Unify save methods, refactor plots, enable OpenMP windows(#180)

Author: StephenNneji

.github/workflows/build_wheel.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        platform: [windows-latest, ubuntu-latest, macos-13, macos-14]
+        platform: [windows-2022, ubuntu-latest, macos-13, macos-14]
     env:
       CIBW_SKIP: 'pp*'
       CIBW_ARCHS: 'auto64'
@@ -34,19 +34,19 @@ jobs:
       - name: Install OMP (MacOS Intel) 
         if: matrix.platform == 'macos-13'
         run: |
-          brew install llvm libomp
-          echo "export CC=/usr/local/opt/llvm/bin/clang" >> ~/.bashrc
-          echo "export CXX=/usr/local/opt/llvm/bin/clang++" >> ~/.bashrc
+          brew install llvm@20 libomp
+          echo "export CC=/usr/local/opt/llvm@20/bin/clang" >> ~/.bashrc
+          echo "export CXX=/usr/local/opt/llvm@20/bin/clang++" >> ~/.bashrc
           echo "export CFLAGS=\"$CFLAGS -I/usr/local/opt/libomp/include\"" >> ~/.bashrc
           echo "export CXXFLAGS=\"$CXXFLAGS -I/usr/local/opt/libomp/include\"" >> ~/.bashrc
           echo "export LDFLAGS=\"$LDFLAGS -Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp\"" >> ~/.bashrc
           source ~/.bashrc
       - name: Install OMP (MacOS M1) 
         if: matrix.platform == 'macos-14'
         run: |
-          brew install llvm libomp
-          echo "export CC=/opt/homebrew/opt/llvm/bin/clang" >> ~/.bashrc
-          echo "export CXX=/opt/homebrew/opt/llvm/bin/clang++" >> ~/.bashrc
+          brew install llvm@20 libomp
+          echo "export CC=/opt/homebrew/opt/llvm@20/bin/clang" >> ~/.bashrc
+          echo "export CXX=/opt/homebrew/opt/llvm@20/bin/clang++" >> ~/.bashrc
           echo "export CFLAGS=\"$CFLAGS -I/opt/homebrew/opt/libomp/include\"" >> ~/.bashrc
           echo "export CXXFLAGS=\"$CXXFLAGS -I/opt/homebrew/opt/libomp/include\"" >> ~/.bashrc
           echo "export LDFLAGS=\"$LDFLAGS -Wl,-rpath,/opt/homebrew/opt/libomp/lib -L/opt/homebrew/opt/libomp/lib -lomp\"" >> ~/.bashrc

.github/workflows/run_tests.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [windows-latest, ubuntu-latest, macos-13, macos-14]
+        platform: [windows-2022, ubuntu-latest, macos-13, macos-14]
         version: ["3.10", "3.13"]
     defaults:
       run:
@@ -38,19 +38,19 @@ jobs:
       - name: Install OMP (MacOS Intel) 
         if: matrix.platform == 'macos-13'
         run: |
-          brew install llvm libomp
-          echo "export CC=/usr/local/opt/llvm/bin/clang" >> ~/.bashrc
-          echo "export CXX=/usr/local/opt/llvm/bin/clang++" >> ~/.bashrc
+          brew install llvm@20 libomp
+          echo "export CC=/usr/local/opt/llvm@20/bin/clang" >> ~/.bashrc
+          echo "export CXX=/usr/local/opt/llvm@20/bin/clang++" >> ~/.bashrc
           echo "export CFLAGS=\"$CFLAGS -I/usr/local/opt/libomp/include\"" >> ~/.bashrc
           echo "export CXXFLAGS=\"$CXXFLAGS -I/usr/local/opt/libomp/include\"" >> ~/.bashrc
           echo "export LDFLAGS=\"$LDFLAGS -Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp\"" >> ~/.bashrc
           source ~/.bashrc
       - name: Install OMP (MacOS M1) 
         if: matrix.platform == 'macos-14'
         run: |
-          brew install llvm libomp
-          echo "export CC=/opt/homebrew/opt/llvm/bin/clang" >> ~/.bashrc
-          echo "export CXX=/opt/homebrew/opt/llvm/bin/clang++" >> ~/.bashrc
+          brew install llvm@20 libomp
+          echo "export CC=/opt/homebrew/opt/llvm@20/bin/clang" >> ~/.bashrc
+          echo "export CXX=/opt/homebrew/opt/llvm@20/bin/clang++" >> ~/.bashrc
           echo "export CFLAGS=\"$CFLAGS -I/opt/homebrew/opt/libomp/include\"" >> ~/.bashrc
           echo "export CXXFLAGS=\"$CXXFLAGS -I/opt/homebrew/opt/libomp/include\"" >> ~/.bashrc
           echo "export LDFLAGS=\"$LDFLAGS -Wl,-rpath,/opt/homebrew/opt/libomp/lib -L/opt/homebrew/opt/libomp/lib -lomp\"" >> ~/.bashrc

