update(Grid): refactor thick and saturated_thick: (#1768)

* update(Grid): refactor thick and saturated_thick:

* Deprecate thick and saturated_thick
* Added cell_thickness and saturated_thickness to Grid 
* changed calls to thick and saturated_thick to cell_thickness and saturated_thickness

* refactor sat_thk to saturated_thickness

autotest/test_grid.py

@@ -909,84 +909,84 @@ def unstructured_grid():
     return GridCases().unstructured_small()
 
 
-def test_structured_thick(structured_grid):
-    thick = structured_grid.thick
-    assert np.allclose(thick, 5.0), "thicknesses != 5."
+def test_structured_thickness(structured_grid):
+    thickness = structured_grid.cell_thickness
+    assert np.allclose(thickness, 5.0), "thicknesses != 5."
 
-    sat_thick = structured_grid.saturated_thick(structured_grid.botm + 10.0)
-    assert np.allclose(sat_thick, thick), "saturated thicknesses != 5."
+    sat_thick = structured_grid.saturated_thickness(structured_grid.botm + 10.0)
+    assert np.allclose(sat_thick, thickness), "saturated thicknesses != 5."
 
-    sat_thick = structured_grid.saturated_thick(structured_grid.botm + 5.0)
-    assert np.allclose(sat_thick, thick), "saturated thicknesses != 5."
+    sat_thick = structured_grid.saturated_thickness(structured_grid.botm + 5.0)
+    assert np.allclose(sat_thick, thickness), "saturated thicknesses != 5."
 
-    sat_thick = structured_grid.saturated_thick(structured_grid.botm + 2.5)
+    sat_thick = structured_grid.saturated_thickness(structured_grid.botm + 2.5)
     assert np.allclose(sat_thick, 2.5), "saturated thicknesses != 2.5"
 
-    sat_thick = structured_grid.saturated_thick(structured_grid.botm)
+    sat_thick = structured_grid.saturated_thickness(structured_grid.botm)
     assert np.allclose(sat_thick, 0.0), "saturated thicknesses != 0."
 
-    sat_thick = structured_grid.saturated_thick(structured_grid.botm - 100.0)
+    sat_thick = structured_grid.saturated_thickness(structured_grid.botm - 100.0)
     assert np.allclose(sat_thick, 0.0), "saturated thicknesses != 0."
 
 
-def test_vertices_thick(vertex_grid):
-    thick = vertex_grid.thick
-    assert np.allclose(thick, 5.0), "thicknesses != 5."
+def test_vertices_thickness(vertex_grid):
+    thickness = vertex_grid.cell_thickness
+    assert np.allclose(thickness, 5.0), "thicknesses != 5."
 
-    sat_thick = vertex_grid.saturated_thick(vertex_grid.botm + 10.0)
-    assert np.allclose(sat_thick, thick), "saturated thicknesses != 5."
+    sat_thick = vertex_grid.saturated_thickness(vertex_grid.botm + 10.0)
+    assert np.allclose(sat_thick, thickness), "saturated thicknesses != 5."
 
-    sat_thick = vertex_grid.saturated_thick(vertex_grid.botm + 5.0)
-    assert np.allclose(sat_thick, thick), "saturated thicknesses != 5."
+    sat_thick = vertex_grid.saturated_thickness(vertex_grid.botm + 5.0)
+    assert np.allclose(sat_thick, thickness), "saturated thicknesses != 5."
 
-    sat_thick = vertex_grid.saturated_thick(vertex_grid.botm + 2.5)
+    sat_thick = vertex_grid.saturated_thickness(vertex_grid.botm + 2.5)
     assert np.allclose(sat_thick, 2.5), "saturated thicknesses != 2.5"
 
-    sat_thick = vertex_grid.saturated_thick(vertex_grid.botm)
+    sat_thick = vertex_grid.saturated_thickness(vertex_grid.botm)
     assert np.allclose(sat_thick, 0.0), "saturated thicknesses != 0."
 
-    sat_thick = vertex_grid.saturated_thick(vertex_grid.botm - 100.0)
+    sat_thick = vertex_grid.saturated_thickness(vertex_grid.botm - 100.0)
     assert np.allclose(sat_thick, 0.0), "saturated thicknesses != 0."
 
