From 8193877ccb8512696795c79c95962ee4ad01c757 Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Wed, 19 Mar 2025 17:10:14 +0000
Subject: [PATCH 1/5] Removes limits struct from input to RAT

---
 RATapi/examples/languages/custom_bilayer.o | Bin 0 -> 34776 bytes
 RATapi/inputs.py                           |  20 ++------
 RATapi/run.py                              |   3 +-
 tests/test_inputs.py                       |  57 ++-------------------
 4 files changed, 9 insertions(+), 71 deletions(-)
 create mode 100644 RATapi/examples/languages/custom_bilayer.o

diff --git a/RATapi/examples/languages/custom_bilayer.o b/RATapi/examples/languages/custom_bilayer.o
new file mode 100644
index 0000000000000000000000000000000000000000..aa967bdbe6367f51cfab56b36ffb069c6bfe46f1
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literal 0
HcmV?d00001

diff --git a/RATapi/inputs.py b/RATapi/inputs.py
index 0bc00284..3798cb0f 100644
--- a/RATapi/inputs.py
+++ b/RATapi/inputs.py
@@ -10,7 +10,7 @@
 import RATapi
 import RATapi.controls
 import RATapi.wrappers
-from RATapi.rat_core import Checks, Control, Limits, NameStore, ProblemDefinition
+from RATapi.rat_core import Checks, Control, NameStore, ProblemDefinition
 from RATapi.utils.enums import Calculations, Languages, LayerModels, TypeOptions
 
 parameter_field = {
@@ -113,7 +113,7 @@ def __len__(self):
         return len(self.files)
 
 
-def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[ProblemDefinition, Limits, Control]:
+def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[ProblemDefinition, Control]:
     """Construct the inputs required for the compiled RAT code using the data defined in the input project and controls.
 
     Parameters
@@ -127,28 +127,14 @@ def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[Prob
     -------
     problem : RAT.rat_core.ProblemDefinition
         The problem input used in the compiled RAT code.
-    limits : RAT.rat_core.Limits
-        A list of min/max values for each parameter defined in the project.
     cpp_controls : RAT.rat_core.Control
         The controls object used in the compiled RAT code.
 
     """
-    limits = Limits()
-
-    for class_list in RATapi.project.parameter_class_lists:
-        setattr(
-            limits,
-            parameter_field[class_list],
-            [[element.min, element.max] for element in getattr(project, class_list)],
-        )
-
-    if project.model == LayerModels.CustomXY:
-        controls.calcSldDuringFit = True
-
     problem = make_problem(project)
     cpp_controls = make_controls(controls)
 
-    return problem, limits, cpp_controls
+    return problem, cpp_controls
 
 
 def make_problem(project: RATapi.Project) -> ProblemDefinition:
diff --git a/RATapi/run.py b/RATapi/run.py
index 17f47ecc..476daa39 100644
--- a/RATapi/run.py
+++ b/RATapi/run.py
@@ -109,7 +109,7 @@ def run(project, controls):
 
     horizontal_line = "\u2500" * 107 + "\n"
     display_on = controls.display != Display.Off
-    problem_definition, limits, cpp_controls = make_input(project, controls)
+    problem_definition, cpp_controls = make_input(project, controls)
 
     if display_on:
         print("Starting RAT " + horizontal_line)
@@ -118,7 +118,6 @@ def run(project, controls):
     with ProgressBar(display=display_on), TextOutput(display=display_on):
         problem_definition, output_results, bayes_results = RATapi.rat_core.RATMain(
             problem_definition,
-            limits,
             cpp_controls,
         )
     end = time.time()
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index d931ff5f..38911ef2 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -9,7 +9,7 @@
 import RATapi
 import RATapi.wrappers
 from RATapi.inputs import FileHandles, check_indices, make_controls, make_input, make_problem
-from RATapi.rat_core import Checks, Control, Limits, NameStore, ProblemDefinition
+from RATapi.rat_core import Checks, Control, NameStore, ProblemDefinition
 from RATapi.utils.enums import (
     BackgroundActions,
     BoundHandling,
@@ -351,36 +351,6 @@ def custom_xy_problem(test_names, test_checks):
     return problem
 
 
-@pytest.fixture
-def normal_limits():
-    """The expected limits object from "standard_layers_project" and "custom_xy_project"."""
-    limits = Limits()
-    limits.params = [[1.0, 5.0], [0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
-    limits.backgroundParams = [[1e-7, 1e-5]]
-    limits.scalefactors = [[0.02, 0.25]]
-    limits.bulkIns = [[0.0, 0.0]]
-    limits.bulkOuts = [[6.2e-6, 6.35e-6]]
-    limits.resolutionParams = [[0.01, 0.05]]
-    limits.domainRatios = []
-
-    return limits
-
-
-@pytest.fixture
-def domains_limits():
-    """The expected limits object from "domains_project"."""
-    limits = Limits()
-    limits.params = [[1.0, 5.0], [0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
-    limits.backgroundParams = [[1e-7, 1e-5]]
-    limits.scalefactors = [[0.02, 0.25]]
-    limits.bulkIns = [[0.0, 0.0]]
-    limits.bulkOuts = [[6.2e-6, 6.35e-6]]
-    limits.resolutionParams = [[0.01, 0.05]]
-    limits.domainRatios = [[0.4, 0.6]]
-
-    return limits
-
-
 @pytest.fixture
 def standard_layers_controls():
     """The expected controls object for input to the compiled RAT code given the default inputs and
@@ -458,55 +428,38 @@ def custom_xy_controls():
 