pyproject.toml

@@ -38,4 +38,5 @@ mark-parentheses = false
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-
+[tool.ruff.lint.isort]
+known-first-party = ["ratapi.rat_core"]

ratapi/controls.py

@@ -233,19 +233,16 @@ def delete_IPC(self):
             os.remove(self._IPCFilePath)
         return None
 
-    def save(self, path: Union[str, Path], filename: str = "controls"):
+    def save(self, filepath: Union[str, Path] = "./controls.json"):
         """Save a controls object to a JSON file.
 
         Parameters
         ----------
-        path : str or Path
-            The directory in which the controls object will be written.
-        filename : str
-            The name for the JSON file containing the controls object.
-
+        filepath : str or Path
+            The path to where the controls file will be written.
         """
-        file = Path(path, f"{filename.removesuffix('.json')}.json")
-        file.write_text(self.model_dump_json())
+        filepath = Path(filepath).with_suffix(".json")
+        filepath.write_text(self.model_dump_json())
 
     @classmethod
     def load(cls, path: Union[str, Path]) -> "Controls":

ratapi/examples/domains/domains_XY_model.py

@@ -1,8 +1,9 @@
 """Custom model file for the domains custom XY example."""
 
-import math
+from math import sqrt
 
 import numpy as np
+from scipy.special import erf
 
 
 def domains_XY_model(params, bulk_in, bulk_out, contrast, domain):
@@ -19,13 +20,13 @@ def domains_XY_model(params, bulk_in, bulk_out, contrast, domain):
     z = np.arange(0, 141)
 
     # Make the volume fraction distribution for our Silicon substrate
-    [vfSilicon, siSurf] = makeLayer(z, -25, 50, 1, subRough, subRough)
+    [vfSilicon, siSurf] = make_layer(z, -25, 50, 1, subRough, subRough)
 
     # ... and the Oxide ...
-    [vfOxide, oxSurface] = makeLayer(z, siSurf, oxideThick, 1, subRough, subRough)
+    [vfOxide, oxSurface] = make_layer(z, siSurf, oxideThick, 1, subRough, subRough)
 
     # ... and also our layer.
-    [vfLayer, laySurface] = makeLayer(z, oxSurface, layerThick, 1, subRough, layerRough)
+    [vfLayer, laySurface] = make_layer(z, oxSurface, layerThick, 1, subRough, layerRough)
 
     # Everything that is not already occupied will be filled will water
     totalVF = vfSilicon + vfOxide + vfLayer
@@ -53,7 +54,7 @@ def domains_XY_model(params, bulk_in, bulk_out, contrast, domain):
     return SLD, subRough
 
 
-def makeLayer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
+def make_layer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
     """Produce a layer, with a defined thickness, height and roughness.
 
