From 0e3004d0511aec56faa6356ba57e8b2598a6a2c9 Mon Sep 17 00:00:00 2001
From: KulaginVladimir <kulagin.vladimir.l@yandex.ru>
Date: Mon, 9 Sep 2024 21:26:52 +0300
Subject: [PATCH 1/7] added a write_at_last parameter

---
 festim/__init__.py                         |   2 +-
 festim/exports/exports.py                  |   3 +-
 festim/exports/txt_export.py               | 107 +++++++++------------
 test/unit/test_exports/test_txt_export.py  |  31 +-----
 test/unit/test_exports/test_txt_exports.py |  28 ------
 5 files changed, 52 insertions(+), 119 deletions(-)
 delete mode 100644 test/unit/test_exports/test_txt_exports.py

diff --git a/festim/__init__.py b/festim/__init__.py
index 10ce0105c..1609104cb 100644
--- a/festim/__init__.py
+++ b/festim/__init__.py
@@ -88,7 +88,7 @@
 
 from .exports.derived_quantities.derived_quantities import DerivedQuantities
 
-from .exports.txt_export import TXTExport, TXTExports
+from .exports.txt_export import TXTExport
 
 
 from .settings import Settings
diff --git a/festim/exports/exports.py b/festim/exports/exports.py
index 45e769a62..c3d61480a 100644
--- a/festim/exports/exports.py
+++ b/festim/exports/exports.py
@@ -129,8 +129,7 @@ def write(self, label_to_function, dx):
                         label_to_function[export.field], self.V_DG1
                     )
                 export.function = label_to_function[export.field]
-                steady = self.final_time == None
-                export.write(self.t, steady)
+                export.write(self.t, self.final_time)
         self.nb_iterations += 1
 
     def initialise_derived_quantities(self, dx, ds, materials):
diff --git a/festim/exports/txt_export.py b/festim/exports/txt_export.py
index 3c7688a99..b306b31e3 100644
--- a/festim/exports/txt_export.py
+++ b/festim/exports/txt_export.py
@@ -20,16 +20,22 @@ class TXTExport(festim.Export):
             Defautls to ".2e".
     """
 
-    def __init__(self, field, filename, times=None, header_format=".2e") -> None:
+    def __init__(
+        self, field, filename, times=None, 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.write_at_last = write_at_last
         self.header_format = header_format
         self._first_time = True
 
+        self.data = None
+        self.header = None
+
     @property
     def filename(self):
         return self._filename
@@ -51,15 +57,21 @@ def is_it_time_to_export(self, current_time):
                 return True
         return False
 
-    def when_is_next_time(self, current_time):
-        if self.times is None:
-            return None
-        for time in self.times:
-            if current_time < time:
-                return time
-        return None
+    def is_last(self, current_time, final_time):
+        if final_time is None:
+            # write if steady
+            return True
+        elif self.times is None:
+            if np.isclose(current_time, final_time, atol=0):
+                # write at final time if exports at each timestep
+                return True
+        else:
+            if np.isclose(current_time, self.times[-1], atol=0):
+                # write at final time if exports at specific times
+                return True
+        return False
 
-    def write(self, current_time, steady):
+    def write(self, current_time, final_time):
         # create a DG1 functionspace
         V_DG1 = f.FunctionSpace(self.function.function_space().mesh(), "DG", 1)
 
@@ -72,62 +84,35 @@ def write(self, current_time, steady):
             if not os.path.exists(dirname):
                 os.makedirs(dirname, exist_ok=True)
 
-            # if steady or it is the first time to export
-            # write data
+            # write data if steady or it is the first time to export
             # else append new column to the existing file
-            if steady or self._first_time:
-                if steady:
-                    header = "x,t=steady"
+            if final_time is None or self._first_time:
+                if final_time is None:
+                    self.header = "x,t=steady"
                 else:
-                    header = f"x,t={format(current_time, self.header_format)}s"
+                    self.header = f"x,t={format(current_time, self.header_format)}s"
+
                 x = f.interpolate(f.Expression("x[0]", degree=1), V_DG1)
                 x_column = np.transpose([x.vector()[:]])
-                data = np.column_stack([x_column, solution_column])
+                self.data = np.column_stack([x_column, solution_column])
                 self._first_time = False
             else:
                 # Update the header
-                old_file = open(self.filename)
-                old_header = old_file.readline().split("\n")[0]
-                old_file.close()
-                header = old_header + f",t={format(current_time, self.header_format)}s"
-                # Append new column
-                old_columns = np.loadtxt(self.filename, delimiter=",", skiprows=1)
-                data = np.column_stack([old_columns, solution_column])
-
-            np.savetxt(self.filename, data, header=header, delimiter=",", comments="")
-
-
-class TXTExports:
-    """
-    Args:
-        fields (list): list of exported fields ("solute", "1", "retention",
-            "T"...)
-        filenames (list): list of the filenames for each field (must end with .txt).
-        times (list, optional): if provided, fields will be
-            exported at these timesteps. Otherwise exports at all
-            timesteps. Defaults to None.
-        header_format (str, optional): the format of column headers.
-            Defautls to ".2e".
-    """
-
-    def __init__(
-        self, fields=[], filenames=[], times=None, header_format=".2e"
-    ) -> None:
-        msg = "TXTExports class will be deprecated in future versions of FESTIM"
-        warnings.warn(msg, DeprecationWarning)
-
-        self.fields = fields
-        if len(self.fields) != len(filenames):
-            raise ValueError(
-                "Number of fields to be exported "
-                "doesn't match number of filenames in txt exports"
-            )
-        if times:
-            self.times = sorted(times)
-        else:
-            self.times = times
-        self.filenames = filenames
-        self.header_format = header_format
-        self.exports = []
-        for function, filename in zip(self.fields, self.filenames):
-            self.exports.append(TXTExport(function, filename, times, header_format))
+                self.header += f",t={format(current_time, self.header_format)}s"
+                # Add new column
+                self.data = np.column_stack([self.data, solution_column])
+
+            if (
+                self.write_at_last and self.is_last(current_time, final_time)
+            ) or not self.write_at_last:
+                if self.is_last(current_time, final_time):
+                    # Sort data by the x-column before at last export time
+                    self.data = self.data[self.data[:, 0].argsort()]
+                # Write data
+                np.savetxt(
+                    self.filename,
+                    self.data,
+                    header=self.header,
+                    delimiter=",",
+                    comments="",
+                )
diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index 58f471081..41417cf76 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -36,14 +36,14 @@ def my_export(self, tmpdir):
     def test_file_exists(self, my_export, function):
         current_time = 1
         my_export.function = function
-        my_export.write(current_time=current_time, steady=False)
+        my_export.write(current_time=current_time, final_time=None)
 
