Tidies up examples

RAT/examples/absorption/absorption.py

@@ -1,13 +1,13 @@
 """Custom layers model including absorption"""
 
+import RAT
 import RAT.utils.plotting
-import RAT.rat_core
 import numpy as np
 
 problem = RAT.Project(name="Absorption example", calculation="non polarised", model="custom layers",
                       geometry="substrate/liquid", absorption=True)
 
-# Add the required parameters (substrate roughness as already there by default)
+# Add the required parameters (substrate roughness is already there by default)
 problem.parameters.append(name="Alloy Thickness", min=100.0, value=135.6, max=200.0, fit=True)
 problem.parameters.append(name="Alloy SLD up", min=6.0e-6, value=9.87e-6, max=1.2e-5, fit=True)
 problem.parameters.append(name="Alloy SLD imaginary up", min=1.0e-9, value=4.87e-8, max=1.0e-7, fit=True)
@@ -43,7 +43,7 @@
 problem.scalefactors.append(name="Scalefactor 3", min=0.5, value=1, max=1.5, fit=True)
 problem.scalefactors.append(name="Scalefactor 4", min=0.5, value=1, max=1.5, fit=True)
 
-# Similarly, use an individual background for each dataset....
+# Similarly, use an individual background for each dataset
 del problem.backgrounds[0]
 del problem.background_parameters[0]
 
@@ -57,7 +57,7 @@
 problem.backgrounds.append(name="Background 3", type="constant", value_1="Background parameter 3")
 problem.backgrounds.append(name="Background 4", type="constant", value_1="Background parameter 4")
 
-# Make the resolution fittable...
+# Make the resolution fittable
 problem.resolution_parameters.set_fields(0, fit=True)
 
 # Now add the data we need
@@ -74,8 +74,7 @@
 problem.data.append(name="H2O_up", data=data_4)
 
 # Add the custom file
-#problem.custom_files.append(name="DPPC absorption", filename="volumeThiolBilayer.m", language="matlab")
-problem.custom_files.append(name="DPPC absorption", filename="volumeThiolBilayer.py", language="python")
+problem.custom_files.append(name="DPPC absorption", filename="volume_thiol_bilayer.py", language="python")
 
 # Finally add the contrasts
 problem.contrasts.append(name="D2O Down", data="D2O_dn", background="Background 1", bulk_in="Silicon",
@@ -94,9 +93,9 @@
                          bulk_out="H2O", scalefactor="Scalefactor 4", resolution="Resolution 1", resample=True,
                          model=["DPPC absorption"])
 
-# Now make a controls block....
+# Now make a controls block
 controls = RAT.set_controls(parallel="contrasts", resampleParams=[0.9, 150.0])
 
+# Run the code and plot the results
 problem, results = RAT.run(problem, controls)
-
 RAT.utils.plotting.plot_ref_sld(problem, results, True)

RAT/examples/absorption/volumeThiolBilayer.py → RAT/examples/absorption/volume_thiol_bilayer.py

@@ -1,4 +1,4 @@
-def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
+def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
     """
     volumeThiolBilayer  RAT Custom Layer Model File.
 
@@ -21,10 +21,6 @@ def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
 
     The second output parameter should be the substrate roughness.
     """
-    #params = np.array(params)
-    #bulk_in = np.array(bulk_in)
-    #bulk_out = np.array(bulk_out)
-
     subRough = params[0]
     alloyThick = params[1]
     alloySLDUp = params[2]
@@ -59,9 +55,9 @@ def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
     bn = 0.936e-4    # Nitrogen
     bd = 0.6671e-4   # Deuterium
 
-    # Work out the total scattering length in each fragment....
-    # Define scattering lengths..
-    # Hydrogenated version....
+    # Work out the total scattering length in each fragment
+    # Define scattering lengths
+    # Hydrogenated version
     COO = (2*bo) + (bc)
     GLYC = (3*bc) + (5*bh)
     CH3 = (1*bc) + (3*bh)
@@ -72,8 +68,8 @@ def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
     H2O = (2*bh) + (1*bo)
     D2O = (2*bd) + (1*bo)
 
-    # And also volumes....
-    vCH3 = 52.7  # CH3 volume in the paper appears to be for 2* CH3's
+    # And also volumes
+    vCH3 = 52.7  # CH3 volume in the paper appears to be for 2 * CH3's
     vCH2 = 28.1
     vCOO = 39.0
     vGLYC = 68.8
@@ -83,13 +79,13 @@ def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
     vCHCH = 42.14
 
     vHead = vCHOL + vPO4 + vGLYC + 2*vCOO
-    vTail = (28*vCH2) + (1*vCHCH) + (2*vCH3)  # Tail_volume
+    vTail = (28*vCH2) + (1*vCHCH) + (2*vCH3)  # Tail volume
 
