Added MOOSE interface Generic File perturbation

doc/user_manual/existing_interfaces.tex

@@ -892,18 +892,27 @@ \subsubsection{Files}
 %
 In the case of any MooseBasedApp, the files typically needed are the following:
 \begin{itemize}
-  \item MooseBasedApp YAML input file
+  \item MooseBasedApp GetPot input file
   \item Restart Files (if the calculation is instantiated from a restart point)
+  \item Mesh Files (in case the mesh is externally specified)
+  \item Any other generic input file (CSVs with Power histories, boundary conditions files, etc.)
 \end{itemize}
 Example:
 \begin{lstlisting}[style=XML]
 <Files>
   <Input name='mooseBasedApp.i' type=''>mooseBasedApp.i</Input>
   <Input name='0020_mesh.cpr' type=''>0020_mesh.cpr</Input>
-  <Input name='0020.xdr.0000'>0020.xdr.0000</Input>
-  <Input name='0020.rd-0'>0020.rd-0</Input>
+  <Input name='0020.xdr.0000' type="">0020.xdr.0000</Input>
+  <Input name='0020.rd-0' type="">0020.rd-0</Input>
+  <Input name='exodus_mesh.e' type="">exodus_mesh.e</Input>
+  <Input name='a_generic_additional_input_file.csv' type="Generic">a_generic_additional_input_file.csv</Input>
 </Files>
 \end{lstlisting}
+If any file is tagged with the type \texttt{Generic}, it will be perturbable with the approach (wildcards)
+ explained in the generic code interface (see  \ref{subsec:genericInterface}).
+
+
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsubsection{Models}
 In the \xmlNode{Models} block particular MooseBasedApp executable needs to be specified.
@@ -994,8 +1003,30 @@ \subsubsection{Samplers}
 ...
 \end{lstlisting}
 %
-In this example, we proceed to do so for both the Grid sampling and the Monte-Carlo sampling.
+In case some variables in external (\texttt{Generic} input files) need to be perturbed, 
+the wildcard approach can be used (for those variables):
+\begin{lstlisting}[style=XML]
+...
+<Samplers>
+  <aSampler name='aUserDefinedName' >
+    <variable name='aWildCard1'>
+      ...
+    </variable>
+        <variable name='aWildCard2'>
+      ...
+    </variable>
+    <variable name='Materials|heatStructure|thermal_conductivity'>
+      ...
+    </variable>
+  </aSampler>
+</Samplers>
+...
+\end{lstlisting}
+In this case the tagged file (\texttt{Generic}) will be parsed to find the variables
+\texttt{\$RAVEN-aWildCard1\$} and \texttt{\$RAVEN-aWildCard1\$} and to replace their values
+with the corresponding sampled variables (for more details, see  \ref{subsec:genericInterface})
 
+In this example, we proceed to do so for both the Grid sampling and the Monte-Carlo sampling.
 \begin{lstlisting}[style=XML,morekeywords={name,type,construction,lowerBound,steps,limit,initialSeed}]
 <Samplers verbosity='debug'>
     <Grid name='myGrid'>
@@ -1011,6 +1042,10 @@ \subsubsection{Samplers}
         <distribution  >ThermalConductivity2</distribution>
         <grid type='value' upperBound='4' construction='equal' steps='1'>0.5</grid>
       </variable>
+      <variable name='aWildCard1'>
+        <distribution  >ThermalConductivity2</distribution>
+        <grid type='value' upperBound='4' construction='equal' steps='1'>0.5</grid>
+      </variable>
     </Grid>
   <MonteCarlo name='MC_Sampler' limit='1000'>
       <variable name='Materials|heatStructure1|thermal_conductivity' >
@@ -1022,6 +1057,9 @@ \subsubsection{Samplers}
       <variable name='Materials|heatStructure2|thermal_conductivity'>
         <distribution  >ThermalConductivity2</distribution>
       </variable>
+      <variable name='aWildCard1'>
+        <distribution  >ThermalConductivity2</distribution>
+      </variable>
   </MonteCarlo>
 </Samplers>
 \end{lstlisting}

framework/CodeInterfaces/MooseBasedApp/MooseBasedAppInterface.py

@@ -21,6 +21,7 @@
 import os
 import copy
 from CodeInterfaceBaseClass import CodeInterfaceBase
+import GenericParser
 import MooseData
 import csvUtilities
 