         assert os.path.exists(my_export.filename)
 
     def test_file_doesnt_exist(self, my_export, function):
         current_time = 10
         my_export.function = function
-        my_export.write(current_time=current_time, steady=False)
+        my_export.write(current_time=current_time, final_time=None)
 
         assert not os.path.exists(my_export.filename)
 
@@ -57,14 +57,14 @@ def test_create_folder(self, my_export, function):
             + "/folder2"
             + my_export.filename[slash_indx:]
         )
-        my_export.write(current_time=current_time, steady=False)
+        my_export.write(current_time=current_time, final_time=None)
 
         assert os.path.exists(my_export.filename)
 
     def test_subspace(self, my_export, function_subspace):
         current_time = 1
         my_export.function = function_subspace
-        my_export.write(current_time=current_time, steady=False)
+        my_export.write(current_time=current_time, final_time=None)
 
         assert os.path.exists(my_export.filename)
 
@@ -99,26 +99,3 @@ def test_false(self, my_export):
         assert not my_export.is_it_time_to_export(0)
         assert not my_export.is_it_time_to_export(5)
         assert not my_export.is_it_time_to_export(1.5)
-
-
-class TestWhenIsNextTime:
-    @pytest.fixture
-    def my_export(self, tmpdir):
-        d = tmpdir.mkdir("test_folder")
-        my_export = TXTExport(
-            "solute",
-            times=[1, 2, 3],
-            filename="{}/solute_label.txt".format(str(Path(d))),
-        )
-
-        return my_export
-
-    def test_there_is_a_next_time(self, my_export):
-        assert my_export.when_is_next_time(2) == 3
-        assert my_export.when_is_next_time(1) == 2
-        assert my_export.when_is_next_time(0) == 1
-        assert my_export.when_is_next_time(0.5) == 1
-
-    def test_last(self, my_export):
-        assert my_export.when_is_next_time(3) is None
-        assert my_export.when_is_next_time(4) is None
diff --git a/test/unit/test_exports/test_txt_exports.py b/test/unit/test_exports/test_txt_exports.py
deleted file mode 100644
index 9d0317f50..000000000
--- a/test/unit/test_exports/test_txt_exports.py
+++ /dev/null
@@ -1,28 +0,0 @@
-from festim import TXTExports
-import pytest
-from pathlib import Path
-
-
-class TestWrite:
-    @pytest.fixture(params=[[1, 2, 3], None])
-    def my_export(self, tmpdir, request):
-        d = tmpdir.mkdir("test_folder")
-        my_export = TXTExports(
-            fields=["solute", "T"],
-            filenames=[
-                "{}/solute_label.txt".format(str(Path(d))),
-                "{}/T_label.txt".format(str(Path(d))),
-            ],
-            times=request.param,
-        )
-
-        return my_export
-
-    def test_txt_exports_times(self, my_export):
-        for export in my_export.exports:
-            assert export.times == my_export.times
-
-
-def test_error_when_fields_and_labels_have_different_lengths():
-    with pytest.raises(ValueError, match="Number of fields to be exported"):
-        TXTExports(["solute", "T"], ["solute_label.txt"], [1])

From 35dc3a7a140cb56c88cf63dab258f4b3e8c7bb4a Mon Sep 17 00:00:00 2001
From: Vladimir Kulagin <kulagin.vladimir.l@yandex.ru>
Date: Fri, 20 Sep 2024 00:23:51 +0300
Subject: [PATCH 2/7] filter duplicates depending on chemical_pot flag

---
 festim/exports/exports.py                 |  4 +-
 festim/exports/txt_export.py              | 52 +++++++++++++---
 festim/generic_simulation.py              |  7 ++-
 test/unit/test_exports/test_txt_export.py | 72 +++++++++++++++++++++--
 4 files changed, 120 insertions(+), 15 deletions(-)

diff --git a/festim/exports/exports.py b/festim/exports/exports.py
index c3d61480a..915f44199 100644
--- a/festim/exports/exports.py
+++ b/festim/exports/exports.py
@@ -71,7 +71,7 @@ def _validate_export(self, value):
             return value
         raise TypeError("festim.Exports must be a list of festim.Export")
 
-    def write(self, label_to_function, dx):
+    def write(self, label_to_function, dx, materials, chemical_pot):
         """writes to file
 
