Mandd/gawithcustomsampler

ravenframework/CodeInterfaceClasses/MooseBasedApp/MooseInputParser.py

@@ -91,6 +91,7 @@ def getpotToInputTree(getpot):
           parentNodes.append(currentNode)
         currentNode = TreeStructure.InputNode(tag=line.strip('[]./'))
         closeEntry = False
+
       #------------------
       # closing node
       elif line.startswith(('[../]', '[]')):

ravenframework/Optimizers/Optimizer.py

@@ -175,12 +175,14 @@ def __init__(self):
     self._constraintFunctions = []      # list of constraint functions
     self._impConstraintFunctions = []   # list of implicit constraint functions
     self._requireSolnExport = True      # optimizers only produce result in solution export
+    self.optAssemblerList = ['DataObjects', 'Distributions', 'Functions', 'Files'] # List of assembler entities required to initialize an optmizer
     # __private
     # additional methods
     self.addAssemblerObject('Constraint', InputData.Quantity.zero_to_infinity)      # Explicit (input-based) constraints
     self.addAssemblerObject('ImplicitConstraint', InputData.Quantity.zero_to_infinity)      # Implicit constraints
     self.addAssemblerObject('Sampler', InputData.Quantity.zero_to_one)          # This Sampler can be used to initialize the optimization initial points (e.g. partially replace the <initial> blocks for some variables)
 
+
     # register adaptive sample identification criteria
     self.registerIdentifier('traj') # the trajectory of interest
 
@@ -208,7 +210,8 @@ def _localGenerateAssembler(self, initDict):
     self.assemblerDict['DataObjects'] = []
     self.assemblerDict['Distributions'] = []
     self.assemblerDict['Functions'] = []
-    for mainClass in ['DataObjects', 'Distributions', 'Functions']:
+    self.assemblerDict['Files'] = []
+    for mainClass in self.optAssemblerList:
       for funct in initDict[mainClass]:
         self.assemblerDict[mainClass].append([mainClass,
                                               initDict[mainClass][funct].type,
@@ -217,7 +220,7 @@ def _localGenerateAssembler(self, initDict):
 
   def localInputAndChecks(self, xmlNode, paramInput):
     """
-      unfortunately-named method that serves as a pass-through for input reading.
+      Method that serves as a pass-through for input reading.
       comes from inheriting from Sampler and _readMoreXML chain.
       @ In, xmlNode, xml.etree.ElementTree.Element, xml element node (don't use!)
       @ In, paramInput, InputData.ParameterInput, parameter specs interpreted
@@ -234,9 +237,8 @@ def _localWhatDoINeed(self):
       @ Out, needDict, dict, list of objects needed
     """
     needDict = {}
-    needDict['Distributions'] = [(None,'all')]
-    needDict['Functions'    ] = [(None,'all')]
-    needDict['DataObjects'  ] = [(None,'all')]
+    for elem in self.optAssemblerList:
+      needDict[elem] = [(None,'all')]
 
     return needDict
 
@@ -401,7 +403,7 @@ def _initializeInitSampler(self, externalSeeding):
     self._initSampler = sampler
     # initialize sampler
     samplerInit = {}
-    for entity in ['Distributions', 'Functions', 'DataObjects']:
+    for entity in self.optAssemblerList:
       samplerInit[entity] = dict((entry[2], entry[3]) for entry in self.assemblerDict.get(entity, []))
     self._initSampler._localGenerateAssembler(samplerInit)
     # assure sampler provides useful info

ravenframework/Samplers/CustomSampler.py

@@ -128,7 +128,7 @@ def _localWhatDoINeed(self):
       This method is a local mirror of the general whatDoINeed method.
       It is implemented by the samplers that need to request special objects
       @ In, None
-      @ Out, needDict, dict, list of objects needed (in this case it is empty, since no distrubtions are needed and the Source is loaded automatically)
+      @ Out, needDict, dict, list of objects needed (in this case it is empty, since no distribtions are needed and the Source is loaded automatically)
     """
     needDict = {}
     needDict['Functions'] = [] # In case functions have been inputted

tests/framework/Optimizers/GeneticAlgorithms/discrete/unconstrained/MaxwReplacement_customsampler/restart.csv