 
 @pytest.mark.parametrize(
-    ["test_project", "test_problem", "test_limits", "test_controls"],
+    ["test_project", "test_problem", "test_controls"],
     [
         (
             "standard_layers_project",
             "standard_layers_problem",
-            "normal_limits",
             "standard_layers_controls",
         ),
         (
             "custom_xy_project",
             "custom_xy_problem",
-            "normal_limits",
             "custom_xy_controls",
         ),
         (
             "domains_project",
             "domains_problem",
-            "domains_limits",
             "standard_layers_controls",
         ),
     ],
 )
-def test_make_input(test_project, test_problem, test_limits, test_controls, request) -> None:
-    """When converting the "project" and "controls", we should obtain the five input objects required for the compiled
+def test_make_input(test_project, test_problem, test_controls, request) -> None:
+    """When converting the "project" and "controls", we should obtain the two input objects required for the compiled
     RAT code.
     """
     test_project = request.getfixturevalue(test_project)
     test_problem = request.getfixturevalue(test_problem)
-    test_limits = request.getfixturevalue(test_limits)
     test_controls = request.getfixturevalue(test_controls)
 
-    parameter_fields = [
-        "params",
-        "backgroundParams",
-        "scalefactors",
-        "bulkIns",
-        "bulkOuts",
-        "resolutionParams",
-        "domainRatios",
-    ]
+    problem, controls = make_input(test_project, RATapi.Controls())
 
-    problem, limits, controls = make_input(test_project, RATapi.Controls())
     problem = pickle.loads(pickle.dumps(problem))
     check_problem_equal(problem, test_problem)
 
-    limits = pickle.loads(pickle.dumps(limits))
-    for limit_field in parameter_fields:
-        assert np.all(getattr(limits, limit_field) == getattr(test_limits, limit_field))
-
     controls = pickle.loads(pickle.dumps(controls))
     check_controls_equal(controls, test_controls)
 

From 16e53d1ad3f07c6788cf53e10af74ac2dce67e1c Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Wed, 19 Mar 2025 18:32:36 +0000
Subject: [PATCH 2/5] Renames "layerSlds" as "layers"

---
 RATapi/outputs.py     |  13 +--
 tests/conftest.py     | 240 +++++++++++++++++++++---------------------
 tests/test_outputs.py |   4 +-
 tests/utils.py        |   2 +-
 4 files changed, 130 insertions(+), 129 deletions(-)