         Args:
@@ -129,7 +129,7 @@ def write(self, label_to_function, dx):
                         label_to_function[export.field], self.V_DG1
                     )
                 export.function = label_to_function[export.field]
-                export.write(self.t, self.final_time)
+                export.write(self.t, self.final_time, materials, chemical_pot)
         self.nb_iterations += 1
 
     def initialise_derived_quantities(self, dx, ds, materials):
diff --git a/festim/exports/txt_export.py b/festim/exports/txt_export.py
index b306b31e3..9144c2b97 100644
--- a/festim/exports/txt_export.py
+++ b/festim/exports/txt_export.py
@@ -71,11 +71,44 @@ def is_last(self, current_time, final_time):
                 return True
         return False
 
-    def write(self, current_time, final_time):
-        # create a DG1 functionspace
-        V_DG1 = f.FunctionSpace(self.function.function_space().mesh(), "DG", 1)
+    def filter_duplicates(self, data, materials):
+        x = data[:, 0]
 
-        solution = f.project(self.function, V_DG1)
+        # Collect all borders
+        borders = []
+        for material in materials:
+            for border in material.borders:
+                borders.append(border)
+        borders = np.unique(borders)
+
+        # Find indices of the closest duplicates to interfaces
+        border_indx = []
+        for border in borders:
+            closest_indx = np.abs(x - border).argmin()
+            closest_x = x[closest_indx]
+            for ind in np.where(x == closest_x)[0]:
+                border_indx.append(ind)
+
+        # Find indices of first elements in duplicated pairs and mesh borders
+        _, unique_indx = np.unique(x, return_index=True)
+
+        # Combine both arrays of indices
+        combined_indx = np.concatenate([border_indx, unique_indx])
+
+        # Sort unique indices to return a slice
+        combined_indx = sorted(np.unique(combined_indx))
+
+        return data[combined_indx, :]
+
+    def write(self, current_time, final_time, materials, chemical_pot):
+        # create a DG1 functionspace if chemical_pot is True
+        # else create a CG1 functionspace
+        if chemical_pot:
+            V = f.FunctionSpace(self.function.function_space().mesh(), "DG", 1)
+        else:
+            V = f.FunctionSpace(self.function.function_space().mesh(), "CG", 1)
+
+        solution = f.project(self.function, V)
         solution_column = np.transpose(solution.vector()[:])
         if self.is_it_time_to_export(current_time):
             # if the directory doesn't exist
@@ -84,7 +117,7 @@ def write(self, current_time, final_time):
             if not os.path.exists(dirname):
                 os.makedirs(dirname, exist_ok=True)
 
-            # write data if steady or it is the first time to export
+            # create header if steady or it is the first time to export
             # else append new column to the existing file
             if final_time is None or self._first_time:
                 if final_time is None:
@@ -92,7 +125,7 @@ def write(self, current_time, final_time):
                 else:
                     self.header = f"x,t={format(current_time, self.header_format)}s"
 
-                x = f.interpolate(f.Expression("x[0]", degree=1), V_DG1)
+                x = f.interpolate(f.Expression("x[0]", degree=1), V)
                 x_column = np.transpose([x.vector()[:]])
                 self.data = np.column_stack([x_column, solution_column])
                 self._first_time = False
@@ -106,8 +139,13 @@ def write(self, current_time, final_time):
                 self.write_at_last and self.is_last(current_time, final_time)
             ) or not self.write_at_last:
                 if self.is_last(current_time, final_time):
-                    # Sort data by the x-column before at last export time
+                    # Sort data by the x-column before the last export time
                     self.data = self.data[self.data[:, 0].argsort()]
+
+                    # Filter duplicates if chemical_pot is True
+                    if chemical_pot:
+                        self.data = self.filter_duplicates(self.data, materials)
+
                 # Write data
                 np.savetxt(
                     self.filename,
diff --git a/festim/generic_simulation.py b/festim/generic_simulation.py
index f8766d1ee..96fa71148 100644
--- a/festim/generic_simulation.py
+++ b/festim/generic_simulation.py
@@ -503,7 +503,12 @@ def run_post_processing(self):
         self.update_post_processing_solutions()
 
         self.exports.t = self.t
-        self.exports.write(self.label_to_function, self.mesh.dx)
+        self.exports.write(
+            self.label_to_function,
+            self.mesh.dx,
+            self.materials,
+            self.settings.chemical_pot,
+        )
 
     def update_post_processing_solutions(self):
         """Creates the post-processing functions by splitting self.u. Projects
diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index 41417cf76..134d88255 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -1,7 +1,8 @@
-from festim import TXTExport, Stepsize
+from festim import TXTExport, Stepsize, Material
 import fenics as f
 import os
 import pytest
+import numpy as np
 from pathlib import Path
 
 
@@ -36,14 +37,24 @@ def my_export(self, tmpdir):
     def test_file_exists(self, my_export, function):
         current_time = 1
         my_export.function = function
-        my_export.write(current_time=current_time, final_time=None)
+        my_export.write(
+            current_time=current_time,
+            final_time=None,
+            materials=None,
+            chemical_pot=False,
+        )
 
         assert os.path.exists(my_export.filename)
 
     def test_file_doesnt_exist(self, my_export, function):
         current_time = 10
         my_export.function = function
-        my_export.write(current_time=current_time, final_time=None)
+        my_export.write(
+            current_time=current_time,
+            final_time=None,
+            materials=None,
+            chemical_pot=False,
+        )
 
         assert not os.path.exists(my_export.filename)
 
