back compatibility with old way of setting diffusion parameters

examples/01_Binary_Precipitation.ipynb

@@ -146,7 +146,7 @@
       "\tbeta\t0.000e+00\t\t0.0000\t\t0.0000e+00\t5.7737e+03\n",
       "\n",
       "N\tTime (s)\tSim Time (s)\tTemperature (K)\tMatrix Comp\n",
-      "3675\t1.8e+06\t\t15.1\t\t723\t\t0.0126\n",
+      "3675\t1.8e+06\t\t12.2\t\t723\t\t0.0126\n",
       "\n",
       "\tPhase\tPrec Density (#/m3)\tVolume Frac\tAvg Radius (m)\tDriving Force (J/mol)\n",
       "\tbeta\t1.374e+22\t\t1.5504\t\t6.1126e-09\t3.2902e+02\n",

examples/06_Single_Phase_Diffusion.ipynb

@@ -115,10 +115,10 @@
      "text": [
       "Iteration\tSim Time (h)\tRun time (s)\n",
       "0\t\t0.0e+00\t\t0.0\n",
-      "100\t\t2.9e+01\t\t2.8\n",
-      "200\t\t5.7e+01\t\t5.3\n",
-      "300\t\t8.6e+01\t\t7.3\n",
-      "349\t\t1.0e+02\t\t8.1\n"
+      "100\t\t2.9e+01\t\t2.5\n",
+      "200\t\t5.7e+01\t\t4.9\n",
+      "300\t\t8.6e+01\t\t6.6\n",
+      "349\t\t1.0e+02\t\t7.2\n"
      ]
     }
    ],

kawin/diffusion/Diffusion.py

@@ -5,7 +5,7 @@
 from kawin.solver.Solver import DESolver, SolverType
 from kawin.GenericModel import GenericModel
 import kawin.diffusion.Plot as diffPlot
-from kawin.diffusion.DiffusionParameters import DiffusionParameters
+from kawin.diffusion.DiffusionParameters import DiffusionParameters, BoundaryConditions
 
 class DiffusionModel(GenericModel):
     #Boundary conditions
@@ -75,6 +75,15 @@ def setThermodynamics(self, thermodynamics):
         '''
         self.therm = thermodynamics
 
+    def setTemperature(self, T):
+        self.parameters.temperature.setIsothermalTemperature(T)
+
+    def setTemperatureArray(self, times, temperatures):
+        self.parameters.temperature.setTemperatureArray(times, temperatures)
+
+    def setTemperatureFunction(self, func):
+        self.parameters.temperature.setTemperatureFunction(func)
+
     def _getVarDict(self):
         '''
         Returns mapping of { variable name : attribute name } for saving
@@ -103,6 +112,15 @@ def load(filename):
         model._loadData(data)
         model.isSetup = True
         return model
+
+    def setHashSensitivity(self, s):
+        self.parameters.hashTable.setHashSensitivity(s)
+
+    def useCache(self, use):
+        self.parameters.hashTable.enableCaching(use)
+
+    def clearCache(self):
+        self.parameters.hashTable.clearCache()
 
