Rename functions following GMG update to 0.7

Project.toml

@@ -1,7 +1,7 @@
 name = "LaMEM"
 uuid = "2e889f3d-35ce-4a77-8ea2-858aecb630f7"
 authors = ["Boris Kaus <kaus@uni-mainz.de>"]
-version = "0.2.13"
+version = "0.3.0"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
@@ -26,7 +26,7 @@ PlotsExt = "Plots"
 DelimitedFiles = "1"
 DocStringExtensions = "0.9"
 GeoParams = "0.4, 0.5"
-GeophysicalModelGenerator = "0.6"
+GeophysicalModelGenerator = "0.7"
 Glob = "1"
 LightXML = "0.9"
 MPICH_jll = "4.1 - 4.1.2"

README.md

@@ -47,7 +47,7 @@ julia> add_phase!(model, sphere, matrix)
 
 Create an initial geometry using the [GeophysicalModelGenerator](https://github.com/JuliaGeodynamics/GeophysicalModelGenerator.jl/tree/main) interface:
 ```Julia
-julia> addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+julia> add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 ```
 and run the simulation with:
 ```julia
@@ -127,19 +127,19 @@ julia> using LaMEM
 ```
 You can first read the `*.pvd` file in the directory to see which timesteps are available. If you used julia to run the simulation (as under 2 above ), this is done with:
 ```julia
-julia> julia> Timestep, Filenames, t = Read_LaMEM_simulation(model)
+julia> julia> Timestep, Filenames, t = read_LaMEM_simulation(model)
 ([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13], ["Timestep_00000000_0.00000000e+00/output.pvtr", "Timestep_00000001_4.40000000e-02/output.pvtr", "Timestep_00000002_9.24000000e-02/output.pvtr", "Timestep_00000003_1.45640000e-01/output.pvtr", "Timestep_00000004_2.04204000e-01/output.pvtr", "Timestep_00000005_2.68624400e-01/output.pvtr", "Timestep_00000006_3.39486840e-01/output.pvtr", "Timestep_00000007_4.17435524e-01/output.pvtr", "Timestep_00000008_5.03179076e-01/output.pvtr", "Timestep_00000009_5.97496984e-01/output.pvtr", "Timestep_00000010_7.01246682e-01/output.pvtr", "Timestep_00000011_8.15371351e-01/output.pvtr", "Timestep_00000012_9.40908486e-01/output.pvtr", "Timestep_00000013_1.07899933e+00/output.pvtr"], [0.0, 0.044, 0.0924, 0.14564, 0.204204, 0.2686244, 0.3394868, 0.4174355, 0.5031791, 0.597497, 0.7012467, 0.8153714, 0.9409085, 1.078999])
 ```
 
 If you instead have an existing LaMEM simulation, you can specify the `*.pvd` file:
 ```julia
 julia> pvdname="output.pvd"
-julia> Timestep, Filenames, t = Read_LaMEM_simulation(pvdname)
+julia> Timestep, Filenames, t = read_LaMEM_simulation(pvdname)
 ```
 
 We can read a particular timestep (say 1) with:
 ```julia
-julia> data, time = Read_LaMEM_timestep(model, 1)
+julia> data, time = read_LaMEM_timestep(model, 1)
 (CartData 
     size    : (17, 17, 17)
     x       ϵ [ -1.0 : 1.0]

docs/src/juliasetup_LaPalma.md

@@ -27,7 +27,7 @@ CartData
 This shows the dimensions of our domain in kilometers. The issue is that this projected topography is not an orthogonal grid, but (slightly) distorted. In any case, we see the approximate dimensions of the grid (in horizontal directions), so we can create an orthogonal grid on which to project this:
 
 ```julia
-julia> Topo_LaMEM = CartData(xyzGrid(-70:.2:70,-60:.2:70,0));
+julia> Topo_LaMEM = CartData(xyz_grid(-70:.2:70,-60:.2:70,0));
 julia> Topo_LaMEM = ProjectCartData(Topo_LaMEM, Topo, proj)
 ```
 
@@ -89,16 +89,16 @@ julia> model.Grid.Phases .= 2;
 
 Now set points above the topography to zero (will be air later), the ones above the topography but below zero to 'water` and below 40 km to mantle (if we had a Moho surface we could use that):
 ```julia
- julia> aboveSurface!(model, Topo_LaMEM, phase=0, T=0)
+ julia> above_surface!(model, Topo_LaMEM, phase=0, T=0)
  julia> model.Grid.Phases[Z.<-0 .&& model.Grid.Phases .== 0] .= 1;
  julia> model.Grid.Phases[Z.<-40] .= 3;
 ```
 