@@ -57,14 +68,24 @@ def test_create_folder(self, my_export, function):
             + "/folder2"
             + my_export.filename[slash_indx:]
         )
-        my_export.write(current_time=current_time, final_time=None)
+        my_export.write(
+            current_time=current_time,
+            final_time=None,
+            materials=None,
+            chemical_pot=False,
+        )
 
         assert os.path.exists(my_export.filename)
 
     def test_subspace(self, my_export, function_subspace):
         current_time = 1
         my_export.function = function_subspace
-        my_export.write(current_time=current_time, final_time=None)
+        my_export.write(
+            current_time=current_time,
+            final_time=None,
+            materials=None,
+            chemical_pot=False,
+        )
 
         assert os.path.exists(my_export.filename)
 
@@ -76,6 +97,47 @@ def test_error_filename_not_a_str(self, my_export):
         with pytest.raises(TypeError, match="filename must be a string"):
             my_export.filename = 2
 
+    def test_sorted_by_x(self, my_export, function):
+        """Checks that the exported data is sorted by x"""
+        current_time = 1
+        my_export.function = function
+        my_export.write(
+            current_time=current_time,
+            final_time=None,
+            materials=None,
+            chemical_pot=False,
+        )
+        assert (np.diff(my_export.data[:, 0]) >= 0).all()
+
+    @pytest.mark.parametrize(
+        "materials,chemical_pot,export_len",
+        [
+            (None, 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,
+                12,  # + 1 duplicate near the interface
+            ),
+        ],
+    )
+    def test_duplicates(self, materials, chemical_pot, export_len, my_export, function):
+        """
+        Checks that the exported data does not contain duplicates
+        except those near interfaces
+        """
+        current_time = 1
+        my_export.function = function
+        my_export.write(
+            current_time=current_time,
+            final_time=None,
+            materials=materials,
+            chemical_pot=chemical_pot,
+        )
+        assert len(my_export.data) == export_len
+
 
 class TestIsItTimeToExport:
     @pytest.fixture

From 72648b20ec4a795334adcab3f751b08a7af24ede Mon Sep 17 00:00:00 2001
From: KulaginVladimir <kulagin.vladimir.l@yandex.ru>
Date: Mon, 7 Oct 2024 02:40:08 +0300
Subject: [PATCH 3/7] refactor filtering

---
 festim/exports/exports.py                 |   4 +-
 festim/exports/txt_export.py              | 125 ++++++++++++----------
 festim/generic_simulation.py              |  58 +++++-----
 test/unit/test_exports/test_txt_export.py |  42 ++++----
 4 files changed, 125 insertions(+), 104 deletions(-)

diff --git a/festim/exports/exports.py b/festim/exports/exports.py
index 915f44199..c3d61480a 100644
--- a/festim/exports/exports.py
+++ b/festim/exports/exports.py
@@ -71,7 +71,7 @@ def _validate_export(self, value):
             return value
         raise TypeError("festim.Exports must be a list of festim.Export")
 
-    def write(self, label_to_function, dx, materials, chemical_pot):
+    def write(self, label_to_function, dx):
         """writes to file
 
         Args:
@@ -129,7 +129,7 @@ def write(self, label_to_function, dx, materials, chemical_pot):
                         label_to_function[export.field], self.V_DG1
                     )
                 export.function = label_to_function[export.field]
-                export.write(self.t, self.final_time, materials, chemical_pot)
+                export.write(self.t, self.final_time)
         self.nb_iterations += 1
 
     def initialise_derived_quantities(self, dx, ds, materials):
diff --git a/festim/exports/txt_export.py b/festim/exports/txt_export.py
index 9144c2b97..7884c69b4 100644
--- a/festim/exports/txt_export.py
+++ b/festim/exports/txt_export.py
@@ -13,11 +13,20 @@ 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.
         header_format (str, optional): the format of column headers.
             Defautls to ".2e".
+
+    Attributes:
+        data (np.array): the data array of the exported field. The first column
+            is the mesh vertices. Each next column is the field profile at the specific
+            export time.
+        header (str): the header of the exported file.
     """
 
     def __init__(
@@ -31,10 +40,11 @@ def __init__(
         self.filename = filename
         self.write_at_last = write_at_last
         self.header_format = header_format
-        self._first_time = True
 
         self.data = None
         self.header = None
+        self._unique_indices = None
+        self._V = None
 
     @property
     def filename(self):
@@ -71,80 +81,81 @@ def is_last(self, current_time, final_time):
                 return True
         return False
 
-    def filter_duplicates(self, data, materials):
-        x = data[:, 0]
-
-        # Collect all borders
-        borders = []
-        for material in materials:
-            for border in material.borders:
-                borders.append(border)
-        borders = np.unique(borders)
-
-        # Find indices of the closest duplicates to interfaces
-        border_indx = []
-        for border in borders:
-            closest_indx = np.abs(x - border).argmin()
-            closest_x = x[closest_indx]
-            for ind in np.where(x == closest_x)[0]:
-                border_indx.append(ind)
+    def initialise_TXTExport(self, mesh, project_to_DG=False, materials=None):
 
