Viezly

docs/examples/3_point_bending.py

@@ -17,7 +17,7 @@
 # Setting up the Beam
 # -------------------
 # First, initialize the setup for the simply supported beam with a distributed load.
-# Define the geometry, the mesh, and the load.
+# Define the geometry, the mesh, and the load. Not defined parameters are set to default values (from class function default_parameters).
 # Note, all parameters must be pint objects:
 
 parameters = {}
@@ -36,6 +36,7 @@
 # Initializing the Linear Elasticity Problem
 # ------------------------------------------
 # Second, initialize the linear elastic problem using the setup object and further material parameters:
+# Again not defined parameters are set to default values (from class function default_parameters).
 
 parameters["rho"] = 7750 * ureg("kg/m^3")
 parameters["E"] = 210e9 * ureg("N/m^2")

docs/examples/cylinder.py

@@ -21,6 +21,7 @@
 # * `mesh_density` (mesh density) in 1/m
 #
 # The parameters must be defined as `pint` objects
+# Parameters required but not defined are set to default values (from class function default_parameters).
 #
 # Example code
 # ------------

environment.yml

@@ -3,8 +3,30 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.10
-  - pip
+  # runtime
+  - fenics-dolfinx=0.6.0
+  - mpi4py=3.1.4
+  - scipy
+  - pint
+  - matplotlib
+  - python-gmsh=4.11.1
+  - meshio=5.3.4
+  - jsonschema
+  # tests
+  - pytest
+  - coverage
+  - toml
+  # docs
+  - sphinx
+  - sphinx-gallery
+  - myst-parser
+  - sphinx_rtd_theme
+  # environment
   - conda-ecosystem-user-package-isolation
-  - fenics-dolfinx
+  # formatting
+  - black
+  - isort
+  - pip
   - pip:
-    - -e .[tests,docs]
+    - -e .
+

pyproject.toml

@@ -12,23 +12,17 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
 ]
-dependencies = [
-  "fenics-dolfinx",
-  "pint",
-  "gmsh",
-  "jsonschema",
-  "scipy",
-]
+dependencies = []
 description = "Implementation of structural problems for concrete structures using FEniCSx"
 license = {file = "LICENSE"}
 name = "fenicsxconcrete"
 readme = "REAMDE.md"
 requires-python = ">=3.10"
 version = "0.0.8"
 
-[project.optional-dependencies]
-tests = ["pytest", "coverage", "toml"]
-docs = ["sphinx", "sphinx-gallery", "sphinx-rtd-theme", "myst-parser", "matplotlib"]
+#[project.optional-dependencies]
+#tests = ["pytest", "coverage", "toml"]
+#docs = ["sphinx", "sphinx-gallery", "sphinx-rtd-theme", "myst-parser", "matplotlib"]
 
 [project.urls]
 repository = "https://github.com/BAMresearch/FenicsXConcrete.git"

src/fenicsxconcrete/experimental_setup/am_multiple_layers.py

@@ -34,13 +34,7 @@ def __init__(self, parameters: dict[str, pint.Quantity]):
 
         """
 
-        # initialize default parameters for the setup
-        default_p = Parameters()
-        # default_p['dummy'] = 'example' * ureg('')  # example default parameter for this class
-
-        # updating parameters, overriding defaults
-        default_p.update(parameters)
-        super().__init__(default_p)
+        super().__init__(parameters)
 
     @staticmethod
     def default_parameters() -> dict[str, pint.Quantity]:
@@ -52,6 +46,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
         """
 
         setup_parameters = {}
+        setup_parameters["degree"] = 2 * ureg("")  # polynomial degree
         # geometry
         setup_parameters["dim"] = 2 * ureg("")
         setup_parameters["num_layers"] = 10 * ureg("")  # number of layers in y

src/fenicsxconcrete/experimental_setup/base_experiment.py

@@ -30,14 +30,33 @@ def __init__(self, parameters: dict[str, pint.Quantity]) -> None:
         """
 
         # initialize parameter attributes
-        default_setup_parameters = Parameters()
-        # setting up default setup parameters
-        default_setup_parameters["degree"] = 2 * ureg("")  # polynomial degree
+        setup_parameters = Parameters()
 
+        # setting up default setup parameters defined in each child
+        default_p = self.default_parameters()
+        setup_parameters.update(default_p)
         # update with input parameters
-        default_setup_parameters.update(parameters)
+        setup_parameters.update(parameters)
+
+        # get logger info which parameters are set to default values
+        # plus check dimensionality of input parameters
+        keys_set_default = []
+        for key in dict(default_p):
+            if key not in parameters:
+                keys_set_default.append(key)
+            else:
+                # check if units are compatible
+                dim_given = parameters[key].dimensionality
+                dim_default = default_p[key].dimensionality
+                if dim_given != dim_default:
+                    raise ValueError(
+                        f"given units for {key} are not compatible with default units: {dim_given} != {dim_default}"
+                    )
+        self.logger.info(f"for the following parameters, the default values are used: {keys_set_default}")
+
         # as attribute
-        self.parameters = default_setup_parameters
+        self.parameters = setup_parameters
+
         # remove units for use in fem model
         self.p = self.parameters.to_magnitude()
 