     def enableRecording(self, dtype = np.float32):
         '''
@@ -194,6 +212,42 @@ def _getPhaseIndex(self, phase = None):
             return 0
         else:
             return self.phases.index(phase)
+
+    def setBC(self, LBCtype = BoundaryConditions.FLUX_BC, LBCValue = 0, RBCType = BoundaryConditions.FLUX_BC, RBCValue = 0, element = None):
+        self.parameters.boundaryConditions.setBoundaryCondition(BoundaryConditions.LEFT, 
+                                                                LBCtype, LBCValue, element)
+        self.parameters.boundaryConditions.setBoundaryCondition(BoundaryConditions.RIGHT,
+                                                                RBCType, RBCValue, element)
+
+    def setCompositionLinear(self, Lvalue, Rvalue, element = None):
+        element = self.elements[0] if element is None else element
+        self.parameters.compositionProfile.clearCompositionBuildSteps(element)
+        self.parameters.compositionProfile.addLinearCompositionStep(element, Lvalue, Rvalue)
+
+    def setCompositionStep(self, Lvalue, Rvalue, z, element = None):
+        element = self.elements[0] if element is None else element
+        self.parameters.compositionProfile.clearCompositionBuildSteps(element)
+        self.parameters.compositionProfile.addStepCompositionStep(element, Lvalue, Rvalue, z)
+
+    def setCompositionSingle(self, value, z, element = None):
+        element = self.elements[0] if element is None else element
+        self.parameters.compositionProfile.clearCompositionBuildSteps(element)
+        self.parameters.compositionProfile.addSingleCompositionStep(element, value, z)
+
+    def setCompositionInBounds(self, value, Lbound, Rbound, element = None):
+        element = self.elements[0] if element is None else element
+        self.parameters.compositionProfile.clearCompositionBuildSteps(element)
+        self.parameters.compositionProfile.addBoundedCompositionStep(element, value, Lbound, Rbound)
+
+    def setCompositionFunction(self, func, element = None):
+        element = self.elements[0] if element is None else element
+        self.parameters.compositionProfile.clearCompositionBuildSteps(element)
+        self.parameters.compositionProfile.addFunctionCompositionStep(element, func)
+
+    def setCompositionProfile(self, z, x, element = None):
+        element = self.elements[0] if element is None else element
+        self.parameters.compositionProfile.clearCompositionBuildSteps(element)
+        self.parameters.compositionProfile.addProfileCompositionStep(element, x, z)
 
     def setup(self):
         '''

kawin/diffusion/DiffusionParameters.py

@@ -440,6 +440,25 @@ def setPostProcessFunction(self, functionName, functionArgs = None):
         Returns post process function
         '''
         self.postProcessParameters = [functionArgs]
+        if isinstance(functionName, str):
+            self._setPostProcessFunctionByStr(functionName)
+        else:
+            self._setPostProcessFunctionByID(functionName)
+
+    def _setPostProcessFunctionByStr(self, functionName):
+        keywords_map = {
+            'none': self.NO_POST,
+            'predefined': self.PREDEFINED,
+            'majority': self.MAJORITY,
+            'exclude': self.EXCLUDE
+        }
+        if functionName in keywords_map:
+            self._setHomogenizationFunctionByID(keywords_map[functionName])
+
+        str_options = ', '.join(list(keywords_map.keys()))
+        raise Exception(f'Error: post process function by str should be {str_options}')
+
+    def _setPostProcessFunctionByID(self, functionName):
         if functionName == self.NO_POST:
             self.postProcessFunction = _postProcessDoNothing
         elif functionName == self.PREDEFINED:
@@ -449,7 +468,9 @@ def setPostProcessFunction(self, functionName, functionArgs = None):
         elif functionName == self.EXCLUDE:
             self.postProcessFunction = _postProcessExcludePhases
         else:
-            raise Exception("Error: post process function should be \'predefined\', \'majority\' or \'exclude\'")
+            func_types = ['NO_POST', 'PREDEFINED', 'MAJORITY', 'EXCLUDE']
+            int_options = ', '.join([f'HomogenizationParameters.{t}' for t in func_types])
+            raise Exception(f'Error: post process function by ID should be {int_options}')
 
     def setHomogenizationFunction(self, function):
         '''
@@ -478,6 +499,7 @@ def _setHomogenizationFunctionByStr(self, function):
         for func_id, keywords in keywords_map.items():
             if all([kw in function for kw in keywords]):
                 self._setHomogenizationFunctionByID(func_id)
+                return
 
         func_types = ['wiener upper', 'wiener lower', 'hashin upper', 'hashin lower', 'labyrinth']
         str_options = ', '.join(func_types)

kawin/diffusion/Homogenization.py

@@ -5,6 +5,18 @@
 import copy
 
 class HomogenizationModel(DiffusionModel):    
+    def setMobilityFunction(self, function):
+        self.parameters.homogenizationParameters.setHomogenizationFunction(function)
+
+    def setLabyrinthFactor(self, n):
+        self.parameters.homogenizationParameters.setLabyrinthFactor(n)
+
+    def setMobilityPostProcessFunction(self, function, functionArgs = None):
+        self.parameters.homogenizationParameters.setPostProcessFunction(function, functionArgs)
+
+    def setIdealEps(self, eps):
+        self.parameters.homogenizationParameters.eps = eps
+
     def _getFluxes(self, t, x_curr):
         '''
         Return fluxes and time interval for the current iteration