-        # Find indices of first elements in duplicated pairs and mesh borders
-        _, unique_indx = np.unique(x, return_index=True)
-
-        # Combine both arrays of indices
-        combined_indx = np.concatenate([border_indx, unique_indx])
+        if project_to_DG:
+            self._V = f.FunctionSpace(mesh, "DG", 1)
+        else:
+            self._V = f.FunctionSpace(mesh, "CG", 1)
+
+        x = f.interpolate(f.Expression("x[0]", degree=1), self._V)
+        x_column = np.transpose([x.vector()[:]])
+
+        # if chemical_pot is True or trap_element_type is DG, get indices of duplicates near interfaces
+        # and indices of the first elements from a pair of duplicates otherwise
+        if project_to_DG:
+            # Collect all borders
+            borders = []
+            for material in materials:
+                if material.borders:
+                    for border in material.borders:
+                        borders.append(border)
+            borders = np.unique(borders)
+
+            # Find indices of the closest duplicates to interfaces
+            border_indices = []
+            for border in borders:
+                closest_indx = np.abs(x_column - border).argmin()
+                closest_x = x_column[closest_indx]
+                for ind in np.where(x_column == closest_x)[0]:
+                    border_indices.append(ind)
+
+            # Find indices of first elements in duplicated pairs and mesh borders
+            _, mesh_indices = np.unique(x_column, return_index=True)
+
+            # Get unique indices from both arrays preserving the order in unsorted x-array
+            unique_indices = []
+            for indx in np.argsort(x_column, axis=0)[:, 0]:
+                if (indx in mesh_indices) or (indx in border_indices):
+                    unique_indices.append(indx)
+
+            self._unique_indices = np.array(unique_indices)
 
-        # Sort unique indices to return a slice
-        combined_indx = sorted(np.unique(combined_indx))
+        else:
+            # Get list of unique indices as integers
+            self._unique_indices = np.argsort(x_column, axis=0)[:, 0]
 
-        return data[combined_indx, :]
+        self.data = x_column[self._unique_indices]
+        self.header = "x"
 
-    def write(self, current_time, final_time, materials, chemical_pot):
-        # create a DG1 functionspace if chemical_pot is True
-        # else create a CG1 functionspace
-        if chemical_pot:
-            V = f.FunctionSpace(self.function.function_space().mesh(), "DG", 1)
-        else:
-            V = f.FunctionSpace(self.function.function_space().mesh(), "CG", 1)
+    def write(self, current_time, final_time):
 
-        solution = f.project(self.function, V)
-        solution_column = np.transpose(solution.vector()[:])
         if self.is_it_time_to_export(current_time):
+            solution = f.project(self.function, self._V)
+            solution_column = np.transpose(solution.vector()[:])
+
             # if the directory doesn't exist
             # create it
             dirname = os.path.dirname(self.filename)
             if not os.path.exists(dirname):
                 os.makedirs(dirname, exist_ok=True)
 
-            # create header if steady or it is the first time to export
-            # else append new column to the existing file
-            if final_time is None or self._first_time:
-                if final_time is None:
-                    self.header = "x,t=steady"
-                else:
-                    self.header = f"x,t={format(current_time, self.header_format)}s"
-
-                x = f.interpolate(f.Expression("x[0]", degree=1), V)
-                x_column = np.transpose([x.vector()[:]])
-                self.data = np.column_stack([x_column, solution_column])
-                self._first_time = False
+            # if steady, add the corresponding label
+            # else append new export time to the header
+            steady = final_time is None
+            if steady:
+                self.header += ",t=steady"
             else:
-                # Update the header
                 self.header += f",t={format(current_time, self.header_format)}s"
-                # Add new column
-                self.data = np.column_stack([self.data, solution_column])
+
+            # Add new column of filtered and sorted data
+            self.data = np.column_stack(
+                [self.data, solution_column[self._unique_indices]]
+            )
 
             if (
                 self.write_at_last and self.is_last(current_time, final_time)
             ) or not self.write_at_last:
-                if self.is_last(current_time, final_time):
-                    # Sort data by the x-column before the last export time
-                    self.data = self.data[self.data[:, 0].argsort()]
-
-                    # Filter duplicates if chemical_pot is True
-                    if chemical_pot:
-                        self.data = self.filter_duplicates(self.data, materials)
 
                 # Write data
                 np.savetxt(
diff --git a/festim/generic_simulation.py b/festim/generic_simulation.py
index 96fa71148..2db764373 100644
--- a/festim/generic_simulation.py
+++ b/festim/generic_simulation.py
@@ -357,11 +357,11 @@ def initialise(self):
 
         self.h_transport_problem.initialise(self.mesh, self.materials, self.dt)
 
-        # raise warning if the derived quantities don't match the type of mesh
-        # eg. SurfaceFlux is used with cylindrical mesh
         for export in self.exports:
             if isinstance(export, festim.DerivedQuantities):
                 for q in export:
+                    # raise warning if the derived quantities don't match the type of mesh
+                    # eg. SurfaceFlux is used with cylindrical mesh
                     if self.mesh.type not in q.allowed_meshes:
                         warnings.warn(
                             f"{type(q)} may not work as intended for {self.mesh.type} meshes"
@@ -381,31 +381,41 @@ def initialise(self):
                                 f"SurfaceKinetics boundary condition must be defined on surface {q.surface} to export data with festim.AdsorbedHydrogen"
                             )
 
-        self.exports.initialise_derived_quantities(
-            self.mesh.dx, self.mesh.ds, self.materials
-        )
-
-        # needed to ensure that data is actually exported at TXTExport.times
-        # see issue 675
-        for export in self.exports:
-            if isinstance(export, festim.TXTExport) and export.times:
-                if not self.dt.milestones:
-                    self.dt.milestones = []
-                for time in export.times:
-                    if time not in self.dt.milestones:
-                        msg = "To ensure that TXTExport exports data at the desired times "
-                        msg += "TXTExport.times are added to milestones"
-                        warnings.warn(msg)
-                        self.dt.milestones.append(time)
-                self.dt.milestones.sort()
-
-            # set Soret to True for SurfaceFlux quantities
-            if isinstance(export, festim.DerivedQuantities):
-                for q in export:
+                    # set Soret to True for SurfaceFlux quantities
                     if isinstance(q, festim.SurfaceFlux):
                         q.soret = self.settings.soret
                         q.T = self.T.T
 