@@ -0,0 +1,11 @@
+x1,x2,x3
+6,6,6
+2,2,6
+4,5,3
+3,4,2
+2,6,1
+1,2,4
+2,2,2
+4,4,3
+2,6,6
+2,1,3

tests/framework/Optimizers/GeneticAlgorithms/discrete/unconstrained/testGAMaxwRep_custom_sampler.xml

@@ -0,0 +1,149 @@
+<?xml version="1.0" ?>
+<Simulation verbosity="debug">
+  <TestInfo>
+    <name>framework/Optimizers/GA.MaxwReplacementCustomSampler</name>
+    <author>mandd</author>
+    <created>2022-02-24</created>
+    <classesTested>GeneticAlgorithm</classesTested>
+    <description>
+      This test assesses the Genetic algorithm when a custom sampler (initialized by file) is used to 
+      initialize the initial population
+    </description>
+    <analytic>
+      This test uses myLocalSum's analytic objective function.
+    </analytic>
+  </TestInfo>
+
+  <RunInfo>
+    <WorkingDir>MaxwReplacement_customsampler</WorkingDir>
+    <Sequence>optimize, print</Sequence>
+    <batchSize>1</batchSize>
+  </RunInfo>
+
+  <Files>
+    <Input name="restart.csv" type="">restart.csv</Input>
+  </Files>
+
+  <Steps>
+    <MultiRun name="optimize" re-seeding="2286">
+      <Input class="DataObjects" type="PointSet">placeholder</Input>
+      <Model class="Models" type="ExternalModel">myLocalSum</Model>
+      <Optimizer class="Optimizers" type="GeneticAlgorithm">GAopt</Optimizer>
+      <SolutionExport class="DataObjects" type="PointSet">opt_export</SolutionExport>
+      <Output class="DataObjects" type="PointSet">optOut</Output>
+      <Output class="OutStreams" type="Print">opt_export</Output>
+    </MultiRun>
+    <IOStep name="print">
+      <Input class="DataObjects" type="PointSet">opt_export</Input>
+      <Input class="DataObjects" type="PointSet">optOut</Input>
+      <Output class="OutStreams" type="Print">opt_export</Output>
+      <Output class="OutStreams" type="Print">optOut</Output>
+      <Output class="OutStreams" type="Plot">opt_path</Output>
+    </IOStep>
+  </Steps>
+
+  <Distributions>
+    <UniformDiscrete name='uniform_dist_Repl_1'>
+      <lowerBound>1</lowerBound>
+      <upperBound>6</upperBound>
+      <strategy>withReplacement</strategy>
+    </UniformDiscrete>
+        <UniformDiscrete name='uniform_dist_woRepl_1'>
+      <lowerBound>1</lowerBound>
+      <upperBound>6</upperBound>
+      <strategy>withoutReplacement</strategy>
+    </UniformDiscrete>
+  </Distributions>
+
+  <Optimizers>
+    <GeneticAlgorithm name="GAopt">
+      <samplerInit>
+        <limit>10</limit>
+        <initialSeed>42</initialSeed>
+        <writeSteps>every</writeSteps>
+        <type>max</type>
