Common Information

In addition to the finite-element mesh, PyLith requires files to specify the simulation parameters. We specify parameters common to all simulations in a directory in pylithapp.cfg. The pylithapp.cfg file contains numerous comments, so we only summarize the parameters here.

Metadata, Mesh, and Output

The pylithapp.metadata section specifies metadata common to all simulations in the directory. We control the verbosity of the output written to stdout using journal.info. We set the parameters for importing the finite-element mesh in pylithapp.mesh_generator.

Physics

These quasi-static simulations solve the poroelasticity equation, so we have a solution field with displacement, pressure, and volumetric strain subfields.

(170)\[\begin{gather} \vec{s} = \left(\vec{u} \quad p \quad \epsilon_v\right)^T, \\ \nabla \cdot \boldsymbol{\sigma}(\vec{u},p) = \vec{0}, \\ \frac{\partial \zeta(\vec{u},p)}{\partial t} + \nabla \cdot \vec{q}(p) = 0, \\ \nabla \cdot \vec{u} - \epsilon_{v} = 0. \end{gather}\]

We specify a basis order of 2 for the displacement subfield, and 1 for each of the remaining subfields. We also adjust the scales for nondimensionalization.

Listing 150 Solution and nondimensionalization parameters for magma-2d examples.

[pylithapp.problem]
solution = pylith.problems.SolnDispPresTracStrain
defaults.quadrature_order = 2

[pylithapp.problem.solution.subfields]
displacement.basis_order = 2
pressure.basis_order = 1
trace_strain.basis_order = 1

[pylithapp.problem]
normalizer = spatialdata.units.NondimElasticQuasistatic
normalizer.length_scale = 100.0*m
normalizer.relaxation_time = 0.2*year
normalizer.shear_modulus = 10.0*GPa

We use the material properties in all of the simulations in this directory, so we specify them in pylithapp.cfg to avoid repeating the information in the file with parameters for each simulation. We create an array of 2 materials; with uniform material properties we use UniformDB spatial databases and set the basis order of the auxiliary subfields to 0.

Listing 151 Material parameters for the magma-2d examples.

[pylithapp.problem]
# We have two different poroelastic materials each with a linear bulk rheology.
materials = [crust, intrusion]
materials.crust = pylith.materials.Poroelasticity
materials.intrusion = pylith.materials.Poroelasticity

[pylithapp.problem.materials]
crust.bulk_rheology = pylith.materials.IsotropicLinearPoroelasticity
intrusion.bulk_rheology = pylith.materials.IsotropicLinearPoroelasticity

[pylithapp.problem.materials.crust]

# `label_value` must match the blocks in `bc.jou` Cubit Journal file.
description = crust
label_value = 1

# We will use uniform material properties, so we use the UniformDB
# spatial database.
db_auxiliary_field = spatialdata.spatialdb.UniformDB
db_auxiliary_field.description = Poroelastic properties for the crust
db_auxiliary_field.values = [solid_density, fluid_density, fluid_viscosity, porosity, shear_modulus, drained_bulk_modulus, biot_coefficient, fluid_bulk_modulus, solid_bulk_modulus, isotropic_permeability]
db_auxiliary_field.data = [ 2500*kg/m**3, 1000*kg/m**3, 0.001*Pa*s, 0.01, 6.0*GPa, 10.0*GPa, 1.0, 2.0*GPa, 20.0*GPa, 1e-15*m**2]

# Set basis order to 0 for uniform properties and a basis order of 1 for Cauchy stress and strain.
auxiliary_subfields.body_force.basis_order = 0
auxiliary_subfields.solid_density.basis_order = 0
auxiliary_subfields.fluid_density.basis_order = 0
auxiliary_subfields.fluid_viscosity.basis_order = 0
auxiliary_subfields.gravitational_acceleration.basis_order = 0
auxiliary_subfields.porosity.basis_order = 0
derived_subfields.cauchy_strain.basis_order = 1
derived_subfields.cauchy_stress.basis_order = 1

[pylithapp.problem.materials.crust.bulk_rheology]
auxiliary_subfields.drained_bulk_modulus.basis_order = 0
auxiliary_subfields.shear_modulus.basis_order = 0
auxiliary_subfields.biot_coefficient.basis_order = 0
auxiliary_subfields.biot_modulus.basis_order = 0
auxiliary_subfields.isotropic_permeability.basis_order = 0


[pylithapp.problem.materials.intrusion]
# `label_value` must match the blocks in `bc.jou` Cubit Journal file.
description = Intrusion
label_value = 2

# We will use uniform material properties, so we use the UniformDB
# spatial database.
db_auxiliary_field = spatialdata.spatialdb.UniformDB
db_auxiliary_field.description = Poroelastic properties
db_auxiliary_field.values = [solid_density, fluid_density, fluid_viscosity, porosity, shear_modulus, drained_bulk_modulus, biot_coefficient, fluid_bulk_modulus, solid_bulk_modulus, isotropic_permeability]
db_auxiliary_field.data = [ 2500*kg/m**3, 1000*kg/m**3, 0.001*Pa*s, 0.1, 6.0*GPa, 10.0*GPa, 0.8,  2.0*GPa, 20.0*GPa, 1e-13*m**2]

auxiliary_subfields.body_force.basis_order = 0
auxiliary_subfields.solid_density.basis_order = 0
auxiliary_subfields.fluid_density.basis_order = 0
auxiliary_subfields.fluid_viscosity.basis_order = 0
auxiliary_subfields.gravitational_acceleration.basis_order = 0
auxiliary_subfields.porosity.basis_order = 0
derived_subfields.cauchy_strain.basis_order = 1
derived_subfields.cauchy_stress.basis_order = 1

[pylithapp.problem.materials.intrusion.bulk_rheology]
# Set basis order to 0 for uniform properties
auxiliary_subfields.drained_bulk_modulus.basis_order = 0
auxiliary_subfields.shear_modulus.basis_order = 0
auxiliary_subfields.biot_coefficient.basis_order = 0
auxiliary_subfields.biot_modulus.basis_order = 0
auxiliary_subfields.isotropic_permeability.basis_order = 0