+            if isinstance(export, festim.TXTExport):
+                # pre-process data depending on the chemical potential flag, trap element type,
+                #  and material borders
+                project_to_DG = (
+                    self.settings.chemical_pot
+                    or self.settings.traps_element_type == "DG"
+                )
+                export.initialise_TXTExport(
+                    self.mesh.mesh,
+                    project_to_DG,
+                    self.materials,
+                )
+
+                # needed to ensure that data is actually exported at TXTExport.times
+                # see issue 675
+                if export.times:
+                    if not self.dt.milestones:
+                        self.dt.milestones = []
+                    for time in export.times:
+                        if time not in self.dt.milestones:
+                            msg = "To ensure that TXTExport exports data at the desired times "
+                            msg += "TXTExport.times are added to milestones"
+                            warnings.warn(msg)
+                            self.dt.milestones.append(time)
+                    self.dt.milestones.sort()
+
+        self.exports.initialise_derived_quantities(
+            self.mesh.dx, self.mesh.ds, self.materials
+        )
+
     def run(self, completion_tone=False):
         """Runs the model.
 
@@ -506,8 +516,6 @@ def run_post_processing(self):
         self.exports.write(
             self.label_to_function,
             self.mesh.dx,
-            self.materials,
-            self.settings.chemical_pot,
         )
 
     def update_post_processing_solutions(self):
diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index 134d88255..5210bf3f3 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -1,4 +1,4 @@
-from festim import TXTExport, Stepsize, Material
+from festim import TXTExport, Material
 import fenics as f
 import os
 import pytest
@@ -7,6 +7,12 @@
 
 
 class TestWrite:
+    @pytest.fixture
+    def mesh(self):
+        mesh = f.UnitIntervalMesh(10)
+
+        return mesh
+
     @pytest.fixture
     def function(self):
         mesh = f.UnitIntervalMesh(10)
@@ -34,31 +40,29 @@ def my_export(self, tmpdir):
 
         return my_export
 
-    def test_file_exists(self, my_export, function):
+    def test_file_exists(self, my_export, function, mesh):
         current_time = 1
         my_export.function = function
+        my_export.initialise_TXTExport(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
-            materials=None,
-            chemical_pot=False,
         )
 
         assert os.path.exists(my_export.filename)
 
-    def test_file_doesnt_exist(self, my_export, function):
+    def test_file_doesnt_exist(self, my_export, function, mesh):
         current_time = 10
         my_export.function = function
+        my_export.initialise_TXTExport(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
-            materials=None,
-            chemical_pot=False,
         )
 
         assert not os.path.exists(my_export.filename)
 
-    def test_create_folder(self, my_export, function):
+    def test_create_folder(self, my_export, function, mesh):
         """Checks that write() creates the folder if it doesn't exist"""
         current_time = 1
         my_export.function = function
@@ -68,23 +72,21 @@ def test_create_folder(self, my_export, function):
             + "/folder2"
             + my_export.filename[slash_indx:]
         )
+        my_export.initialise_TXTExport(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
-            materials=None,
-            chemical_pot=False,
         )
 
         assert os.path.exists(my_export.filename)
 
-    def test_subspace(self, my_export, function_subspace):
+    def test_subspace(self, my_export, function_subspace, mesh):
         current_time = 1
         my_export.function = function_subspace
+        my_export.initialise_TXTExport(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
-            materials=None,
-            chemical_pot=False,
         )
 
         assert os.path.exists(my_export.filename)
@@ -97,20 +99,19 @@ def test_error_filename_not_a_str(self, my_export):
         with pytest.raises(TypeError, match="filename must be a string"):
             my_export.filename = 2
 
-    def test_sorted_by_x(self, my_export, function):
+    def test_sorted_by_x(self, my_export, function, mesh):
         """Checks that the exported data is sorted by x"""
         current_time = 1
         my_export.function = function
+        my_export.initialise_TXTExport(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
-            materials=None,
-            chemical_pot=False,
         )
         assert (np.diff(my_export.data[:, 0]) >= 0).all()
 
     @pytest.mark.parametrize(
-        "materials,chemical_pot,export_len",
+        "materials,project_to_DG,export_len",
         [
             (None, False, 11),
             (
@@ -123,18 +124,19 @@ def test_sorted_by_x(self, my_export, function):
             ),
         ],
     )
-    def test_duplicates(self, materials, chemical_pot, export_len, my_export, function):
+    def test_duplicates(
+        self, materials, project_to_DG, 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.initialise_TXTExport(mesh, project_to_DG, materials)
         my_export.write(
             current_time=current_time,
             final_time=None,
-            materials=materials,
-            chemical_pot=chemical_pot,
         )
         assert len(my_export.data) == export_len
 

From 7ca79976e5bb685d9a69a652179664fc39eaeeba Mon Sep 17 00:00:00 2001
From: KulaginVladimir <kulagin.vladimir.l@yandex.ru>
Date: Mon, 7 Oct 2024 03:17:53 +0300
Subject: [PATCH 4/7] test is_last