+      </samplerInit>
+
+      <GAparams>
+        <populationSize>10</populationSize>
+        <parentSelection>rouletteWheel</parentSelection>
+        <reproduction>
+          <crossover type="onePointCrossover">
+            <crossoverProb>0.8</crossoverProb>
+          </crossover>
+          <mutation type="swapMutator">
+            <mutationProb>0.9</mutationProb>
+          </mutation>
+        </reproduction>
+        <fitness type="invLinear">
+          <a>2.0</a>
+          <b>1.0</b>
+        </fitness>
+        <survivorSelection>fitnessBased</survivorSelection>
+      </GAparams>
+
+      <convergence>
+        <AHDp>0.1</AHDp>
+      </convergence>
+
+      <variable name="x1">
+        <distribution>uniform_dist_Repl_1</distribution>
+      </variable>
+
+      <variable name="x2">
+        <distribution>uniform_dist_Repl_1</distribution>
+      </variable>
+
+      <variable name="x3">
+        <distribution>uniform_dist_Repl_1</distribution>
+      </variable>
+
+      <objective>ans</objective>
+      <TargetEvaluation class="DataObjects" type="PointSet">optOut</TargetEvaluation>
+    <Sampler class="Samplers" type="CustomSampler">restartSampler</Sampler>
+    </GeneticAlgorithm>
+  </Optimizers>
+
+  <Samplers>
+    <CustomSampler name="restartSampler">
+      <Source class="Files" type="">restart.csv</Source>
+      <variable name="x1"/>
+      <variable name="x2"/>
+      <variable name="x3"/>
+    </CustomSampler>
+  </Samplers>
+
+    <Models>
+      <ExternalModel ModuleToLoad="../../../../../AnalyticModels/optimizing/myLocalSum.py" name="myLocalSum" subType="">
+        <variables>x1,x2,x3,ans</variables>
+      </ExternalModel>
+    </Models>
+
+    <DataObjects>
+      <PointSet name="placeholder"/>
+      <PointSet name="optOut">
+        <Input>x1,x2,x3</Input>
+        <Output>ans</Output>
+      </PointSet>
+      <PointSet name="opt_export">
+        <Input>trajID</Input>
+        <Output>x1,x2,x3,ans,age,batchId,fitness,iteration,accepted,AHDp,conv_AHDp</Output>
+      </PointSet>
+    </DataObjects>
+
+    <OutStreams>
+      <Print name="optOut">
+        <type>csv</type>
+        <source>optOut</source>
+      </Print>
+      <Print name="opt_export">
+        <type>csv</type>
+        <source>opt_export</source>
+        <clusterLabel>trajID</clusterLabel>
+      </Print>
+      <Plot name="opt_path" subType="OptPath">
+        <source>opt_export</source>
+        <vars>x1,x2,x3,ans</vars>
+      </Plot>
+    </OutStreams>
+</Simulation>

