added filter flag

festim/exports/txt_export.py

@@ -13,12 +13,15 @@ class TXTExport(festim.Export):
         field (str): the exported field ("solute", "1", "retention",
             "T"...)
         filename (str): the filename (must end with .txt).
-        write_at_last (bool): if True, the data will be exported at
-            the last export time. Otherwise, the data will be exported
-            at each export time. Defaults to False.
         times (list, optional): if provided, the field will be
             exported at these timesteps. Otherwise exports at all
             timesteps. Defaults to None.
+        filter (bool): if True and the field is projected to a DG function space,
+            the duplicated vertices in the output file array are filtered except those near interfaces.
+            Defaults to True.
+        write_at_last (bool): if True, the data will be exported at
+            the last export time. Otherwise, the data will be exported
+            at each export time. Defaults to False.
         header_format (str, optional): the format of column headers.
             Defautls to ".2e".
 
@@ -29,17 +32,28 @@ class TXTExport(festim.Export):
         header (str): the header of the exported file.
         V (fenics.FunctionSpace): the vector-function space for the exported field.
 
+    .. note::
+        The exported field is projected to DG if conservation of chemical potential is considered or
+        ``traps_element_type`` is "DG".
+
     """
 
     def __init__(
-        self, field, filename, times=None, write_at_last=False, header_format=".2e"
+        self,
+        field,
+        filename,
+        times=None,
+        filter=True,
+        write_at_last=False,
+        header_format=".2e",
     ) -> None:
         super().__init__(field=field)
         if times:
             self.times = sorted(times)
         else:
             self.times = times
         self.filename = filename
+        self.filter = filter
         self.write_at_last = write_at_last
         self.header_format = header_format
 
@@ -116,7 +130,7 @@ def initialise(self, mesh, project_to_DG=False, materials=None):
         The array is then used to obtain indices of sorted elements for the data export.
 
         .. note::
-            If DG1 is used, the duplicated vertices in the array are filtered except those near interfaces,
+            If DG1 is used and filter flag is True, the duplicated vertices in the array are filtered except those near interfaces,
             The interfaces are defined by ``material.borders`` in the ``Materials`` list.
 
         Args:
@@ -134,9 +148,9 @@ def initialise(self, mesh, project_to_DG=False, materials=None):
         x = f.interpolate(f.Expression("x[0]", degree=1), self.V)
         x_column = np.transpose([x.vector()[:]])
 
-        # if project_to_DG is True, get indices of duplicates near interfaces
+        # if filter is True, get indices of duplicates near interfaces
         # and indices of the first elements from a pair of duplicates otherwise
-        if project_to_DG:
+        if project_to_DG and self.filter:
             # Collect all borders
             borders = []
             for material in materials:
@@ -165,7 +179,7 @@ def initialise(self, mesh, project_to_DG=False, materials=None):
             self._unique_indices = np.array(unique_indices)
 
         else:
-            # Get list of unique indices
+            # Get list of sorted indices
             self._unique_indices = np.argsort(x_column, axis=0)[:, 0]
 
         self.data = x_column[self._unique_indices]

test/unit/test_exports/test_txt_export.py

@@ -111,33 +111,45 @@ def test_sorted_by_x(self, my_export, function, mesh):
         assert (np.diff(my_export.data[:, 0]) >= 0).all()
 
     @pytest.mark.parametrize(
-        "materials,project_to_DG,export_len",
+        "materials,project_to_DG,filter,export_len",
         [
-            (None, False, 11),
+            (None, False, False, 11),
             (
                 [
                     Material(id=1, D_0=1, E_D=0, S_0=1, E_S=0, borders=[0, 0.5]),
                     Material(id=2, D_0=2, E_D=0, S_0=2, E_S=0, borders=[0.5, 1]),
                 ],
                 True,
+                True,
                 12,  # + 1 duplicate near the interface
             ),
+            (
+                [
+                    Material(id=1, D_0=1, E_D=0, S_0=1, E_S=0, borders=[0, 0.5]),
+                    Material(id=2, D_0=2, E_D=0, S_0=2, E_S=0, borders=[0.5, 1]),
+                ],
+                True,
+                False,
+                20,  # 2 * (len_vertices - 1)
+            ),
         ],
     )
     def test_duplicates(
-        self, materials, project_to_DG, export_len, my_export, function, mesh
+        self, materials, project_to_DG, filter, export_len, my_export, function, mesh
     ):
         """
         Checks that the exported data does not contain duplicates
         except those near interfaces
         """
         current_time = 1
         my_export.function = function
+        my_export.filter = filter
         my_export.initialise(mesh, project_to_DG, materials)
         my_export.write(
             current_time=current_time,
             final_time=None,
         )
+        print(my_export._unique_indices)
         assert len(my_export.data) == export_len