@@ -78,11 +79,15 @@ def createNewInput(self,currentInputFiles,oriInputFiles,samplerType,**Kwargs):
       self._samplersDictionary[samplerType] = self.pointSamplerForMooseBasedApp
 
     found = False
-    for index, inputFile in enumerate(currentInputFiles):
-      inputFile = inputFile.getAbsFile()
-      if inputFile.endswith(self.getInputExtension()):
+    genericInput, genericOriInput = [], []
+    for i, inputFile in enumerate(currentInputFiles):
+      inFile = inputFile.getAbsFile()
+      if inFile.endswith(self.getInputExtension()):
+        index = i
         found = True
-        break
+      if inputFile.getType().lower() == "generic":
+        genericInput.append(inputFile)
+        genericOriInput.append(oriInputFiles[i])
     if not found:
       raise IOError('None of the input files has one of the following extensions: ' + ' '.join(self.getInputExtension()))
     outName = self.outputPrefix+currentInputFiles[index].getBase()
@@ -98,6 +103,12 @@ def createNewInput(self,currentInputFiles,oriInputFiles,samplerType,**Kwargs):
     #make input
     parser.printInput(currentInputFiles[index].getAbsFile())
     self.vectorPPFound, self.vectorPPDict = parser.vectorPostProcessor()
+
+    if genericInput:
+      parser = GenericParser.GenericParser(genericInput)
+      parser.modifyInternalDictionary(**Kwargs)
+      parser.writeNewInput(genericInput,genericOriInput)
+
     return currentInputFiles
 
   def pointSamplerForMooseBasedApp(self,**Kwargs):
@@ -124,7 +135,6 @@ def dynamicEventTreeForMooseBasedApp(self,**Kwargs):
     """
     listDict = []
     raise IOError('dynamicEventTreeForMooseBasedApp not yet implemented')
-    return listDict
 
   def finalizeCodeOutput(self,command,output,workingDir):
     """

tests/framework/CodeInterfaceTests/MOOSEBaseApps/MooseExample18OnlyGenericFile/ex18.i

@@ -0,0 +1,151 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+  xmin = 0
+  xmax = 1
+  ymin = 0
+  ymax = 1
+  nx = 10
+  ny = 10
+  elem_type = QUAD4
+[]
+
+[Functions]
+  # ODEs
+  [./exact_x_fn]
+    type = ParsedFunction
+    value = (-1/3)*exp(-t)+(4/3)*exp(5*t)
+  [../]
+  [./exact_y_fn]
+    type = ParsedFunction
+    value = (2/3)*exp(-t)+(4/3)*exp(5*t)
+  [../]
+[]
+
+[Variables]
+  [./diffused]
+    order = FIRST
+    family = LAGRANGE
+  [../]
+
+  # ODE variables
+  [./x]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 1
+  [../]
+  [./y]
+    family = SCALAR
+    order = FIRST
+    initial_condition = 2
+  [../]
+
+[]
+
+[Kernels]
+  [./td]
+    type = TimeDerivative
+    variable = diffused
+  [../]
+  [./diff]
+    type = Diffusion
+    variable = diffused
+  [../]
+[]
+
+[ScalarKernels]
+  [./td1]
+    type = ODETimeDerivative
+    variable = x
+  [../]
+  [./ode1]
+    type = ImplicitODEx
+    variable = x
+    y = y
+  [../]
+
+  [./td2]
+    type = ODETimeDerivative
+    variable = y
+  [../]
+  [./ode2]
+    type = ImplicitODEy
+    variable = y
+    x = x
+  [../]
+[]
+
+
+[BCs]
+  [./right]
+    type = ScalarDirichletBC
+    variable = diffused
+    boundary = 1
+    scalar_var = x
+  [../]
+
+  [./left]
+    type = ScalarDirichletBC
+    variable = diffused
+    boundary = 3
+    scalar_var = y
+  [../]
+[]
+
+[Postprocessors]
+  # to print the values of x, y into a file so we can plot it
+  [./x]
+    type = ScalarVariable
+    variable = x
+    execute_on = timestep_end
+  [../]
+
+  [./y]
+    type = ScalarVariable
+    variable = y
+    execute_on = timestep_end
+  [../]
+
+  [./exact_x]
+    type = FunctionValuePostprocessor
+    function = exact_x_fn
+    execute_on = timestep_end
+    point = '0 0 0'
+  [../]
+
+  [./exact_y]
+    type = FunctionValuePostprocessor
+    function = exact_y_fn
+    execute_on = timestep_end
+    point = '0 0 0'
+  [../]
+
+  # Measure the error in ODE solution for 'x'.
+  [./l2err_x]
+    type = ScalarL2Error
+    variable = x
+    function = exact_x_fn
+  [../]
+
+  # Measure the error in ODE solution for 'y'.
+  [./l2err_y]
+    type = ScalarL2Error
+    variable = y
+    function = exact_y_fn
+  [../]
+[]
+
+
+[Executioner]
+  type = Transient
+  start_time = 0
+  dt = 0.01
+  num_steps = 10
+
+  #Preconditioned JFNK (default)
+  solve_type = 'PJFNK'
+[]
+
+[Outputs]
+  exodus = true
+[]