 Finally, we define some magma chambers:
 ```julia 
-julia> addSphere!(model, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200));
-julia> addEllipsoid!(model, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200));
-julia> addEllipsoid!(model, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> add_sphere!(model, cen=(0,0,-35), radius=5, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> add_ellipsoid!(model, cen=(-1,0,-11), axes=(3,3,8), StrikeAngle=225, DipAngle=45, phase=ConstantPhase(5), T=ConstantTemp(1200));
+julia> add_ellipsoid!(model, cen=(-0,0,-23), axes=(8,8,2), StrikeAngle=0, DipAngle=0, phase=ConstantPhase(5), T=ConstantTemp(1200));
 ```
 
  We can plot a cross-section through the model:

docs/src/juliasetup_TMSubduction.md

@@ -106,7 +106,7 @@ If you want to see what each of these parameters mean, you can get some basic he
 
 ```julia
 help?> Time
-search: Time time Timer time_ns timedwait mtime ctime @time @timev @timed @time_imports @showtime optimize_ticks optimize_datetime_ticks Read_LaMEM_timestep
+search: Time time Timer time_ns timedwait mtime ctime @time @timev @timed @time_imports @showtime optimize_ticks optimize_datetime_ticks read_LaMEM_timestep
 
   Structure that contains the LaMEM timestepping information. An explanation of the paramneters is given in the struct `Time_info`
     •  time_end::Float64: simulation end time
@@ -266,10 +266,10 @@ model.Grid.Phases[model.Grid.Grid.Z .> 0.0 ] .= 5;
 ```
 
 ##### Add left oceanic plate
-An oceanic plate can be added using the `addBox!()` function of the `GeophysicalModelGenerator` package (see `?GeophysicalModelGenerator.addBox!` for more information, or check out the online [help](https://juliageodynamics.github.io/GeophysicalModelGenerator.jl/dev/man/lamem/) of the package). The lithosphere to asthenosphere temperature is set to 1250°C. If temperature of the plate is > 1250°C then the material is turned to asthenosphere. The temperature profile of the plate is set using a half space cooling temperature and a spreading rate velocity of 0.5 cm/yr with the ridge prescribed to be at the "left" of the box.
+An oceanic plate can be added using the `add_box!()` function of the `GeophysicalModelGenerator` package (see `?GeophysicalModelGenerator.add_box!` for more information, or check out the online [help](https://juliageodynamics.github.io/GeophysicalModelGenerator.jl/dev/man/lamem/) of the package). The lithosphere to asthenosphere temperature is set to 1250°C. If temperature of the plate is > 1250°C then the material is turned to asthenosphere. The temperature profile of the plate is set using a half space cooling temperature and a spreading rate velocity of 0.5 cm/yr with the ridge prescribed to be at the "left" of the box.
 
 ```julia
-addBox!(model;  xlim    = (-2000.0, 0.0), 
+add_box!(model;  xlim    = (-2000.0, 0.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -286,7 +286,7 @@ addBox!(model;  xlim    = (-2000.0, 0.0),
 Same for the plate on the right:
 
 ```julia
-addBox!(model;  xlim    = (1500, 2000), 
+add_box!(model;  xlim    = (1500, 2000), 
                 ylim    = (model.Grid.coord_y..., ), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -303,7 +303,7 @@ addBox!(model;  xlim    = (1500, 2000),
 For the overriding plate margin the age is fixed to 90 Ma using `HalfspaceCoolingTemp()`.
 
 ```julia
-addBox!(model;  xlim    = (0.0, 400.0), 
+add_box!(model;  xlim    = (0.0, 400.0), 
                 ylim    = (model.Grid.coord_y[1], model.Grid.coord_y[2]), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -316,7 +316,7 @@ addBox!(model;  xlim    = (0.0, 400.0),
 ##### Add overriding plate craton
 
 ```julia
-addBox!(model;  xlim    = (400.0, 1500.0), 
+add_box!(model;  xlim    = (400.0, 1500.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -330,7 +330,7 @@ addBox!(model;  xlim    = (400.0, 1500.0),
 Here we change the dip angle of the box to 30° to initiates subduction:
 
 ```julia
-addBox!(model;  xlim    = (0.0, 300), 
+add_box!(model;  xlim    = (0.0, 300), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=30,

docs/src/juliasetup_example_sphere.md

@@ -69,7 +69,7 @@ julia> add_phase!(model, sphere, matrix)
 #### 1.3 Set initial model geometry
 We also need to specify an initial model geometry. The julia package `GeophysicalModelGenerator` has a number of functions for that, which can be used here. For the current setup, we just add a sphere: 
 ```julia
-julia> addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+julia> add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 ```
 It is often useful to plot the initial model setup. You can do this with the `heatmap` function from the `Plots.jl` package, for which we provide a LaMEM plugin that allows you to specify a cross-section through a 3D LaMEM setup:
 

