Merge pull request #88 from joergbuchwald/ogs6py_ng

make timesteps in output optional
joergbuchwald · Jul 4, 2024 · 5bb9ac7 · 5bb9ac7
2 parents fc95659 + 72559c4
commit 5bb9ac7
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Showing 3 changed files with 32 additions and 24 deletions.
diff --git a/examples/example_THM.py b/examples/example_THM.py
@@ -3,7 +3,7 @@
 # if MKL set vars vars script should be executed before OGS
 # model = OGS(PROJECT_FILE="thm_test.prj", MKL=True, OMP_NUM_THREADS=4)
 model = OGS(PROJECT_FILE="thm_test.prj", OMP_NUM_THREADS=4)
-model.geo.add_geom(filename="square_1x1_thm.gml")
+model.geometry.add_geometry(filename="square_1x1_thm.gml")
 model.mesh.add_mesh(filename="quarter_002_2nd.vtu", axially_symmetric="true")
 model.processes.set_process(
     name="THERMO_HYDRO_MECHANICS",
@@ -115,27 +115,27 @@
 model.media.add_property(medium_id="0",
                             name="thermal_conductivity",
                             type="EffectiveThermalConductivityPorosityMixing")
-model.timeloop.add_process(process="THERMO_HYDRO_MECHANICS",
+model.time_loop.add_process(process="THERMO_HYDRO_MECHANICS",
                           nonlinear_solver_name="basic_newton",
                           convergence_type="PerComponentDeltaX",
                           norm_type="NORM2",
                           abstols="1e-5 1e-5 1e-5 1e-5",
                           time_discretization="BackwardEuler")
-model.timeloop.set_stepping(process="THERMO_HYDRO_MECHANICS",
+model.time_loop.set_stepping(process="THERMO_HYDRO_MECHANICS",
                            type="FixedTimeStepping",
                            t_initial="0",
                            t_end="50000",
                            repeat="10",
                            delta_t="5000")
-model.timeloop.add_output(
+model.time_loop.add_output(
     type="VTK",
     prefix="blubb",
     repeat="1",
     each_steps="10",
     variables=["displacement", "pressure", "temperature", "sigma", "epsilon"],
     fixed_output_times=[1,2,3])
-model.timeloop.add_time_stepping_pair(process="THERMO_HYDRO_MECHANICS", repeat="15", delta_t="32")
-model.timeloop.add_output_pair(repeat="12", each_steps="11")
+model.time_loop.add_time_stepping_pair(process="THERMO_HYDRO_MECHANICS", repeat="15", delta_t="32")
+model.time_loop.add_output_pair(repeat="12", each_steps="11")
 model.parameters.add_parameter(name="E", type="Constant", value="5000000000")
 model.parameters.add_parameter(name="nu", type="Constant", value="0.3")
 model.parameters.add_parameter(name="T0", type="Constant", value="273.15")
@@ -159,65 +159,65 @@
                               value="150")
 model.curves.add_curve(name="time_curve", coords=[0.0, 1e6, 1.1e6, 5e6],
                 values=[1.0, 1.0, 2.0, 2.0])
-model.processvars.set_ic(process_variable_name="displacement",
+model.process_variables.set_ic(process_variable_name="displacement",
                         components="2",
                         order="2",
                         initial_condition="displacement0")
-model.processvars.add_bc(process_variable_name="displacement",
+model.process_variables.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",
+model.process_variables.add_bc(process_variable_name="displacement",
                         geometrical_set="square_1x1_geometry",
                         geometry="bottom",
                         type="Dirichlet",
                         component="1",
                         parameter="dirichlet0")
-model.processvars.set_ic(process_variable_name="pressure",
+model.process_variables.set_ic(process_variable_name="pressure",
                         components="1",
                         order="1",
                         initial_condition="pressure_ic")
-model.processvars.add_bc(process_variable_name="pressure",
+model.process_variables.add_bc(process_variable_name="pressure",
                         geometrical_set="square_1x1_geometry",
                         geometry="out",
                         type="Dirichlet",
                         component="0",
                         parameter="pressure_bc_left")
-model.processvars.set_ic(process_variable_name="temperature",
+model.process_variables.set_ic(process_variable_name="temperature",
                         components="1",
                         order="1",
                         initial_condition="temperature_ic")
-model.processvars.add_bc(process_variable_name="temperature",
+model.process_variables.add_bc(process_variable_name="temperature",
                         geometrical_set="square_1x1_geometry",
                         geometry="out",
                         type="Dirichlet",
                         component="0",
                         parameter="temperature_bc_left")
-model.processvars.add_st(process_variable_name="temperature",
+model.process_variables.add_st(process_variable_name="temperature",
                         geometrical_set="square_1x1_geometry",
                         geometry="center",
                         type="Nodal",