     # Calculate sum_b's for other fragments
     sumbHead = CHOL + PO4 + GLYC + 2*COO
     sumbTail = (28*CH2) + (2*CH) + 2*CH3
 
-    # Calculate SLD's and Thickness'
+    # Calculate SLDs and Thickness
     sldHead = sumbHead/vHead
     thickHead = vHead/thiolAPM
 
@@ -100,7 +96,7 @@ def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
     thiolHeadHydr = thiolHeadHydr/100
     sldHead = (sldHead * (1 - thiolHeadHydr) + (thiolHeadHydr * bulk_out[contrast]))
 
-    # Now correct both the SLD's for the coverage parameter
+    # Now correct both the SLDs for the coverage parameter
     sldTail = (thiolCoverage*sldTail) + ((1-thiolCoverage) * bulk_out[contrast])
     sldHead = (thiolCoverage*sldHead) + ((1-thiolCoverage) * bulk_out[contrast])
 
@@ -109,7 +105,7 @@ def volumeThiolBilayer(params, bulk_in, bulk_out, contrast):
 
     # Now do the same for the bilayer
     vHead = vCHOL + vPO4 + vGLYC + 2*vCOO
-    vTail = (28*vCH2)  # Tail_volume
+    vTail = (28*vCH2)  # Tail volume
     vMe = (2*vCH3)
 
     sumbHead = CHOL + PO4 + GLYC + 2*COO

RAT/examples/domains/alloyDomains.py → RAT/examples/domains/alloy_domains.py

@@ -1,10 +1,10 @@
 
-def alloyDomains(params, bulkIn, bulkOut, contrast, domain):
-    """Simple custom model for testing incoherent summing...
-    Simple two layer of permalloy / gold, with up/down domains..
+def alloy_domains(params, bulkIn, bulkOut, contrast, domain):
+    """Simple custom model for testing incoherent summing.
+    Simple two layer of permalloy / gold, with up/down domains.
     """
 
-    # Split up the parameters....
+    # Split up the parameters
     subRough = params[0]
     alloyThick = params[1]
     alloySLDup = params[2]
@@ -14,7 +14,7 @@ def alloyDomains(params, bulkIn, bulkOut, contrast, domain):
     goldSLD = params[6]
     goldRough = params[7]
 
-    # Make the layers....
+    # Make the layers
     alloyUp = [alloyThick, alloySLDup, alloyRough]
     alloyDn = [alloyThick, alloySLDdn, alloyRough]
     gold = [goldThick, goldSLD, goldRough]

RAT/examples/domains/domains_XY.py

@@ -1,7 +1,7 @@
 """Simple example of a layer containing domains using a custom XY model"""
+
 import RAT
 import RAT.utils.plotting
-import RAT.rat_core
 
 problem = RAT.Project(calculation="domains", model="custom xy", geometry="substrate/liquid")
 
@@ -18,7 +18,7 @@
 problem.bulk_out.append(name="SLD H2O", min=-0.6e-6, value=-0.56e-6, max=-0.5e-6)
 
 # Add the custom file
-problem.custom_files.append(name="Domain Layer", filename="domainsXY.m", language="matlab")
+problem.custom_files.append(name="Domain Layer", filename="domains_XY_model.py", language="python")
 
 # Make contrasts
 problem.contrasts.append(name="D2O", background="Background 1", resolution="Resolution 1", scalefactor="Scalefactor 1",

RAT/examples/domains/domainsXY.py → RAT/examples/domains/domains_XY_model.py

@@ -1,64 +1,60 @@
 import numpy as np
 import scipy as sp
 
-def domainsXY(params, bulk_in, bulk_out, contrast, domain):
 
-    debugPlot = False      # optional debug plot
+def domains_XY_model(params, bulk_in, bulk_out, contrast, domain):
 
-    # Split up the parameters for convenience...
+    # Split up the parameters for convenience
     subRough = params[0]
     oxideThick = params[1]
     layerThick = params[2]
     layerSLD = params[3]
     layerRough = params[4]
     domainSLD = params[5]
 
-    # Make an array of z values for our model...
+    # Make an array of z values for our model
     z = np.arange(0, 141)
 