docs/src/juliasetups.md

@@ -96,7 +96,7 @@ In order to run a simulation, we need to define at least 1 phase and heterogenei
 The easiest way to do that is to use routines from the `GeophyicalModelGenerator` package, for which we created simple interfaces to many of the relevant routines:
 ```julia
 julia> using GeophysicalModelGenerator
-julia> addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+julia> add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 ```
 
 For the sake of this example, lets add another phase:

docs/src/readtimesteps.md

@@ -8,12 +8,12 @@ You can first read the `*.pvd` file in the directory to see which timesteps are
 ```julia
 julia> FileName="FB_multigrid"
 julia> DirName ="test"
-julia> Timestep, Filenames, Time = Read_LaMEM_simulation(FileName, DirName)
+julia> Timestep, Filenames, Time = read_LaMEM_simulation(FileName, DirName)
 ([0, 1], ["Timestep_00000000_0.00000000e+00/FB_multigrid.pvtr", "Timestep_00000001_6.72970343e+00/FB_multigrid.pvtr"], [0.0, 6.729703])
 ```
 We can read a particular timestep (say 1) with:
 ```julia
-julia> data, time = Read_LaMEM_timestep(FileName, 1, DirName)
+julia> data, time = read_LaMEM_timestep(FileName, 1, DirName)
 (CartData 
     size    : (33, 33, 33)
     x       ϵ [ 0.0 : 1.0]
@@ -27,7 +27,7 @@ The output is in a `CartData` structure (as defined in GeophysicalModelGenerator
 
 If you do not indicate a directory name (`DirName`) it'll look in your current directory. The default above will load the main LaMEM simulation output. Alternatively, you can also load the `phase` information by specify the optional keyword `phase=true`:
 ```julia
-julia> data, time = Read_LaMEM_timestep(FileName, 1, DirName, phase=true)
+julia> data, time = read_LaMEM_timestep(FileName, 1, DirName, phase=true)
 (CartData 
     size    : (96, 96, 96)
     x       ϵ [ 0.0052083334885537624 : 0.9947916269302368]
@@ -41,12 +41,12 @@ In the same way, you can load the internal free surface with `surf=true` (if tha
 If you don't want to load all the fields in the file back to julia, you can check which fields are available:
 
 ```julia
-julia> Read_LaMEM_fieldnames(FileName, DirName)
+julia> read_LaMEM_fieldnames(FileName, DirName)
 ("phase [ ]", "visc_total [ ]", "visc_creep [ ]", "velocity [ ]", "pressure [ ]", "strain_rate [ ]", "j2_dev_stress [ ]", "j2_strain_rate [ ]")
 ```
 and load only part of those:
 ```julia
-julia> data, time = Read_LaMEM_timestep(FileName, 1, DirName, fields=("phase [ ]", "visc_total [ ]","velocity [ ]"))
+julia> data, time = read_LaMEM_timestep(FileName, 1, DirName, fields=("phase [ ]", "visc_total [ ]","velocity [ ]"))
 (CartData 
     size    : (33, 33, 33)
     x       ϵ [ 0.0 : 1.0]

ext/PlotsExt.jl

@@ -2,7 +2,7 @@ module PlotsExt
 
 using Plots
 using GeophysicalModelGenerator, Statistics, DelimitedFiles
-import LaMEM: cross_section, Model, Read_LaMEM_timestep, Read_LaMEM_simulation, read_phase_diagram
+import LaMEM: cross_section, Model, read_LaMEM_timestep, read_LaMEM_simulation, read_phase_diagram
 import LaMEM: plot_topo, plot_cross_section, plot_phasediagram, plot_cross_section_simulation
 export plot_topo, plot_cross_section, plot_phasediagram, plot_cross_section_simulation
 
@@ -24,7 +24,7 @@ function plot_cross_section(model::Union{Model,CartData}, args...; field::Symbol
 
     if !isnothing(timestep)
         # load a particular timestep
-        data_cart, time = Read_LaMEM_timestep(model,timestep)
+        data_cart, time = read_LaMEM_timestep(model,timestep)
         model = data_cart
     end
 