diff --git a/RATapi/outputs.py b/RATapi/outputs.py
index 84b3222d..af3c7a69 100644
--- a/RATapi/outputs.py
+++ b/RATapi/outputs.py
@@ -141,12 +141,13 @@ class Results:
         The background for each contrast defined over the simulation range.
     resolutions : list
         The resolution for each contrast defined over the simulation range.
-    layerSlds : list
-        The array of layer parameter values for each contrast.
     sldProfiles : list
         The SLD profiles for each contrast.
+    layers : list
+        The array of layer parameter values for each contrast.
     resampledLayers : list
-        If resampling is used, the SLD for each contrast after resampling has been performed.
+        If resampling is used, the array of layer parameter values for each contrast after resampling has been
+        performed.
     calculationResults : CalculationResults
         The chi-squared fit results from the final calculation and fit.
     contrastParams : ContrastParams
@@ -164,8 +165,8 @@ class Results:
     shiftedData: list
     backgrounds: list
     resolutions: list
-    layerSlds: list
     sldProfiles: list
+    layers: list
     resampledLayers: list
     calculationResults: CalculationResults
     contrastParams: ContrastParams
@@ -502,8 +503,8 @@ def make_results(
             shiftedData=output_results.shiftedData,
             backgrounds=output_results.backgrounds,
             resolutions=output_results.resolutions,
-            layerSlds=output_results.layerSlds,
             sldProfiles=output_results.sldProfiles,
+            layers=output_results.layers,
             resampledLayers=output_results.resampledLayers,
             calculationResults=calculation_results,
             contrastParams=contrast_params,
@@ -524,8 +525,8 @@ def make_results(
             shiftedData=output_results.shiftedData,
             backgrounds=output_results.backgrounds,
             resolutions=output_results.resolutions,
-            layerSlds=output_results.layerSlds,
             sldProfiles=output_results.sldProfiles,
+            layers=output_results.layers,
             resampledLayers=output_results.resampledLayers,
             calculationResults=calculation_results,
             contrastParams=contrast_params,
diff --git a/tests/conftest.py b/tests/conftest.py
index ce580c15..7d987a9f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -774,36 +774,6 @@ def reflectivity_calculation_output_results():
             ]
         ),
     ]
-    results.layerSlds = [
-        [
-            np.array(
-                [
-                    [1.954000e01, 4.001499e-06, 3.000000e00],
-                    [2.266000e01, -6.586988e-08, 3.000000e00],
-                    [8.560000e00, 3.672535e-06, 5.640000e00],
-                    [1.712000e01, 5.980000e-06, 5.640000e00],
-                    [1.070000e01, 3.100365e-06, 6.014000e00],
-                    [1.782000e01, 6.751924e-07, 6.014000e00],
-                    [1.782000e01, 6.751924e-07, 6.014000e00],
-                    [1.070000e01, 3.100365e-06, 6.014000e00],
-                ],
-            ),
-        ],
-        [
-            np.array(
-                [
-                    [1.9540000e01, 3.1114020e-06, 3.0000000e00],
-                    [2.2660000e01, -2.6387028e-07, 3.0000000e00],
-                    [8.5600000e00, 1.9590700e-06, 5.6400000e00],
-                    [1.7120000e01, 2.2100000e-06, 5.6400000e00],
-                    [1.0700000e01, 1.7375100e-06, 6.0140000e00],
-                    [1.7820000e01, 1.0164400e-08, 6.0140000e00],
-                    [1.7820000e01, 1.0164400e-08, 6.0140000e00],
-                    [1.0700000e01, 1.7375100e-06, 6.0140000e00],
-                ],
-            ),
-        ],
-    ]
     results.sldProfiles = [
         [
             np.array(
@@ -866,6 +836,36 @@ def reflectivity_calculation_output_results():
             ),
         ],
     ]
+    results.layers = [
+        [
+            np.array(
+                [
+                    [1.954000e01, 4.001499e-06, 3.000000e00],
+                    [2.266000e01, -6.586988e-08, 3.000000e00],
+                    [8.560000e00, 3.672535e-06, 5.640000e00],
+                    [1.712000e01, 5.980000e-06, 5.640000e00],
+                    [1.070000e01, 3.100365e-06, 6.014000e00],
+                    [1.782000e01, 6.751924e-07, 6.014000e00],
+                    [1.782000e01, 6.751924e-07, 6.014000e00],
+                    [1.070000e01, 3.100365e-06, 6.014000e00],
+                ],
+            ),
+        ],
+        [
+            np.array(
+                [
+                    [1.9540000e01, 3.1114020e-06, 3.0000000e00],
+                    [2.2660000e01, -2.6387028e-07, 3.0000000e00],
+                    [8.5600000e00, 1.9590700e-06, 5.6400000e00],
+                    [1.7120000e01, 2.2100000e-06, 5.6400000e00],
+                    [1.0700000e01, 1.7375100e-06, 6.0140000e00],
+                    [1.7820000e01, 1.0164400e-08, 6.0140000e00],
+                    [1.7820000e01, 1.0164400e-08, 6.0140000e00],
+                    [1.0700000e01, 1.7375100e-06, 6.0140000e00],
+                ],
+            ),
+        ],
+    ]
     results.resampledLayers = [[np.array([[0.0, 0.0, 0.0]])], [np.array([[0.0, 0.0, 0.0]])]]
     results.calculationResults = RATapi.rat_core.Calculation()
     results.calculationResults.chiValues = np.array([202.83057377, 1641.4024969])
@@ -1430,36 +1430,6 @@ def reflectivity_calculation_results():
                 ]
             ),
         ],
-        layerSlds=[
-            [
-                np.array(
-                    [
-                        [1.954000e01, 4.001499e-06, 3.000000e00],
-                        [2.266000e01, -6.586988e-08, 3.000000e00],