-    # Make the volume fraction distribution for our Silicon substrate....
-    [vfSilicon, siSurf] = makeLayer(z,-25,50,1,subRough,subRough)
+    # Make the volume fraction distribution for our Silicon substrate
+    [vfSilicon, siSurf] = makeLayer(z, -25, 50, 1, subRough, subRough)
 
-    # ..and the Oxide....
-    [vfOxide, oxSurface] = makeLayer(z,siSurf,oxideThick,1,subRough,subRough)
+    # ... and the Oxide ...
+    [vfOxide, oxSurface] = makeLayer(z, siSurf, oxideThick, 1, subRough, subRough)
 
-    # ..also our layer.
-    [vfLayer, laySurface] = makeLayer(z,oxSurface,layerThick,1,subRough,layerRough)
+    # ... and also our layer.
+    [vfLayer, laySurface] = makeLayer(z, oxSurface, layerThick, 1, subRough, layerRough)
 
-    # Everything that is not already occupied will be filled will water..
+    # Everything that is not already occupied will be filled will water
     totalVF = vfSilicon + vfOxide + vfLayer
     vfWater = 1 - totalVF
 
-    # Now convert the Volume Fractions to SLD's...
+    # Now convert the Volume Fractions to SLDs
     siSLD = vfSilicon * bulk_in
     oxSLD = vfOxide * 3.41e-6
 
-    # Layer SLD depends on whether we are calculating the domain or not...
+    # Layer SLD depends on whether we are calculating the domain or not
     if domain == 1:
         laySLD = vfLayer * layerSLD
     else:
         laySLD = vfLayer * domainSLD
 
-    #...finally the water.
-    waterSLD = vfWater * bulk_out(contrast)
+    # ... and finally the water SLD.
+    waterSLD = vfWater * bulk_out[contrast]
 
-    # Make the total SLD by just adding them all up..
+    # Make the total SLD by just adding them all up
     totalSLD = siSLD + oxSLD + laySLD + waterSLD
 
-    # The output is just a [n x 2] array of z against SLD..
-    SLD = [z, totalSLD]
+    # The output is just a [n x 2] array of z against SLD
+    SLD = np.column_stack([z, totalSLD])
 
     return SLD, subRough
 
 
-# -------------------------------------------------------------------------
-
-
 def makeLayer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
     """ This produces a layer, with a defined thickness, height and roughness.
     Each side of the layer has its own roughness value.
     """
-    # Find the edges.....
+    # Find the edges
     l = prevLaySurf
     r = prevLaySurf + thickness
 
@@ -69,4 +65,4 @@ def makeLayer(z, prevLaySurf, thickness, height, Sigma_L, Sigma_R):
 
     thisLaySurf = r
 
-    return VF, thisLaySurf
+    return VF, thisLaySurf

RAT/examples/domains/domains_custom_layers.py

@@ -1,7 +1,7 @@
 """An example custom layers domains project involving incoherent summing on a permalloy layer"""
+
 import RAT
 import RAT.utils.plotting
-import RAT.rat_core
 
 problem = RAT.Project(calculation="domains", model="custom layers", geometry="substrate/liquid")
 
@@ -17,15 +17,15 @@
 # Set the bulk SLD
 problem.bulk_in.set_fields(0, name="Silicon", value=2.073e-6, max=1.0)
 
-# Add the custom file...
-problem.custom_files.append(name="Alloy domains", filename="alloyDomains.m", language="matlab")
+# Add the custom file
+problem.custom_files.append(name="Alloy domains", filename="alloy_domains.py", language="python")
 
-# Make a contrast...
+# Make a contrast
 problem.contrasts.append(name="D2O Contrast", data="Simulation", background="Background 1", bulk_in="Silicon",
                          bulk_out="SLD D2O", scalefactor="Scalefactor 1", resolution="Resolution 1", resample=False,
                          domain_ratio="Domain Ratio 1", model=["Alloy domains"])
 
 controls = RAT.set_controls()
-problem, results = RAT.run(problem, controls)
 
+problem, results = RAT.run(problem, controls)
 RAT.utils.plotting.plot_ref_sld(problem, results, True)

RAT/examples/domains/standard_layers.py

@@ -1,10 +1,9 @@
 import RAT
 import RAT.utils.plotting
-import RAT.rat_core
 
 problem = RAT.Project(calculation="domains")
 
