Update lattice strain fitting example

Author: morganjwilliams

docs/source/conf.py

@@ -343,7 +343,6 @@ def reset_mpl(gallery_conf, fname):
     )
     + "</dl>"
 )
-print(refcomps)
 rst_prolog = """
 .. |br| raw:: html
 

docs/source/gallery/examples/geochem/mineral_lattice.py

@@ -58,7 +58,7 @@
 # get the Shannon ionic radii for the elements in the 2+ site
 site2radii = [
     get_ionic_radii("Na", charge=1, coordination=8),
-    *[get_ionic_radii(el, charge=2, coordination=8) for el in ["Ca", "Eu", "Sr"]],
+    *get_ionic_radii(["Ca", "Eu", "Sr"], charge=2, coordination=8),
 ]
 # plot the relative paritioning curve for cations in the 2+ site
 site2Ds = D_Ca * np.array(
@@ -89,7 +89,7 @@
 #
 site3labels = REE(dropPm=True)
 # get the Shannon ionic radii for the elements in the 3+ site
-site3radii = [get_ionic_radii(x, charge=3, coordination=8) for x in REE(dropPm=True)]
+site3radii = get_ionic_radii([x for x in REE(dropPm=True)], charge=3, coordination=8)
 site3Ds = D_La * np.array(
     [strain_coefficient(rLa, rx, r0=r03, E=E_3, T=Tk) for rx in site3radii]
 )
@@ -103,9 +103,7 @@
     ax.annotate(
         l, xy=(r, d), xycoords="data", ha="right", va="bottom", fontsize=fontsize
     )
-ax.set_yscale("log")
-ax.set_ylabel("$D_X$")
-ax.set_xlabel("Radii ($\AA$)")
+ax.set(ylabel="$D_X$", xlabel="Radii ($\AA$)", yscale="log")
 fig
 ########################################################################################
 # As europium is commonly present as a mixture of both :math:`Eu^{2+}`
@@ -134,6 +132,8 @@
 ax.legend(bbox_to_anchor=(1.05, 1))
 fig
 ########################################################################################
+# Fitting Lattice Strain Models
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # Given the lattice strain model and a partitioning profile (for e.g. REE data),
 # we can also fit a model to a given curve; here we fit to our REE data above,
 # for which we have some known parameters to compare to:
@@ -158,8 +158,8 @@
 #
 from pyrolite.plot.spider import REE_v_radii
 
-ax = REE_v_radii()
-
+ax = REE_v_radii(index="radii")
+ax.set(ylabel="$D_X$", xlabel="Radii ($\AA$)")
 ax.plot(site3radii, site3Ds, label="True", color="k")
 ax.plot(
     site3radii,
@@ -169,18 +169,15 @@
     color="0.5",
 )
 
-ax.plot(site3radii, fit_lattice_strain._opt(site3radii, _ri, _tk, _D, z=3), label="Fit")
-
+ax.plot(
+    site3radii,
+    _lattice_opt_function(site3radii, _ri, _tk, _D, z=3),
+    label="Fit",
+    color="r",
+)
+ax.legend()
 ax.figure
 ########################################################################################
-# .. [#ref_1] Blundy, J., Wood, B., 1994. Prediction of crystal–melt partition coefficients
-#             from elastic moduli. Nature 372, 452.
-#             doi: `10.1038/372452A0 <https://doi.org/10.1038/372452A0>`__
-#
-# .. [#ref_2] Dohmen, R., Blundy, J., 2014. A predictive thermodynamic model for element partitioning
-#             between plagioclase and melt as a function of pressure, temperature and composition.
-#             American Journal of Science 314, 1319–1372.
-#             doi: `10.2475/09.2014.04 <https://doi.org/10.2475/09.2014.04>`__
 #
 # .. seealso::
 #
@@ -191,4 +188,18 @@
 #   Functions:
 #     :func:`~pyrolite.mineral.lattice.strain_coefficient`,
 #     :func:`~pyrolite.mineral.lattice.youngs_modulus_approximation`,
+#     :func:`~pyrolite.mineral.lattice.fit_lattice_strain`
 #     :func:`~pyrolite.geochem.get_ionic_radii`
+#
+# References
+# ~~~~~~~~~~~
+# .. [#ref_1] Blundy, J., Wood, B., 1994. Prediction of crystal–melt partition coefficients
+#             from elastic moduli. Nature 372, 452.
+#             doi: `10.1038/372452A0 <https://doi.org/10.1038/372452A0>`__
+#
+# .. [#ref_2] Dohmen, R., Blundy, J., 2014. A predictive thermodynamic model for element partitioning
+#             between plagioclase and melt as a function of pressure, temperature and composition.
+#             American Journal of Science 314, 1319–1372.
+#             doi: `10.2475/09.2014.04 <https://doi.org/10.2475/09.2014.04>`__
+#
+

pyrolite/geochem/ind.py

@@ -459,18 +459,20 @@ def get_ionic_radii(
     * Implement interpolation for coordination +/- charge.
     """
     if isinstance(element, list):
-        return [
-            get_ionic_radii(
-                e,
-                charge=charge,
-                coordination=coordination,
-                variant=variant,
-                source=source,
-                pauling=pauling,
-                **kwargs,
-            )
-            for e in element
-        ]
+        return np.array(
+            [
+                get_ionic_radii(
+                    e,
+                    charge=charge,
+                    coordination=coordination,
+                    variant=variant,
+                    source=source,
+                    pauling=pauling,
+                    **kwargs,
+                )
+                for e in element
+            ]
+        )
 
     if "shannon" in source.lower():
         df = __radii__["shannon"]
@@ -491,7 +493,7 @@ def get_ionic_radii(
         if charge in df.loc[elfltr, "charge"].unique():
             fltrs *= df.charge == charge
         else:
-            logger.warn("Charge {:d} not in table.".format(int(charge)))
+            logger.warning("Charge {:d} not in table.".format(int(charge)))
             # try to interpolate over charge?..
             # interpolate_charge=True
     else:
@@ -502,7 +504,7 @@ def get_ionic_radii(
         if coordination in df.loc[elfltr, "coordination"].unique():
             fltrs *= df.coordination == coordination
         else:
-            logger.warn("Coordination {:d} not in table.".format(int(coordination)))
+            logger.warning("Coordination {:d} not in table.".format(int(coordination)))
             # try to interpolate over coordination
             # interpolate_coordination=True