# Step 1: Magma inflation ```{include} step01_inflation-synopsis.md ``` ## Simulation parameter This example uses poroelasticity to model flow of magma up through a conduit and into a magma reservoir. The magma reseroir and conduit have a higher permeability than the surrounding crust. We generate flow by imposing a pressure on the external boundary of the conduit that is higher than the uniform initial pressure in the domain. {numref}`fig:example:magma:2d:step01:diagram` shows the boundary conditions on the domain. The parameters specific to this example are in `step01_inflation.cfg`. :::{figure-md} fig:example:magma:2d:step01:diagram Boundary and initial conditions for magma inflation. We apply roller boundary conditions on the +x, -x, and -y boundaries. We impose zero pressure (undrained conditions) on the +y boundary and a pressure on the external boundary of the conduit to generate fluid flow. ::: ```{code-block} cfg --- caption: Time stepping parameters for Step 1. --- [pylithapp.timedependent] start_time = -0.2*year initial_dt = 0.2*year end_time = 10.0*year ``` ```{code-block} cfg --- caption: Initial condition parameters for Step 1. We impose an initial fluid pressure of 5 MPa over the entire domain. --- [pylithapp.problem] ic = [domain] ic.domain = pylith.problems.InitialConditionDomain [pylithapp.problem.ic.domain] db = spatialdata.spatialdb.UniformDB db.description = Initial conditions for domain db.values = [displacement_x, displacement_y, pressure, trace_strain] db.data = [0.0*m, 0.0*m, 5.0*MPa, 0.0] ``` We create an array of 5 Dirichlet boundary conditions: 3 for displacement and 2 for fluid pressure. We have zero displacement perpendicular to the -x, +x, and -y boundaries, zero pressure on the +y boundary, and 10 MPa of fluid pressure on the external boundary of the conduit. ```{code-block} cfg --- caption: Dirichlet boundary conditions for Step 1. --- [pylithapp.problem] bc = [bc_xneg, bc_xpos, bc_yneg, bc_ypos, bc_flow] bc.bc_xneg = pylith.bc.DirichletTimeDependent bc.bc_xpos = pylith.bc.DirichletTimeDependent bc.bc_yneg = pylith.bc.DirichletTimeDependent bc.bc_ypos = pylith.bc.DirichletTimeDependent bc.bc_flow = pylith.bc.DirichletTimeDependent [pylithapp.problem.bc.bc_xneg] constrained_dof = [0] label = boundary_xneg field = displacement db_auxiliary_field = pylith.bc.ZeroDB db_auxiliary_field.description = Dirichlet BC -x [pylithapp.problem.bc.bc_xpos] constrained_dof = [0] label = boundary_xpos field = displacement db_auxiliary_field = pylith.bc.ZeroDB db_auxiliary_field.description = Dirichlet BC +x [pylithapp.problem.bc.bc_yneg] constrained_dof = [1] label = boundary_yneg field = displacement db_auxiliary_field = pylith.bc.ZeroDB db_auxiliary_field.description = Dirichlet BC -y [pylithapp.problem.bc.bc_ypos] constrained_dof = [0] label = boundary_ypos field = pressure db_auxiliary_field = pylith.bc.ZeroDB db_auxiliary_field.description = Dirichlet BC +z [pylithapp.problem.bc.bc_flow] constrained_dof = [0] label = boundary_flow field = pressure db_auxiliary_field = spatialdata.spatialdb.UniformDB db_auxiliary_field.description = Flow into external boundary of conduit db_auxiliary_field.values = [initial_amplitude] db_auxiliary_field.data = [10.0*MPa] ``` ## Running the simulation ```{code-block} console --- caption: Run Step 1 simulation --- $ pylith step01_inflation.cfg # The output should look something like the following. >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/meshio/MeshIOObj.py:44:read -- meshiocubit(info) -- Reading finite-element mesh >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:157:void pylith::meshio::MeshIOCubit::_readVertices(pylith::meshio::ExodusII &, pylith::scalar_array *, int *, int *) const -- meshiocubit(info) -- Component 'reader': Reading 747 vertices. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:217:void pylith::meshio::MeshIOCubit::_readCells(pylith::meshio::ExodusII &, pylith::int_array *, pylith::int_array *, int *, int *) const -- meshiocubit(info) -- Component 'reader': Reading 705 cells in 2 blocks. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:279:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &) -- meshiocubit(info) -- Component 'reader': Found 5 node sets. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:305:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &) -- meshiocubit(info) -- Component 'reader': Reading node set 'boundary_xneg' with id 20 containing 21 nodes. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:305:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &) -- meshiocubit(info) -- Component 'reader': Reading node set 'boundary_xpos' with id 21 containing 21 nodes. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:305:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &) -- meshiocubit(info) -- Component 'reader': Reading node set 'boundary_yneg' with id 22 containing 23 nodes. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:305:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &) -- meshiocubit(info) -- Component 'reader': Reading node set 'boundary_ypos' with id 23 containing 21 nodes. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIOCubit.cc:305:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII &) -- meshiocubit(info) -- Component 'reader': Reading node set 'boundary_flow' with id 24 containing 3 nodes. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/meshio/MeshIO.cc:94:void pylith::meshio::MeshIO::read(topology::Mesh *) -- meshiocubit(info) -- Component 'reader': Domain bounding box: (0, 20000) (-20000, 0) >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/problems/Problem.py:116:preinitialize -- timedependent(info) -- Performing minimal initialization before verifying configuration. >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/problems/Solution.py:44:preinitialize -- solution(info) -- Performing minimal initialization of solution. >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/problems/Problem.py:175:verifyConfiguration -- timedependent(info) -- Verifying compatibility of problem configuration. >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/problems/Problem.py:221:_printInfo -- timedependent(info) -- Scales for nondimensionalization: Length scale: 100*m Time scale: 6.31152e+06*s Pressure scale: 1e+10*m**-1*kg*s**-2 Density scale: 3.98353e+19*m**-3*kg Temperature scale: 1*K >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/problems/Problem.py:186:initialize -- timedependent(info) -- Initializing timedependent problem with quasistatic formulation. >> /Users/baagaard/src/cig/pylith/libsrc/pylith/utils/PetscOptions.cc:235:static void pylith::utils::_PetscOptions::write(pythia::journal::info_t &, const char *, const pylith::utils::PetscOptions &) -- petscoptions(info) -- Setting PETSc options: ksp_atol = 1.0e-12 ksp_converged_reason = true ksp_error_if_not_converged = true ksp_rtol = 1.0e-12 pc_type = lu snes_atol = 1.0e-9 snes_converged_reason = true snes_error_if_not_converged = true snes_monitor = true snes_rtol = 1.0e-12 ts_error_if_step_fails = true ts_monitor = true ts_type = beuler # -- many lines ommitted -- 50 TS dt 1. time 49. 0 SNES Function norm 3.049429649018e-03 Linear solve converged due to CONVERGED_ATOL iterations 1 1 SNES Function norm 5.567219918314e-16 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 51 TS dt 1. time 50. >> /Users/baagaard/software/unix/py39-venv/pylith-debug/lib/python3.9/site-packages/pylith/problems/Problem.py:201:finalize -- timedependent(info) -- Finalizing problem. ``` At the beginning of the output written to the terminal, we see that PyLith is reading the mesh using the `MeshIOCubit` reader and that it found the domain to extend from 0 to 20 km in the x direction and from -20 km to 0 in the y direction. The scales for nondimensionalization . PyLith detects the use of poroelasticity without a fault and selects appropriate preconditioning options as discussed in {ref}`sec-user-run-pylith-petsc-options`. At the end of the output written to the terminal, we see that the solver advanced the solution 51 time steps. At each time step, the linear converges in 1 iteration and the norm of the residual met the absolute convergence tolerance (`ksp_atol`) . The nonlinear solve converged in 1 iteration, which we expect because this is a linear problem, and the residual met the absolute convergence tolerance (`snes_atol`). ## Visualizing the results The `output` directory contains the simulation output. Each "observer" writes its own set of files, so the solution over the domain is in one set of files, the boundary condition information is in another set of files, and the material information is in yet another set of files. The HDF5 (`.h5`) files contain the mesh geometry and topology information along with the solution fields. The Xdmf (`.xmf`) files contain metadata that allow visualization tools like ParaView to know where to find the information in the HDF5 files. To visualize the data using ParaView or Visit, load the Xdmf files. In {numref}`fig:example:magma:2d:step01:solution` we use ParaView to visualize the y displacement field using the `viz/plot_dispwarp.py` Python script. First, we start ParaView from the `examples/magma-2d` directory. ```{code-block} console --- caption: Open ParaView using the command line. --- $ PATH_TO_PARAVIEW/paraview # For macOS, it will be something like $ /Applications/ParaView-5.10.1.app/Contents/MacOS/paraview ``` Next we run the `viz/plot_dispwarp.py` Python script as described in {ref}`sec-paraview-python-scripts`. For Step 1 we do not need to change any of the default values. :::{figure-md} fig:example:magma:2d:step01:solution Solution for Step 1 at t=100 yr. The colors indicate the fluid pressure, and the deformation is exaggerated by a factor of 1000. Solution for Step 1 at t=100 yr. The colors of the shaded surface indicate the fluid pressure, and the deformation is exaggerated by a factor of 1000. :::