-                        [8.560000e00, 3.672535e-06, 5.640000e00],
-                        [1.712000e01, 5.980000e-06, 5.640000e00],
-                        [1.070000e01, 3.100365e-06, 6.014000e00],
-                        [1.782000e01, 6.751924e-07, 6.014000e00],
-                        [1.782000e01, 6.751924e-07, 6.014000e00],
-                        [1.070000e01, 3.100365e-06, 6.014000e00],
-                    ],
-                ),
-            ],
-            [
-                np.array(
-                    [
-                        [1.9540000e01, 3.1114020e-06, 3.0000000e00],
-                        [2.2660000e01, -2.6387028e-07, 3.0000000e00],
-                        [8.5600000e00, 1.9590700e-06, 5.6400000e00],
-                        [1.7120000e01, 2.2100000e-06, 5.6400000e00],
-                        [1.0700000e01, 1.7375100e-06, 6.0140000e00],
-                        [1.7820000e01, 1.0164400e-08, 6.0140000e00],
-                        [1.7820000e01, 1.0164400e-08, 6.0140000e00],
-                        [1.0700000e01, 1.7375100e-06, 6.0140000e00],
-                    ],
-                ),
-            ],
-        ],
         sldProfiles=[
             [
                 np.array(
@@ -1522,6 +1492,36 @@ def reflectivity_calculation_results():
                 ),
             ],
         ],
+        layers=[
+            [
+                np.array(
+                    [
+                        [1.954000e01, 4.001499e-06, 3.000000e00],
+                        [2.266000e01, -6.586988e-08, 3.000000e00],
+                        [8.560000e00, 3.672535e-06, 5.640000e00],
+                        [1.712000e01, 5.980000e-06, 5.640000e00],
+                        [1.070000e01, 3.100365e-06, 6.014000e00],
+                        [1.782000e01, 6.751924e-07, 6.014000e00],
+                        [1.782000e01, 6.751924e-07, 6.014000e00],
+                        [1.070000e01, 3.100365e-06, 6.014000e00],
+                    ],
+                ),
+            ],
+            [
+                np.array(
+                    [
+                        [1.9540000e01, 3.1114020e-06, 3.0000000e00],
+                        [2.2660000e01, -2.6387028e-07, 3.0000000e00],
+                        [8.5600000e00, 1.9590700e-06, 5.6400000e00],
+                        [1.7120000e01, 2.2100000e-06, 5.6400000e00],
+                        [1.0700000e01, 1.7375100e-06, 6.0140000e00],
+                        [1.7820000e01, 1.0164400e-08, 6.0140000e00],
+                        [1.7820000e01, 1.0164400e-08, 6.0140000e00],
+                        [1.0700000e01, 1.7375100e-06, 6.0140000e00],
+                    ],
+                ),
+            ],
+        ],
         resampledLayers=[[np.array([[0.0, 0.0, 0.0]])], [np.array([[0.0, 0.0, 0.0]])]],
         calculationResults=RATapi.outputs.CalculationResults(
             chiValues=np.array([202.83057377, 1641.4024969]),
@@ -2091,36 +2091,6 @@ def dream_output_results():
             ]
         ),
     ]
-    results.layerSlds = [
-        [
-            np.array(
-                [
-                    [3.15755349e01, 3.35278238e-06, 4.16625659e00],
-                    [3.61791464e01, 7.68327921e-07, 4.16625659e00],
-                    [1.00488530e01, 2.06044530e-06, 2.78042232e01],
-                    [1.08043784e01, 3.29384190e-06, 2.78042232e01],
-                    [2.42251646e01, 2.35556998e-06, 1.55593097e01],
-                    [1.49022278e01, 7.42138004e-07, 1.55593097e01],
-                    [1.49022278e01, 7.42138004e-07, 1.55593097e01],
-                    [2.42251646e01, 2.35556998e-06, 1.55593097e01],
-                ],
-            ),
-        ],
-        [
-            np.array(
-                [
-                    [3.15755349e01, 4.11636356e-06, 4.16625659e00],
-                    [3.61791464e01, 1.39268494e-06, 4.16625659e00],
-                    [1.00488530e01, 2.45715680e-06, 2.78042232e01],
-                    [1.08043784e01, 5.26668495e-06, 2.78042232e01],
-                    [2.42251646e01, 3.31348777e-06, 1.55593097e01],
-                    [1.49022278e01, 1.37428245e-06, 1.55593097e01],
-                    [1.49022278e01, 1.37428245e-06, 1.55593097e01],
-                    [2.42251646e01, 3.31348777e-06, 1.55593097e01],
-                ],
-            ),
-        ],
-    ]
     results.sldProfiles = [
         [
             np.array(
@@ -2191,6 +2161,36 @@ def dream_output_results():
             ),
         ],
     ]
+    results.layers = [
+        [
+            np.array(
+                [
+                    [3.15755349e01, 3.35278238e-06, 4.16625659e00],
+                    [3.61791464e01, 7.68327921e-07, 4.16625659e00],
+                    [1.00488530e01, 2.06044530e-06, 2.78042232e01],
+                    [1.08043784e01, 3.29384190e-06, 2.78042232e01],
+                    [2.42251646e01, 2.35556998e-06, 1.55593097e01],
+                    [1.49022278e01, 7.42138004e-07, 1.55593097e01],
+                    [1.49022278e01, 7.42138004e-07, 1.55593097e01],
+                    [2.42251646e01, 2.35556998e-06, 1.55593097e01],
+                ],
+            ),
+        ],
+        [
+            np.array(
+                [
+                    [3.15755349e01, 4.11636356e-06, 4.16625659e00],
+                    [3.61791464e01, 1.39268494e-06, 4.16625659e00],
+                    [1.00488530e01, 2.45715680e-06, 2.78042232e01],
+                    [1.08043784e01, 5.26668495e-06, 2.78042232e01],
+                    [2.42251646e01, 3.31348777e-06, 1.55593097e01],
+                    [1.49022278e01, 1.37428245e-06, 1.55593097e01],
+                    [1.49022278e01, 1.37428245e-06, 1.55593097e01],
