From a23b6cb13ae7f0e27f07f6b283b2460969252265 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 16:45:13 +0200
Subject: [PATCH 01/20] restore to state from previous PR

---
 .../derived_quantities/average_surface.py     | 29 ++++++-
 .../derived_quantities/average_volume.py      | 30 ++++++-
 .../derived_quantities/derived_quantities.py  | 12 ++-
 .../derived_quantities/derived_quantity.py    | 30 ++++---
 .../derived_quantities/hydrogen_flux.py       | 35 +++++++-
 .../derived_quantities/maximum_surface.py     | 38 +++++++--
 .../derived_quantities/maximum_volume.py      | 34 +++++++-
 .../derived_quantities/minimum_surface.py     | 38 +++++++--
 .../derived_quantities/minimum_volume.py      | 34 +++++++-
 .../exports/derived_quantities/point_value.py | 33 ++++++--
 .../derived_quantities/surface_flux.py        | 79 ++++++++++++++++---
 .../derived_quantities/thermal_flux.py        | 35 ++++++++
 .../derived_quantities/total_surface.py       | 48 ++++++++++-
 .../derived_quantities/total_volume.py        | 48 ++++++++++-
 festim/exports/exports.py                     |  2 +-
 .../test_derived_quantities.py                | 60 +++++++++++++-
 .../test_hydrogen_flux.py                     | 23 ++++++
 .../test_surface_flux.py                      | 21 +++++
 .../test_thermal_flux.py                      | 24 ++++++
 .../test_total_surface.py                     | 21 +++++
 .../test_total_volume.py                      | 21 +++++
 .../test_derived_quantities/tools.py          | 13 +++
 22 files changed, 648 insertions(+), 60 deletions(-)
 create mode 100644 test/unit/test_exports/test_derived_quantities/tools.py

diff --git a/festim/exports/derived_quantities/average_surface.py b/festim/exports/derived_quantities/average_surface.py
index 32007dcb4..cc0dd42dd 100644
--- a/festim/exports/derived_quantities/average_surface.py
+++ b/festim/exports/derived_quantities/average_surface.py
@@ -3,9 +3,36 @@
 
 
 class AverageSurface(SurfaceQuantity):
+    """
+    Computes the average value of a field on a given surface
+    int( f dx) / int (1 * dx)
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        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.title = "Average {} surface {}".format(self.field, self.surface)
+
+    @property
+    def title(self):
+        quantity_title = f"Average {self.field} surface {self.surface}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self):
         return f.assemble(self.function * self.ds(self.surface)) / f.assemble(
diff --git a/festim/exports/derived_quantities/average_volume.py b/festim/exports/derived_quantities/average_volume.py
index 49372e721..2d7fb87e0 100644
--- a/festim/exports/derived_quantities/average_volume.py
+++ b/festim/exports/derived_quantities/average_volume.py
@@ -3,9 +3,35 @@
 
 
 class AverageVolume(VolumeQuantity):
+    """
+    Computes the average value of a field in a given volume
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
+        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, volume: int) -> None:
-        super().__init__(field, volume)
-        self.title = "Average {} volume {}".format(self.field, self.volume)
+        super().__init__(field=field, volume=volume)
+
+    @property
+    def title(self):
+        quantity_title = f"Average {self.field} volume {self.volume}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self):
         return f.assemble(self.function * self.dx(self.volume)) / f.assemble(
diff --git a/festim/exports/derived_quantities/derived_quantities.py b/festim/exports/derived_quantities/derived_quantities.py
index 0cb0e108d..3cef88ad9 100644
--- a/festim/exports/derived_quantities/derived_quantities.py
+++ b/festim/exports/derived_quantities/derived_quantities.py
@@ -23,6 +23,8 @@ class DerivedQuantities(list):
         nb_iterations_between_exports (int, optional): number of
             iterations between each export. If None, the file will be
             exported at the last timestep. Defaults to None.
+        show_units (bool, optional): will show the units of each
+            derived quantity in the title in export
     """
 
     def __init__(
@@ -31,6 +33,7 @@ def __init__(
         filename: str = None,
         nb_iterations_between_compute: int = 1,
         nb_iterations_between_exports: int = None,
+        show_units=False,
     ) -> None:
         # checks that input is list
         if len(args) == 0:
@@ -43,8 +46,9 @@ def __init__(
         self.filename = filename
         self.nb_iterations_between_compute = nb_iterations_between_compute
         self.nb_iterations_between_exports = nb_iterations_between_exports
+        self.show_units = show_units
 
-        self.data = [self.make_header()]
+        self.data = []
         self.t = []
 
     @property
@@ -108,6 +112,7 @@ def filename(self, value):
     def make_header(self):
         header = ["t(s)"]
         for quantity in self:
+            quantity.show_units = self.show_units
             header.append(quantity.title)
         return header
 
@@ -139,6 +144,11 @@ def compute(self, t):
                 value = quantity.compute(self.volume_markers)
             else:
                 value = quantity.compute()
+
+            # check if first time writing data
+            if len(self.data) == 0:
+                self.data = [self.make_header()]
+
             quantity.data.append(value)
             quantity.t.append(t)
             row.append(value)
diff --git a/festim/exports/derived_quantities/derived_quantity.py b/festim/exports/derived_quantities/derived_quantity.py
index 113ac26ba..489ab3fa6 100644
--- a/festim/exports/derived_quantities/derived_quantity.py
+++ b/festim/exports/derived_quantities/derived_quantity.py
@@ -3,6 +3,8 @@
 
 class DerivedQuantity(Export):
     """
+    Parent class of all derived quantities
+
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
     """
@@ -18,16 +20,19 @@ def __init__(self, field) -> None:
         self.Q = None
         self.data = []
         self.t = []
+        self.show_units = False
 
 
 class VolumeQuantity(DerivedQuantity):
-    def __init__(self, field: str or int, volume: int) -> None:
-        """DerivedQuantity relative to a volume
+    """DerivedQuantity relative to a volume
+
+    Args:
+        field (str, int): the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
 
-        Args:
-            field (str, int): the field ("solute", 0, 1, "T", "retention")
-            volume (int): the volume id
-        """
+    """
+
+    def __init__(self, field: str or int, volume: int) -> None:
         super().__init__(field)
         self.volume = volume
 
@@ -44,13 +49,16 @@ def volume(self, value):
 
 
 class SurfaceQuantity(DerivedQuantity):
+    """DerivedQuantity relative to a surface
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+
+    """
+
     def __init__(self, field: str or int, surface: int) -> None:
-        """DerivedQuantity relative to a surface
 
-        Args:
-            field (str, int):  the field ("solute", 0, 1, "T", "retention")
-            surface (int): the surface id
-        """
         super().__init__(field)
         self.surface = surface
 
diff --git a/festim/exports/derived_quantities/hydrogen_flux.py b/festim/exports/derived_quantities/hydrogen_flux.py
index 09f6b9d70..e81370ab8 100644
--- a/festim/exports/derived_quantities/hydrogen_flux.py
+++ b/festim/exports/derived_quantities/hydrogen_flux.py
@@ -2,7 +2,40 @@
 
 
 class HydrogenFlux(SurfaceFlux):
-    """Equivalent to SurfaceFlux("solute", ...)"""
+    """
+    Computes the surface flux of hydrogen at a given surface
+
+    Args:
+        surface (int): the surface id
+
+    Attribtutes
+        field (str, int): the hydrogen solute field
+        surface (int): the surface id
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        title (str): the title of the derived quantity
+        function (dolfin.function.function.Function): the solution function of
+            the hydrogen solute field
+
+    Notes:
+        units are in H/m2/s in 1D, H/m/s in 2D and H/s in 3D domains
+
+    """
 
     def __init__(self, surface) -> None:
         super().__init__(field="solute", surface=surface)
+
+    @property
+    def title(self):
+        quantity_title = f"Flux surface {self.surface}: {self.field}"
+        if self.show_units:
+            # obtain domain dimension
+            dim = self.function.function_space().mesh().topology().dim()
+            if dim == 1:
+                return quantity_title + " (H m-2 s-1)"
+            if dim == 2:
+                return quantity_title + " (H m-1 s-1)"
+            if dim == 3:
+                return quantity_title + " (H s-1)"
+        else:
+            return quantity_title
diff --git a/festim/exports/derived_quantities/maximum_surface.py b/festim/exports/derived_quantities/maximum_surface.py
index 35eab5f16..54726c87e 100644
--- a/festim/exports/derived_quantities/maximum_surface.py
+++ b/festim/exports/derived_quantities/maximum_surface.py
@@ -1,20 +1,42 @@
-from festim import DerivedQuantity
+from festim import SurfaceQuantity
 import fenics as f
 import numpy as np
 