-# Define the parameters we need to define our two domains...
+# Define the parameters we need to define our two domains
 problem.parameters.append(name="L1 Thickness", min=5.0, value=20.0, max=60.0, fit=True)
 problem.parameters.append(name="L1 SLD", min=3.0e-6, value=4.1e-6, max=5.0e-6, fit=False)
 problem.parameters.append(name="L1 Roughness", min=2.0, value=5.0, max=20.0, fit=True)
@@ -28,10 +27,8 @@
 problem.layers.append(name="Layer 2", thickness="L2 Thickness", SLD="L2 SLD", roughness="L2 Roughness",
                       hydration="L2 Hydration", hydrate_with="bulk out")
 
-#problem.layers.append(name="Layer 3", thickness="L3 Thickness", SLD="L3 SLD", roughness="L3 Roughness",
-#                      hydration="L3 Hydration", hydrate_with="bulk out")
-problem.layers.append(name="Layer 3", thickness="L2 Thickness", SLD="L2 SLD", roughness="L2 Roughness",
-                      hydration="L2 Hydration", hydrate_with="bulk out")
+problem.layers.append(name="Layer 3", thickness="L3 Thickness", SLD="L3 SLD", roughness="L3 Roughness",
+                      hydration="L3 Hydration", hydrate_with="bulk out")
 
 
 # If we look at the project, there are two extra groups as compared to a normal standard layers calculation:
@@ -45,8 +42,8 @@
                          domain_ratio="Domain Ratio 1", data="Simulation", model=["Domain 1", "Domain 2"])
 
 
-# Now we can run our simulation as usual, and plot the results....
+# Now we can run our simulation as usual, and plot the results
 controls = RAT.set_controls()
-problem, results = RAT.run(problem, controls)
 
+problem, results = RAT.run(problem, controls)
 RAT.utils.plotting.plot_ref_sld(problem, results, True)

RAT/examples/languages/customBilayer.cpp → RAT/examples/languages/custom_bilayer.cpp

@@ -1,4 +1,4 @@
-//customBilayer.cpp
+//custom_bilayer.cpp
 
 #include <vector>
 
@@ -8,10 +8,10 @@
 #define LIB_EXPORT
 #endif
 
-// We user extern "C" decorator to avoid name mangling....
+// We user extern "C" decorator to avoid name mangling
 extern "C" {
 
-    LIB_EXPORT void customBilayer(std::vector<double>& params, std::vector<double>& bulkIn, std::vector<double>& bulkOut, int contrast, std::vector<double>& output, double* outputSize, double* rough)
+    LIB_EXPORT void custom_bilayer(std::vector<double>& params, std::vector<double>& bulkIn, std::vector<double>& bulkOut, int contrast, std::vector<double>& output, double* outputSize, double* rough)
     {
         double subRough = params[0];
         double oxideThick = params[1];
@@ -25,19 +25,19 @@ extern "C" {
         // We have a constant SLD for the oxide
         double oxideSLD = 3.41e-6;
 
-        // Now make the lipid layers..
+        // Now make the lipid layers
         // Use known lipid volume and compositions
         // to make the layers
 
-        // define all the neutron b's.
+        // define all the neutron b's
         double bc = 0.6646e-4;     //Carbon
         double bo = 0.5843e-4;     //Oxygen
         double bh = -0.3739e-4;	   //Hydrogen
         double bp = 0.513e-4;      //Phosphorus
         double bn = 0.936e-4;      //Nitrogen
         double bd = 0.6671e-4;     //Deuterium
 
-        // Now make the lipid groups..
+        // Now make the lipid groups
         double COO = (4*bo) + (2*bc);
         double GLYC = (3*bc) + (5*bh);
         double CH3 = (2*bc) + (6*bh);
@@ -54,12 +54,12 @@ extern "C" {
         double vHead = 319;
         double vTail = 782;
 
-        // we use the volumes to calculate the SLD's
+        // we use the volumes to calculate the SLDs
         double SLDhead = Head / vHead;
         double SLDtail = Tails / vTail;
 
-        // We calculate the layer thickness' from
-        // the volumes and the APM...
+        // We calculate the layer thickness from
+        // the volumes and the APM
         double headThick = vHead / lipidAPM;
         double tailThick = vTail / lipidAPM;
 
@@ -102,7 +102,7 @@ extern "C" {
 
         *rough = subRough;
 
-        outputSize[0] = 6;     // row - Necessary to ouptut how many layers in stack
+        outputSize[0] = 6;     // row - Necessary to output how many layers in stack
         outputSize[1] = 3;     // col - Should be different depending on calculation 
     }
 } // extern "C"