diff --git a/cpp/RAT b/cpp/RAT
index 16f3ebef..aae3dc14 160000
--- a/cpp/RAT
+++ b/cpp/RAT
@@ -1 +1 @@
-Subproject commit 16f3ebef737f4c85ca601046f7a30ffabee4eb47
+Subproject commit aae3dc141b6a10c6e10dfb47cd62e07a2a11857d
diff --git a/ratapi/inputs.py b/ratapi/inputs.py
index 890066f9..7d0a8720 100644
--- a/ratapi/inputs.py
+++ b/ratapi/inputs.py
@@ -302,7 +302,7 @@ def make_problem(project: ratapi.Project) -> ProblemDefinition:
     problem.numberOfContrasts = len(project.contrasts)
     problem.geometry = project.geometry
     problem.useImaginary = project.absorption
-    problem.repeatLayers = [1] * len(project.contrasts)
+    problem.repeatLayers = [contrast.repeat_layers for contrast in project.contrasts]
     problem.contrastBackgroundParams = contrast_background_params
     problem.contrastBackgroundTypes = contrast_background_types
     problem.contrastBackgroundActions = [contrast.background_action for contrast in project.contrasts]
diff --git a/ratapi/models.py b/ratapi/models.py
index e882af65..7d0d4f74 100644
--- a/ratapi/models.py
+++ b/ratapi/models.py
@@ -163,6 +163,8 @@ class Contrast(RATModel):
         The name of the instrument resolution for this contrast.
     resample : bool
         Whether adaptive resampling should be used for interface microslicing.
+    repeat_layers : int
+        For standard layers, the number of times the set of layers defined in the model should be repeated.
     model : list[str]
         If this is a standard layers model, this should be a list of layer names
         that make up the slab model for this contrast.
@@ -180,6 +182,7 @@ class Contrast(RATModel):
     scalefactor: str = ""
     resolution: str = ""
     resample: bool = False
+    repeat_layers: int = Field(default=1, gt=0)
     model: list[str] = []
 
     @model_validator(mode="before")
@@ -208,6 +211,7 @@ def __str__(self):
                 self.scalefactor,
                 self.resolution,
                 self.resample,
+                self.repeat_layers,
                 model_entry,
             ]
         )
@@ -238,6 +242,8 @@ class ContrastWithRatio(RATModel):
         The name of the instrument resolution for this contrast.
     resample : bool
         Whether adaptive resampling should be used for interface microslicing.
+    repeat_layers : int
+        For standard layers, the number of times the set of layers defined in the model should be repeated.
     domain_ratio : str
         The name of the domain ratio parameter describing how the first domain should be weighted
         relative to the second.
@@ -258,6 +264,7 @@ class ContrastWithRatio(RATModel):
     scalefactor: str = ""
     resolution: str = ""
     resample: bool = False
+    repeat_layers: int = Field(default=1, gt=0)
     domain_ratio: str = ""
     model: list[str] = []
 
@@ -276,6 +283,8 @@ def __str__(self):
                 self.scalefactor,
                 self.resolution,
                 self.resample,
+                self.repeat_layers,
+                self.domain_ratio,
                 model_entry,
             ]
         )
diff --git a/ratapi/project.py b/ratapi/project.py
index 860f23b7..88555539 100644
--- a/ratapi/project.py
+++ b/ratapi/project.py
@@ -361,8 +361,8 @@ def model_post_init(self, __context: Any) -> None:
         """Set up the Class to protect against disallowed modification.
 