 
-def test_unstructured_thick(unstructured_grid):
-    thick = unstructured_grid.thick
-    assert np.allclose(thick, 5.0), "thicknesses != 5."
+def test_unstructured_thickness(unstructured_grid):
+    thickness = unstructured_grid.cell_thickness
+    assert np.allclose(thickness, 5.0), "thicknesses != 5."
 
-    sat_thick = unstructured_grid.saturated_thick(
+    sat_thick = unstructured_grid.saturated_thickness(
         unstructured_grid.botm + 10.0
     )
-    assert np.allclose(sat_thick, thick), "saturated thicknesses != 5."
+    assert np.allclose(sat_thick, thickness), "saturated thicknesses != 5."
 
-    sat_thick = unstructured_grid.saturated_thick(unstructured_grid.botm + 5.0)
-    assert np.allclose(sat_thick, thick), "saturated thicknesses != 5."
+    sat_thick = unstructured_grid.saturated_thickness(unstructured_grid.botm + 5.0)
+    assert np.allclose(sat_thick, thickness), "saturated thicknesses != 5."
 
-    sat_thick = unstructured_grid.saturated_thick(unstructured_grid.botm + 2.5)
+    sat_thick = unstructured_grid.saturated_thickness(unstructured_grid.botm + 2.5)
     assert np.allclose(sat_thick, 2.5), "saturated thicknesses != 2.5"
 
-    sat_thick = unstructured_grid.saturated_thick(unstructured_grid.botm)
+    sat_thick = unstructured_grid.saturated_thickness(unstructured_grid.botm)
     assert np.allclose(sat_thick, 0.0), "saturated thicknesses != 0."
 
-    sat_thick = unstructured_grid.saturated_thick(
+    sat_thick = unstructured_grid.saturated_thickness(
         unstructured_grid.botm - 100.0
     )
     assert np.allclose(sat_thick, 0.0), "saturated thicknesses != 0."
 
 
 @parametrize_with_cases("grid", cases=GridCases, prefix="structured_cbd")
-def test_structured_ncb_thick(grid):
-    thick = grid.thick
+def test_structured_ncb_thickness(grid):
+    thickness = grid.cell_thickness
 
-    assert thick.shape[0] == grid.nlay + np.count_nonzero(
+    assert thickness.shape[0] == grid.nlay + np.count_nonzero(
         grid.laycbd
-    ), "grid thick attribute returns incorrect shape"
+    ), "grid cell_thickness attribute returns incorrect shape"
 
-    thick = grid.remove_confining_beds(grid.thick)
+    thickness = grid.remove_confining_beds(grid.cell_thickness)
     assert (
-        thick.shape == grid.shape
+        thickness.shape == grid.shape
     ), "quasi3d confining beds not properly removed"
 
-    sat_thick = grid.saturated_thick(grid.thick)
+    sat_thick = grid.saturated_thickness(grid.cell_thickness)
     assert (
         sat_thick.shape == grid.shape
     ), "saturated_thickness confining beds not removed"

autotest/test_modflow.py

@@ -316,11 +316,11 @@ def test_load_twri_grid(example_data_path):
     assert (
         mg.shape == shape
     ), f"modelgrid shape {mg.shape} not equal to {shape}"
-    thick = mg.thick
+    thickness = mg.cell_thickness
     shape = (5, 15, 15)
     assert (
-        thick.shape == shape
-    ), f"thickness shape {thick.shape} not equal to {shape}"
+        thickness.shape == shape
+    ), f"cell_thickness shape {thickness.shape} not equal to {shape}"
 
 
 def test_mg(function_tmpdir):
@@ -347,7 +347,7 @@ def test_mg(function_tmpdir):
         botm=botm,
     )
     bas = ModflowBas(ms, ifrefm=True)
-    t = ms.modelgrid.thick
+    t = ms.modelgrid.cell_thickness
 
     # test instantiation of an empty basic Structured Grid
     mg = StructuredGrid(dis.delc.array, dis.delr.array)

autotest/test_postprocessing.py

@@ -297,7 +297,7 @@ def test_get_sat_thickness_gradients(function_tmpdir):
     dz = np.array([np.nan, -0.9])
     assert np.nansum(np.abs(dh / dz - grad[:, 1, 0])) < 1e-6
 
