LaMEM

In order to generate geodynamic simulations from setups created with GeophysicalModelGenerator.jl, we provide a few routines that directly create marker input files for the 3D geodynamic modelling software LaMEM, which is an open-source cartesian code to perform crustal and lithospheric-scale simulations. If you want to learn how to run LaMEM simulations, the easiest way to get started is by looking at LaMEM.jl which is integrated with GMG

The routines provided here have the following functionality:

Read LaMEM *.dat files (to get the size of the domain)
Read LaMEM processor partitioning file
Save LaMEM marker files in serial or in parallel
Read a LaMEM timestep

GeophysicalModelGenerator.read_LaMEM_inputfile — Function

Grid::LaMEM_grid = read_LaMEM_inputfile(file, args::Union{String,Nothing}=nothing)

Parses a LaMEM input file and stores grid information in the Grid structure. Optionally, you can pass LaMEM command-line arguments as well.

Example 1

julia> Grid = read_LaMEM_inputfile("SaltModels.dat")
LaMEM Grid:
nel         : (32, 32, 32)
marker/cell : (3, 3, 3)
markers     : (96, 96, 96)
x           ϵ [-3.0 : 3.0]
y           ϵ [-2.0 : 2.0]
z           ϵ [-2.0 : 0.0]

Example 2 (with command-line arguments)

julia> Grid = read_LaMEM_inputfile("SaltModels.dat", args="-nel_x 64 -coord_x -4,4")
LaMEM Grid:
  nel         : (64, 32, 32)
  marker/cell : (3, 3, 3)
  markers     : (192, 96, 96)
  x           ϵ [-4.0 : 4.0]
  y           ϵ [-2.0 : 2.0]
  z           ϵ [-2.0 : 0.0]

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GeophysicalModelGenerator.get_processor_partitioning — Function

nProcX,nProcY,nProcZ, xc,yc,zc, nNodeX,nNodeY,nNodeZ = get_processor_partitioning(filename; is64bit=false)

Reads a LaMEM processor partitioning file, used to create marker files, and returns the parallel layout. By default this is done for a 32bit PETSc installation, which will fail if you actually use a 64bit version.

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GeophysicalModelGenerator.save_LaMEM_topography — Function

save_LaMEM_topography(Topo::CartData, filename::String)

This writes a topography file Topo for use in LaMEM, which should have size (nx,ny,1) and contain the field :Topography

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GeophysicalModelGenerator.save_LaMEM_markers_parallel — Function

save_LaMEM_markers_parallel(Grid::CartData; PartitioningFile=empty, directory="./markers", verbose=true, is64bit=false)

Saves a LaMEM marker file from the CartData structure Grid. It must have a field called Phases, holding phase information (as integers) and optionally a field Temp with temperature info. It is possible to provide a LaMEM partitioning file PartitioningFile. If not, output is assumed to be for one processor. By default it is assumed that the partitioning file was generated on a 32bit PETSc installation. If Int64 was used instead, set the flag.

The size of Grid should be consistent with what is provided in the LaMEM input file. In practice, the size of the mesh can be retrieved from a LaMEM input file using read_LaMEM_inputfile.

Example

julia> Grid    = read_LaMEM_inputfile("LaMEM_input_file.dat")
julia> Phases  = zeros(Int32,size(Grid.X));
julia> Temp    = ones(Float64,size(Grid.X));
julia> Model3D = CartData(Grid, (Phases=Phases,Temp=Temp))
julia> save_LaMEM_markers_parallel(Model3D)
Writing LaMEM marker file -> ./markers/mdb.00000000.dat

If you want to create a LaMEM input file for multiple processors:

julia> save_LaMEM_markers_parallel(Model3D, PartitioningFile="ProcessorPartitioning_4cpu_1.2.2.bin")
Writing LaMEM marker file -> ./markers/mdb.00000000.dat
Writing LaMEM marker file -> ./markers/mdb.00000001.dat
Writing LaMEM marker file -> ./markers/mdb.00000002.dat
Writing LaMEM marker file -> ./markers/mdb.00000003.dat

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GeophysicalModelGenerator.read_data_PVTR — Function

Data::ParaviewData = read_data_PVTR(fname, dir)

Reads a parallel, rectilinear, *.vts file with the name fname and located in dir and create a 3D Data struct from it.

Example

julia> Data = read_data_PVTR("Haaksbergen.pvtr", "./Timestep_00000005_3.35780500e-01/")
ParaviewData
  size  : (33, 33, 33)
  x     ϵ [ -3.0 : 3.0]
  y     ϵ [ -2.0 : 2.0]
  z     ϵ [ -2.0 : 0.0]
  fields: (:phase, :density, :visc_total, :visc_creep, :velocity, :pressure, :temperature, :dev_stress, :strain_rate, :j2_dev_stress, :j2_strain_rate, :plast_strain, :plast_dissip, :tot_displ, :yield, :moment_res, :cont_res)

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GeophysicalModelGenerator.LaMEM_grid — Type

Structure that holds information about the LaMEM grid (usually read from an input file).

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GeophysicalModelGenerator.create_partitioning_file — Function

create_partitioning_file(LaMEM_input::String, NumProc::Int64; LaMEM_dir::String=pwd(), LaMEM_options::String="", MPI_dir="", verbose=true)

This executes LaMEM for the input file LaMEM_input & creates a parallel partitioning file for NumProc processors. The directory where the LaMEM binary is can be specified; if not it is assumed to be in the current directory. Likewise for the mpiexec directory (if not specified it is assumed to be available on the command line).

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