 
-class MaximumSurface(DerivedQuantity):
+class MaximumSurface(SurfaceQuantity):
     """
+    Computes the maximum value of a field on a given surface
+
     Args:
-        field (str): the field from which the maximum
-            is computed (ex: "solute", "retention", "T"...)
-        surface (int): the surface id where the maximum is computed
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        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)
-        self.surface = surface
-        self.title = "Maximum {} surface {}".format(self.field, self.surface)
+        super().__init__(field=field, surface=surface)
+
+    @property
+    def title(self):
+        quantity_title = f"Maximum {self.field} surface {self.surface}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self, surface_markers):
         """Maximum of f over subdomains facets marked with self.surface"""
diff --git a/festim/exports/derived_quantities/maximum_volume.py b/festim/exports/derived_quantities/maximum_volume.py
index 1c7c66d75..315c5a79a 100644
--- a/festim/exports/derived_quantities/maximum_volume.py
+++ b/festim/exports/derived_quantities/maximum_volume.py
@@ -4,9 +4,39 @@
 
 
 class MaximumVolume(VolumeQuantity):
+    """
+    Computes the maximum value in a field in a given volume
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
+
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        volume (int): the volume id
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        function (dolfin.function.function.Function): the solution function for
+            the field
+
+    notes:
+        Units are in H/m3 for hydrogen concentration and K for temperature
+
+    """
+
     def __init__(self, field, volume) -> None:
-        super().__init__(field, volume=volume)
-        self.title = "Maximum {} volume {}".format(self.field, self.volume)
+        super().__init__(field=field, volume=volume)
+
+    @property
+    def title(self):
+        quantity_title = f"Maximum {self.field} volume {self.volume}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self, volume_markers):
         """Minimum of f over subdomains cells marked with self.volume"""
diff --git a/festim/exports/derived_quantities/minimum_surface.py b/festim/exports/derived_quantities/minimum_surface.py
index 2ea9c7bc5..6da9f6b16 100644
--- a/festim/exports/derived_quantities/minimum_surface.py
+++ b/festim/exports/derived_quantities/minimum_surface.py
@@ -1,20 +1,42 @@
-from festim import DerivedQuantity
+from festim import SurfaceQuantity
 import fenics as f
 import numpy as np
 
 
-class MinimumSurface(DerivedQuantity):
+class MinimumSurface(SurfaceQuantity):
     """
+    Computes the minimum value of a field on a given surface
+
     Args:
-        field (str): the field from which the minimum
-            is computed (ex: "solute", "retention", "T"...)
-        surface (int): the surface id where the minimum is computed
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        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)
-        self.surface = surface
-        self.title = "Minimum {} surface {}".format(self.field, self.surface)
+        super().__init__(field=field, surface=surface)
+
+    @property
+    def title(self):
+        quantity_title = f"Minimum {self.field} surface {self.surface}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self, surface_markers):
         """Minimum of f over subdomains facets marked with self.surface"""
diff --git a/festim/exports/derived_quantities/minimum_volume.py b/festim/exports/derived_quantities/minimum_volume.py
index 02b064789..36cd4c01e 100644
--- a/festim/exports/derived_quantities/minimum_volume.py
+++ b/festim/exports/derived_quantities/minimum_volume.py
@@ -4,9 +4,39 @@
 
 
 class MinimumVolume(VolumeQuantity):
+    """
+    Computes the minimum value in a field in a given volume
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        function (dolfin.function.function.Function): the solution function for
+            the field
+
+    notes:
+        Units are in H/m3 for hydrogen concentration and K for temperature
+
+    """
+
     def __init__(self, field, volume) -> None:
-        super().__init__(field, volume=volume)
-        self.title = "Minimum {} volume {}".format(self.field, self.volume)
+        super().__init__(field=field, volume=volume)
+
+    @property
+    def title(self):
+        quantity_title = f"Minimum {self.field} volume {self.volume}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self, volume_markers):
         """Minimum of f over subdomains cells marked with self.volume"""
diff --git a/festim/exports/derived_quantities/point_value.py b/festim/exports/derived_quantities/point_value.py
index 10b046560..d038c2a2c 100644
--- a/festim/exports/derived_quantities/point_value.py
+++ b/festim/exports/derived_quantities/point_value.py
@@ -2,20 +2,43 @@
 
 
 class PointValue(DerivedQuantity):
-    """DerivedQuantity relative to a point
+    """
+    Computes the value of a field at a given point
 
     Args:
-        field (str, int): the field ("solute", 0, 1, "T", "retention")
-        point (int, float, tuple, list): the point coordinates
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        x (int, float, tuple, list): the point coordinates
+
+    Attributes:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        x (int, float, tuple, list): the point coordinates
+        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: str or int, x: int or float or tuple or list) -> None:
-        super().__init__(field)
+        super().__init__(field=field)
         # make sure x is an iterable
         if not hasattr(x, "__iter__"):
             x = [x]
         self.x = x
-        self.title = "{} value at {}".format(field, x)
+
+    @property
+    def title(self):
+        quantity_title = f"{self.field} value at {self.x}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (K)"
+            else:
+                return quantity_title + " (H m-3)"
+        else:
+            return quantity_title
 
     def compute(self):
         """The value at the point"""
diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index 227da62e3..0d6e9b7ad 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -4,24 +4,59 @@
 
 
 class SurfaceFlux(SurfaceQuantity):
-    def __init__(self, field, surface) -> None:
-        """
+    """
+    Computes the surface flux of a field at a given surface
+
+    Args:
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+
+    Attribtutes
+        field (str, int):  the field ("solute", 0, 1, "T", "retention")
+        surface (int): the surface id
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        title (str): the title of the derived quantity
+        function (dolfin.function.function.Function): the solution function of
+            the hydrogen solute field
+
+    Notes:
         Object to compute the flux J of a field u through a surface
         J = integral(-prop * grad(u) . n ds)
         where prop is the property of the field (D, thermal conductivity, etc)
         u is the field
         n is the normal vector of the surface
         ds is the surface measure.
+        units are in H/m2/s in 1D, H/m/s in 2D and H/s in 3D domains for hydrogen
+        concentration and W/m2 in 1D, W/m in 2D and W in 3D domains for temperature
 
-        Note: this will probably won't work correctly for axisymmetric meshes.
-        Use only with cartesian coordinates.
+    """
 
-        Args:
-            field (str, int):  the field ("solute", 0, 1, "T", "retention")
-            surface (int): the surface id
-        """
+    def __init__(self, field, surface) -> None:
         super().__init__(field=field, surface=surface)
-        self.title = "Flux surface {}: {}".format(self.surface, self.field)
+
+    @property
+    def title(self):
+        quantity_title = f"Flux surface {self.surface}: {self.field}"
+        if self.show_units:
+            # obtain domain dimension
+            dim = self.function.function_space().mesh().topology().dim()
+            if self.field == "T":
+                if dim == 1:
+                    return quantity_title + " (W m-2)"
+                if dim == 2:
+                    return quantity_title + " (W m-1)"
+                if dim == 3:
+                    return quantity_title + " (W)"
+            else:
+                if dim == 1:
+                    return quantity_title + " (H m-2 s-1)"
+                if dim == 2:
+                    return quantity_title + " (H m-1 s-1)"
+                if dim == 3:
+                    return quantity_title + " (H s-1)"
+        else:
+            return quantity_title
 
     @property
     def prop(self):
@@ -69,10 +104,21 @@ class SurfaceFluxCylindrical(SurfaceFlux):
     """
 
     def __init__(self, field, surface, azimuth_range=(0, 2 * np.pi)) -> None:
-        super().__init__(field, surface)
+        super().__init__(field=field, surface=surface)
         self.r = None
         self.azimuth_range = azimuth_range
 
+    @property
+    def title(self):
+        quantity_title = f"Cylindrical flux surface {self.surface}: {self.field}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (W)"
+            else:
+                return quantity_title + " (H s-1)"
+        else:
+            return quantity_title
+
     @property
     def azimuth_range(self):
         return self._azimuth_range
@@ -134,11 +180,22 @@ class SurfaceFluxSpherical(SurfaceFlux):
     def __init__(
         self, field, surface, azimuth_range=(0, np.pi), polar_range=(-np.pi, np.pi)
     ) -> None:
-        super().__init__(field, surface)
+        super().__init__(field=field, surface=surface)
         self.r = None
         self.polar_range = polar_range
         self.azimuth_range = azimuth_range
 
+    @property
+    def title(self):
+        quantity_title = f"Spherical flux surface {self.surface}: {self.field}"
+        if self.show_units:
+            if self.field == "T":
+                return quantity_title + " (W)"
+            else:
+                return quantity_title + " (H s-1)"
+        else:
+            return quantity_title
+
     @property
     def polar_range(self):
         return self._polar_range
diff --git a/festim/exports/derived_quantities/thermal_flux.py b/festim/exports/derived_quantities/thermal_flux.py
index 176df3799..69cfe7c17 100644
--- a/festim/exports/derived_quantities/thermal_flux.py
+++ b/festim/exports/derived_quantities/thermal_flux.py
@@ -2,5 +2,40 @@
 
 
 class ThermalFlux(SurfaceFlux):
+    """
+    Computes the surface flux of heat at a given surface
+
+    Args:
+        surface (int): the surface id
+
+    Attribtutes
+        surface (int): the surface id
+        field (str): the temperature field
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        title (str): the title of the derived quantity
+        function (dolfin.function.function.Function): the solution function of
+            the temperature field
+
+    Notes:
+        units are in W/m2 in 1D, W/m in 2D and W in 3D domains
+
+    """
+
     def __init__(self, surface) -> None:
         super().__init__(field="T", surface=surface)
+
+    @property
+    def title(self):
+        quantity_title = f"Flux surface {self.surface}: {self.field}"
+        if self.show_units:
+            # obtain domain dimension
+            dim = self.function.function_space().mesh().topology().dim()
+            if dim == 1:
+                return quantity_title + " (W m-2)"
+            if dim == 2:
+                return quantity_title + " (W m-1)"
+            if dim == 3:
+                return quantity_title + " (W)"
+        else:
+            return quantity_title
diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 057d7f9af..48717a8cb 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -3,9 +3,53 @@
 
