Make argument names consistent, update docstring, & add units

.github/workflows/pytest.yaml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        py: ["3.9", "3.10", "3.11"]
+        py: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: "actions/checkout@v3"

examples/Atom_Grid.ipynb

@@ -17,12 +17,12 @@
         "\n",
         "[AtomGrid](https://grid.qcdevs.org/pyapi/grid.atomgrid.html#grid.atomgrid.AtomGrid) constructs an atomic grid by combining a radial and angular components for evaluation, integration, interpolation, and differentiation in three-dimensional (3D) space. In quantum chemistry, this is typically used for computations of atomic properties. However, this is a general purpose grid that can be used for any function in 3D space.\n",
         "\n",
-        "This notebook showcases various functionalities of [AtomGrid](https://grid.qcdevs.org/pyapi/grid.atomgrid.html#grid.atomgrid.AtomGrid). For computing properties on the grid, we use $\\textbf{He}$ in the triplet state ($1s^1 2s^1$) as an example. The corresponding wavefunction is obtained from formatted checkpoint file `\"doc/notebooks/He_t.fchk\"`. The [`qc-iodata`](https://github.com/theochem/iodata) package is used for parsing the wavefuction data from the fchk file, and [`qc-gbasis`](https://github.com/theochem/gbasis) package is used for analytical evaluation of various properties in the grid.\n"
+        "This notebook showcases various functionalities of [AtomGrid](https://grid.qcdevs.org/pyapi/grid.atomgrid.html#grid.atomgrid.AtomGrid). For computing properties on the grid, we use $\\textbf{He}$ in the triplet state ($1s^1 2s^1$) as an example. The corresponding wavefunction is obtained from formatted checkpoint file `\"doc/notebooks/He_t.fchk\"`. The [qc-iodata](https://github.com/theochem/iodata) package is used for parsing the wavefuction data from the fchk file, and [qc-gbasis](https://github.com/theochem/gbasis) package is used for analytical evaluation of various properties in the grid.\n"
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 2,
+      "execution_count": 8,
       "metadata": {},
       "outputs": [
         {
@@ -57,12 +57,12 @@
         "\n",
         "There are multiple ways to construct an atomic grid, for a complete description see the [Atomic_Grid_Construction.ipynb]().\n",
         "\n",
-        "Here we construct an atomic grid from a radial grid instance and the degrees of the angular grid centered at the position of $\\textbf{He}$ nucleus. The radial grid is constructed by specifying the number of radial grid points. For more details on the radial and angular grids see [Radial_Grid.ipynb]() and [Angular_Grid.ipynb]().\n"
+        "Here we construct an atomic grid from a radial grid instance and the degrees of the angular grid centered at the position of $\\textbf{He}$ nucleus. The radial grid is constructed by specifying the number of radial grid points. For more details on the radial and angular grids see [One_dimensional_grids.ipynb](https://grid.qcdevs.org/notebooks/one_dimensional_grids.html) and [Angular_Grid.ipynb](https://grid.qcdevs.org/notebooks/angular_grid.html).\n"
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 3,
+      "execution_count": 9,
       "metadata": {},
       "outputs": [
         {
@@ -112,12 +112,12 @@
       "source": [
         "### Example: Integrate Electron Density\n",
         "\n",
-        "To integrate a scalar function over the atomic grid, we first need to evaluate the function on the grid points. Here, we compute the electron density $\\rho(\\mathbf{r})$ of the $\\textbf{He}$ in the triplet state ($1s^1 2s^1$) using the [`gbasis.evals.density`]() function of the [`qc-gbasis`](https://github.com/theochem/gbasis) package. The wavefunction data are loaded from the formatted checkpoint file using [`load_one`](https://iodata.readthedocs.io/en/latest/pyapi/iodata.api.html#iodata.api.load_one) function of [`qc-iodata`](https://github.com/theochem/iodata)package. The density values are then integrated using the [`AtomGrid.integrate`](https://grid.qcdevs.org/pyapi/grid.basegrid.html#grid.basegrid.Grid.integrate) method.\n"
+        "To integrate a scalar function over the atomic grid, we first need to evaluate the function on the grid points. Here, we compute the electron density $\\rho(\\mathbf{r})$ of the $\\textbf{He}$ in the triplet state ($1s^1 2s^1$) using the [gbasis.evals.density](https://gbasis.qcdevs.org/_autosummary/gbasis.evals.html#gbasis.evals.density.evaluate_density) function of the [qc-gbasis](https://github.com/theochem/gbasis) package. The wavefunction data are loaded from the formatted checkpoint file using [load_one](https://iodata.readthedocs.io/en/latest/pyapi/iodata.api.html#iodata.api.load_one) function of [qc-iodata](https://github.com/theochem/iodata)package. The density values are then integrated using the [AtomGrid.integrate](https://grid.qcdevs.org/pyapi/grid.basegrid.html#grid.basegrid.Grid.integrate) method.\n"
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 4,
+      "execution_count": 10,
       "metadata": {},
       "outputs": [
         {
@@ -171,7 +171,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 5,
+      "execution_count": 11,
       "metadata": {},
       "outputs": [
         {
@@ -222,12 +222,12 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "To identify the local maxima of radial electron density and corresponding radii, the [`scipy.signal.find_peaks`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.find_peaks.html) is used.\n"
+        "To identify the local maxima of radial electron density and corresponding radii, the [scipy.signal.find_peaks](https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.find_peaks.html) is used.\n"
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 13,
+      "execution_count": 12,
       "metadata": {},
       "outputs": [
         {
@@ -265,7 +265,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 7,
+      "execution_count": 13,
       "metadata": {},
       "outputs": [
         {
@@ -300,12 +300,12 @@
         "$$\n",
         "\n",
         "where $\\mathbf{r}$ and $w(\\mathbf{r})$ represent the coordinates and weights of grid points.\n",
-        "When $i = j$, the denominator is zero denominator and the energy is undefined. To ensure that grid points do not coincide, different grids are used for $\\mathbf{r}_i$ and $\\mathbf{r}_j$ within the same spatial domain. This can be easily done by introducing a second atomic grid with different angular degree or one less radial grid points. The electron density values on this second grid can be either directly computed or obtained by interpolating from the values on the first grid using the [`AtomGrid.interpolate`](https://grid.qcdevs.org/pyapi/grid.atomgrid.html#grid.atomgrid.AtomGrid.interpolate) method.\n"
+        "When $i = j$, the denominator is zero denominator and the energy is undefined. To ensure that grid points do not coincide, different grids are used for $\\mathbf{r}_i$ and $\\mathbf{r}_j$ within the same spatial domain. This can be easily done by introducing a second atomic grid with different angular degree or one less radial grid points. The electron density values on this second grid can be either directly computed or obtained by interpolating from the values on the first grid using the [AtomGrid.interpolate](https://grid.qcdevs.org/pyapi/grid.atomgrid.html#grid.atomgrid.AtomGrid.interpolate) method.\n"
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 8,
+      "execution_count": 14,
       "metadata": {},
       "outputs": [
         {