         We initialise the class handle in the ClassLists for empty data fields, set protected parameters, get names of
-        all defined parameters, determine the contents of the "model" field in contrasts,
-        and wrap ClassList routines to control revalidation.
+        all defined parameters, determine the contents of the "model" field in contrasts, and wrap ClassList routines
+        to control revalidation.
         """
         # Ensure all ClassLists have the correct _class_handle defined
         for field in (fields := Project.model_fields):
@@ -454,6 +454,33 @@ def set_layers(self) -> "Project":
             self.layers.data = []
         return self
 
+    @model_validator(mode="after")
+    def set_repeat_layers(self) -> "Project":
+        """If we are not using a standard layers model, warn that the repeat layers setting is not valid."""
+        if self.model != LayerModels.StandardLayers:
+            for contrast in self.contrasts:
+                if "repeat_layers" in contrast.model_fields_set and contrast.repeat_layers != 1:
+                    warnings.warn(
+                        'For a custom layers or custom XY calculation, the "repeat_layers" setting for each '
+                        "contrast is not valid - resetting to 1.",
+                        stacklevel=2,
+                    )
+                contrast.repeat_layers = 1
+        return self
+
+    @model_validator(mode="after")
+    def set_resample(self) -> "Project":
+        """If we are using a custom XY model, warn that the resample setting for each contrast must always be True."""
+        if self.model == LayerModels.CustomXY:
+            for contrast in self.contrasts:
+                if "resample" in contrast.model_fields_set and contrast.resample is False:
+                    warnings.warn(
+                        'For a custom XY calculation, "resample" must be True for each contrast - resetting to True.',
+                        stacklevel=2,
+                    )
+                contrast.resample = True
+        return self
+
     @model_validator(mode="after")
     def set_calculation(self) -> "Project":
         """Apply the calc setting to the project."""
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index db5b6646..e7a1560e 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -306,7 +306,7 @@ def custom_xy_problem(test_names, test_checks):
     problem.contrastResolutionTypes = ["constant"]
     problem.contrastCustomFiles = [1]
     problem.contrastDomainRatios = [0]
-    problem.resample = [False]
+    problem.resample = [True]
     problem.dataPresent = [0]
     problem.data = [np.empty([0, 6])]
     problem.dataLimits = [[0.0, 0.0]]
diff --git a/tests/test_project.py b/tests/test_project.py
index c2ea92a2..7683dec9 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -443,6 +443,46 @@ def test_set_layers(project_parameters: dict) -> None:
     assert project.layers == []
 
 
+@pytest.mark.parametrize(
+    "project_parameters",
+    [
+        (
+            {
+                "model": LayerModels.CustomLayers,
+                "contrasts": [ratapi.models.Contrast(name="Test Contrast", repeat_layers=2)],
+            }
+        ),
+        ({"model": LayerModels.CustomXY, "contrasts": [ratapi.models.Contrast(name="Test Contrast", repeat_layers=2)]}),
+    ],
+)
+def test_set_repeat_layers(project_parameters: dict) -> None:
+    """If we are using a custom layers of custom XY model, the "resample" field of all the contrasts should always
+    be 1."""
+    with pytest.warns(
+        match='For a custom layers or custom XY calculation, the "repeat_layers" setting for each '
+        "contrast is not valid - resetting to 1."
+    ):
+        project = ratapi.Project(**project_parameters)
+    assert all(contrast.repeat_layers == 1 for contrast in project.contrasts)
+
+
+@pytest.mark.parametrize(
+    "project_parameters",
+    [
+        ({"model": LayerModels.CustomXY, "contrasts": [ratapi.models.Contrast(name="Test Contrast")]}),
+    ],
+)
+def test_set_resample(project_parameters: dict) -> None:
+    """If we are using a custom XY model, the "resample" field of all the contrasts should always be True."""
+    project = ratapi.Project(**project_parameters)
+    assert all(contrast.resample for contrast in project.contrasts)
+    with pytest.warns(
+        match='For a custom XY calculation, "resample" must be True for each contrast - resetting to True.'
+    ):
+        project.contrasts.append(name="New Contrast", resample=False)
+    assert all(contrast.resample for contrast in project.contrasts)
+
+
 @pytest.mark.parametrize(
     ["input_calculation", "input_contrast", "new_calculation", "new_contrast_model", "num_domain_ratios"],
     [