+                    [2.42251646e01, 3.31348777e-06, 1.55593097e01],
+                ],
+            ),
+        ],
+    ]
     results.resampledLayers = [[np.array([[0.0, 0.0, 0.0]])], [np.array([[0.0, 0.0, 0.0]])]]
     results.calculationResults = RATapi.rat_core.Calculation()
     results.calculationResults.chiValues = (np.array([4.6077885, 7.00028098]),)
@@ -4576,36 +4576,6 @@ def dream_results():
                 ]
             ),
         ],
-        layerSlds=[
-            [
-                np.array(
-                    [
-                        [3.15755349e01, 3.35278238e-06, 4.16625659e00],
-                        [3.61791464e01, 7.68327921e-07, 4.16625659e00],
-                        [1.00488530e01, 2.06044530e-06, 2.78042232e01],
-                        [1.08043784e01, 3.29384190e-06, 2.78042232e01],
-                        [2.42251646e01, 2.35556998e-06, 1.55593097e01],
-                        [1.49022278e01, 7.42138004e-07, 1.55593097e01],
-                        [1.49022278e01, 7.42138004e-07, 1.55593097e01],
-                        [2.42251646e01, 2.35556998e-06, 1.55593097e01],
-                    ],
-                ),
-            ],
-            [
-                np.array(
-                    [
-                        [3.15755349e01, 4.11636356e-06, 4.16625659e00],
-                        [3.61791464e01, 1.39268494e-06, 4.16625659e00],
-                        [1.00488530e01, 2.45715680e-06, 2.78042232e01],
-                        [1.08043784e01, 5.26668495e-06, 2.78042232e01],
-                        [2.42251646e01, 3.31348777e-06, 1.55593097e01],
-                        [1.49022278e01, 1.37428245e-06, 1.55593097e01],
-                        [1.49022278e01, 1.37428245e-06, 1.55593097e01],
-                        [2.42251646e01, 3.31348777e-06, 1.55593097e01],
-                    ],
-                ),
-            ],
-        ],
         sldProfiles=[
             [
                 np.array(
@@ -4676,6 +4646,36 @@ def dream_results():
                 ),
             ],
         ],
+        layers=[
+            [
+                np.array(
+                    [
+                        [3.15755349e01, 3.35278238e-06, 4.16625659e00],
+                        [3.61791464e01, 7.68327921e-07, 4.16625659e00],
+                        [1.00488530e01, 2.06044530e-06, 2.78042232e01],
+                        [1.08043784e01, 3.29384190e-06, 2.78042232e01],
+                        [2.42251646e01, 2.35556998e-06, 1.55593097e01],
+                        [1.49022278e01, 7.42138004e-07, 1.55593097e01],
+                        [1.49022278e01, 7.42138004e-07, 1.55593097e01],
+                        [2.42251646e01, 2.35556998e-06, 1.55593097e01],
+                    ],
+                ),
+            ],
+            [
+                np.array(
+                    [
+                        [3.15755349e01, 4.11636356e-06, 4.16625659e00],
+                        [3.61791464e01, 1.39268494e-06, 4.16625659e00],
+                        [1.00488530e01, 2.45715680e-06, 2.78042232e01],
+                        [1.08043784e01, 5.26668495e-06, 2.78042232e01],
+                        [2.42251646e01, 3.31348777e-06, 1.55593097e01],
+                        [1.49022278e01, 1.37428245e-06, 1.55593097e01],
+                        [1.49022278e01, 1.37428245e-06, 1.55593097e01],
+                        [2.42251646e01, 3.31348777e-06, 1.55593097e01],
+                    ],
+                ),
+            ],
+        ],
         resampledLayers=[[np.array([[0.0, 0.0, 0.0]])], [np.array([[0.0, 0.0, 0.0]])]],
         calculationResults=RATapi.outputs.CalculationResults(
             chiValues=np.array([4.6077885, 7.00028098]),
diff --git a/tests/test_outputs.py b/tests/test_outputs.py
index 7d9a0afd..a0f91af9 100644
--- a/tests/test_outputs.py
+++ b/tests/test_outputs.py
@@ -24,8 +24,8 @@ def reflectivity_calculation_str():
         "shiftedData = [Data array: [21 x 3], Data array: [21 x 3]],\n"
         "backgrounds = [Data array: [82 x 3], Data array: [82 x 3]],\n"
         "resolutions = [Data array: [82 x 2], Data array: [82 x 2]],\n"
-        "layerSlds = [[Data array: [8 x 3]], [Data array: [8 x 3]]],\n"
         "sldProfiles = [[Data array: [25 x 2], Data array: [25 x 2]]],\n"
+        "layers = [[Data array: [8 x 3]], [Data array: [8 x 3]]],\n"
         "resampledLayers = [[Data array: [1 x 3]], [Data array: [1 x 3]]],\n"
         "calculationResults = CalculationResults(\n"
         "\tchiValues = [ 202.83057377 1641.4024969 ],\n"
@@ -59,8 +59,8 @@ def dream_str():
         "shiftedData = [Data array: [21 x 3], Data array: [21 x 3]],\n"
         "backgrounds = [Data array: [82 x 3], Data array: [82 x 3]],\n"
         "resolutions = [Data array: [82 x 2], Data array: [82 x 2]],\n"
-        "layerSlds = [[Data array: [8 x 3]], [Data array: [8 x 3]]],\n"
         "sldProfiles = [[Data array: [29 x 2], Data array: [29 x 2]]],\n"
+        "layers = [[Data array: [8 x 3]], [Data array: [8 x 3]]],\n"
         "resampledLayers = [[Data array: [1 x 3]], [Data array: [1 x 3]]],\n"
         "calculationResults = CalculationResults(\n"
         "\tchiValues = [4.6077885  7.00028098],\n"
diff --git a/tests/utils.py b/tests/utils.py
index a9411aac..36805e6d 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -31,7 +31,7 @@ def check_results_equal(actual_results, expected_results) -> None:
     "CalculationResults" and "ContrastParams".
     """
     list_fields = ["reflectivity", "simulation", "shiftedData", "backgrounds", "resolutions"]
-    double_list_fields = ["layerSlds", "sldProfiles", "resampledLayers"]
+    double_list_fields = ["sldProfiles", "layers", "resampledLayers"]
     contrast_param_fields = [
         "scalefactors",
         "bulkIn",