---
 test/unit/test_exports/test_txt_export.py | 26 +++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index 5210bf3f3..177b6c853 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -163,3 +163,29 @@ def test_false(self, my_export):
         assert not my_export.is_it_time_to_export(0)
         assert not my_export.is_it_time_to_export(5)
         assert not my_export.is_it_time_to_export(1.5)
+
+
+class TestIsLast:
+    @pytest.fixture
+    def my_export(self, tmpdir):
+        d = tmpdir.mkdir("test_folder")
+        my_export = TXTExport(
+            "solute",
+            filename="{}/solute_label.txt".format(str(Path(d))),
+        )
+
+        return my_export
+
+    def test_final_time_none(self, my_export):
+        assert my_export.is_last(1, None) == True
+
+    @pytest.mark.parametrize("current_time,output", [(1, False), (3, False), (5, True)])
+    def test_times_not_none(self, current_time, output, my_export):
+        final_time = 5
+        assert my_export.is_last(current_time, final_time) == output
+
+    @pytest.mark.parametrize("current_time,output", [(1, False), (2, False), (3, True)])
+    def test_times_not_none(self, current_time, output, my_export):
+        my_export.times = [1, 2, 3]
+        final_time = 5
+        assert my_export.is_last(current_time, final_time) == output

From 4903d7edbef943be31e1e3facd8e044058ac424f Mon Sep 17 00:00:00 2001
From: KulaginVladimir <kulagin.vladimir.l@yandex.ru>
Date: Mon, 7 Oct 2024 03:37:29 +0300
Subject: [PATCH 5/7] fix typo

---
 test/unit/test_exports/test_txt_export.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index 177b6c853..e34b08e7b 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -176,11 +176,11 @@ def my_export(self, tmpdir):
 
         return my_export
 
-    def test_final_time_none(self, my_export):
+    def test_final_time_is_none(self, my_export):
         assert my_export.is_last(1, None) == True
 
     @pytest.mark.parametrize("current_time,output", [(1, False), (3, False), (5, True)])
-    def test_times_not_none(self, current_time, output, my_export):
+    def test_times_is_none(self, current_time, output, my_export):
         final_time = 5
         assert my_export.is_last(current_time, final_time) == output
 

From 9ef34ad938a1446d4fcc3e89488893932636b605 Mon Sep 17 00:00:00 2001
From: KulaginVladimir <kulagin.vladimir.l@yandex.ru>
Date: Mon, 7 Oct 2024 22:43:34 +0300
Subject: [PATCH 6/7] added docstrings

---
 docs/source/api/exports.rst               |  4 --
 festim/exports/txt_export.py              | 67 ++++++++++++++++++++---
 festim/generic_simulation.py              |  2 +-
 test/unit/test_exports/test_txt_export.py | 12 ++--
 4 files changed, 66 insertions(+), 19 deletions(-)

diff --git a/docs/source/api/exports.rst b/docs/source/api/exports.rst
index abde0afbc..0bf38fdfc 100644
--- a/docs/source/api/exports.rst
+++ b/docs/source/api/exports.rst
@@ -15,10 +15,6 @@ Exports
     :members:
     :show-inheritance:
 
-.. autoclass:: TXTExports
-    :members:
-    :show-inheritance:
-
 .. autoclass:: TrapDensityXDMF
     :members:
     :show-inheritance:
diff --git a/festim/exports/txt_export.py b/festim/exports/txt_export.py
index 7884c69b4..0dadd4614 100644
--- a/festim/exports/txt_export.py
+++ b/festim/exports/txt_export.py
@@ -27,6 +27,8 @@ class TXTExport(festim.Export):
             is the mesh vertices. Each next column is the field profile at the specific
             export time.
         header (str): the header of the exported file.
+        V (fenics.FunctionSpace): the vector-function space for the exported field.
+
     """
 
     def __init__(
@@ -43,8 +45,8 @@ def __init__(
 
         self.data = None
         self.header = None
+        self.V = None
         self._unique_indices = None
-        self._V = None
 
     @property
     def filename(self):
@@ -60,6 +62,17 @@ def filename(self, value):
         self._filename = value
 
     def is_it_time_to_export(self, current_time):
+        """
+        Checks if the exported field should be written to a file or not
+        based on the current time and the TXTExport.times
+
+        Args:
+            current_time (float): the current simulation time
+
+        Returns:
+            bool: True if the exported field should be written to a file, else False
+        """
+
         if self.times is None:
             return True
         for time in self.times:
@@ -68,6 +81,21 @@ def is_it_time_to_export(self, current_time):
         return False
 
     def is_last(self, current_time, final_time):
+        """
+        Checks if the current simulation step equals to the last export time.
+        based on the final simulation time, TXTExport.times, and the current time
+
+        Args:
+            current_time (float): the current simulation time.
+            final_time (float, None): the final simulation time.
+
+        Returns:
+            bool: True if simulation is steady (final_time is None), if TXTExport.times
+                are not provided and the current time equals to the final time, or if
+                TXTExport.times are provided and the current time equals to the last time in
+                TXTExport.times, else False.
+        """
+
         if final_time is None:
             # write if steady
             return True
@@ -81,17 +109,32 @@ def is_last(self, current_time, final_time):
                 return True
         return False
 