@@ -59,6 +78,8 @@ def default_parameters() -> dict[str, pint.Quantity]:
 
         """
 
+        pass
+
     @abstractmethod
     def create_displacement_boundary(self, V: df.fem.FunctionSpace) -> list[df.fem.bcs.DirichletBCMetaClass] | None:
         """defines empty displacement boundary conditions (to be done in child)

src/fenicsxconcrete/experimental_setup/cantilever_beam.py

@@ -27,14 +27,7 @@ def __init__(self, parameters: dict[str, pint.Quantity] | None = None):
 
         """
 
-        # initialize default parameters for the setup
-        default_p = Parameters()
-        # default_p['dummy'] = 'example' * ureg('')  # example default parameter for this class
-
-        # updating parameters, overriding defaults
-        default_p.update(parameters)
-
-        super().__init__(default_p)
+        super().__init__(parameters)
 
     def setup(self) -> None:
         """defines the mesh for 2D or 3D
@@ -77,6 +70,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
         """
 
         setup_parameters = {}
+
         setup_parameters["length"] = 1 * ureg("m")
         setup_parameters["height"] = 0.3 * ureg("m")
         setup_parameters["width"] = 0.3 * ureg("m")  # only relevant for 3D case

src/fenicsxconcrete/experimental_setup/compression_cylinder.py

@@ -90,12 +90,7 @@ def __init__(self, parameters: dict[str, pint.Quantity] | None = None) -> None:
 
         """
 
-        # initialize a set of default parameters
-        p = Parameters()
-
-        p.update(parameters)
-
-        super().__init__(p)
+        super().__init__(parameters)
 
         # initialize variable top_displacement
         self.top_displacement = df.fem.Constant(domain=self.mesh, c=0.0)  # applied via fkt: apply_displ_load(...)
@@ -127,7 +122,7 @@ def setup(self) -> None:
             # until the bottom surface area matches that of a circle with the initially defined radius
             def create_cylinder_mesh(radius, p):
                 # generate cylinder mesh using gmsh
-                mesh = generate_cylinder_mesh(radius, p["height"], p["mesh_density"], p["degree"])
+                mesh = generate_cylinder_mesh(radius, p["height"], p["mesh_density"], p["element_order"])
                 facets = df.mesh.locate_entities_boundary(mesh, 2, plane_at(0.0, 2))
                 tdim = mesh.topology.dim
                 f_v = mesh.topology.connectivity(tdim - 1, 0).array.reshape(-1, 3)
@@ -169,6 +164,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
         """
 
         default_parameters = {}
+        default_parameters["element_order"] = 2 * ureg("")  # polynomial degree
 
         # boundary setting
         default_parameters["bc_setting"] = "free" * ureg("")  # boundary setting, two options available: fixed and free

src/fenicsxconcrete/experimental_setup/simple_beam.py

@@ -31,14 +31,7 @@ def __init__(self, parameters: dict[str, pint.Quantity]) -> None:
 
         """
 
-        # initialize default parameters for the setup
-        default_p = Parameters()
-        default_p["degree"] = 2 * ureg("")  # polynomial degree
-
-        # updating parameters, overriding defaults
-        default_p.update(parameters)
-
-        super().__init__(default_p)
+        super().__init__(parameters)
 
     def setup(self):
         """defines the mesh for 2D or 3D
@@ -81,6 +74,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
         """
 
         setup_parameters = {}
+
         setup_parameters["load"] = 10000 * ureg("N/m^2")
         setup_parameters["length"] = 1 * ureg("m")
         setup_parameters["height"] = 0.3 * ureg("m")

src/fenicsxconcrete/experimental_setup/simple_cube.py

@@ -9,7 +9,7 @@
 
 from fenicsxconcrete.boundary_conditions.bcs import BoundaryConditions
 from fenicsxconcrete.experimental_setup.base_experiment import Experiment
-from fenicsxconcrete.util import Parameters, ureg
+from fenicsxconcrete.util import LogMixin, Parameters, ureg
 
 
 class SimpleCube(Experiment):
@@ -33,17 +33,7 @@ def __init__(self, parameters: dict[str, pint.Quantity] | None = None) -> None:
                         see default_parameters for a first guess
         """
 
-        # initialize a set of default parameters
-        default_p = Parameters()
-        default_p["height"] = 1 * ureg("m")
-        default_p["width"] = 1 * ureg("m")
-        default_p["length"] = 1 * ureg("m")
-        default_p["T_0"] = ureg.Quantity(20.0, ureg.degC)
-        default_p["T_bc"] = ureg.Quantity(20.0, ureg.degC)
-
-        default_p.update(parameters)
-
-        super().__init__(default_p)
+        super().__init__(parameters)
 