 
 class TotalSurface(SurfaceQuantity):
+    """
+    Computes the total value of a field on a given surface
+
+    Args:
+        field (str, int): the field
+        surface (int): the surface id
+
+    Attribtutes
+        field (str, int): the field
+        surface (int): the surface id
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        title (str): the title of the derived quantity
+        function (dolfin.function.function.Function): the solution function of
+            the hydrogen solute field
+
+    Notes:
+        units are in H/m2 in 1D, H/m in 2D and H in 3D domains for hydrogen
+        concentration and K in 1D, K m in 2D and K m2 in 3D domains for temperature
+
+    """
+
     def __init__(self, field, surface) -> None:
-        super().__init__(field, surface=surface)
-        self.title = "Total {} surface {}".format(self.field, self.surface)
+        super().__init__(field=field, surface=surface)
+
+    @property
+    def title(self):
+        quantity_title = f"Total {self.field} surface {self.surface}"
+        if self.show_units:
+            # obtain domain dimension
+            dim = self.function.function_space().mesh().topology().dim()
+            if self.field == "T":
+                if dim == 1:
+                    return quantity_title + " (K)"
+                elif dim == 2:
+                    return quantity_title + " (K m)"
+                elif dim == 3:
+                    return quantity_title + " (K m2)"
+            else:
+                if dim == 1:
+                    return quantity_title + " (H m-2)"
+                elif dim == 2:
+                    return quantity_title + " (H m-1)"
+                elif dim == 3:
+                    return quantity_title + " (H)"
+        else:
+            return quantity_title
 
     def compute(self):
         return f.assemble(self.function * self.ds(self.surface))
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index 497db138b..b91e0f003 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -3,9 +3,53 @@
 
 
 class TotalVolume(VolumeQuantity):
+    """
+    Computes the total value of a field in a given volume
+
+    Args:
+        field (str, int): the field
+        volume (int): the volume id
+
+    Attribtutes
+        field (str, int): the field
+        volume (int): the volume id
+        show_units (bool): show the units in the title in the derived quantities
+            file
+        title (str): the title of the derived quantity
+        function (dolfin.function.function.Function): the solution function of
+            the hydrogen solute field
+
+    Notes:
+        units are in H/m2 in 1D, H/m in 2D and H in 3D domains for hydrogen
+        concentration and K m in 1D, K m2 in 2D and K m3 in 3D domains for temperature
+
+    """
+
     def __init__(self, field, volume) -> None:
-        super().__init__(field, volume=volume)
-        self.title = "Total {} volume {}".format(self.field, self.volume)
+        super().__init__(field=field, volume=volume)
+
+    @property
+    def title(self):
+        quantity_title = f"Total {self.field} volume {self.volume}"
+        if self.show_units:
+            # obtain domain dimension
+            dim = self.function.function_space().mesh().topology().dim()
+            if self.field == "T":
+                if dim == 1:
+                    return quantity_title + " (K m)"
+                elif dim == 2:
+                    return quantity_title + " (K m2)"
+                elif dim == 3:
+                    return quantity_title + " (K m3)"
+            else:
+                if dim == 1:
+                    return quantity_title + " (H m-2)"
+                elif dim == 2:
+                    return quantity_title + " (H m-1)"
+                elif dim == 3:
+                    return quantity_title + " (H)"
+        else:
+            return quantity_title
 
     def compute(self):
         return f.assemble(self.function * self.dx(self.volume))
diff --git a/festim/exports/exports.py b/festim/exports/exports.py
index a84e80d9e..b79cd2f2b 100644
--- a/festim/exports/exports.py
+++ b/festim/exports/exports.py
@@ -136,6 +136,6 @@ def initialise_derived_quantities(self, dx, ds, materials):
         """
         for export in self:
             if isinstance(export, festim.DerivedQuantities):
-                export.data = [export.make_header()]
+                export.data = []
                 export.assign_measures_to_quantities(dx, ds)
                 export.assign_properties_to_quantities(materials)
diff --git a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
index 1a81e91c5..2928d2fdc 100644
--- a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
+++ b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
@@ -6,6 +6,10 @@
     TotalVolume,
     MaximumVolume,
     MinimumVolume,
+    MinimumSurface,
+    MaximumSurface,
+    AverageSurface,
+    PointValue,
     Materials,
 )
 import fenics as f
@@ -23,7 +27,17 @@ class TestMakeHeader:
     tot_surf_2 = TotalSurface("trap1", 7)
     tot_vol_1 = TotalVolume("trap2", 5)
     min_vol_1 = MinimumVolume("retention", 2)
+    min_vol_2 = MinimumVolume("T", 2)
     max_vol_1 = MaximumVolume("T", 2)
+    max_vol_2 = MaximumVolume("trap2", 2)
+    min_surface_1 = MinimumSurface("solute", 1)
+    min_surface_2 = MinimumSurface("T", 2)
+    max_surface_1 = MaximumSurface("solute", 8)
+    max_surface_2 = MaximumSurface("T", 9)
+    avg_surface_1 = AverageSurface("solute", 4)
+    avg_surface_2 = AverageSurface("T", 6)
+    point_1 = PointValue(field="retention", x=2)
+    point_2 = PointValue(field="T", x=9)
 
     def test_simple(self):
         """
@@ -76,6 +90,46 @@ def test_all_quantities(self):
         ]
         assert header == expected_header
 
+    def test_with_units_simple(self):
+        """Test with quantities that don't require mesh dimension for unit"""
+        my_derv_quant = DerivedQuantities(
+            [
+                self.average_vol_1,
+                self.average_vol_2,
+                self.min_vol_1,
+                self.min_vol_2,
+                self.max_vol_1,
+                self.max_vol_2,
+                self.min_surface_1,
+                self.min_surface_2,
+                self.max_surface_1,
+                self.max_surface_2,
+                self.avg_surface_1,
+                self.avg_surface_2,
+                self.point_1,
+                self.point_2,
+            ],
+            show_units=True,
+        )
+        header = my_derv_quant.make_header()
+        expected_header = ["t(s)"] + [
+            "Average solute volume 3 (H m-3)",
+            "Average T volume 4 (K)",
+            "Minimum retention volume 2 (H m-3)",
+            "Minimum T volume 2 (K)",
+            "Maximum T volume 2 (K)",
+            "Maximum trap2 volume 2 (H m-3)",
+            "Minimum solute surface 1 (H m-3)",
+            "Minimum T surface 2 (K)",
+            "Maximum solute surface 8 (H m-3)",
+            "Maximum T surface 9 (K)",
+            "Average solute surface 4 (H m-3)",
+            "Average T surface 6 (K)",
+            "retention value at [2] (H m-3)",
+            "T value at [9] (K)",
+        ]
+        assert header == expected_header
+
 
 class TestAssignMeasuresToQuantities:
     """
@@ -211,7 +265,7 @@ def test_simple(self):
 
         my_derv_quant.data = []
         my_derv_quant.compute(t)
-        assert my_derv_quant.data[0] == expected_data
+        assert my_derv_quant.data[1] == expected_data
 
     def test_two_quantities(self):
         """Check for the case of two festim.DerivedQuantity objects"""
@@ -232,7 +286,7 @@ def test_two_quantities(self):
         my_derv_quant.data = []
         my_derv_quant.compute(t)
 
-        assert my_derv_quant.data[0] == expected_data
+        assert my_derv_quant.data[1] == expected_data
 
     def test_all_quantities(self):
         """Check for the case of many festim.DerivedQuantity objects"""
@@ -262,7 +316,7 @@ def test_all_quantities(self):
         my_derv_quant.data = []
         my_derv_quant.compute(t)
 
-        assert my_derv_quant.data[0] == expected_data
+        assert my_derv_quant.data[1] == expected_data
 
 
 class TestWrite:
diff --git a/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py b/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py
index 1b1b71181..bfc9e1b34 100644
--- a/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py
@@ -1,4 +1,6 @@
 from festim import HydrogenFlux
+from .tools import c_1D, c_2D, c_3D
+import pytest
 
 
 def test_field_is_solute():
@@ -9,3 +11,24 @@ def test_field_is_solute():
 
     my_flux = HydrogenFlux(2)
     assert my_flux.field == "solute"
+
+
+@pytest.mark.parametrize(
+    "function, expected_title",
+    [
+        (c_1D, "Flux surface 3: solute (H m-2 s-1)"),
+        (c_2D, "Flux surface 3: solute (H m-1 s-1)"),
+        (c_3D, "Flux surface 3: solute (H s-1)"),
+    ],
+)
+def test_title_with_units(function, expected_title):
+    my_flux = HydrogenFlux(3)
+    my_flux.function = function
+    my_flux.show_units = True
+
+    assert my_flux.title == expected_title
+
+
+def test_title_without_units():
+    my_flux = HydrogenFlux(4)
+    assert my_flux.title == "Flux surface 4: solute"
diff --git a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
index 55446254e..16b142e55 100644
--- a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
@@ -3,6 +3,8 @@
 import math
 import numpy as np
 import pytest
+from festim import SurfaceFlux, k_B
+from .tools import c_1D, c_2D, c_3D
 
