Average surface and volume derived quantities in Cylindrical and Spherical

festim/__init__.py

@@ -74,14 +74,22 @@
 )
 from .exports.derived_quantities.hydrogen_flux import HydrogenFlux
 from .exports.derived_quantities.thermal_flux import ThermalFlux
-from .exports.derived_quantities.average_volume import AverageVolume
+from .exports.derived_quantities.average_volume import (
+    AverageVolume,
+    AverageVolumeCylindrical,
+    AverageVolumeSpherical,
+)
 from .exports.derived_quantities.maximum_volume import MaximumVolume
 from .exports.derived_quantities.minimum_volume import MinimumVolume
 from .exports.derived_quantities.minimum_surface import MinimumSurface
 from .exports.derived_quantities.maximum_surface import MaximumSurface
 from .exports.derived_quantities.total_surface import TotalSurface
 from .exports.derived_quantities.total_volume import TotalVolume
-from .exports.derived_quantities.average_surface import AverageSurface
+from .exports.derived_quantities.average_surface import (
+    AverageSurface,
+    AverageSurfaceCylindrical,
+    AverageSurfaceSpherical,
+)
 from .exports.derived_quantities.point_value import PointValue
 
 from .exports.derived_quantities.derived_quantities import DerivedQuantities

festim/exports/derived_quantities/average_surface.py

@@ -1,5 +1,6 @@
 from festim import SurfaceQuantity
 import fenics as f
+import numpy as np
 
 
 class AverageSurface(SurfaceQuantity):
@@ -43,3 +44,91 @@
         return f.assemble(self.function * self.ds(self.surface)) / f.assemble(
             1 * self.ds(self.surface)
         )
+
+
+class AverageSurfaceCylindrical(AverageSurface):
+    """
+    Computes the average value of a field on a given surface
+    int(f ds) / int (1 * ds)
+    ds is the surface measure in cylindrical coordinates.
+    ds = r dr dtheta
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        title (str): the title of the derived quantity
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        function (dolfin.function.function.Function): the solution function of
+            the field
+
+    Notes:
+        Units are in H/m3 for hydrogen concentration and K for temperature
+    """
+
+    def __init__(self, field, surface) -> None:
+        super().__init__(field=field, surface=surface)
+        self.r = None
+
+    def compute(self):
+
+        if self.r is None:
+            mesh = (
+                self.function.function_space().mesh()
+            )  # get the mesh from the function
+            rthetaz = f.SpatialCoordinate(mesh)  # get the coordinates from the mesh
+            self.r = rthetaz[0]  # only care about r here
+
+        # dS_z = r dr dtheta , assuming axisymmetry dS_z = theta r dr
+        # dS_r = r dz dtheta , assuming axisymmetry dS_r = theta r dz
+        # in both cases the expression with self.dx is the same
+
+        avg_surf = f.assemble(
+            self.function * self.r * self.ds(self.surface)
+        ) / f.assemble(1 * self.r * self.ds(self.surface))
+
+        return avg_surf
+
+
+class AverageSurfaceSpherical(AverageSurface):
+    """
+    Computes the average value of a field in a given volume
+    int(f ds) / int (1 * ds)
+    ds is the surface measure in cylindrical coordinates.
+    ds = r^2 sin(theta) dtheta dphi
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        title (str): the title of the derived quantity
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        function (dolfin.function.function.Function): the solution function of
+            the field
+
+    Notes:
+        Units are in H/m3 for hydrogen concentration and K for temperature
+    """
+
+    def __init__(self, field, surface) -> None:
+        super().__init__(field=field, surface=surface)
+        self.r = None
+
+    def compute(self):
+
+        if self.r is None:
+            mesh = (
+                self.function.function_space().mesh()
+            )  # get the mesh from the function
+            rthetaz = f.SpatialCoordinate(mesh)  # get the coordinates from the mesh
+            self.r = rthetaz[0]  # only care about r here
+
+        # dV_z = r dr dtheta , assuming axisymmetry dV_z = theta r dr
+        # dV_r = r dz dtheta , assuming axisymmetry dV_r = theta r dz
+        # in both cases the expression with self.dx is the same
+
+        avg_surf = f.assemble(
+            self.function * self.r**2 * self.ds(self.surface)
+        ) / f.assemble(1 * self.r**2 * self.ds(self.surface))
+
+        return avg_surf

festim/exports/derived_quantities/average_volume.py

@@ -1,5 +1,6 @@
 from festim import VolumeQuantity
 import fenics as f
+import numpy as np
 
 
 class AverageVolume(VolumeQuantity):
@@ -42,3 +43,81 @@
         return f.assemble(self.function * self.dx(self.volume)) / f.assemble(
             1 * self.dx(self.volume)
         )
+
+
+class AverageVolumeCylindrical(AverageVolume):
+    """
+    Computes the average value of a field in a given volume
+    int(f dx) / int (1 * dx)
+    dx is the volume measure in cylindrical coordinates.
+    dx = r dr dz dtheta
+
+    Note: for particle fluxes J is given in H/s, for heat fluxes J is given in W
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
+        title (str): the title of the derived quantity
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        function (dolfin.function.function.Function): the solution function of
+            the field
+    """
+
+    def __init__(self, field, volume) -> None:
+        super().__init__(field=field, volume=volume)
+        self.r = None
+
+    def compute(self):
+
+        if self.r is None:
+            mesh = (
+                self.function.function_space().mesh()
+            )  # get the mesh from the function
+            rthetaz = f.SpatialCoordinate(mesh)  # get the coordinates from the mesh
+            self.r = rthetaz[0]  # only care about r here
+
+        avg_vol = f.assemble(
+            self.function * self.r * self.dx(self.volume)
+        ) / f.assemble(1 * self.r * self.dx(self.volume))
+
+        return avg_vol
+
+
+class AverageVolumeSpherical(AverageVolume):
+    """
+    Computes the average value of a field in a given volume
+    int(f dx) / int (1 * dx)
+    dx is the volume measure in cylindrical coordinates.
+    dx = rho dtheta dphi
+
+    Note: for particle fluxes J is given in H/s, for heat fluxes J is given in W
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
+        title (str): the title of the derived quantity
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        function (dolfin.function.function.Function): the solution function of
+            the field
+    """
+
+    def __init__(self, field, volume) -> None:
+        super().__init__(field=field, volume=volume)
+        self.r = None
+
+    def compute(self):
+
+        if self.r is None:
+            mesh = (
+                self.function.function_space().mesh()
+            )  # get the mesh from the function
+            rthetaphi = f.SpatialCoordinate(mesh)  # get the coordinates from the mesh
+            self.r = rthetaphi[0]  # only care about r here
+
+        avg_vol = f.assemble(
+            self.function * self.r**2 * self.dx(self.volume)
+        ) / f.assemble(1 * self.r**2 * self.dx(self.volume))
+
+        return avg_vol