ogs6py

ogs6py is a python-API for the OpenGeoSys finite element sofware. Its main functionalities include creating and altering OGS6 input files as well as executing OGS. The package allows to streamline OGS-workflows with python or Julia entirely in jupyter or pluto notebooks as demonstrated in the following video:

Documentation reference

To alter and execute OGS input, e.g., for looping over parameter ranges, two approaches exist:

1. creating a new input file using python method calls
2. altering existing input files

0. Installation

clone the repository and use pip/pip3 to install the package.

# git clone https://github.com/joergbuchwald/ogs6py.git
# cd ogs6py
# pip install --user .

CAUTION: naming style of methods has changed (2021-05-20)

1. Creating a new input file

The following example consists of a simple mechanics problem. The source file can be found in the examples directory The names of the method calls are based on the corresponing XML tags. The MKL=True option executes source /opt/intel/mkl/bin/mklvars.sh intel64 before the ogs call.

from ogs6py import ogs

model = ogs.OGS(PROJECT_FILE="simple_mechanics.prj")
model.geo.add_geom(filename="square_1x1.gml")
model.mesh.add_mesh(filename="square_1x1_quad_1e2.vtu")
model.processes.set_process(name="SD",
                           type="SMALL_DEFORMATION",
                           integration_order="2",
                           solid_density="rho_sr",
                           specific_body_force="0 0")
model.processes.set_constitutive_relation(type="LinearElasticIsotropic",
                                        youngs_modulus="E",
                                        poissons_ratio="nu")
model.processes.add_process_variable(process_variable="process_variable",
                                   process_variable_name="displacement")
model.processes.add_process_variable(secondary_variable="sigma",
                                   output_name="sigma")
model.timeloop.add_process(process="SD",
                          nonlinear_solver_name="basic_newton",
                          convergence_type="DeltaX",
                          norm_type="NORM2",
                          abstol="1e-15",
                          time_discretization="BackwardEuler")
model.timeloop.set_stepping(process="SD", type="FixedTimeStepping",
                           t_initial="0",
                           t_end="1",
                           repeat="4",
                           delta_t="0.25")
model.timeloop.add_output(type="VTK",
                         prefix="blubb",
                         repeat="1",
                         each_steps="10",
                         variables=["displacement", "sigma"])
model.parameters.add_parameter(name="E", type="Constant", value="1")
model.parameters.add_parameter(name="nu", type="Constant", value="0.3")
model.parameters.add_parameter(name="rho_sr", type="Constant", value="1")
model.parameters.add_parameter(name="displacement0",
                              type="Constant",
                              values="0 0")
model.parameters.add_parameter(name="dirichlet0", type="Constant", value="0")
model.parameters.add_parameter(name="dirichlet1", type="Constant", value="0.05")
model.processvars.set_ic(process_variable_name="displacement",
                        components="2",
                        order="1",
                        initial_condition="displacement0")
model.processvars.add_bc(process_variable_name="displacement",
                        geometrical_set="square_1x1_geometry",
                        geometry="left",
                        type="Dirichlet",
                        component="0",
                        parameter="dirichlet0")
model.processvars.add_bc(process_variable_name="displacement",
                        geometrical_set="square_1x1_geometry",
                        geometry="bottom",
                        type="Dirichlet",
                        component="1",
                        parameter="dirichlet0")
model.processvars.add_bc(process_variable_name="displacement",
                        geometrical_set="square_1x1_geometry",
                        geometry="top",
                        type="Dirichlet",
                        component="1",
                        parameter="dirichlet1")
model.nonlinsolvers.add_non_lin_solver(name="basic_newton",
                                    type="Newton",
                                    max_iter="4",
                                    linear_solver="general_linear_solver")
model.linsolvers.add_lin_solver(name="general_linear_solver",
                              kind="lis",
                              solver_type="cg",
                              precon_type="jacobi",
                              max_iteration_step="10000",
                              error_tolerance="1e-16")
model.linsolvers.add_lin_solver(name="general_linear_solver",
                              kind="eigen",
                              solver_type="CG",
                              precon_type="DIAGONAL",
                              max_iteration_step="10000",
                              error_tolerance="1e-16")
model.linsolvers.add_lin_solver(name="general_linear_solver",
                              kind="petsc",
                              prefix="sd",
                              solver_type="cg",
                              precon_type="bjacobi",
                              max_iteration_step="10000",
                              error_tolerance="1e-16")
model.write_input()
model.run_model(logfile="out.log")

model.runModel(path="~/github/ogs/build_mkl/bin")

An example using the MPL can be find in example_THM.py.

2. Alternatively it is possible to alter existing files using the available replace methods:

E.g., to iterate over three Young's moduli one can use the replace parameter method:

Es = [1,2,3]
filename = "simple_mechanics.prj"
for E in Es:
    model = OGS(INPUT_FILE=filename, PROJECT_FILE=filename, MKL=True)
    model.replace_parameter(name="E", value=E)
    model.replace_text("out_E="+str(E), xpath="./time_loop/output/prefix")
    model.write_input()
    model.run_model(path="~/github/ogs/build_mkl/bin")

Instead of the replaceParameter method, the more general replaceTxt method can be used

model.replace_text(E, xpath="./parameters/parameter[name='E']/value")

The Young's modulus in this file can also be accessed through 0'th occurrence of the place addressed by the xpath ./parameters/parameter/value

model.replace_text(E, xpath="./parameters/parameter/value", occurrence=0)

For MPL based processes, there exist specific functions to set phase and medium properties: E.g.,

model.replace_phase_property(mediumid=0, phase="Solid", name="thermal_expansivity", value="42")

for a phse property and

model.replace_medium_property(mediumid=0, name="porosity", value="0.24")

for a property that lives on the medium level.

3. Log-Parser

To parse the output that is piped into a file named out.log you can simply do:

df = model.parse_out("examples/out_thm.log")