@@ -68,7 +68,7 @@ As `plot_cross_section`, but for the entire simulation instead of a single times
 function plot_cross_section_simulation(model::Union{Model,CartData}, args...; field::Symbol=:phase, 
         dim=1, x=nothing, y=nothing, z=nothing, aspect_ratio::Union{Real, Symbol}=:equal)
 
-    Timesteps,_,_ = Read_LaMEM_simulation(model);
+    Timesteps,_,_ = read_LaMEM_simulation(model);
     for timestep_val in Timesteps
         plot_cross_section(model, args, field=field, timestep=timestep_val, dim=dim, x=x, y=y, z=z, aspect_ratio=aspect_ratio)
     end

notebooks/FallingSphere_1.jl

@@ -91,7 +91,7 @@ We also need to specify an initial model geometry. The julia package `Geophysica
 """
 
 # ╔═╡ a3afc50b-2fcd-4067-895d-fde7fb7f8742
-addSphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
+add_sphere!(model,cen=(0.0,0.0,0.0), radius=(0.5, ))
 
 # ╔═╡ e0411cc1-60ae-43cf-9500-93a246e62e1b
 md"""
@@ -129,7 +129,7 @@ We can read all timesteps of the simulation with:
 """
 
 # ╔═╡ 3040c159-7281-4971-80ad-8104abb3a6d9
-timesteps,_,_ = Read_LaMEM_simulation(model)
+timesteps,_,_ = read_LaMEM_simulation(model)
 
 # ╔═╡ b7ca7625-4910-4faf-919c-4b785438c574
 md"""
@@ -153,7 +153,7 @@ If you want to know which fields have been saved, you can read a timestep back i
 """
 
 # ╔═╡ c72ffd0d-dbf7-4b88-af5e-de4f76d5ec33
-data_cart, time = Read_LaMEM_timestep(model,1)
+data_cart, time = read_LaMEM_timestep(model,1)
 
 # ╔═╡ e73a3f02-c1f4-46d8-a0c2-c6f6058e1ca1
 md"""

notebooks/subduction_example.ipynb

@@ -140,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "addBox!(model, xlim=(-700,100), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=0, T=ConstantTemp(1000))"
+    "add_box!(model, xlim=(-700,100), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=0, T=ConstantTemp(1000))"
    ]
   },
   {
@@ -150,7 +150,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "addBox!(model, xlim=(100,300), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=30, T=ConstantTemp(1000))"
+    "add_box!(model, xlim=(100,300), zlim=(-60,0), phase=LithosphericPhases(Layers=[20 60], Phases=[1 2 0]), DipAngle=30, T=ConstantTemp(1000))"
    ]
   },
   {
@@ -6397,7 +6397,7 @@
     }
    ],
    "source": [
-    "timesteps,_,_ = Read_LaMEM_simulation(model)"
+    "timesteps,_,_ = read_LaMEM_simulation(model)"
    ]
   },
   {

scripts/Subduction3D.jl

@@ -40,10 +40,10 @@ model = Model(
 # Next, we specify the geometry of the model, using the `AddBox!` function from `GeophysicalModelGenerator`.
 # We start with the horizontal part of the slab. The function `AddBox!` allows you to specify a layered lithosphere; here we have a crust and mantle. It also allows specifying a thermal structure. 
 # Since the current setup is only mechanical, we don't specify that here. 
-AddBox!(model, xlim=(-3000,-1000), ylim=(0,1000), zlim=(-80,0), phase=LithosphericPhases(Layers=[20,60], Phases=[1,2]))
+add_box!(model, xlim=(-3000,-1000), ylim=(0,1000), zlim=(-80,0), phase=LithosphericPhases(Layers=[20,60], Phases=[1,2]))
 
 # The inclined part of the slab is generate by giving it a dip:
-AddBox!(model, xlim=(-1000,-810), ylim=(0,1000), zlim=(-80,0), phase=LithosphericPhases(Layers=[20,60], Phases=[1,2]), DipAngle=16)
+add_box!(model, xlim=(-1000,-810), ylim=(0,1000), zlim=(-80,0), phase=LithosphericPhases(Layers=[20,60], Phases=[1,2]), DipAngle=16)
 
 # There is a simple way to have a quick look at this setup by using the `Plots.jl` package:
 using Plots 

scripts/TM_Subduction_example.jl

@@ -62,7 +62,7 @@ model.Grid.Temp[model.Grid.Grid.Z .> 0]    .=  Tair;
 model.Grid.Phases[model.Grid.Grid.Z .> 0.0 ] .= 5;
 