     Each side of the layer has its own roughness value.
@@ -63,12 +64,9 @@ def makeLayer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
     right = prevLaySurf + thickness
 
     # Make our heaviside
-    a = (z - left) / ((2**0.5) * Sigma_L)
-    b = (z - right) / ((2**0.5) * Sigma_R)
+    erf_left = erf((z - left) / (sqrt(2) * Sigma_L))
+    erf_right = erf((z - right) / (sqrt(2) * Sigma_R))
 
-    erf_a = np.array([math.erf(value) for value in a])
-    erf_b = np.array([math.erf(value) for value in b])
-
-    VF = np.array((height / 2) * (erf_a - erf_b))
+    VF = np.array((0.5 * height) * (erf_left - erf_right))
 
     return VF, right

ratapi/examples/normal_reflectivity/custom_XY_DSPC.py

@@ -1,8 +1,9 @@
 """A custom XY model for a supported DSPC bilayer."""
 
-import math
+from math import sqrt
 
 import numpy as np
+from scipy.special import erf
 
 
 def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
@@ -51,10 +52,10 @@ def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
     z = np.arange(0, 141)
 
     # Make our Silicon substrate
-    vfSilicon, siSurf = layer(z, -25, 50, 1, subRough, subRough)
+    vfSilicon, siSurf = make_layer(z, -25, 50, 1, subRough, subRough)
 
     # Add the Oxide
-    vfOxide, oxSurface = layer(z, siSurf, oxideThick, 1, subRough, subRough)
+    vfOxide, oxSurface = make_layer(z, siSurf, oxideThick, 1, subRough, subRough)
 
     # We fill in the water at the end, but there may be a hydration layer between the bilayer and the oxide,
     # so we start the bilayer stack an appropriate distance away
@@ -65,15 +66,15 @@ def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
     headThick = vHead / lipidAPM
 
     # ... and make a box for the volume fraction (1 for now, we correct for coverage later)
-    vfHeadL, headLSurface = layer(z, watSurface, headThick, 1, bilayerRough, bilayerRough)
+    vfHeadL, headLSurface = make_layer(z, watSurface, headThick, 1, bilayerRough, bilayerRough)
 
     # ... also do the same for the tails
     # We'll make both together, so the thickness will be twice the volume
     tailsThick = (2 * vTail) / lipidAPM
-    vfTails, tailsSurf = layer(z, headLSurface, tailsThick, 1, bilayerRough, bilayerRough)
+    vfTails, tailsSurf = make_layer(z, headLSurface, tailsThick, 1, bilayerRough, bilayerRough)
 
     # Finally the upper head ...
-    vfHeadR, headSurface = layer(z, tailsSurf, headThick, 1, bilayerRough, bilayerRough)
+    vfHeadR, headSurface = make_layer(z, tailsSurf, headThick, 1, bilayerRough, bilayerRough)
 
     # Making the model
     # We've created the volume fraction profiles corresponding to each of the groups.
@@ -114,12 +115,12 @@ def custom_XY_DSPC(params, bulk_in, bulk_out, contrast):
     totSLD = sldSilicon + sldOxide + sldHeadL + sldTails + sldHeadR + sldWat
 
     # Make the SLD array for output
-    SLD = [[a, b] for (a, b) in zip(z, totSLD)]
+    SLD = np.column_stack((z, totSLD))
 
     return SLD, subRough
 
 
-def layer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
+def make_layer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
     """Produce a layer, with a defined thickness, height and roughness.
 
     Each side of the layer has its own roughness value.
@@ -129,12 +130,9 @@ def layer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
     right = prevLaySurf + thickness
 
     # Make our heaviside
-    a = (z - left) / ((2**0.5) * Sigma_L)
-    b = (z - right) / ((2**0.5) * Sigma_R)
+    erf_left = erf((z - left) / (sqrt(2) * Sigma_L))
+    erf_right = erf((z - right) / (sqrt(2) * Sigma_R))
 
-    erf_a = np.array([math.erf(value) for value in a])
-    erf_b = np.array([math.erf(value) for value in b])
-
-    VF = np.array((height / 2) * (erf_a - erf_b))
+    VF = np.array((0.5 * height) * (erf_left - erf_right))
 
     return VF, right