-    def initialise_TXTExport(self, mesh, project_to_DG=False, materials=None):
+    def initialise(self, mesh, project_to_DG=False, materials=None):
+        """
+        Initialises TXTExport. Depending on the project_to_DG flag, defines a function space (DG1 or CG1)
+        for projection of the exported field. After that, an unsorted array of mesh vertices is created for export.
+        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,
+            The interfaces are defined by ``material.borders`` in the ``Materials`` list.
+
+        Args:
+            mesh (fenics.Mesh): the mesh.
+            project_to_DG (bool): if True, the exported field is projected to a DG1 function space.
+                Defaults to False.
+            materials (festim.Materials): the materials. Defaults to None.
+        """
 
         if project_to_DG:
-            self._V = f.FunctionSpace(mesh, "DG", 1)
+            self.V = f.FunctionSpace(mesh, "DG", 1)
         else:
-            self._V = f.FunctionSpace(mesh, "CG", 1)
+            self.V = f.FunctionSpace(mesh, "CG", 1)
 
-        x = f.interpolate(f.Expression("x[0]", degree=1), self._V)
+        x = f.interpolate(f.Expression("x[0]", degree=1), self.V)
         x_column = np.transpose([x.vector()[:]])
 
-        # if chemical_pot is True or trap_element_type is DG, get indices of duplicates near interfaces
+        # if project_to_DG is True, get indices of duplicates near interfaces
         # and indices of the first elements from a pair of duplicates otherwise
         if project_to_DG:
             # Collect all borders
@@ -122,16 +165,24 @@ def initialise_TXTExport(self, mesh, project_to_DG=False, materials=None):
             self._unique_indices = np.array(unique_indices)
 
         else:
-            # Get list of unique indices as integers
+            # Get list of unique indices
             self._unique_indices = np.argsort(x_column, axis=0)[:, 0]
 
         self.data = x_column[self._unique_indices]
         self.header = "x"
 
     def write(self, current_time, final_time):
+        """
+        Modifies the header and writes the data to a file depending on
+        the current and the final times of a simulation.
+
+        Args:
+            current_time (float): the current simulation time.
+            final_time (float, None): the final simulation time.
+        """
 
         if self.is_it_time_to_export(current_time):
-            solution = f.project(self.function, self._V)
+            solution = f.project(self.function, self.V)
             solution_column = np.transpose(solution.vector()[:])
 
             # if the directory doesn't exist
diff --git a/festim/generic_simulation.py b/festim/generic_simulation.py
index 2db764373..d8167d955 100644
--- a/festim/generic_simulation.py
+++ b/festim/generic_simulation.py
@@ -393,7 +393,7 @@ def initialise(self):
                     self.settings.chemical_pot
                     or self.settings.traps_element_type == "DG"
                 )
-                export.initialise_TXTExport(
+                export.initialise(
                     self.mesh.mesh,
                     project_to_DG,
                     self.materials,
diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index e34b08e7b..fe9493e78 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -43,7 +43,7 @@ def my_export(self, tmpdir):
     def test_file_exists(self, my_export, function, mesh):
         current_time = 1
         my_export.function = function
-        my_export.initialise_TXTExport(mesh)
+        my_export.initialise(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
@@ -54,7 +54,7 @@ def test_file_exists(self, my_export, function, mesh):
     def test_file_doesnt_exist(self, my_export, function, mesh):
         current_time = 10
         my_export.function = function
-        my_export.initialise_TXTExport(mesh)
+        my_export.initialise(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
@@ -72,7 +72,7 @@ def test_create_folder(self, my_export, function, mesh):
             + "/folder2"
             + my_export.filename[slash_indx:]
         )
-        my_export.initialise_TXTExport(mesh)
+        my_export.initialise(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
@@ -83,7 +83,7 @@ def test_create_folder(self, my_export, function, mesh):
     def test_subspace(self, my_export, function_subspace, mesh):
         current_time = 1
         my_export.function = function_subspace
-        my_export.initialise_TXTExport(mesh)
+        my_export.initialise(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
@@ -103,7 +103,7 @@ def test_sorted_by_x(self, my_export, function, mesh):
         """Checks that the exported data is sorted by x"""
         current_time = 1
         my_export.function = function
-        my_export.initialise_TXTExport(mesh)
+        my_export.initialise(mesh)
         my_export.write(
             current_time=current_time,
             final_time=None,
@@ -133,7 +133,7 @@ def test_duplicates(
         """
         current_time = 1
         my_export.function = function
-        my_export.initialise_TXTExport(mesh, project_to_DG, materials)
+        my_export.initialise(mesh, project_to_DG, materials)
         my_export.write(
             current_time=current_time,
             final_time=None,

From f639d2a2ea1506d21c1f1fe65ba0dc55d7dd22d5 Mon Sep 17 00:00:00 2001
From: KulaginVladimir <kulagin.vladimir.l@yandex.ru>
Date: Sun, 27 Oct 2024 23:19:43 +0300
Subject: [PATCH 7/7] added filter flag

---
 festim/exports/txt_export.py              | 30 +++++++++++++++++------
 test/unit/test_exports/test_txt_export.py | 18 +++++++++++---
 2 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/festim/exports/txt_export.py b/festim/exports/txt_export.py
index 0dadd4614..f148716f6 100644
--- a/festim/exports/txt_export.py
+++ b/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".
 
@@ -29,10 +32,20 @@ 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:
@@ -40,6 +53,7 @@ def __init__(
         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]
diff --git a/test/unit/test_exports/test_txt_export.py b/test/unit/test_exports/test_txt_export.py
index fe9493e78..1d86f32c0 100644
--- a/test/unit/test_exports/test_txt_export.py
+++ b/test/unit/test_exports/test_txt_export.py
@@ -111,21 +111,31 @@ 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
@@ -133,11 +143,13 @@ def test_duplicates(
         """
         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