v2.7.3

Author: fbordignon

src/ltrace/ltrace/pore_networks/functions.py

@@ -314,12 +314,7 @@ def geo2pnf(
         input_x = pore_dict["pore.coords_0"][i] * scale_factor
         input_y = pore_dict["pore.coords_1"][i] * scale_factor
         input_z = pore_dict["pore.coords_2"][i] * scale_factor
-        if axis == "x":
-            p_z, p_y, p_x = input_x, input_y, input_z
-        elif axis == "y":
-            p_y, p_z, p_x = input_x, input_y, input_z
-        elif axis == "z":
-            p_x, p_y, p_z = input_x, input_y, input_z
+        p_z, p_y, p_x = input_x, input_y, input_z
         coordinate_number = len(pores_conns_pores[i])
         is_inlet = int(pore_dict[f"pore.{axis}max"][i])
         is_outlet = int(pore_dict[f"pore.{axis}min"][i])

src/ltrace/ltrace/pore_networks/functions_simulation.py

@@ -371,6 +371,8 @@ def single_phase_permeability(
     pore_network,
     in_face="xmin",
     out_face="xmax",
+    pressure_drop=101325,  # Pa
+    viscosity=0.001,  # Pa.s
     subresolution_function=None,
     subres_porositymodifier=1.0,
     subres_shape_factor=0.041,
@@ -424,6 +426,7 @@ def single_phase_permeability(
 
     water = openpnm.phase.Water(network=sub_proj.network)
     water.add_model_collection(openpnm.models.collections.physics.standard)
+    water["pore.viscosity"] = viscosity
     sub_proj["throat.hydraulic_conductance"] = sub_proj["throat.conductance"]
     sub_proj["pore.phase"][...] = 1
     perm = openpnm.algorithms.StokesFlow(
@@ -434,7 +437,7 @@ def single_phase_permeability(
     perm.settings["x_rtol"] = 1e-11
     # print("\n\n############## OpenPNM flow ###########\n\n", perm, "\n\n##############################\n\n")
     perm.set_value_BC(
-        pores=sub_proj.pores(in_face), values=101325, mode="overwrite"
+        pores=sub_proj.pores(in_face), values=pressure_drop, mode="overwrite"
     )  # pressure in pa: 101325 pa = 1 atm
     perm.set_value_BC(pores=sub_proj.pores(out_face), values=0, mode="overwrite")
     inlets = perm.network[f"pore.{in_face}"].astype(np.int32)

src/ltrace/ltrace/pore_networks/krel_result.py

@@ -363,7 +363,19 @@ def _linspace(max_x, number_of_points=201):
 
     @staticmethod
     def _interpolate(interpolated_x, x_values, y_values):
-        return np.interp(interpolated_x, x_values, y_values, left=np.nan, right=np.nan)
+        interpolated_y = np.interp(interpolated_x, x_values, y_values, left=np.nan, right=np.nan)
+
+        # Ensure first and last data are represented in the interpolated data
+        extra_x_over_limit = interpolated_x > x_values[-1]
+        if np.any(extra_x_over_limit):
+            first_out_of_bounds = np.where(extra_x_over_limit == True)[0][0]
+            interpolated_y[first_out_of_bounds] = y_values[-1]
+        extra_x_under_limit = interpolated_x < x_values[0]
+        if np.any(extra_x_under_limit):
+            last_out_of_bounds = np.where(extra_x_under_limit == True)[0][-1]
+            interpolated_y[last_out_of_bounds] = y_values[0]
+
+        return interpolated_y
 
     @staticmethod
     def _interpolate_table(table, id, interpolated_x, cycles_id_list):
@@ -435,9 +447,9 @@ def _get_prefixes(table_dict):
 
 class KrelParameterParser:
     def __init__(self):
-        self.input_regex = re.compile(f"{INPUT_PREFIX}(\S+)")
-        self.result_regex = re.compile(f"{RESULT_PREFIX}(\S+)")
-        self.error_regex = re.compile(f"{ERROR_PREFIX}(\S+)")
+        self.input_regex = re.compile(f"{INPUT_PREFIX}(\\S+)")
+        self.result_regex = re.compile(f"{RESULT_PREFIX}(\\S+)")
+        self.error_regex = re.compile(f"{ERROR_PREFIX}(\\S+)")
 
     def get_input_name(self, column_name):
         match = self.input_regex.match(column_name)

src/ltrace/ltrace/pore_networks/pnflow_parameter_defs.py

@@ -340,6 +340,16 @@
             "Model 3 (Morrow curve)": "3",
         },
     }
+    PARAMETERS[f"{i}_contact_distribution"] = {
+        "display_name": "Distribution",
+        "layout": i,
+        "dtype": "combobox",
+        "default_value": 1,
+        "display_names": {
+            "Weibull": "weibull",
+            "Gaussian": "gaussian",
+        },
+    }
     PARAMETERS[f"{i}_contact_angle"] = {
         "display_name": "CA center (deg)",
         "tooltip": "Contact angle distribution center (degrees)",
@@ -358,6 +368,12 @@
         "max_value": 180.0,
         "layout": i,
     }
+    PARAMETERS[f"{i}_contact_angle_sig"] = {
+        "display_name": "Standard deviation",
+        "dtype": "multifloat",
+        "default_value": 5.0,
+        "layout": i,
+    }
     PARAMETERS[f"{i}_contact_angle_del"] = {
         "display_name": "Delta",
         "dtype": "multifloat",