 # Left ocanic plate:
-addBox!(model;  xlim    = (-2000.0, 0.0), 
+add_box!(model;  xlim    = (-2000.0, 0.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -74,7 +74,7 @@ addBox!(model;  xlim    = (-2000.0, 0.0),
                                                 AgeRidge    = 0.01;
                                                 maxAge      = 80.0      ) )
 # Add right oceanic plate:
-addBox!(model;  xlim    = (1500, 2000), 
+add_box!(model;  xlim    = (1500, 2000), 
                 ylim    = (model.Grid.coord_y..., ), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -87,7 +87,7 @@ addBox!(model;  xlim    = (1500, 2000),
                                                 maxAge      = 80.0      ) )
 
 # Add overriding plate margin
-addBox!(model;  xlim    = (0.0, 400.0), 
+add_box!(model;  xlim    = (0.0, 400.0), 
                 ylim    = (model.Grid.coord_y[1], model.Grid.coord_y[2]), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -98,7 +98,7 @@ addBox!(model;  xlim    = (0.0, 400.0),
 
 
 # Overriding plate craton
-addBox!(model;  xlim    = (400.0, 1500.0), 
+add_box!(model;  xlim    = (400.0, 1500.0), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=0,
@@ -107,7 +107,7 @@ addBox!(model;  xlim    = (400.0, 1500.0),
                                                     Tmantle     = Tmantle,
                                                     Age         = 120      ) )
 #   Add pre-subducted slab                                                  
-addBox!(model;  xlim    = (0.0, 300), 
+add_box!(model;  xlim    = (0.0, 300), 
                 ylim    = (model.Grid.coord_y...,), 
                 zlim    = (-660.0, 0.0),
                 Origin  = nothing, StrikeAngle=0, DipAngle=30,

src/IO_functions.jl

@@ -2,7 +2,7 @@ module IO_functions
 # this contains I/O routines of LaMEM, which don't require LaMEM_jll
 
 include("read_timestep.jl")
-export Read_LaMEM_PVTR_File, Read_LaMEM_PVTS_File, field_names, readPVD, Read_LaMEM_PVTU_File
+export read_LaMEM_PVTR_file, read_LaMEM_PVTS_file, field_names, readPVD, read_LaMEM_PVTU_file
 
 
 include("utils_IO.jl")

src/LaMEM.jl

@@ -8,9 +8,9 @@ export NO_units, GEO_units, SI_units, km, m, Pa, Pas, kg, cm, yr
 # Functions to read LaMEM output
 include("IO_functions.jl")
 using .IO_functions
-export Read_LaMEM_PVTR_File, Read_LaMEM_PVTS_File, Read_LaMEM_PVTU_File
-export Read_LaMEM_simulation, Read_LaMEM_timestep, Read_LaMEM_fieldnames
-export PassiveTracer_Time
+export read_LaMEM_PVTR_file, read_LaMEM_PVTS_file, read_LaMEM_PVTU_file
+export read_LaMEM_simulation, read_LaMEM_timestep, read_LaMEM_fieldnames
+export passivetracer_time
 export clean_directory, changefolder, read_phase_diagram, read_LaMEM_logfile
 export compress_vtr_file, compress_pvd
 
@@ -25,17 +25,17 @@ include("DocUtils.jl")
 # Functions that help running LaMEM directly from julia
 include("LaMEM_ModelGeneration/LaMEM_Model.jl")
 using .LaMEM_Model
-export  LaMEM_Model, Model, Write_LaMEM_InputFile, create_initialsetup,
+export  LaMEM_Model, Model, write_LaMEM_inputFile, create_initialsetup,
         Scaling, Grid, Time, FreeSurface, BoundaryConditions, VelocityBox, BCBlock, VelCylinder, SolutionParams,
         Solver, ModelSetup, 
-        geom_Sphere, geom_Ellipsoid, geom_Box, geom_RidgeSeg, geom_Hex, geom_Layer, geom_Cylinder,
+        GeomSphere, GeomEllipsoid, GeomBox, GeomRidgeSeg, GeomHex, GeomLayer, GeomCylinder,
         Output,
         Multigrid, print_short, 
         Materials, Phase, Softening, PhaseTransition, PhaseAggregate, Dike, PassiveTracers,
         add_vbox!, rm_vbox!, rm_last_vbox!, 
         add_phase!, rm_phase!, rm_last_phase!, replace_phase!, add_petsc!, add_softening!, add_phaseaggregate!,
         add_phasetransition!, add_dike!, add_geom!, rm_geom!, set_air, copy_phase,
-        add_topography!, aboveSurface!, belowSurface!,
+        add_topography!, above_surface!, below_surface!,
         prepare_lamem, isdefault, hasplasticity,
         add_geoparams_rheologies,
         stress_strainrate_0D