 
 @pytest.mark.parametrize("field,surface", [("solute", 1), ("T", 2)])
@@ -264,3 +266,22 @@ def test_soret_raises_error_spherical():
     my_flux = SurfaceFluxSpherical("T", 1)
     with pytest.raises(NotImplementedError):
         my_flux.compute(soret=True)
+
+
+@pytest.mark.parametrize(
+    "function, field, expected_title",
+    [
+        (c_1D, "solute", "Flux surface 3: solute (H m-2 s-1)"),
+        (c_1D, "T", "Flux surface 3: T (W m-2)"),
+        (c_2D, "solute", "Flux surface 3: solute (H m-1 s-1)"),
+        (c_2D, "T", "Flux surface 3: T (W m-1)"),
+        (c_3D, "solute", "Flux surface 3: solute (H s-1)"),
+        (c_3D, "T", "Flux surface 3: T (W)"),
+    ],
+)
+def test_title_with_units(function, field, expected_title):
+    my_flux = SurfaceFlux(field=field, surface=3)
+    my_flux.function = function
+    my_flux.show_units = True
+
+    assert my_flux.title == expected_title
diff --git a/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py b/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py
index fac0e5f46..4c78881bc 100644
--- a/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py
@@ -1,4 +1,6 @@
 from festim import ThermalFlux
+import pytest
+from .tools import c_1D, c_2D, c_3D
 
 
 def test_field_is_T():
@@ -8,3 +10,25 @@ def test_field_is_T():
     """
     my_flux = ThermalFlux(2)
     assert my_flux.field == "T"
+
+
+@pytest.mark.parametrize(
+    "function, expected_title",
+    [
+        (c_1D, "Flux surface 5: T (W m-2)"),
+        (c_2D, "Flux surface 5: T (W m-1)"),
+        (c_3D, "Flux surface 5: T (W)"),
+    ],
+)
+def test_title_with_units(function, expected_title):
+    my_flux = ThermalFlux(5)
+    my_flux.function = function
+    my_flux.show_units = True
+
+    assert my_flux.title == expected_title
+
+
+def test_title_without_units():
+    my_flux = ThermalFlux(5)
+
+    assert my_flux.title == "Flux surface 5: T"
diff --git a/test/unit/test_exports/test_derived_quantities/test_total_surface.py b/test/unit/test_exports/test_derived_quantities/test_total_surface.py
index f5e152595..ea0cd8354 100644
--- a/test/unit/test_exports/test_derived_quantities/test_total_surface.py
+++ b/test/unit/test_exports/test_derived_quantities/test_total_surface.py
@@ -2,6 +2,8 @@
 from festim import TotalSurface
 import fenics as f
 import pytest
+from .tools import c_1D, c_2D, c_3D
+import pytest
 
 
 @pytest.mark.parametrize("field,surface", [("solute", 1), ("T", 2)])
@@ -43,3 +45,22 @@ def test_minimum(self):
 
         produced = self.my_total.compute()
         assert produced == expected
+
+
+@pytest.mark.parametrize(
+    "function, field, expected_title",
+    [
+        (c_1D, "solute", "Total solute surface 8 (H m-2)"),
+        (c_1D, "T", "Total T surface 8 (K)"),
+        (c_2D, "solute", "Total solute surface 8 (H m-1)"),
+        (c_2D, "T", "Total T surface 8 (K m)"),
+        (c_3D, "solute", "Total solute surface 8 (H)"),
+        (c_3D, "T", "Total T surface 8 (K m2)"),
+    ],
+)
+def test_title_with_units(function, field, expected_title):
+    my_export = TotalSurface(surface=8, field=field)
+    my_export.function = function
+    my_export.show_units = True
+
+    assert my_export.title == expected_title
diff --git a/test/unit/test_exports/test_derived_quantities/test_total_volume.py b/test/unit/test_exports/test_derived_quantities/test_total_volume.py
index 8f2e3cfa5..5fd3a8cb3 100644
--- a/test/unit/test_exports/test_derived_quantities/test_total_volume.py
+++ b/test/unit/test_exports/test_derived_quantities/test_total_volume.py
@@ -1,6 +1,8 @@
 from festim import TotalVolume
 import fenics as f
 import pytest
+from .tools import c_1D, c_2D, c_3D
+import pytest
 
 
 @pytest.mark.parametrize("field,volume", [("solute", 1), ("T", 2)])
@@ -42,3 +44,22 @@ def test_minimum(self):
 
         produced = self.my_total.compute()
         assert produced == expected
+
+
+@pytest.mark.parametrize(
+    "function, field, expected_title",
+    [
+        (c_1D, "solute", "Total solute volume 2 (H m-2)"),
+        (c_1D, "T", "Total T volume 2 (K m)"),
+        (c_2D, "solute", "Total solute volume 2 (H m-1)"),
+        (c_2D, "T", "Total T volume 2 (K m2)"),
+        (c_3D, "solute", "Total solute volume 2 (H)"),
+        (c_3D, "T", "Total T volume 2 (K m3)"),
+    ],
+)
+def test_title_with_units(function, field, expected_title):
+    my_export = TotalVolume(volume=2, field=field)
+    my_export.function = function
+    my_export.show_units = True
+
+    assert my_export.title == expected_title
diff --git a/test/unit/test_exports/test_derived_quantities/tools.py b/test/unit/test_exports/test_derived_quantities/tools.py
new file mode 100644
index 000000000..8f9ce3089
--- /dev/null
+++ b/test/unit/test_exports/test_derived_quantities/tools.py
@@ -0,0 +1,13 @@
+import fenics as f
+
+mesh_1D = f.UnitIntervalMesh(10)
+V_1D = f.FunctionSpace(mesh_1D, "P", 1)
+c_1D = f.interpolate(f.Expression("x[0]", degree=1), V_1D)
+
+mesh_2D = f.UnitSquareMesh(10, 10)
+V_2D = f.FunctionSpace(mesh_2D, "P", 1)
+c_2D = f.interpolate(f.Expression("x[0]", degree=1), V_2D)
+
+mesh_3D = f.UnitCubeMesh(10, 10, 10)
+V_3D = f.FunctionSpace(mesh_3D, "P", 1)
+c_3D = f.interpolate(f.Expression("x[0]", degree=1), V_3D)

From 2518e09c42ae2be3bf38da16b3adad47b2902356 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:08:11 +0200
Subject: [PATCH 02/20] changes for comments from reveiw

---
 .../exports/derived_quantities/average_surface.py |  6 +++++-
 .../exports/derived_quantities/average_volume.py  |  4 ++++
 .../exports/derived_quantities/hydrogen_flux.py   | 15 ---------------
 festim/exports/derived_quantities/surface_flux.py |  4 ++--
 festim/exports/derived_quantities/thermal_flux.py | 15 ---------------
 .../exports/derived_quantities/total_surface.py   |  1 +
 festim/exports/derived_quantities/total_volume.py |  1 +
 7 files changed, 13 insertions(+), 33 deletions(-)

diff --git a/festim/exports/derived_quantities/average_surface.py b/festim/exports/derived_quantities/average_surface.py
index cc0dd42dd..18ed890c0 100644
--- a/festim/exports/derived_quantities/average_surface.py
+++ b/festim/exports/derived_quantities/average_surface.py
@@ -5,10 +5,12 @@
 class AverageSurface(SurfaceQuantity):
     """
     Computes the average value of a field on a given surface
-    int( f dx) / int (1 * dx)
+    int( f ds) / int (1 * ds)
+
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
         surface (int): the surface id
+
     Attributes:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
         surface (int): the surface id
@@ -16,8 +18,10 @@ class AverageSurface(SurfaceQuantity):
             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:
diff --git a/festim/exports/derived_quantities/average_volume.py b/festim/exports/derived_quantities/average_volume.py
index 2d7fb87e0..f385631c4 100644
--- a/festim/exports/derived_quantities/average_volume.py
+++ b/festim/exports/derived_quantities/average_volume.py
@@ -5,9 +5,12 @@
 class AverageVolume(VolumeQuantity):
     """
     Computes the average value of a field in a given volume
+    int( f ds) / int (1 * ds)
+
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
         volume (int): the volume id
+
     Attributes:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
         volume (int): the volume id
@@ -15,6 +18,7 @@ class AverageVolume(VolumeQuantity):
             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
     """
diff --git a/festim/exports/derived_quantities/hydrogen_flux.py b/festim/exports/derived_quantities/hydrogen_flux.py
index e81370ab8..4226e6f1b 100644
--- a/festim/exports/derived_quantities/hydrogen_flux.py
+++ b/festim/exports/derived_quantities/hydrogen_flux.py
@@ -24,18 +24,3 @@ class HydrogenFlux(SurfaceFlux):
 
     def __init__(self, surface) -> None:
         super().__init__(field="solute", surface=surface)
-
-    @property
-    def title(self):
-        quantity_title = f"Flux surface {self.surface}: {self.field}"
-        if self.show_units:
-            # obtain domain dimension
-            dim = self.function.function_space().mesh().topology().dim()
-            if dim == 1:
-                return quantity_title + " (H m-2 s-1)"
-            if dim == 2:
-                return quantity_title + " (H m-1 s-1)"
-            if dim == 3:
-                return quantity_title + " (H s-1)"
-        else:
-            return quantity_title
diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index 0d6e9b7ad..f428979be 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -5,7 +5,7 @@
 
 class SurfaceFlux(SurfaceQuantity):
     """
-    Computes the surface flux of a field at a given surface
+    Computes the surface flux of a field at a given surface in cartesian coordinates
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
@@ -18,7 +18,7 @@ class SurfaceFlux(SurfaceQuantity):
             file
         title (str): the title of the derived quantity
         function (dolfin.function.function.Function): the solution function of
-            the hydrogen solute field
+            the field
 
     Notes:
         Object to compute the flux J of a field u through a surface
diff --git a/festim/exports/derived_quantities/thermal_flux.py b/festim/exports/derived_quantities/thermal_flux.py
index 69cfe7c17..3095908fe 100644
--- a/festim/exports/derived_quantities/thermal_flux.py
+++ b/festim/exports/derived_quantities/thermal_flux.py
@@ -24,18 +24,3 @@ class ThermalFlux(SurfaceFlux):
 
     def __init__(self, surface) -> None:
         super().__init__(field="T", surface=surface)
-
-    @property
-    def title(self):
-        quantity_title = f"Flux surface {self.surface}: {self.field}"
-        if self.show_units:
-            # obtain domain dimension
-            dim = self.function.function_space().mesh().topology().dim()
-            if dim == 1:
-                return quantity_title + " (W m-2)"
-            if dim == 2:
-                return quantity_title + " (W m-1)"
-            if dim == 3:
-                return quantity_title + " (W)"
-        else:
-            return quantity_title
diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 48717a8cb..2cd821883 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -5,6 +5,7 @@
 class TotalSurface(SurfaceQuantity):
     """
     Computes the total value of a field on a given surface
+    int(f ds)
 