src/ltrace/ltrace/pore_networks/visualization_model.py

@@ -12,7 +12,7 @@
 ARROW_TYPE = 3
 
 
-def visualize_vtu(
+def _visualize_vtu(
     filepath,
     cycle,
     scale_factor=10**3,
@@ -30,6 +30,19 @@ def visualize_vtu(
         Must be 'w' for wetting phase (usually waater) injection cycles and 'o'
         for non-wetting phase (usually oil) injection cycles
     """
+    if axis == "x":
+        arrow_x = 0
+        arrow_y = 0
+        arrow_z = 1
+    elif axis == "y":
+        arrow_x = 0
+        arrow_y = 1
+        arrow_z = 0
+    elif axis == "z":
+        arrow_x = 1
+        arrow_y = 0
+        arrow_z = 0
+
     reader = vtk.vtkXMLUnstructuredGridReader()
     reader.SetFileName(filepath)
     reader.Update()
@@ -116,7 +129,7 @@ def visualize_vtu(
         arrows_saturations.InsertTuple1(i, arrow_saturation)
         arrows_condW.InsertTuple1(i, 0)
         arrows_condO.InsertTuple1(i, 0)
-        arrows_direction.InsertTuple3(i, 0, 0, 1)
+        arrows_direction.InsertTuple3(i, arrow_x, arrow_y, arrow_z)
         arrows_position.InsertTuple3(i, *arrow_position)
         arrows_type.InsertTuple1(i, ARROW_TYPE)
         arrows_id.InsertTuple1(i, object_id)
@@ -193,13 +206,17 @@ def visualize_vtu(
     return pressure, merger
 
 
-def generate_model_variable_scalar(temp_folder, is_multiscale=False):
+def generate_model_variable_scalar(temp_folder, is_multiscale=False, **kwargs):
     file_names = sorted([i for i in os.listdir(temp_folder) if i[-4:] == ".vtu"])
 
     pressures = []
     base_filepath = os.path.join(temp_folder, file_names[0])
-    pressure, pore_mesh = visualize_vtu(
-        base_filepath, create_model=False, cycle=file_names[0][2].lower(), normalize_radius=is_multiscale
+    pressure, pore_mesh = _visualize_vtu(
+        base_filepath,
+        create_model=False,
+        cycle=file_names[0][2].lower(),
+        normalize_radius=is_multiscale,
+        **kwargs,
     )
     point_data = pore_mesh.GetOutput().GetPointData()
     pressures.append(pressure)
@@ -214,8 +231,12 @@ def generate_model_variable_scalar(temp_folder, is_multiscale=False):
 
     for data_point, file_name in enumerate(file_names[1:], start=1):
         filepath = os.path.join(temp_folder, file_name)
-        pressure, poly_data = visualize_vtu(
-            filepath, cycle=file_name[2].lower(), create_model=False, normalize_radius=is_multiscale
+        pressure, poly_data = _visualize_vtu(
+            filepath,
+            cycle=file_name[2].lower(),
+            create_model=False,
+            normalize_radius=is_multiscale,
+            **kwargs,
         )
         saturation = poly_data.GetOutput().GetPointData().GetArray("saturation")
         new_array = vtk.util.numpy_support.vtk_to_numpy(saturation)
@@ -285,6 +306,13 @@ def _unstructured_grid_to_dict(
     Returns:
         dict: model elements data
     """
+    if axis == "x":
+        arrow_displacement_axis = 2
+    elif axis == "y":
+        arrow_displacement_axis = 1
+    elif axis == "z":
+        arrow_displacement_axis = 0
+
     n_points = unstructured_grid.GetNumberOfPoints()
     n_cells = unstructured_grid.GetNumberOfCells()
 
@@ -347,8 +375,7 @@ def _unstructured_grid_to_dict(
         radius = unstructured_grid.GetPointData().GetArray("radius").GetComponent(pore_id, 0)
         sw = unstructured_grid.GetPointData().GetArray("Sw").GetComponent(pore_id, 0)
 
-        if axis == "x":
-            position = position[-1::-1]
+        position = position[-1::-1]
 
         is_inlet = unstructured_grid.GetPointData().GetArray("inlets").GetComponent(pore_id, 0)
         if is_inlet == 1:
@@ -400,9 +427,11 @@ def _unstructured_grid_to_dict(
     volume_side = volume ** (1.0 / 3.0)
 
     inlet_arrows_positions = position_list[inlet_bool_list] * scale_factor
-    inlet_arrows_positions[:, 2] -= volume_side * arrow_scale + pore_radius_list[inlet_bool_list] / 2
+    inlet_arrows_positions[:, arrow_displacement_axis] -= (
+        volume_side * arrow_scale + pore_radius_list[inlet_bool_list] / 2
+    )
     outlet_arrows_positions = position_list[outlet_bool_list] * scale_factor
-    outlet_arrows_positions[:, 2] += pore_radius_list[outlet_bool_list] / 2
+    outlet_arrows_positions[:, arrow_displacement_axis] += pore_radius_list[outlet_bool_list] / 2
 
     arrows = []
     for i, sw in enumerate(sw_list[inlet_bool_list]):