-    sat_thick = m.modelgrid.saturated_thick(hds, mask=nodata)
+    sat_thick = m.modelgrid.saturated_thickness(hds, mask=nodata)
     assert (
         np.abs(np.sum(sat_thick[:, 1, 1] - np.array([0.2, 1.0, 1.0]))) < 1e-6
     ), "failed saturated thickness comparison (grid.thick())"

examples/Notebooks/flopy3_Modflow_postprocessing_example.ipynb

@@ -372,7 +372,7 @@
    "metadata": {},
    "source": [
     "### Get the saturated thickness of a layer\n",
-    "`m.modelgrid.saturated_thick()` returns an nlay, nrow, ncol array of saturated thicknesses."
+    "`m.modelgrid.saturated_thickness()` returns an nlay, nrow, ncol array of saturated thicknesses."
    ]
   },
   {
@@ -399,7 +399,7 @@
     }
    ],
    "source": [
-    "st = m.modelgrid.saturated_thick(hds, mask=-9999.0)\n",
+    "st = m.modelgrid.saturated_thickness(hds, mask=-9999.0)\n",
     "\n",
     "plt.imshow(st[0])\n",
     "plt.colorbar(label=\"Saturated thickness\")\n",
@@ -633,7 +633,7 @@
     }
    ],
    "source": [
-    "m.modelgrid.thick[:, r, c]"
+    "m.modelgrid.cell_thickness[:, r, c]"
    ]
   },
   {
@@ -674,7 +674,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,

examples/Notebooks/flopy3_SEAWAT_henry_problem.ipynb

@@ -57,7 +57,6 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {
-    "collapsed": false,
     "execution": {
      "iopub.execute_input": "2023-02-22T02:45:17.582730Z",
      "iopub.status.busy": "2023-02-22T02:45:17.582364Z",
@@ -474,13 +473,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Util2d:hk layer 1: resetting 'how' to external\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "Util2d:hk layer 1: resetting 'how' to external\n",
       " Elapsed run time:  8.265 Seconds\n",
       "\n",
       " Normal termination of SEAWAT\n"
@@ -518,7 +511,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -532,7 +525,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,

examples/Notebooks/flopy3_demo_of_modelgrid_classes.ipynb

@@ -1290,7 +1290,7 @@
     "   - `nnodes` : returns the number of cells in the model\n",
     "   - `top` : returns an array of the top elevation of the model or for unstructured grids the top elevation of all cells\n",
     "   - `botm` : retuns an array of the botm elevations of model cells\n",
-    "   - `thick` : returns an array of model cell thickness\n",
+    "   - `cell_thickness` : returns an array of model cell thickness\n",
     "   - `idomain` : retruns the idomain array associated with the model\n",
     "   - `xvertices` : returns an array of x-vertices for model cells\n",
     "   - `yvertices` : returns an array of y-vertices for model cells\n",
@@ -1409,7 +1409,7 @@
     "    nrows=1, ncols=3, figsize=(18, 6), subplot_kw={\"aspect\": \"equal\"}\n",
     ")\n",
     "\n",
-    "arrays = [modelgrid.top, modelgrid.botm, modelgrid.thick]\n",
+    "arrays = [modelgrid.top, modelgrid.botm, modelgrid.cell_thickness]\n",
     "\n",
     "labels = [\"top\", \"botm\", \"thickness\"]\n",
     "\n",
@@ -1450,7 +1450,7 @@
     "   - `get_coords()` : Method to convert model coordinates to real-world coordinates based on coordinate reference information\n",
     "   - `get_local_coords()` : Method to convert real-world coordinates to model coordinates based on coordinate reference information\n",
     "   - `intersect()` : Method to get the cellid (`StructuredGrid`=(row, column) OR `VertexGrid` & `UnstrucuturedGrid`=node number) from either model coordinates or from real-world coordinates\n",
-    "   - `saturated_thick()` : Method to get the saturated thickness\n",
+    "   - `saturated_thickness()` : Method to get the saturated thickness\n",
     "   - `write_shapefile()` : Method to write a shapefile of the grid with just the cellid attributes"
    ]
   },
@@ -1715,7 +1715,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### saturated_thick()\n",
+    "#### saturated_thickness()\n",
     "\n",
     "Method to calculate the saturated thickness of each model cell from an array of elevations. Input parameters to this method include:\n",
     "\n",
@@ -1802,10 +1802,10 @@
     "head = hds.get_alldata()[0]\n",
     "\n",
     "# calculate saturated thickness\n",
-    "sat_thk = ml.modelgrid.saturated_thick(head, mask=[1e30])\n",
+    "sat_thk = ml.modelgrid.saturated_thickness(head, mask=[1e30])\n",
     "\n",
     "# get thick for comparison\n",
-    "thk = ml.modelgrid.thick\n",
+    "thk = ml.modelgrid.cell_thickness\n",
     "\n",
     "# plot thickness and saturated thickness for comparison\n",
     "fig, ax = plt.subplots(\n",
@@ -1898,7 +1898,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,