     Args:
         field (str, int): the field
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index b91e0f003..89d21bda0 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -5,6 +5,7 @@
 class TotalVolume(VolumeQuantity):
     """
     Computes the total value of a field in a given volume
+    int(f dx)
 
     Args:
         field (str, int): the field

From fdf066852c4afd323fe2a96d43460399d2744758 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:08:17 +0200
Subject: [PATCH 03/20] increase coverage

---
 .../test_derived_quantities.py                     | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
index 2928d2fdc..3cdde3821 100644
--- a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
+++ b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
@@ -10,6 +10,8 @@
     MaximumSurface,
     AverageSurface,
     PointValue,
+    SurfaceFluxCylindrical,
+    SurfaceFluxSpherical,
     Materials,
 )
 import fenics as f
@@ -38,6 +40,10 @@ class TestMakeHeader:
     avg_surface_2 = AverageSurface("T", 6)
     point_1 = PointValue(field="retention", x=2)
     point_2 = PointValue(field="T", x=9)
+    cyl_surface_flux_1 = SurfaceFluxCylindrical("solute", 2)
+    cyl_surface_flux_2 = SurfaceFluxCylindrical("T", 3)
+    sph_surface_flux_1 = SurfaceFluxSpherical("solute", 5)
+    sph_surface_flux_2 = SurfaceFluxSpherical("T", 6)
 
     def test_simple(self):
         """
@@ -108,6 +114,10 @@ def test_with_units_simple(self):
                 self.avg_surface_2,
                 self.point_1,
                 self.point_2,
+                self.cyl_surface_flux_1,
+                self.cyl_surface_flux_2,
+                self.sph_surface_flux_1,
+                self.sph_surface_flux_2,
             ],
             show_units=True,
         )
@@ -127,6 +137,10 @@ def test_with_units_simple(self):
             "Average T surface 6 (K)",
             "retention value at [2] (H m-3)",
             "T value at [9] (K)",
+            "Cylindrical flux surface 2: solute (H s-1)",
+            "Cylindrical flux surface 3: T (W)",
+            "Spherical flux surface 5: solute (H s-1)",
+            "Spherical flux surface 6: T (W)",
         ]
         assert header == expected_header
 

From 070cb1d92dd10a0e464f2d903e7189f6423a3b59 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:16:29 +0200
Subject: [PATCH 04/20] remove whitespace

---
 festim/exports/derived_quantities/average_surface.py | 2 +-
 festim/exports/derived_quantities/average_volume.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/festim/exports/derived_quantities/average_surface.py b/festim/exports/derived_quantities/average_surface.py
index 18ed890c0..8ae471231 100644
--- a/festim/exports/derived_quantities/average_surface.py
+++ b/festim/exports/derived_quantities/average_surface.py
@@ -5,7 +5,7 @@
 class AverageSurface(SurfaceQuantity):
     """
     Computes the average value of a field on a given surface
-    int( f ds) / int (1 * ds)
+    int(f ds) / int (1 * ds)
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
diff --git a/festim/exports/derived_quantities/average_volume.py b/festim/exports/derived_quantities/average_volume.py
index f385631c4..5add33232 100644
--- a/festim/exports/derived_quantities/average_volume.py
+++ b/festim/exports/derived_quantities/average_volume.py
@@ -5,7 +5,7 @@
 class AverageVolume(VolumeQuantity):
     """
     Computes the average value of a field in a given volume
-    int( f ds) / int (1 * ds)
+    int(f ds) / int (1 * ds)
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")

From 8c02f7191607e6fed20d80e719f92a7b7e4a0bdd Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:20:47 +0200
Subject: [PATCH 05/20] can only be str

---
 festim/exports/derived_quantities/hydrogen_flux.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/festim/exports/derived_quantities/hydrogen_flux.py b/festim/exports/derived_quantities/hydrogen_flux.py
index 4226e6f1b..24a668a46 100644
--- a/festim/exports/derived_quantities/hydrogen_flux.py
+++ b/festim/exports/derived_quantities/hydrogen_flux.py
@@ -9,7 +9,7 @@ class HydrogenFlux(SurfaceFlux):
         surface (int): the surface id
 
     Attribtutes
-        field (str, int): the hydrogen solute field
+        field (str): the hydrogen solute field
         surface (int): the surface id
         show_units (bool): show the units in the title in the derived quantities
             file

From 4b8248b29adafb25a03a996a7368a840e7a2ba77 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:21:08 +0200
Subject: [PATCH 06/20] better consistency in doc strings

---
 festim/exports/derived_quantities/total_surface.py | 4 ++--
 festim/exports/derived_quantities/total_volume.py  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 2cd821883..44f5b3d8d 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -8,11 +8,11 @@ class TotalSurface(SurfaceQuantity):
     int(f ds)
 
     Args:
-        field (str, int): the field
+        field (str, int): the field ("solute", 0, 1, "T", "retention")
         surface (int): the surface id
 
     Attribtutes
-        field (str, int): the field
+        field (str, int): the field ("solute", 0, 1, "T", "retention")
         surface (int): the surface id
         show_units (bool): show the units in the title in the derived quantities
             file
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index 89d21bda0..96f236e53 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -8,11 +8,11 @@ class TotalVolume(VolumeQuantity):
     int(f dx)
 
     Args:
-        field (str, int): the field
+        field (str, int): the field ("solute", 0, 1, "T", "retention")
         volume (int): the volume id
 
     Attribtutes
-        field (str, int): the field
+        field (str, int): the field ("solute", 0, 1, "T", "retention")
         volume (int): the volume id
         show_units (bool): show the units in the title in the derived quantities
             file

From d49cf9e2319a9376c83caea791bc04a5228e9f1d Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:24:42 +0200
Subject: [PATCH 07/20] added clarification inline comment

---
 .../test_derived_quantities/test_derived_quantities.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
index 3cdde3821..652c96f5a 100644
--- a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
+++ b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
@@ -279,6 +279,10 @@ def test_simple(self):
 
         my_derv_quant.data = []
         my_derv_quant.compute(t)
+
+        # title created in compute() method and appended to data
+        # so test line 2 for first data entry
+
         assert my_derv_quant.data[1] == expected_data
 
     def test_two_quantities(self):
@@ -300,6 +304,9 @@ def test_two_quantities(self):
         my_derv_quant.data = []
         my_derv_quant.compute(t)
 
+        # title created in compute() method and appended to data
+        # so test line 2 for first data entry
+
         assert my_derv_quant.data[1] == expected_data
 
     def test_all_quantities(self):
@@ -330,6 +337,9 @@ def test_all_quantities(self):
         my_derv_quant.data = []
         my_derv_quant.compute(t)
 
+        # title created in compute() method and appended to data
+        # so test line 2 for first data entry
+
         assert my_derv_quant.data[1] == expected_data
 
 

From 1282110583f81fb067e2c00f8454ca42f8feabeb Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 17:29:14 +0200
Subject: [PATCH 08/20] title is an attribute

---
 festim/exports/derived_quantities/average_surface.py | 1 +
 festim/exports/derived_quantities/average_volume.py  | 1 +
 festim/exports/derived_quantities/hydrogen_flux.py   | 2 +-
 festim/exports/derived_quantities/maximum_surface.py | 1 +
 festim/exports/derived_quantities/maximum_volume.py  | 1 +
 festim/exports/derived_quantities/minimum_surface.py | 1 +
 festim/exports/derived_quantities/minimum_volume.py  | 1 +
 festim/exports/derived_quantities/point_value.py     | 1 +
 festim/exports/derived_quantities/surface_flux.py    | 2 +-
 festim/exports/derived_quantities/thermal_flux.py    | 2 +-
 festim/exports/derived_quantities/total_surface.py   | 2 +-
 festim/exports/derived_quantities/total_volume.py    | 2 +-
 12 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/festim/exports/derived_quantities/average_surface.py b/festim/exports/derived_quantities/average_surface.py
index 8ae471231..a6d994c02 100644
--- a/festim/exports/derived_quantities/average_surface.py
+++ b/festim/exports/derived_quantities/average_surface.py
@@ -14,6 +14,7 @@ class AverageSurface(SurfaceQuantity):
     Attributes:
         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
diff --git a/festim/exports/derived_quantities/average_volume.py b/festim/exports/derived_quantities/average_volume.py
index 5add33232..651751f70 100644
--- a/festim/exports/derived_quantities/average_volume.py
+++ b/festim/exports/derived_quantities/average_volume.py
@@ -14,6 +14,7 @@ class AverageVolume(VolumeQuantity):
     Attributes:
         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
diff --git a/festim/exports/derived_quantities/hydrogen_flux.py b/festim/exports/derived_quantities/hydrogen_flux.py
index 24a668a46..26f39626c 100644
--- a/festim/exports/derived_quantities/hydrogen_flux.py
+++ b/festim/exports/derived_quantities/hydrogen_flux.py
@@ -11,9 +11,9 @@ class HydrogenFlux(SurfaceFlux):
     Attribtutes
         field (str): the hydrogen solute field
         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
-        title (str): the title of the derived quantity
         function (dolfin.function.function.Function): the solution function of
             the hydrogen solute field
 
