filter duplicates depending on chemical_pot flag

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):

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
@@ -84,15 +117,15 @@ 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:
                     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_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,

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

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