tests/framework/Optimizers/GeneticAlgorithms/gold/discrete/unconstrained/MaxwReplacement_customsampler/opt_export_0.csv

@@ -0,0 +1,52 @@
+x1,x2,x3,ans,age,batchId,fitness,iteration,accepted,AHDp,conv_AHDp
+6.0,6.0,6.0,36.0,0.0,1.0,72.0,0.0,first,,0.0
+2.0,2.0,6.0,24.0,0.0,1.0,48.0,0.0,first,,0.0
+4.0,5.0,3.0,23.0,0.0,1.0,46.0,0.0,first,,0.0
+3.0,4.0,2.0,17.0,0.0,1.0,34.0,0.0,first,,0.0
+2.0,6.0,1.0,17.0,0.0,1.0,34.0,0.0,first,,0.0
+1.0,2.0,4.0,17.0,0.0,1.0,34.0,0.0,first,,0.0
+2.0,2.0,2.0,12.0,0.0,1.0,24.0,0.0,first,,0.0
+4.0,4.0,3.0,21.0,0.0,1.0,42.0,0.0,first,,0.0
+2.0,6.0,6.0,32.0,0.0,1.0,64.0,0.0,first,,0.0
+2.0,1.0,3.0,13.0,0.0,1.0,26.0,0.0,first,,0.0
+3.0,4.0,4.0,23.0,0.0,2.0,46.0,1.0,accepted,2.44051339313,0.0
+4.0,2.0,1.0,11.0,0.0,2.0,22.0,1.0,accepted,2.44051339313,0.0
+6.0,4.0,4.0,26.0,0.0,2.0,52.0,1.0,accepted,2.44051339313,0.0
+3.0,6.0,6.0,33.0,0.0,2.0,66.0,1.0,accepted,2.44051339313,0.0
+3.0,4.0,4.0,23.0,0.0,2.0,46.0,1.0,accepted,2.44051339313,0.0
+6.0,2.0,2.0,16.0,0.0,2.0,32.0,1.0,accepted,2.44051339313,0.0
+6.0,6.0,1.0,21.0,0.0,2.0,42.0,1.0,accepted,2.44051339313,0.0
+4.0,2.0,6.0,26.0,0.0,2.0,52.0,1.0,accepted,2.44051339313,0.0
+6.0,2.0,1.0,13.0,0.0,2.0,26.0,1.0,accepted,2.44051339313,0.0
+4.0,2.0,2.0,14.0,0.0,2.0,28.0,1.0,accepted,2.44051339313,0.0
+6.0,6.0,6.0,36.0,0.0,3.0,72.0,2.0,accepted,2.15036705544,0.0
+6.0,6.0,3.0,27.0,0.0,3.0,54.0,2.0,accepted,2.15036705544,0.0
+1.0,6.0,6.0,31.0,0.0,3.0,62.0,2.0,accepted,2.15036705544,0.0
+6.0,6.0,6.0,36.0,0.0,3.0,72.0,2.0,accepted,2.15036705544,0.0
+3.0,5.0,6.0,31.0,0.0,3.0,62.0,2.0,accepted,2.15036705544,0.0
+4.0,6.0,6.0,34.0,0.0,3.0,68.0,2.0,accepted,2.15036705544,0.0
+1.0,6.0,3.0,22.0,0.0,3.0,44.0,2.0,accepted,2.15036705544,0.0
+6.0,6.0,6.0,36.0,0.0,3.0,72.0,2.0,accepted,2.15036705544,0.0
+3.0,6.0,3.0,24.0,0.0,3.0,48.0,2.0,accepted,2.15036705544,0.0
+6.0,5.0,4.0,28.0,0.0,3.0,56.0,2.0,accepted,2.15036705544,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,2.0,6.0,28.0,0.0,4.0,56.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,2.0,6.0,28.0,0.0,4.0,56.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,0.0,4.0,72.0,3.0,accepted,2.98811264988,0.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,accepted,0.0,1.0
+6.0,6.0,6.0,36.0,1.0,5.0,72.0,4.0,final,0.0,1.0

tests/framework/Optimizers/GeneticAlgorithms/tests

@@ -70,6 +70,17 @@
     [../]
   [../]
 
+  [./MaxwReplacementCustomSampler]
+    type = 'RavenFramework'
+    input = 'discrete/unconstrained/testGAMaxwRep_custom_sampler.xml'
+    [./data]
+      type = OrderedCSV
+      output = 'discrete/unconstrained/MaxwReplacement_customsampler/opt_export_0.csv'
+      rel_err = 1e-3
+      zero_threshold = 1e-5
+    [../]
+  [../]
+
   [./MaxwReplacementDiffDist]
     type = 'RavenFramework'
     input = 'discrete/unconstrained/testGAMaxwRepDifferentDist.xml'

tests/framework/ROM/TimeSeries/ARMA/tests

@@ -295,9 +295,9 @@
   [./InterpolatedMaxCycles]
     type = 'RavenFramework'
     input = 'interpolated_maxcycles.xml'
-    csv = 'InterpolatedMaxCycles/synthetic.csv InterpolatedMaxCycles/resynthetic.csv'
+    output = 'InterpolatedMaxCycles/synthetic.csv InterpolatedMaxCycles/resynthetic.csv'
     #not consistent, see 1351
-    rel_err = 10000.0
+    #rel_err = 10000.0
   [../]
 
   [./CloudPlot]