diff --git a/festim/exports/derived_quantities/maximum_surface.py b/festim/exports/derived_quantities/maximum_surface.py
index 54726c87e..f4b790755 100644
--- a/festim/exports/derived_quantities/maximum_surface.py
+++ b/festim/exports/derived_quantities/maximum_surface.py
@@ -14,6 +14,7 @@ class MaximumSurface(SurfaceQuantity):
     Attributes:
         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
diff --git a/festim/exports/derived_quantities/maximum_volume.py b/festim/exports/derived_quantities/maximum_volume.py
index 315c5a79a..62eee2100 100644
--- a/festim/exports/derived_quantities/maximum_volume.py
+++ b/festim/exports/derived_quantities/maximum_volume.py
@@ -14,6 +14,7 @@ class MaximumVolume(VolumeQuantity):
     Attributes:
         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 for
diff --git a/festim/exports/derived_quantities/minimum_surface.py b/festim/exports/derived_quantities/minimum_surface.py
index 6da9f6b16..f782db5f0 100644
--- a/festim/exports/derived_quantities/minimum_surface.py
+++ b/festim/exports/derived_quantities/minimum_surface.py
@@ -14,6 +14,7 @@ class MinimumSurface(SurfaceQuantity):
     Attributes:
         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
diff --git a/festim/exports/derived_quantities/minimum_volume.py b/festim/exports/derived_quantities/minimum_volume.py
index 36cd4c01e..e3277c522 100644
--- a/festim/exports/derived_quantities/minimum_volume.py
+++ b/festim/exports/derived_quantities/minimum_volume.py
@@ -14,6 +14,7 @@ class MinimumVolume(VolumeQuantity):
     Attributes:
         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 for
diff --git a/festim/exports/derived_quantities/point_value.py b/festim/exports/derived_quantities/point_value.py
index d038c2a2c..80d5a82e0 100644
--- a/festim/exports/derived_quantities/point_value.py
+++ b/festim/exports/derived_quantities/point_value.py
@@ -12,6 +12,7 @@ class PointValue(DerivedQuantity):
     Attributes:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
         x (int, float, tuple, list): the point coordinates
+        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
diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index f428979be..1e106a033 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -14,9 +14,9 @@ class SurfaceFlux(SurfaceQuantity):
     Attribtutes
         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
-        title (str): the title of the derived quantity
         function (dolfin.function.function.Function): the solution function of
             the field
 
diff --git a/festim/exports/derived_quantities/thermal_flux.py b/festim/exports/derived_quantities/thermal_flux.py
index 3095908fe..8dd4b4032 100644
--- a/festim/exports/derived_quantities/thermal_flux.py
+++ b/festim/exports/derived_quantities/thermal_flux.py
@@ -11,9 +11,9 @@ class ThermalFlux(SurfaceFlux):
     Attribtutes
         surface (int): the surface id
         field (str): the temperature field
+        title (str): the title of the derived quantity
         show_units (bool): show the units in the title in the derived quantities
             file
-        title (str): the title of the derived quantity
         function (dolfin.function.function.Function): the solution function of
             the temperature field
 
diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 44f5b3d8d..2fe7d8c0e 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -14,9 +14,9 @@ class TotalSurface(SurfaceQuantity):
     Attribtutes
         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
-        title (str): the title of the derived quantity
         function (dolfin.function.function.Function): the solution function of
             the hydrogen solute field
 
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index 96f236e53..f61675cec 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -14,9 +14,9 @@ class TotalVolume(VolumeQuantity):
     Attribtutes
         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
-        title (str): the title of the derived quantity
         function (dolfin.function.function.Function): the solution function of
             the hydrogen solute field
 

From c833b4b0402d5a79a27599cc0f02f8b217717575 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 18:05:31 +0200
Subject: [PATCH 09/20] new title naming scheme for fluxes

---
 .../derived_quantities/surface_flux.py        | 15 ++++++++--
 .../test_derived_quantities.py                |  8 +++---
 .../test_hydrogen_flux.py                     |  6 ++--
 .../test_surface_flux.py                      | 28 +++++++++++++++----
 .../test_thermal_flux.py                      |  6 ++--
 5 files changed, 45 insertions(+), 18 deletions(-)

diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index 1e106a033..81b82cfc3 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -41,7 +41,10 @@ def title(self):
         if self.show_units:
             # obtain domain dimension
             dim = self.function.function_space().mesh().topology().dim()
+            # new title but only with show_units to not introduce breaking change
+            quantity_title = f"{self.field} flux surface {self.surface}"
             if self.field == "T":
+                quantity_title = f"Heat flux surface {self.surface}"
                 if dim == 1:
                     return quantity_title + " (W m-2)"
                 if dim == 2:
@@ -110,7 +113,11 @@ def __init__(self, field, surface, azimuth_range=(0, 2 * np.pi)) -> None:
 
     @property
     def title(self):
-        quantity_title = f"Cylindrical flux surface {self.surface}: {self.field}"
+        if self.field == "T":
+            quantity_title = f"Heat flux surface {self.surface}"
+        else:
+            quantity_title = f"{self.field} flux surface {self.surface}"
+
         if self.show_units:
             if self.field == "T":
                 return quantity_title + " (W)"
@@ -187,7 +194,11 @@ def __init__(
 
     @property
     def title(self):
-        quantity_title = f"Spherical flux surface {self.surface}: {self.field}"
+        if self.field == "T":
+            quantity_title = f"Heat flux surface {self.surface}"
+        else:
+            quantity_title = f"{self.field} flux surface {self.surface}"
+
         if self.show_units:
             if self.field == "T":
                 return quantity_title + " (W)"
diff --git a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
index 652c96f5a..b6b198df4 100644
--- a/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
+++ b/test/unit/test_exports/test_derived_quantities/test_derived_quantities.py
@@ -137,10 +137,10 @@ def test_with_units_simple(self):
             "Average T surface 6 (K)",
             "retention value at [2] (H m-3)",
             "T value at [9] (K)",
-            "Cylindrical flux surface 2: solute (H s-1)",
-            "Cylindrical flux surface 3: T (W)",
-            "Spherical flux surface 5: solute (H s-1)",
-            "Spherical flux surface 6: T (W)",
+            "solute flux surface 2 (H s-1)",
+            "Heat flux surface 3 (W)",
+            "solute flux surface 5 (H s-1)",
+            "Heat flux surface 6 (W)",
         ]
         assert header == expected_header
 
diff --git a/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py b/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py
index bfc9e1b34..96aa175e4 100644
--- a/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_hydrogen_flux.py
@@ -16,9 +16,9 @@ def test_field_is_solute():
 @pytest.mark.parametrize(
     "function, expected_title",
     [
-        (c_1D, "Flux surface 3: solute (H m-2 s-1)"),
-        (c_2D, "Flux surface 3: solute (H m-1 s-1)"),
-        (c_3D, "Flux surface 3: solute (H s-1)"),
+        (c_1D, "solute flux surface 3 (H m-2 s-1)"),
+        (c_2D, "solute flux surface 3 (H m-1 s-1)"),
+        (c_3D, "solute flux surface 3 (H s-1)"),
     ],
 )
 def test_title_with_units(function, expected_title):
diff --git a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
index 16b142e55..8b7df3908 100644
--- a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
@@ -271,12 +271,12 @@ def test_soret_raises_error_spherical():
 @pytest.mark.parametrize(
     "function, field, expected_title",
     [
-        (c_1D, "solute", "Flux surface 3: solute (H m-2 s-1)"),
-        (c_1D, "T", "Flux surface 3: T (W m-2)"),
-        (c_2D, "solute", "Flux surface 3: solute (H m-1 s-1)"),
-        (c_2D, "T", "Flux surface 3: T (W m-1)"),
-        (c_3D, "solute", "Flux surface 3: solute (H s-1)"),
-        (c_3D, "T", "Flux surface 3: T (W)"),
+        (c_1D, "solute", "solute flux surface 3 (H m-2 s-1)"),
+        (c_1D, "T", "Heat flux surface 3 (W m-2)"),
+        (c_2D, "solute", "solute flux surface 3 (H m-1 s-1)"),
+        (c_2D, "T", "Heat flux surface 3 (W m-1)"),
+        (c_3D, "solute", "solute flux surface 3 (H s-1)"),
+        (c_3D, "T", "Heat flux surface 3 (W)"),
     ],
 )
 def test_title_with_units(function, field, expected_title):
@@ -285,3 +285,19 @@ def test_title_with_units(function, field, expected_title):
     my_flux.show_units = True
 
     assert my_flux.title == expected_title
+
+
+def test_cyldrical_flux_title_no_units_solute():
+    """A simple test to check that the title is set correctly in
+    festim.CylindricalSurfaceFlux with a solute field without units"""
+
+    my_h_flux = SurfaceFluxCylindrical("solute", 2)
+    assert my_h_flux.title == "solute flux surface 2"
+
+
+def test_cyldrical_flux_title_no_units_temperature():
+    """A simple test to check that the title is set correctly in
+    festim.CylindricalSurfaceFlux with a solute field without units"""
+
+    my_heat_flux = SurfaceFluxCylindrical("T", 4)
+    assert my_heat_flux.title == "Heat flux surface 4"
diff --git a/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py b/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py
index 4c78881bc..92776a1b9 100644
--- a/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_thermal_flux.py
@@ -15,9 +15,9 @@ def test_field_is_T():
 @pytest.mark.parametrize(
     "function, expected_title",
     [
-        (c_1D, "Flux surface 5: T (W m-2)"),
-        (c_2D, "Flux surface 5: T (W m-1)"),
-        (c_3D, "Flux surface 5: T (W)"),
+        (c_1D, "Heat flux surface 5 (W m-2)"),
+        (c_2D, "Heat flux surface 5 (W m-1)"),
+        (c_3D, "Heat flux surface 5 (W)"),
     ],
 )
 def test_title_with_units(function, expected_title):

