model
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Functionwrite_LaMEM_inputFile(d::Model,fname::String; dir=pwd())
Writes a LaMEM input file based on the data stored in Model
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::BoundaryConditions)
Writes the boundary conditions related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::FreeSurface)
Writes the free surface related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomBox)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomCylinder)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomEllipsoid)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomHex)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomLayer)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomRidgeSeg)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomSphere)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_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])
+digitsep(12345678, seperator= "-", per_separator=4) # "1234-5678"
sourceLaMEM.LaMEM_Model.flatten — MethodCreates a 2D array out of a cross-section and a specified data field
sourceLaMEM.LaMEM_Model.hasplasticity — Methodhasplasticity(p::Phase)
true if p contains plastic parameters (cohesion or friction angle)
sourceLaMEM.LaMEM_Model.is_rectilinear — Methodis_rectilinear(topography::CartData)
Checks whether topography is rectilinear
sourceLaMEM.LaMEM_Model.isdefault — Methodisdefault(s1::S, s_default::S)
Checks whether a struct s1 has default parameters s_default
sourceLaMEM.LaMEM_Model.prepare_lamem — Functionprepare_lamem(model::Model, cores::Int64=1, args:String=""; verbose=false)
Prepares a LaMEM run for the parameters that are 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)
Set model.Output.write_VTK_setup to true if you want to write a VTK file of the model setup
sourceLaMEM.LaMEM_Model.print_short — MethodThis creates a single string, so we can use it in the command line
sourceLaMEM.LaMEM_Model.replace_phase! — Methodreplace_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.
sourceLaMEM.LaMEM_Model.rm_geom! — Methodrm_geom!(model::Model)
This removes all existing geometric objects from model
sourceLaMEM.LaMEM_Model.rm_last_phase! — Methodrm_last_phase!(model::Model, phase::Phase)
This removes the last added phase from model
sourceLaMEM.LaMEM_Model.rm_last_vbox! — Methodrmlastvbox!(model::Model) This removes the last added vbox from model
sourceLaMEM.LaMEM_Model.rm_phase! — Methodrm_phase!(model::Model, ID::Int64)
This removes a phase with ID from model
sourceLaMEM.LaMEM_Model.rm_phase! — Methodrm_phase!(model::Model)
This removes all existing phases from model
sourceLaMEM.LaMEM_Model.rm_vbox! — Methodrm_vbox!(model::Model)
This removes all existing velocity boxes from model
sourceLaMEM.LaMEM_Model.set_air — Methodset_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
sourceLaMEM.LaMEM_Model.set_geom! — MethodThis sets the geometry
sourceLaMEM.LaMEM_Model.stress_strainrate_0D — Methodτ = 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).
sourceLaMEM.LaMEM_Model.within_bounds — Methodwithin_bounds(model::Model, topography::CartData)
Verifies that the bounds of the topography grid are larger than that of the model
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Functionwrite_LaMEM_inputFile(d::Model,fname::String; dir=pwd())
Writes a LaMEM input file based on the data stored in Model
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::BoundaryConditions)
Writes the boundary conditions related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::FreeSurface)
Writes the free surface related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomBox)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomCylinder)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomEllipsoid)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomHex)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomLayer)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomRidgeSeg)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomSphere)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_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)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::Output)
Writes the free surface related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::ModelSetup)
Writes options related to the Model Setup to disk
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::Output)
Writes the free surface related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::PassiveTracers)
Writes the boundary conditions related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::SolutionParams)
Writes the boundary conditions related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::Solver)
Writes the free surface related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — MethodWrites the Time related parameters to file
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomSphere)
sourceLaMEM.LaMEM_Model.write_LaMEM_inputFile_PETSc — Methodwrite_LaMEM_inputFile_PETSc(io, d::Solver)
Writes the (optional) PETSc options to file
sourceLaMEM.Run.run_lamem — Functionrun_lamem(model::Model, cores::Int64=1, args:String=""; wait=true)
Performs a LaMEM run for the parameters that are specified in model
sourceSettings
This document was generated with Documenter.jl version 1.4.1 on Friday 24 May 2024. Using Julia version 1.9.4.
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::Output)Writes the free surface related parameters to file
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::ModelSetup)Writes options related to the Model Setup to disk
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::Output)Writes the free surface related parameters to file
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::PassiveTracers)Writes the boundary conditions related parameters to file
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::SolutionParams)Writes the boundary conditions related parameters to file
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::Solver)Writes the free surface related parameters to file
LaMEM.LaMEM_Model.write_LaMEM_inputFile — MethodWrites the Time related parameters to file
LaMEM.LaMEM_Model.write_LaMEM_inputFile — Methodwrite_LaMEM_inputFile(io, d::GeomSphere)LaMEM.LaMEM_Model.write_LaMEM_inputFile_PETSc — Methodwrite_LaMEM_inputFile_PETSc(io, d::Solver)Writes the (optional) PETSc options to file
LaMEM.Run.run_lamem — Functionrun_lamem(model::Model, cores::Int64=1, args:String=""; wait=true)Performs a LaMEM run for the parameters that are specified in model
Note that this is a significantly higher resolution than the original paper, which was run on an HPC system (admittedly, this was 20 years ago).