From 269ecea2157771d3e33d7cf0e939fc81f4bbd1af Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Tue, 25 Mar 2025 12:45:07 +0000
Subject: [PATCH 3/5] Updates submodule and build

---
 RATapi/examples/languages/custom_bilayer.o | Bin 34776 -> 0 bytes
 RATapi/outputs.py                          |   4 --
 cpp/RAT                                    |   2 +-
 cpp/includes/defines.h                     |  11 ++-
 cpp/rat.cpp                                |  77 ++++-----------------
 tests/conftest.py                          |   2 -
 tests/test_inputs.py                       |   2 +-
 tests/test_outputs.py                      |   1 -
 tests/utils.py                             |   2 +-
 9 files changed, 19 insertions(+), 82 deletions(-)
 delete mode 100644 RATapi/examples/languages/custom_bilayer.o

diff --git a/RATapi/examples/languages/custom_bilayer.o b/RATapi/examples/languages/custom_bilayer.o
deleted file mode 100644
index aa967bdbe6367f51cfab56b36ffb069c6bfe46f1..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/RATapi/outputs.py b/RATapi/outputs.py
index af3c7a69..150ebc2d 100644
--- a/RATapi/outputs.py
+++ b/RATapi/outputs.py
@@ -324,8 +324,6 @@ class DreamOutput(RATResult):
         The runtime of the DREAM algorithm in seconds.
     iteration : float
         The number of iterations performed.
-    modelOutput : float
-        Unused. Will always be 0.
     AR : np.ndarray
         A two-column array where ``DreamOutput.AR[i, 0]`` is an iteration number
         and ``DreamOutput.AR[i, 1]`` is the average acceptance rate of chain step
@@ -345,7 +343,6 @@ class DreamOutput(RATResult):
     outlierChains: np.ndarray
     runtime: float
     iteration: float
-    modelOutput: float
     AR: np.ndarray
     R_stat: np.ndarray
     CR: np.ndarray
@@ -484,7 +481,6 @@ def make_results(
             outlierChains=bayes_results.dreamOutput.outlierChains,
             runtime=bayes_results.dreamOutput.runtime,
             iteration=bayes_results.dreamOutput.iteration,
-            modelOutput=bayes_results.dreamOutput.modelOutput,
             AR=bayes_results.dreamOutput.AR,
             R_stat=bayes_results.dreamOutput.R_stat,
             CR=bayes_results.dreamOutput.CR,
diff --git a/cpp/RAT b/cpp/RAT
index 282d17be..b33f77a0 160000
--- a/cpp/RAT
+++ b/cpp/RAT
@@ -1 +1 @@
-Subproject commit 282d17beb964af0855c1b2cc412e0b187b1a4140
+Subproject commit b33f77a0cbab9c9493cfe06120e3e1ac97d3e8f8
diff --git a/cpp/includes/defines.h b/cpp/includes/defines.h
index ffecaec3..90e6e544 100644
--- a/cpp/includes/defines.h
+++ b/cpp/includes/defines.h
@@ -237,8 +237,6 @@ runtime : float
     The runtime of the DREAM algorithm in seconds.
 iteration : float
     The number of iterations performed.
-modelOutput : float
-    Unused. Will always be 0.
 AR : np.ndarray[np.float]
     A two-column array where ``DreamOutput.AR[i, 0]`` is an iteration number
     and ``DreamOutput.AR[i, 1]`` is the average acceptance rate of chain step
@@ -259,7 +257,6 @@ struct DreamOutput
     py::array_t<real_T> outlierChains;
     real_T runtime;
     real_T iteration;
-    real_T modelOutput;
     py::array_t<real_T> AR;
     py::array_t<real_T> R_stat;
     py::array_t<real_T> CR;
@@ -354,12 +351,12 @@ backgrounds : list
     The background for each contrast defined over the simulation range.
 resolutions : list
     The resolution for each contrast defined over the simulation range.
-layerSlds : list
-    The array of layer parameter values for each contrast.
 sldProfiles : list
     The SLD profiles for each contrast.
+layers : list
+    The array of layer parameter values for each contrast.
 resampledLayers : list
-    If resampling is used, the SLD for each contrast after resampling has been performed.
+    If resampling is used, the array of layer parameter values for each contrast after resampling has been performed.
 calculationResults : RATapi.rat_core.Calculation
     The chi-squared fit results from the final calculation and fit.
 contrastParams : RATapi.rat_core.ContrastParams
@@ -377,8 +374,8 @@ struct OutputResult {
     py::list shiftedData;
     py::list backgrounds;
     py::list resolutions;
-    py::list layerSlds;
     py::list sldProfiles;
+    py::list layers;
     py::list resampledLayers;
     Calculation calculationResults {};
     ContrastParams contrastParams {};
diff --git a/cpp/rat.cpp b/cpp/rat.cpp
index d8d48d68..a92dc49d 100644
--- a/cpp/rat.cpp
+++ b/cpp/rat.cpp
@@ -301,21 +301,6 @@ RAT::b_ProblemDefinition createProblemDefinitionStruct(const ProblemDefinition&
 }
 
 
-RAT::ProblemLimits createProblemLimitsStruct(const Limits& limits)
-{
-    RAT::ProblemLimits limits_struct;
-    limits_struct.params = customCaller("Limits.params", pyArrayToRatArray2d, limits.params);
-    limits_struct.backgroundParams = customCaller("Limits.backgroundParams", pyArrayToRatArray2d, limits.backgroundParams);
-    limits_struct.scalefactors = customCaller("Limits.scalefactors", pyArrayToRatArray2d, limits.scalefactors);
-    limits_struct.bulkIns = customCaller("Limits.bulkIns", pyArrayToRatArray2d, limits.bulkIns);
-    limits_struct.bulkOuts = customCaller("Limits.bulkOuts", pyArrayToRatArray2d, limits.bulkOuts);
-    limits_struct.resolutionParams = customCaller("Limits.resolutionParams", pyArrayToRatArray2d, limits.resolutionParams);
-    limits_struct.domainRatios = customCaller("Limits.domainRatios", pyArrayToRatArray2d, limits.domainRatios);
-    
-    return limits_struct;
-}
-
-
 RAT::Controls createControlsStruct(const Control& control)
 {
     RAT::Controls control_struct;
@@ -391,26 +376,26 @@ OutputResult OutputResultFromStruct(const RAT::Results result)
         output_result.resolutions.append(array);
     }
 
-    for (int32_T idx0{0}; idx0 < result.layerSlds.size(0); idx0++) {
+    for (int32_T idx0{0}; idx0 < result.sldProfiles.size(0); idx0++) {
         py::list inner_list;
-        for (int32_T idx1{0}; idx1 < result.layerSlds.size(1); idx1++) {
-            auto tmp = result.layerSlds[idx0 +  result.layerSlds.size(0) * idx1];
+        for (int32_T idx1{0}; idx1 < result.sldProfiles.size(1); idx1++) {
+            auto tmp = result.sldProfiles[idx0 +  result.sldProfiles.size(0) * idx1];
             auto array = py::array_t<real_T, py::array::f_style>({tmp.f1.size(0), tmp.f1.size(1)});
             std::memcpy(array.request().ptr, tmp.f1.data(), array.nbytes());
             inner_list.append(array);
         }
-        output_result.layerSlds.append(inner_list);
+        output_result.sldProfiles.append(inner_list);
     }
 