From 05d7a2078e0fdbe60cf9296492c536545e7fd33a Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 18:07:41 +0200
Subject: [PATCH 10/20] typo and better coverage

---
 .../test_surface_flux.py                      | 22 ++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
index 8b7df3908..47dff6a72 100644
--- a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
@@ -287,7 +287,7 @@ def test_title_with_units(function, field, expected_title):
     assert my_flux.title == expected_title
 
 
-def test_cyldrical_flux_title_no_units_solute():
+def test_cylindrical_flux_title_no_units_solute():
     """A simple test to check that the title is set correctly in
     festim.CylindricalSurfaceFlux with a solute field without units"""
 
@@ -295,9 +295,25 @@ def test_cyldrical_flux_title_no_units_solute():
     assert my_h_flux.title == "solute flux surface 2"
 
 
-def test_cyldrical_flux_title_no_units_temperature():
+def test_cylindrical_flux_title_no_units_temperature():
     """A simple test to check that the title is set correctly in
-    festim.CylindricalSurfaceFlux with a solute field without units"""
+    festim.CylindricalSurfaceFlux with a T field without units"""
 
     my_heat_flux = SurfaceFluxCylindrical("T", 4)
     assert my_heat_flux.title == "Heat flux surface 4"
+
+
+def test_spherical_flux_title_no_units_solute():
+    """A simple test to check that the title is set correctly in
+    festim.SphericalSurfaceFlux with a solute field without units"""
+
+    my_h_flux = SurfaceFluxCylindrical("solute", 3)
+    assert my_h_flux.title == "solute flux surface 3"
+
+
+def test_spherical_flux_title_no_units_temperature():
+    """A simple test to check that the title is set correctly in
+    festim.CSphericalSurfaceFlux with a T field without units"""
+
+    my_heat_flux = SurfaceFluxCylindrical("T", 5)
+    assert my_heat_flux.title == "Heat flux surface 5"

From 1f728b142a946eddca473e0b7cf17c38acff9ff3 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 18:18:35 +0200
Subject: [PATCH 11/20] typo

---
 .../test_exports/test_derived_quantities/test_surface_flux.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
index 47dff6a72..b6d3323be 100644
--- a/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
+++ b/test/unit/test_exports/test_derived_quantities/test_surface_flux.py
@@ -307,7 +307,7 @@ def test_spherical_flux_title_no_units_solute():
     """A simple test to check that the title is set correctly in
     festim.SphericalSurfaceFlux with a solute field without units"""
 
-    my_h_flux = SurfaceFluxCylindrical("solute", 3)
+    my_h_flux = SurfaceFluxSpherical("solute", 3)
     assert my_h_flux.title == "solute flux surface 3"
 
 
@@ -315,5 +315,5 @@ def test_spherical_flux_title_no_units_temperature():
     """A simple test to check that the title is set correctly in
     festim.CSphericalSurfaceFlux with a T field without units"""
 
-    my_heat_flux = SurfaceFluxCylindrical("T", 5)
+    my_heat_flux = SurfaceFluxSpherical("T", 5)
     assert my_heat_flux.title == "Heat flux surface 5"

From 8f5e09b7d88f944c1f7425f10fa687f82695dcdd Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 20:15:44 +0200
Subject: [PATCH 12/20] fixed doc string, unit property

---
 .../derived_quantities/surface_flux.py        | 42 +++++++++++--------
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index 81b82cfc3..33a6517d4 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -14,6 +14,7 @@ class SurfaceFlux(SurfaceQuantity):
     Attribtutes
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
         surface (int): the surface id
+        export_unit (str): the unit of the derived quantity in the export file
         title (str): the title of the derived quantity
         show_units (bool): show the units in the title in the derived quantities
             file
@@ -22,7 +23,7 @@ class SurfaceFlux(SurfaceQuantity):
 
     Notes:
         Object to compute the flux J of a field u through a surface
-        J = integral(-prop * grad(u) . n ds)
+        J = integral(+prop * grad(u) . n ds)
         where prop is the property of the field (D, thermal conductivity, etc)
         u is the field
         n is the normal vector of the surface
@@ -35,29 +36,36 @@ class SurfaceFlux(SurfaceQuantity):
     def __init__(self, field, surface) -> None:
         super().__init__(field=field, surface=surface)
 
+    @property
+    def export_unit(self):
+        # obtain domain dimension
+        dim = self.function.function_space().mesh().topology().dim()
+        if self.field == "T":
+            if dim == 1:
+                return "W m-2"
+            if dim == 2:
+                return "W m-1"
+            if dim == 3:
+                return "W"
+        else:
+            if dim == 1:
+                return "H m-2 s-1"
+            if dim == 2:
+                return "H m-1 s-1"
+            if dim == 3:
+                return "H s-1"
+
     @property
     def title(self):
         quantity_title = f"Flux surface {self.surface}: {self.field}"
         if self.show_units:
-            # obtain domain dimension
-            dim = self.function.function_space().mesh().topology().dim()
-            # new title but only with show_units to not introduce breaking change
-            quantity_title = f"{self.field} flux surface {self.surface}"
             if self.field == "T":
                 quantity_title = f"Heat flux surface {self.surface}"
-                if dim == 1:
-                    return quantity_title + " (W m-2)"
-                if dim == 2:
-                    return quantity_title + " (W m-1)"
-                if dim == 3:
-                    return quantity_title + " (W)"
             else:
-                if dim == 1:
-                    return quantity_title + " (H m-2 s-1)"
-                if dim == 2:
-                    return quantity_title + " (H m-1 s-1)"
-                if dim == 3:
-                    return quantity_title + " (H s-1)"
+                quantity_title = f"{self.field} flux surface {self.surface}"
+
+            return quantity_title + f" ({self.export_unit})"
+
         else:
             return quantity_title
 

From 73a963b1856fb0ceb3dfc6b7bea05b7c9118ed66 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 20:16:27 +0200
Subject: [PATCH 13/20] warning if show_units False

---
 festim/exports/derived_quantities/derived_quantities.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/festim/exports/derived_quantities/derived_quantities.py b/festim/exports/derived_quantities/derived_quantities.py
index 3cef88ad9..2d5defe70 100644
--- a/festim/exports/derived_quantities/derived_quantities.py
+++ b/festim/exports/derived_quantities/derived_quantities.py
@@ -113,6 +113,11 @@ def make_header(self):
         header = ["t(s)"]
         for quantity in self:
             quantity.show_units = self.show_units
+            if self.show_units is False:
+                warnings.warn(
+                    "The derived_quantities ti will be deprecated in a future release, please use festim.DerivedQuantities as a list instead",
+                    DeprecationWarning,
+                )
             header.append(quantity.title)
         return header
 

From f930d5dd2ead273ffe71d21fc4640139ab5d83c9 Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 21:32:42 +0200
Subject: [PATCH 14/20] different warning

---
 festim/exports/derived_quantities/derived_quantities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/festim/exports/derived_quantities/derived_quantities.py b/festim/exports/derived_quantities/derived_quantities.py
index 2d5defe70..4664f0ad5 100644
--- a/festim/exports/derived_quantities/derived_quantities.py
+++ b/festim/exports/derived_quantities/derived_quantities.py
@@ -115,7 +115,7 @@ def make_header(self):
             quantity.show_units = self.show_units
             if self.show_units is False:
                 warnings.warn(
-                    "The derived_quantities ti will be deprecated in a future release, please use festim.DerivedQuantities as a list instead",
+                    "The current derived_quantities title style will be deprecated in a future release, please use show_units=True instead",
                     DeprecationWarning,
                 )
             header.append(quantity.title)

From 7eb4e31c9e41b301fbda8859da304fd4903e918f Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Thu, 4 Apr 2024 21:33:34 +0200
Subject: [PATCH 15/20] total values with export unit property

---
 .../derived_quantities/total_surface.py       | 37 +++++++++++--------
 .../derived_quantities/total_volume.py        | 37 +++++++++++--------
 2 files changed, 42 insertions(+), 32 deletions(-)

diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 2fe7d8c0e..04a3a6a25 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -14,6 +14,7 @@ class TotalSurface(SurfaceQuantity):
     Attribtutes
         field (str, int): the field ("solute", 0, 1, "T", "retention")
         surface (int): the surface id
+        export_unit (str): the unit of the derived quantity for exporting
         title (str): the title of the derived quantity
         show_units (bool): show the units in the title in the derived quantities
             file
@@ -29,26 +30,30 @@ class TotalSurface(SurfaceQuantity):
     def __init__(self, field, surface) -> None:
         super().__init__(field=field, surface=surface)
 
+    @property
+    def export_unit(self):
+        # obtain domain dimension
+        dim = self.function.function_space().mesh().topology().dim()
+        if self.field == "T":
+            if dim == 1:
+                return "K"
+            if dim == 2:
+                return "K m"
+            if dim == 3:
+                return "K m2"
+        else:
+            if dim == 1:
+                return "H m-2"
+            if dim == 2:
+                return "H m-1"
+            if dim == 3:
+                return "H"
+
     @property
     def title(self):
         quantity_title = f"Total {self.field} surface {self.surface}"
         if self.show_units:
-            # obtain domain dimension
-            dim = self.function.function_space().mesh().topology().dim()
-            if self.field == "T":
-                if dim == 1:
-                    return quantity_title + " (K)"
-                elif dim == 2:
-                    return quantity_title + " (K m)"
-                elif dim == 3:
-                    return quantity_title + " (K m2)"
-            else:
-                if dim == 1:
-                    return quantity_title + " (H m-2)"
-                elif dim == 2:
-                    return quantity_title + " (H m-1)"
-                elif dim == 3:
-                    return quantity_title + " (H)"
+            return quantity_title + f" ({self.export_unit})"
         else:
             return quantity_title
 