tests/framework/CodeInterfaceTests/MOOSEBaseApps/MooseExample18OnlyGenericFile/generic_external_file.csv

@@ -0,0 +1,5 @@
+time,power
+0.,10
+1.0,20
+2.0,$RAVEN-p2.0$
+3.0,$RAVEN-p3.0$

tests/framework/CodeInterfaceTests/MOOSEBaseApps/MooseExample18OnlyGenericFile/myMC/1/out~ex18.csv

@@ -0,0 +1,12 @@
+time,exact_x,exact_y,l2err_x,l2err_y,x,y
+0,0,0,0,0,1,2
+0.01,1.0716781839183,2.0617280176675,0.0017975847110658,0.0018467608635113,1.0734757686294,2.063574778531
+0.02,1.1468283329986,2.1270270063054,0.0037839718620896,0.0038813479623196,1.1506123048607,2.1309083542677
+0.03,1.2256304791215,2.19607601267,0.0059738448989899,0.0061184592775807,1.2316043240205,2.2021944719476
+0.04,1.3082738644961,2.2690633036484,0.008382904883361,0.0085738102126549,1.3166567693795,2.2776371138611
+0.05,1.3949574140834,2.3461868385841,0.011027936581653,0.011264199685733,1.4059853506651,2.3574510382699
+0.06,1.4858902322399,2.4276547658242,0.013926878676188,0.014207580343858,1.4998171109161,2.441862346168
+0.07,1.5812921248224,2.5136859447283,0.017098898346571,0.017423133144702,1.5983910231689,2.531109077873
+0.08,1.6813941480595,2.6045104944461,0.020564470486559,0.020931346578875,1.701958618546,2.625441841025
+0.09,1.7864391855631,2.7003703708344,0.024345461837806,0.024754100802847,1.810784647401,2.7251244716372
+0.1,1.8966825549215,2.8015199729575,0.028465220336359,0.028914756989218,1.9251477752579,2.8304347299467

tests/framework/CodeInterfaceTests/MOOSEBaseApps/MooseExample18OnlyGenericFile/myMC/2/out~ex18.csv

@@ -0,0 +1,12 @@
+time,exact_x,exact_y,l2err_x,l2err_y,x,y
+0,0,0,0,0,1,2
+0.01,1.0716781839183,2.0617280176675,0.0017975847110658,0.0018467608635113,1.0734757686294,2.063574778531
+0.02,1.1468283329986,2.1270270063054,0.0037839718620896,0.0038813479623196,1.1506123048607,2.1309083542677
+0.03,1.2256304791215,2.19607601267,0.0059738448989899,0.0061184592775807,1.2316043240205,2.2021944719476
+0.04,1.3082738644961,2.2690633036484,0.008382904883361,0.0085738102126549,1.3166567693795,2.2776371138611
+0.05,1.3949574140834,2.3461868385841,0.011027936581653,0.011264199685733,1.4059853506651,2.3574510382699
+0.06,1.4858902322399,2.4276547658242,0.013926878676188,0.014207580343858,1.4998171109161,2.441862346168
+0.07,1.5812921248224,2.5136859447283,0.017098898346571,0.017423133144702,1.5983910231689,2.531109077873
+0.08,1.6813941480595,2.6045104944461,0.020564470486559,0.020931346578875,1.701958618546,2.625441841025
+0.09,1.7864391855631,2.7003703708344,0.024345461837806,0.024754100802847,1.810784647401,2.7251244716372
+0.1,1.8966825549215,2.8015199729575,0.028465220336359,0.028914756989218,1.9251477752579,2.8304347299467