flopy/discretization/grid.py

@@ -1,5 +1,6 @@
 import copy
 import os
+import warnings
 
 import numpy as np
 
@@ -299,7 +300,7 @@ def laycbd(self):
             return self._laycbd
 
     @property
-    def thick(self):
+    def cell_thickness(self):
         """
         Get the cell thickness for a structured, vertex, or unstructured grid.
 
@@ -309,7 +310,24 @@ def thick(self):
         """
         return -np.diff(self.top_botm, axis=0).reshape(self._botm.shape)
 
-    def saturated_thick(self, array, mask=None):
+    @property
+    def thick(self):
+        """
+        DEPRECATED method. thick will be removed in version 3.3.9
+
+        Get the cell thickness for a structured, vertex, or unstructured grid.
+
+        Returns
+        -------
+            thick : calculated thickness
+        """
+        warnings.warn(
+            "thick has been replaced with cell_thickness and will be removed in version 3.3.9,",
+            DeprecationWarning,
+        )
+        return self.cell_thickness
+
+    def saturated_thickness(self, array, mask=None):
         """
         Get the saturated thickness for a structured, vertex, or unstructured
         grid. If the optional array is passed then thickness is returned
@@ -325,26 +343,52 @@ def saturated_thick(self, array, mask=None):
 
         Returns
         -------
-            thick : calculated saturated thickness
+            thickness : calculated saturated thickness
         """
-        thick = self.thick
-        top = self.top_botm[:-1].reshape(thick.shape)
-        bot = self.top_botm[1:].reshape(thick.shape)
-        thick = self.remove_confining_beds(thick)
+        thickness = self.cell_thickness
+        top = self.top_botm[:-1].reshape(thickness.shape)
+        bot = self.top_botm[1:].reshape(thickness.shape)
+        thickness = self.remove_confining_beds(thickness)
         top = self.remove_confining_beds(top)
         bot = self.remove_confining_beds(bot)
         array = self.remove_confining_beds(array)
 
         idx = np.where((array < top) & (array > bot))
-        thick[idx] = array[idx] - bot[idx]
+        thickness[idx] = array[idx] - bot[idx]
         idx = np.where(array <= bot)
-        thick[idx] = 0.0
+        thickness[idx] = 0.0
         if mask is not None:
             if isinstance(mask, (float, int)):
                 mask = [float(mask)]
             for mask_value in mask:
-                thick[np.where(array == mask_value)] = np.nan
-        return thick
+                thickness[np.where(array == mask_value)] = np.nan
+        return thickness
+
+    def saturated_thick(self, array, mask=None):
+        """
+        DEPRECATED method. saturated_thick will be removed in version 3.3.9
+
+        Get the saturated thickness for a structured, vertex, or unstructured
+        grid. If the optional array is passed then thickness is returned
+        relative to array values (saturated thickness). Returned values
+        ranges from zero to cell thickness if optional array is passed.
+
+        Parameters
+        ----------
+        array : ndarray
+            array of elevations that will be used to adjust the cell thickness
+        mask: float, list, tuple, ndarray
+            array values to replace with a nan value.
+
+        Returns
+        -------
+            thick : calculated saturated thickness
+        """
+        warnings.warn(
+            "saturated_thick has been replaced with saturated_thickness and will be removed in version 3.3.9,",
+            DeprecationWarning,
+        )
+        return self.saturated_thickness(array, mask)
 
     @property
     def units(self):