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index f61675cec..141e8cada 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -14,6 +14,7 @@ class TotalVolume(VolumeQuantity):
     Attribtutes
         field (str, int): the field ("solute", 0, 1, "T", "retention")
         volume (int): the volume id
+        export_unit (str): the unit of the derived quantity for exporting
         title (str): the title of the derived quantity
         show_units (bool): show the units in the title in the derived quantities
             file
@@ -29,26 +30,30 @@ class TotalVolume(VolumeQuantity):
     def __init__(self, field, volume) -> None:
         super().__init__(field=field, volume=volume)
 
+    @property
+    def export_unit(self):
+        # obtain domain dimension
+        dim = self.function.function_space().mesh().topology().dim()
+        if self.field == "T":
+            if dim == 1:
+                return "K m"
+            if dim == 2:
+                return "K m2"
+            if dim == 3:
+                return "K m3"
+        else:
+            if dim == 1:
+                return "H m-2"
+            if dim == 2:
+                return "H m-1"
+            if dim == 3:
+                return "H"
+
     @property
     def title(self):
         quantity_title = f"Total {self.field} volume {self.volume}"
         if self.show_units:
-            # obtain domain dimension
-            dim = self.function.function_space().mesh().topology().dim()
-            if self.field == "T":
-                if dim == 1:
-                    return quantity_title + " (K m)"
-                elif dim == 2:
-                    return quantity_title + " (K m2)"
-                elif dim == 3:
-                    return quantity_title + " (K m3)"
-            else:
-                if dim == 1:
-                    return quantity_title + " (H m-2)"
-                elif dim == 2:
-                    return quantity_title + " (H m-1)"
-                elif dim == 3:
-                    return quantity_title + " (H)"
+            return quantity_title + f" ({self.export_unit})"
         else:
             return quantity_title
 

From 29e06c897dde6e2b344242191d785d43a7176a62 Mon Sep 17 00:00:00 2001
From: James Dark <65899899+jhdark@users.noreply.github.com>
Date: Fri, 5 Apr 2024 06:14:56 +0000
Subject: [PATCH 16/20] changes from reveiw comments

---
 festim/exports/derived_quantities/average_volume.py | 2 +-
 festim/exports/derived_quantities/maximum_volume.py | 2 +-
 festim/exports/derived_quantities/minimum_volume.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/festim/exports/derived_quantities/average_volume.py b/festim/exports/derived_quantities/average_volume.py
index 651751f70..9c4140161 100644
--- a/festim/exports/derived_quantities/average_volume.py
+++ b/festim/exports/derived_quantities/average_volume.py
@@ -5,7 +5,7 @@
 class AverageVolume(VolumeQuantity):
     """
     Computes the average value of a field in a given volume
-    int(f ds) / int (1 * ds)
+    int(f dx) / int (1 * dx)
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
diff --git a/festim/exports/derived_quantities/maximum_volume.py b/festim/exports/derived_quantities/maximum_volume.py
index 62eee2100..7dc7f0b18 100644
--- a/festim/exports/derived_quantities/maximum_volume.py
+++ b/festim/exports/derived_quantities/maximum_volume.py
@@ -5,7 +5,7 @@
 
 class MaximumVolume(VolumeQuantity):
     """
-    Computes the maximum value in a field in a given volume
+    Computes the maximum value of a field in a given volume
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")
diff --git a/festim/exports/derived_quantities/minimum_volume.py b/festim/exports/derived_quantities/minimum_volume.py
index e3277c522..b11e6bb21 100644
--- a/festim/exports/derived_quantities/minimum_volume.py
+++ b/festim/exports/derived_quantities/minimum_volume.py
@@ -5,7 +5,7 @@
 
 class MinimumVolume(VolumeQuantity):
     """
-    Computes the minimum value in a field in a given volume
+    Computes the minimum value of a field in a given volume
 
     Args:
         field (str, int):  the field ("solute", 0, 1, "T", "retention")

From 1aac50327b33925bda38cd18bf9c73cc665cf028 Mon Sep 17 00:00:00 2001
From: James Dark <65899899+jhdark@users.noreply.github.com>
Date: Sat, 6 Apr 2024 18:39:42 +0200
Subject: [PATCH 17/20] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Rémi Delaporte-Mathurin <40028739+RemDelaporteMathurin@users.noreply.github.com>
---
 festim/exports/derived_quantities/surface_flux.py  | 14 ++------------
 festim/exports/derived_quantities/total_surface.py | 14 ++------------
 festim/exports/derived_quantities/total_volume.py  | 14 ++------------
 3 files changed, 6 insertions(+), 36 deletions(-)

diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index 33a6517d4..3c27d2a3e 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -41,19 +41,9 @@ def export_unit(self):
         # obtain domain dimension
         dim = self.function.function_space().mesh().topology().dim()
         if self.field == "T":
-            if dim == 1:
-                return "W m-2"
-            if dim == 2:
-                return "W m-1"
-            if dim == 3:
-                return "W"
+            return f"W m{dim-3}".replace(" m0", "")
         else:
-            if dim == 1:
-                return "H m-2 s-1"
-            if dim == 2:
-                return "H m-1 s-1"
-            if dim == 3:
-                return "H s-1"
+            return f"H m{dim-3} s-1".replace(" m0", "")
 
     @property
     def title(self):
diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 04a3a6a25..5eb9b8e25 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -35,19 +35,9 @@ def export_unit(self):
         # obtain domain dimension
         dim = self.function.function_space().mesh().topology().dim()
         if self.field == "T":
-            if dim == 1:
-                return "K"
-            if dim == 2:
-                return "K m"
-            if dim == 3:
-                return "K m2"
+            return f"K m{dim-1}".replace(" m0", "")
         else:
-            if dim == 1:
-                return "H m-2"
-            if dim == 2:
-                return "H m-1"
-            if dim == 3:
-                return "H"
+            return f"H m{dim-3}".replace(" m0", "")
 
     @property
     def title(self):
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index 141e8cada..56117c76e 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -35,19 +35,9 @@ def export_unit(self):
         # obtain domain dimension
         dim = self.function.function_space().mesh().topology().dim()
         if self.field == "T":
-            if dim == 1:
-                return "K m"
-            if dim == 2:
-                return "K m2"
-            if dim == 3:
-                return "K m3"
+            return f"K m{dim}".replace("1", "")
         else:
-            if dim == 1:
-                return "H m-2"
-            if dim == 2:
-                return "H m-1"
-            if dim == 3:
-                return "H"
+            return f"H m{dim-3}".replace(" m0", "")
 
     @property
     def title(self):

From 62cf7193ee2ddf734c535a69830689bf87555e1f Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Sat, 6 Apr 2024 18:47:38 +0200
Subject: [PATCH 18/20] added inline comment

---
 festim/exports/derived_quantities/surface_flux.py | 1 +
 festim/exports/derived_quantities/total_volume.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/festim/exports/derived_quantities/surface_flux.py b/festim/exports/derived_quantities/surface_flux.py
index 3c27d2a3e..7c1d73c21 100644
--- a/festim/exports/derived_quantities/surface_flux.py
+++ b/festim/exports/derived_quantities/surface_flux.py
@@ -40,6 +40,7 @@ def __init__(self, field, surface) -> None:
     def export_unit(self):
         # obtain domain dimension
         dim = self.function.function_space().mesh().topology().dim()
+        # return unit depending on field and dimension of domain
         if self.field == "T":
             return f"W m{dim-3}".replace(" m0", "")
         else:
diff --git a/festim/exports/derived_quantities/total_volume.py b/festim/exports/derived_quantities/total_volume.py
index 56117c76e..164c55f54 100644
--- a/festim/exports/derived_quantities/total_volume.py
+++ b/festim/exports/derived_quantities/total_volume.py
@@ -34,6 +34,7 @@ def __init__(self, field, volume) -> None:
     def export_unit(self):
         # obtain domain dimension
         dim = self.function.function_space().mesh().topology().dim()
+        # return unit depending on field and dimension of domain
         if self.field == "T":
             return f"K m{dim}".replace("1", "")
         else:

From 4f1e2c60bc8a7f9cb3a13f65e54bdfa879a925fd Mon Sep 17 00:00:00 2001
From: J Dark <james.dark.95@gmail.com>
Date: Sat, 6 Apr 2024 18:47:57 +0200
Subject: [PATCH 19/20] comment and fix for m1 case

---
 festim/exports/derived_quantities/total_surface.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/festim/exports/derived_quantities/total_surface.py b/festim/exports/derived_quantities/total_surface.py
index 5eb9b8e25..649c1308b 100644
--- a/festim/exports/derived_quantities/total_surface.py
+++ b/festim/exports/derived_quantities/total_surface.py
@@ -34,8 +34,9 @@ def __init__(self, field, surface) -> None:
     def export_unit(self):
         # obtain domain dimension
         dim = self.function.function_space().mesh().topology().dim()
+        # return unit depending on field and dimension of domain
         if self.field == "T":
-            return f"K m{dim-1}".replace(" m0", "")
+            return f"K m{dim-1}".replace(" m0", "").replace(" m1", " m")
         else:
             return f"H m{dim-3}".replace(" m0", "")
 

From 04adb23b31f1c550d3125f9fd337093c67724b46 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Thu, 18 Apr 2024 08:24:53 -0400
Subject: [PATCH 20/20] update to v4 on main

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9a6da3054..d5bce7d4c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,6 +34,6 @@ jobs:
         pytest test/ --cov festim --cov-report xml --cov-report term
     
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}