-    for (int32_T idx0{0}; idx0 < result.sldProfiles.size(0); idx0++) {
+    for (int32_T idx0{0}; idx0 < result.layers.size(0); idx0++) {
         py::list inner_list;
-        for (int32_T idx1{0}; idx1 < result.sldProfiles.size(1); idx1++) {
-            auto tmp = result.sldProfiles[idx0 +  result.sldProfiles.size(0) * idx1];
+        for (int32_T idx1{0}; idx1 < result.layers.size(1); idx1++) {
+            auto tmp = result.layers[idx0 +  result.layers.size(0) * idx1];
             auto array = py::array_t<real_T, py::array::f_style>({tmp.f1.size(0), tmp.f1.size(1)});
             std::memcpy(array.request().ptr, tmp.f1.data(), array.nbytes());
             inner_list.append(array);
         }
-        output_result.sldProfiles.append(inner_list);
+        output_result.layers.append(inner_list);
     }
 
     for (int32_T idx0{0}; idx0 < result.resampledLayers.size(0); idx0++) {
@@ -548,7 +533,6 @@ BayesResults bayesResultsFromStruct(const RAT::BayesResults results)
     bayesResults.dreamOutput.outlierChains = pyArray2dFromBoundedArray<coder::bounded_array<real_T, 2000U, 2U>>(results.dreamOutput.outlierChains);
     bayesResults.dreamOutput.runtime = results.dreamOutput.runtime;
     bayesResults.dreamOutput.iteration = results.dreamOutput.iteration;
-    bayesResults.dreamOutput.modelOutput = results.dreamOutput.modelOutput;
     bayesResults.dreamOutput.R_stat = pyArrayFromRatArray2d(results.dreamOutput.R_stat);
     bayesResults.dreamOutput.CR = pyArrayFromRatArray2d(results.dreamOutput.CR);
     bayesResults.dreamOutput.AR = pyArray2dFromBoundedArray<coder::bounded_array<real_T, 2000U, 2U>>(results.dreamOutput.AR);
@@ -582,8 +566,6 @@ Parameters
 ----------
 problem_def : Rat.rat_core.ProblemDefinition
     The project input for the RAT calculation.
-limits : RATapi.rat_core.Limits
-    Min and max values for each parameter defined in the problem definition.
 control : RATapi.rat_core.Control
     The controls object for the RAT calculation.
 
@@ -597,16 +579,15 @@ bayes_result : Rat.rat_core.BayesResults
     The extra results if RAT calculation is Bayesian.
 )";
 
-py::tuple RATMain(const ProblemDefinition& problem_def, const Limits& limits, const Control& control)
+py::tuple RATMain(const ProblemDefinition& problem_def, const Control& control)
 {
     RAT::b_ProblemDefinition problem_def_struct = createProblemDefinitionStruct(problem_def);
-    RAT::ProblemLimits limits_struct = createProblemLimitsStruct(limits);
     RAT::Controls control_struct = createControlsStruct(control);
     // Output
     RAT::Results results;
     RAT::BayesResults bayesResults;
     // Call the entry-point
-    RAT::RATMain(&problem_def_struct, &limits_struct, &control_struct, &results, &bayesResults);
+    RAT::RATMain(&problem_def_struct, &control_struct, &results, &bayesResults);
     // Copy result to output
     auto out_problem_def = problemDefinitionFromStruct(problem_def_struct);
     out_problem_def.customFiles = problem_def.customFiles.attr("copy")(); 
@@ -802,7 +783,6 @@ PYBIND11_MODULE(rat_core, m) {
         .def_readwrite("outlierChains", &DreamOutput::outlierChains)
         .def_readwrite("runtime", &DreamOutput::runtime)
         .def_readwrite("iteration", &DreamOutput::iteration)
-        .def_readwrite("modelOutput", &DreamOutput::modelOutput)
         .def_readwrite("AR", &DreamOutput::AR)
         .def_readwrite("R_stat", &DreamOutput::R_stat)
         .def_readwrite("CR", &DreamOutput::CR);
@@ -836,8 +816,8 @@ PYBIND11_MODULE(rat_core, m) {
         .def_readwrite("shiftedData", &OutputResult::shiftedData)
         .def_readwrite("backgrounds", &OutputResult::backgrounds)
         .def_readwrite("resolutions", &OutputResult::resolutions)
-        .def_readwrite("layerSlds", &OutputResult::layerSlds)
         .def_readwrite("sldProfiles", &OutputResult::sldProfiles)
+        .def_readwrite("layers", &OutputResult::layers)
         .def_readwrite("resampledLayers", &OutputResult::resampledLayers)
         .def_readwrite("calculationResults", &OutputResult::calculationResults)
         .def_readwrite("contrastParams", &OutputResult::contrastParams)        
@@ -912,39 +892,6 @@ PYBIND11_MODULE(rat_core, m) {
                 return chk;
             }));
 
-    py::class_<Limits>(m, "Limits", docsLimits.c_str())
-        .def(py::init<>())
-        .def_readwrite("params", &Limits::params)
-        .def_readwrite("backgroundParams", &Limits::backgroundParams)
-        .def_readwrite("scalefactors", &Limits::scalefactors)
-        .def_readwrite("bulkIns", &Limits::bulkIns)
-        .def_readwrite("bulkOuts", &Limits::bulkOuts)
-        .def_readwrite("resolutionParams", &Limits::resolutionParams)
-        .def_readwrite("domainRatios", &Limits::domainRatios)
-        .def(py::pickle(
-            [](const Limits &lim) { // __getstate__
-                /* Return a tuple that fully encodes the state of the object */
-                return py::make_tuple(lim.params, lim.backgroundParams, lim.scalefactors, lim.bulkIns, lim.bulkOuts, 
-                                      lim.resolutionParams, lim.domainRatios);
-            },
-            [](py::tuple t) { // __setstate__
-                if (t.size() != 7)
-                    throw std::runtime_error("Encountered invalid state unpickling Limits object!");
-
-                /* Create a new C++ instance */
-                Limits lim;
-
-                lim.params = t[0].cast<py::array_t<real_T>>(); 
-                lim.backgroundParams = t[1].cast<py::array_t<real_T>>(); 
-                lim.scalefactors = t[2].cast<py::array_t<real_T>>(); 
-                lim.bulkIns = t[3].cast<py::array_t<real_T>>(); 
-                lim.bulkOuts = t[4].cast<py::array_t<real_T>>(); 
-                lim.resolutionParams = t[5].cast<py::array_t<real_T>>(); 
-                lim.domainRatios = t[6].cast<py::array_t<real_T>>();
-
-                return lim;
-            }));
-
     py::class_<Control>(m, "Control", docsControl.c_str())
         .def(py::init<>())
         .def_readwrite("parallel", &Control::parallel)
@@ -1150,7 +1097,7 @@ PYBIND11_MODULE(rat_core, m) {
                 return p;
             }));
 