                         parameter="temperature_source_term")
-model.nonlinsolvers.add_non_lin_solver(name="basic_newton",
+model.nonlinear_solvers.add_non_lin_solver(name="basic_newton",
                                     type="Newton",
                                     max_iter="50",
                                     linear_solver="general_linear_solver")
-model.linsolvers.add_lin_solver(name="general_linear_solver",
+model.linear_solvers.add_lin_solver(name="general_linear_solver",
                               kind="lis",
                               solver_type="bicgstab",
                               precon_type="ilu",
                               max_iteration_step="10000",
                               error_tolerance="1e-16")
-model.linsolvers.add_lin_solver(name="general_linear_solver",
+model.linear_solvers.add_lin_solver(name="general_linear_solver",
                               kind="eigen",
                               solver_type="SparseLU",
                               precon_type="DIAGONAL",
                               max_iteration_step="10000",
                               error_tolerance="1e-8",
                               scaling="1")
-model.linsolvers.add_lin_solver(name="general_linear_solver",
+model.linear_solvers.add_lin_solver(name="general_linear_solver",
                               kind="petsc",
                               prefix="sd",
                               solver_type="cg",

diff --git a/examples/thm_test.prj b/examples/thm_test.prj
@@ -1,14 +1,12 @@
 <?xml version='1.0' encoding='ISO-8859-1'?>
 <OpenGeoSysProject>
-    <geometry>square_1x1_thm.gml</geometry>
     <mesh axially_symmetric="true">quarter_002_2nd.vtu</mesh>
     <processes>
         <process>
             <name>THERMO_HYDRO_MECHANICS</name>
             <type>THERMO_HYDRO_MECHANICS</type>
             <integration_order>4</integration_order>
             <dimension>2</dimension>
-            <reference_temperature>T0</reference_temperature>
             <specific_body_force>0 0</specific_body_force>
             <constitutive_relation>
                 <type>LinearElasticIsotropic</type>
@@ -49,7 +47,12 @@
                             <independent_variable>
                                 <variable_name>temperature</variable_name>
                                 <reference_condition>273.15</reference_condition>
-                                <slope>-4e-4</slope>
+                                <slope>-0.0004</slope>
+                            </independent_variable>
+                            <independent_variable>
+                                <variable_name>phase_pressure</variable_name>
+                                <reference_condition>100000.0</reference_condition>
+                                <slope>1e-20</slope>
                             </independent_variable>
                         </property>
                         <property>
@@ -111,6 +114,10 @@
                     <type>Constant</type>
                     <value>1.0</value>
                 </property>
+                <property>
+                    <name>thermal_conductivity</name>
+                    <type>EffectiveThermalConductivityPorosityMixing</type>
+                </property>
             </properties>
         </medium>
     </media>
@@ -305,7 +312,7 @@
             <name>general_linear_solver</name>
             <lis>-i bicgstab -p ilu -tol 1e-16 -maxiter 10000</lis>
             <eigen>
-                <solver_type>PardisoLU</solver_type>
+                <solver_type>SparseLU</solver_type>
                 <precon_type>DIAGONAL</precon_type>
                 <max_iteration_step>10000</max_iteration_step>
                 <error_tolerance>1e-8</error_tolerance>
@@ -317,4 +324,5 @@
             </petsc>
         </linear_solver>
     </linear_solvers>
+    <geometry>square_1x1_thm.gml</geometry>
 </OpenGeoSysProject>
diff --git a/ogs6py/classes/timeloop.py b/ogs6py/classes/timeloop.py
@@ -211,8 +211,8 @@ def add_output(self, **args):
                 for mesh in args["meshes"]:
                     self.populate_tree(meshes, 'mesh', text=mesh)
                     # material_id attribute missing
-        timesteps = self.populate_tree(self.output, 'timesteps')
         if "repeat" in args:
+            timesteps = self.populate_tree(self.output, 'timesteps')
             if "each_steps" not in args:
                 raise KeyError("each_steps is a required tag if repeat is given.")
             if isinstance(args["repeat"], list) and isinstance(args["each_steps"], list):
@@ -286,7 +286,7 @@ def add_output_pair(self, **args):
         each_steps : `int` or `str` or `list`
         """
         self._convertargs(args)
-        timesteps = self.output.find("./timesteps")
+        timesteps = self.populate_tree(self.output, 'timesteps', overwrite=True)
         if "repeat" in args and "each_steps" in args:
             if isinstance(args["repeat"], list) and isinstance(args["each_steps"], list):
                 for i, entry in enumerate(args["repeat"]):