From f0a83115097613f331b1c9b858115a4aa1605d56 Mon Sep 17 00:00:00 2001
From: Mathieu Doucet <matd10@yahoo.com>
Date: Tue, 10 Sep 2024 17:01:51 -0400
Subject: [PATCH] Add hydration model

---
 docs/index.rst                       |  8 ----
 src/refl1d_models/hydration_model.py | 56 ++++++++++++++++++++++++++++
 tests/test_hydration_model.py        |  9 +++++
 3 files changed, 65 insertions(+), 8 deletions(-)
 create mode 100644 src/refl1d_models/hydration_model.py
 create mode 100644 tests/test_hydration_model.py

diff --git a/docs/index.rst b/docs/index.rst
index 1b5768e..5388370 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -7,11 +7,3 @@ Refl1d example models
    :caption: Contents:
 
    README
-
-=========================================
-Indices and tables
-=========================================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/src/refl1d_models/hydration_model.py b/src/refl1d_models/hydration_model.py
new file mode 100644
index 0000000..129e4b8
--- /dev/null
+++ b/src/refl1d_models/hydration_model.py
@@ -0,0 +1,56 @@
+"""
+Hydration model example
+"""
+
+import numpy as np
+from refl1d.names import SLD, Experiment, FitProblem, Parameter, QProbe
+
+# PRobe ########################################################################
+q = np.logspace(np.log10(0.009), np.log10(0.18), num=150)
+dq = 0.025 * q / 2.35
+
+probe = QProbe(q, dq)
+
+# Materials ####################################################################
+silicon = SLD(name="Si", rho=2.07, irho=0.0)
+d2o = SLD(name="D2O", rho=6.13, irho=0.0)
+titanium = SLD(name="Ti", rho=-1.238, irho=0.0)
+copper = SLD(name="Cu", rho=6.446, irho=0.0)
+material = SLD(name="material", rho=-1.648, irho=0.1)
+sei = SLD(name="SEI", rho=4.581, irho=0.1)
+
+# Film definition ##############################################################
+sample = (
+    d2o(0, 43.77) | sei(177.7, 23.04) | material(21.73, 18.22) | copper(566.1, 9.736) | titanium(52.91, 12.7) | silicon
+)
+
+# Parameter ranges #############################################################
+sample["Ti"].thickness.range(20.0, 60.0)
+sample["Ti"].material.rho.range(-2.0, 0.0)
+sample["Ti"].interface.range(1.0, 20.0)
+sample["Cu"].thickness.range(10.0, 800.0)
+sample["Cu"].interface.range(8.0, 15.0)
+sample["material"].thickness.range(15.0, 100.0)
+sample["material"].material.rho.range(-3.0, 8.0)
+sample["material"].interface.range(1.0, 35.0)
+sample["SEI"].thickness.range(100.0, 300.0)
+sample["SEI"].interface.range(5.0, 25.0)
+
+# Define a base SLD value for the SEI layer
+base_sld = Parameter(value=3, name="base_sld").range(-3.0, 8.0)
+
+# Define a solvent penetration parameter for the SEI layer
+solvent_penetration = Parameter(value=0.0, name="penetration").range(0, 1)
+
+# The SLD of the SEI layer is a linear combination of the base SLD and the solvent SLD,
+# according to the solvent penetration parameter
+sample["SEI"].material.rho = base_sld * (1 - solvent_penetration) + sample["D2O"].material.rho * solvent_penetration
+
+# The probe has a normalization parameter and a background parameter
+probe.intensity = Parameter(value=1.0, name="normalization")
+probe.background.range(0.0, 1e-05)
+sample["D2O"].interface.range(25.0, 150.0)
+
+# Create the experiment and the problem objects
+experiment = Experiment(probe=probe, sample=sample)
+problem = FitProblem(experiment)
diff --git a/tests/test_hydration_model.py b/tests/test_hydration_model.py
new file mode 100644
index 0000000..e35ed6d
--- /dev/null
+++ b/tests/test_hydration_model.py
@@ -0,0 +1,9 @@
+from refl1d_models.hydration_model import experiment
+
+
+def test_hydration_model():
+    """
+    Example use and test of the hydration model
+    """
+    r, dr = experiment.reflectivity()
+    assert len(r) == 150