-    m.def("RATMain", &RATMain, docsRATMain.c_str(), py::arg("problem_def"), py::arg("limits"), py::arg("control"));
+    m.def("RATMain", &RATMain, docsRATMain.c_str(), py::arg("problem_def"), py::arg("control"));
 
     m.def("makeSLDProfileXY", &makeSLDProfileXY, docsMakeSLDProfileXY.c_str(), 
           py::arg("bulk_in"), py::arg("bulk_out"), py::arg("ssub"), py::arg("layers"), py::arg("number_of_repeats") = DEFAULT_NREPEATS);
diff --git a/tests/conftest.py b/tests/conftest.py
index 7d987a9f..50fbc11c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -3984,7 +3984,6 @@ def dream_bayes():
     bayes.dreamOutput.outlierChains = np.array([[0.0, 0.0]])
     bayes.dreamOutput.runtime = 2.6e-06
     bayes.dreamOutput.iteration = 2.0
-    bayes.dreamOutput.modelOutput = 0.0
     bayes.dreamOutput.AR = np.array([[1.0, np.nan]])
     bayes.dreamOutput.R_stat = np.array(
         [
@@ -6463,7 +6462,6 @@ def dream_results():
             outlierChains=np.array([[0.0, 0.0]]),
             runtime=2.6e-06,
             iteration=2.0,
-            modelOutput=0.0,
             AR=np.array([[1.0, np.nan]]),
             R_stat=np.array(
                 [
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index 38911ef2..2874a888 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -397,7 +397,7 @@ def custom_xy_controls():
     controls = Control()
     controls.procedure = Procedures.Calculate
     controls.parallel = Parallel.Single
-    controls.calcSldDuringFit = True
+    controls.calcSldDuringFit = False
     controls.resampleMinAngle = 0.9
     controls.resampleNPoints = 50.0
     controls.display = Display.Iter
diff --git a/tests/test_outputs.py b/tests/test_outputs.py
index a0f91af9..37a4c631 100644
--- a/tests/test_outputs.py
+++ b/tests/test_outputs.py
@@ -119,7 +119,6 @@ def dream_str():
         "\toutlierChains = Data array: [1 x 2],\n"
         "\truntime = 2.6e-06,\n"
         "\titeration = 2.0,\n"
-        "\tmodelOutput = 0.0,\n"
         "\tAR = Data array: [1 x 2],\n"
         "\tR_stat = Data array: [1 x 19],\n"
         "\tCR = Data array: [1 x 4],\n"
diff --git a/tests/utils.py b/tests/utils.py
index 36805e6d..40524fd0 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -109,7 +109,7 @@ def check_bayes_fields_equal(actual_results, expected_results) -> None:
             "IO",
             "storeOutput",
         ],
-        "dreamOutput": ["runtime", "iteration", "modelOutput"],
+        "dreamOutput": ["runtime", "iteration"],
         "nestedSamplerOutput": ["logZ"],
     }
 

From 111f739db794b8b28d8a387fef027bc1700f165d Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Thu, 27 Mar 2025 15:35:08 +0000
Subject: [PATCH 4/5] Updates submodule

---
 cpp/RAT | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cpp/RAT b/cpp/RAT
index b33f77a0..df626113 160000
--- a/cpp/RAT
+++ b/cpp/RAT
@@ -1 +1 @@
-Subproject commit b33f77a0cbab9c9493cfe06120e3e1ac97d3e8f8
+Subproject commit df626113d7a930cfa23c1ab47fdf9b1111b52123

From b1d1f2480eca5a2b6a878a8cd98e9e02d62908de Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Thu, 27 Mar 2025 15:56:10 +0000
Subject: [PATCH 5/5] Updates defines.h

---
 cpp/includes/defines.h | 31 -------------------------------
 1 file changed, 31 deletions(-)

diff --git a/cpp/includes/defines.h b/cpp/includes/defines.h
index 90e6e544..67b0fda7 100644
--- a/cpp/includes/defines.h
+++ b/cpp/includes/defines.h
@@ -383,37 +383,6 @@ struct OutputResult {
     py::list fitNames;
 };
 
-const std::string docsLimits = R"(The Python binding for the C++ limit struct which contains
-Min and max values for each parameter defined in the project.
-
-Parameters
-----------
-params : np.ndarray[np.float] 
-    Limits for params in the problem definition.
-backgroundParams : np.ndarray[np.float] 
-    Limits for backgroundParams in the problem definition.
-scalefactors : np.ndarray[np.float] 
-    Limits for scalefactors in the problem definition.
-bulkIns : np.ndarray[np.float] 
-    Limits for bulkIns in the problem definition.
-bulkOuts : np.ndarray[np.float] 
-    Limits for bulkOuts in the problem definition.
-resolutionParams : np.ndarray[np.float] 
-    Limits for resolutionParams in the problem definition.
-domainRatios : np.ndarray[np.float] 
-    Limits for domainRatios in the problem definition.
-)";
-
-struct Limits {
-    py::array_t<real_T> params;
-    py::array_t<real_T> backgroundParams;
-    py::array_t<real_T> scalefactors;
-    py::array_t<real_T> bulkIns;
-    py::array_t<real_T> bulkOuts;
-    py::array_t<real_T> resolutionParams;
-    py::array_t<real_T> domainRatios;
-};
-
 const std::string docsNameStore = R"(The Python binding for the C++ names struct which 
 contains names of all parameters in the project.