     @staticmethod
     def default_parameters() -> dict[str, pint.Quantity]:
@@ -56,6 +46,11 @@ def default_parameters() -> dict[str, pint.Quantity]:
 
         setup_parameters = {}
 
+        setup_parameters["height"] = 1 * ureg("m")
+        setup_parameters["width"] = 1 * ureg("m")
+        setup_parameters["length"] = 1 * ureg("m")
+        setup_parameters["T_0"] = ureg.Quantity(20.0, ureg.degC)
+        setup_parameters["T_bc"] = ureg.Quantity(20.0, ureg.degC)
         setup_parameters["dim"] = 3 * ureg("")
         setup_parameters["num_elements_length"] = 2 * ureg("")
         setup_parameters["num_elements_width"] = 2 * ureg("")

src/fenicsxconcrete/experimental_setup/tensile_beam.py

@@ -26,14 +26,8 @@ def __init__(self, parameters: dict[str, pint.Quantity] | None = None) -> None:
                         see default_parameters for a first guess
 
         """
-        # initialize a set of "basic parameters"
-        default_p = Parameters()
-        # default_p['dummy'] = 'example' * ureg('')  # example default parameter for this class
 
-        # updating parameters, overriding defaults
-        default_p.update(parameters)
-
-        super().__init__(default_p)
+        super().__init__(parameters)
 
     def setup(self) -> None:
         """defines the mesh for 2D or 3D
@@ -76,6 +70,7 @@ def default_parameters() -> dict[str, pint.Quantity]:
         """
 
         setup_parameters = {}
+
         setup_parameters["length"] = 1 * ureg("m")
         setup_parameters["height"] = 0.3 * ureg("m")
         setup_parameters["width"] = 0.3 * ureg("m")  # only relevant for 3D case

src/fenicsxconcrete/finite_element_problem/base_material.py

@@ -62,6 +62,7 @@ class QuadratureFields:
     strain: ufl.core.expr.Expr | df.fem.Function | None = None
     degree_of_hydration: ufl.core.expr.Expr | df.fem.Function | None = None
     damage: ufl.core.expr.Expr | df.fem.Function | None = None
+    temperature: ufl.core.expr.Expr | df.fem.Function | None = None
     compressive_strength: ufl.core.expr.Expr | df.fem.Function | None = None
     tensile_strength: ufl.core.expr.Expr | df.fem.Function | None = None
     youngs_modulus: ufl.core.expr.Expr | df.fem.Function | None = None
@@ -92,16 +93,35 @@ def __init__(
         self.experiment = experiment
         self.mesh = self.experiment.mesh
 
-        # setting up default material parameters
-        default_fem_parameters = Parameters()
-        default_fem_parameters["g"] = 9.81 * ureg("m/s^2")
-        default_fem_parameters["dt"] = 1.0 * ureg("s")
-
-        # adding experimental parameters to dictionary to combine to one
-        default_fem_parameters.update(self.experiment.parameters)
+        # initialize parameter attributes
+        setup_parameters = Parameters()
+        # setting up default setup parameters defined in each child
+        _, default_p = self.default_parameters()
+        setup_parameters.update(default_p)
+        # update with experiment parameters
+        setup_parameters.update(self.experiment.parameters)
         # update with input parameters
-        default_fem_parameters.update(parameters)
-        self.parameters = default_fem_parameters
+        setup_parameters.update(parameters)
+
+        # get logger info which input parameters are set to default values
+        # plus check dimensionality of input parameters
+        keys_set_default = []
+        for key in dict(default_p):
+            if key not in parameters:
+                keys_set_default.append(key)
+            else:
+                # check if units are compatible
+                if not isinstance(parameters[key], bool):
+                    dim_given = parameters[key].dimensionality
+                    dim_default = default_p[key].dimensionality
+                    if dim_given != dim_default:
+                        raise ValueError(
+                            f"given units for {key} are not compatible with default units: {dim_given} != {dim_default}"
+                        )
+        self.logger.info(f"for the following parameters, the default values are used: {keys_set_default}")
+
+        # set parameters as attribute
+        self.parameters = setup_parameters
         # remove units for use in fem model
         self.p = self.parameters.to_magnitude()
         self.experiment.p = self.p  # update experimental parameter list for use in e.g. boundary definition
@@ -135,6 +155,8 @@ def default_parameters() -> tuple[Experiment, dict[str, pint.Quantity]]:
         """returns a dictionary with required parameters and a set of working values as example"""
         # this must de defined in each setup class
 
+        pass
+
     @abstractmethod
     def setup(self) -> None:
         # initialization of this specific problem