examples/Interpolation_and_Poisson.ipynb

@@ -40,7 +40,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 1,
+      "execution_count": 5,
       "metadata": {
         "ExecuteTime": {
           "end_time": "2024-01-08T20:58:10.192004233Z",
@@ -61,7 +61,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 2,
+      "execution_count": 6,
       "metadata": {
         "ExecuteTime": {
           "end_time": "2024-01-08T20:58:10.461254804Z",
@@ -80,12 +80,12 @@
         "btf = BeckeRTransform(rmin=1e-30, R=1.5)\n",
         "radial = btf.transform_1d_grid(oned)\n",
         "degree = 29\n",
-        "atgrid = AtomGrid.from_pruned(radial, 1, sectors_r=[], sectors_degree=[degree], center=center)"
+        "atgrid = AtomGrid.from_pruned(radial, 1, r_sectors=[], d_sectors=[degree], center=center)"
       ]
     },
     {
       "cell_type": "code",
-      "execution_count": 3,
+      "execution_count": 7,
       "metadata": {
         "ExecuteTime": {
           "end_time": "2024-01-08T20:58:10.840072685Z",
@@ -99,11 +99,11 @@
           "output_type": "stream",
           "text": [
             "Error difference between interpolation and true:\n",
-            "[1.89178096e-11 5.27372802e-11 5.82772147e-11 4.10898563e-15\n",
-            " 1.64881470e-11 2.55238009e-11 1.29296147e-12 2.59097473e-12\n",
-            " 2.75023420e-10 5.08640456e-11 8.28065238e-12 7.54837099e-10\n",
-            " 2.51240298e-11 6.69289698e-12 2.82764424e-11 2.35286288e-11\n",
-            " 4.27065323e-11 3.41960277e-11 5.42822891e-11 5.25577287e-11]\n"
+            "[5.50204594e-11 4.97960712e-11 9.96328462e-11 1.50277207e-11\n",
+            " 3.25926654e-11 2.01591117e-11 3.26607444e-11 8.44455422e-11\n",
+            " 4.00808614e-11 5.06480266e-10 7.52775412e-11 3.48676058e-11\n",
+            " 4.13636728e-11 1.11618694e-11 4.14768677e-11 4.12894238e-11\n",
+            " 7.26674645e-11 8.43535809e-11 5.25728962e-11 6.84093102e-11]\n"
           ]
         }
       ],
@@ -150,7 +150,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 4,
+      "execution_count": 8,
       "metadata": {
         "ExecuteTime": {
           "end_time": "2024-01-08T20:58:17.855028023Z",
@@ -164,8 +164,8 @@
           "output_type": "stream",
           "text": [
             "The maximum error: 1.4653770128456663e-06\n",
-            "The mean error: 1.1070838082589734e-06\n",
-            "The standard dev: 4.6000482348200205e-07\n"
+            "The mean error: 1.1070838082577226e-06\n",
+            "The standard dev: 4.600048234819135e-07\n"
           ]
         }
       ],
@@ -211,14 +211,14 @@
     "language_info": {
       "codemirror_mode": {
         "name": "ipython",
-        "version": 2
+        "version": 3
       },
       "file_extension": ".py",
       "mimetype": "text/x-python",
       "name": "python",
       "nbconvert_exporter": "python",
-      "pygments_lexer": "ipython2",
-      "version": "2.7.6"
+      "pygments_lexer": "ipython3",
+      "version": "3.10.12"
     }
   },
   "nbformat": 4,