WIP making ODEs work in Julia

Author: B-rando1

code/drasil-code/lib/Data/Drasil/ExternalLibraries/ODELibraries.hs

@@ -2,6 +2,8 @@
 module Data.Drasil.ExternalLibraries.ODELibraries (
   -- * SciPy Library (Python)
   scipyODEPckg, scipyODESymbols,
+  -- DifferentialEquations.jl Library (Julia)
+  jlODEPckg, jlODESymbols,
   -- * Oslo Library (C#)
   osloPckg, osloSymbols, arrayVecDepVar,
   -- * Apache Commons (Java)
@@ -23,7 +25,7 @@ import Language.Drasil.Code (Lang(..), ExternalLibrary, Step, Argument,
   lockedNamedArg, inlineArg, inlineNamedArg, preDefinedArg, functionArg,
   customObjArg, recordArg, lockedParam, unnamedParam, customClass,
   implementation, constructorInfo, methodInfo, methodInfoNoReturn,
-  appendCurrSol, populateSolList, assignArrayIndex, assignSolFromObj,
+  appendCurrSol, populateSolList, populateSolList', assignArrayIndex, assignSolFromObj,
   initSolListFromArray, initSolListWithVal, solveAndPopulateWhile,
   returnExprList, fixedReturn',
   ExternalLibraryCall, externalLibCall, choiceStepsFill, choiceStepFill,
@@ -164,6 +166,88 @@ odeintFunc = quantfunc $ implVar "odeint_scipy" (nounPhrase
   "method that solves a system of ODE using lsoda from the FORTRAN library odepack.")
   (Array Real) (label "odeint")
 
+-- DifferentialEquations.jl Library (Julia)
+jlODEPckg :: ODELibPckg
+jlODEPckg = mkODELibNoPath "DifferentialEquations.jl" "7.13.0" jlODE jlODECall [Julia]
+
+jlODESymbols :: [QuantityDict]
+jlODESymbols = map qw [jlMthdArg, jlRelTolArg, jlAbsTolArg, jlSaveAtArg] ++
+  map qw [jlR, jlP, t_span, jlSol, jlMthd, jlSp] ++
+  map qw [jlODEProblem, jlF, jlODESolve, jlODEDP5]
+
+jlODE :: ExternalLibrary
+jlODE = externalLib [
+  mandatorySteps $ [
+    callStep $ libFunctionWithResult jlODEImport
+      jlODEProblem [
+        functionArg jlF (map unnamedParam [Array Real, Real, Real])
+        returnExprList, inlineArg (Array Real), preDefinedArg t_span] jlR,
+    callStep $ libFunctionWithResult jlODEImport
+      jlODEDP5 [] jlMthd,
+    callStep $ libFunctionWithResult jlODEImport
+      jlODESolve [lockedArg (sy jlR), lockedNamedArg jlMthdArg (sy jlMthd),
+      inlineNamedArg jlRelTolArg Real, inlineNamedArg jlAbsTolArg Real,
+      inlineNamedArg jlSaveAtArg Real] jlSol] ++
+    populateSolList' jlSol jlSp] -- TODO: this should probably be populateSolList, but we don't have structs
+
+jlODECall :: ODEInfo -> ExternalLibraryCall
+jlODECall info = [
+  mandatoryStepsFill $ [
+    callStepFill $ libCallFill (functionArgFill
+      (map unnamedParamFill [depVar info, jlP, indepVar info])
+      (returnExprListFill $ odeSyst info) : map (basicArgFill . matrix)
+        [[initVal info], [[tInit info, tFinal info]]]),
+    callStepFill $ libCallFill [],
+    callStepFill $ libCallFill $ map basicArgFill
+      [relTol $ odeOpts info, absTol $ odeOpts info, stepSize $ odeOpts info]] ++
+    populateSolListFill (depVar info)]
+
+jlODEImport :: String
+jlODEImport = "DifferentialEquations"
+
+jlMthdArg, jlRelTolArg, jlAbsTolArg, jlSaveAtArg :: NamedArgument
+jlMthdArg = narg $ implVar "mthd_arg_jlODE" (nounPhrase
+  "chosen method for solving ODE" "chosen methods for solving ODE")
+  String (label "alg")
+jlRelTolArg = narg $ implVar "jl_arg_reltol" (nounPhrase
+  "Chosen relative tolerance" "Chosen relative tolerances")
+  Real (label "reltol")
+jlAbsTolArg = narg $ implVar "jl_arg_abstol" (nounPhrase
+  "Chosen absolute tolerance" "Chosen absolute tolerances")
+  Real (label "abstol")
+jlSaveAtArg = narg $ implVar "jl_arg_saveat" (nounPhrase
+  "Chosen time step" "Chosen time step")
+  Real (label "saveat")
+
+jlR, jlP, t_span, jlSol, jlMthd, jlSp :: CodeVarChunk
+jlR = quantvar $ implVar "r" (nounPhrase "ODE struct" "ODE structs")
+  odeT2 (label "r")
+jlP = quantvar $ implVar "params" (nounPhrase "param?" "params?")
+  Void (label "p") -- TODO: this should be a struct of some sort
+t_span = quantvar $ implVar "t_span" (nounPhrase "Timespan" "Timespans")
+  (Array Real) (label "t_span")
+jlSol = quantvar $ implVar "jl_solve" (nounPhrase "Solution" "Solutions")
+  Void (label "sol") -- TODO: this should be a struct of some sort
+jlMthd = quantvar $ implVar "jl_method" (nounPhrase
+  "chosen method for solving ODE" "chosen methods for solving ODE")
+  String (label "algorithm")
+jlSp = quantvar $ implVar "sp_julia" (nounPhrase "ODE solution point"
+  "ODE solution points") Real (label "sp")
+
+jlF, jlODEProblem, jlODESolve, jlODEDP5 :: CodeFuncChunk
+jlF = quantfunc $ implVar "f_jlODE" (nounPhrase "function representing ODE system"
+  "functions representing ODE system") (Array Real) (label "f")
+jlODEProblem = quantfunc $ implVar "jl_ode_problem" (nounPhrase
+  "function for defining an ODE for jlODE"
+  "functions for defining an ODE for jlODE") odeT2 (label "ODEProblem")
+jlODESolve = quantfunc $ implVar "jl_ode_solve" (nounPhrase
+  "function for solving an ODE for jlODE"
+  "functions for solving an ODE for jlODE") odeT2 (label "solve")
+jlODEDP5 = quantfunc $ implVar "jl_ode_dp5" (nounPhrase "DP5" "DP5s") odeT2 (label "DP5")
+
+odeT2 :: Space
+odeT2 = Void -- TODO: this should be a struct/function? of some sort
+
 -- Oslo Library (C#)
 
 -- | [Oslo](https://www.microsoft.com/en-us/research/project/open-solving-library-for-odes/) ODE library package.

code/drasil-code/lib/Language/Drasil/Code.hs

@@ -20,7 +20,7 @@ module Language.Drasil.Code (
   inlineArg, inlineNamedArg, preDefinedArg, preDefinedNamedArg, functionArg,
   customObjArg, recordArg, lockedParam, unnamedParam, customClass,
   implementation, constructorInfo, methodInfo, methodInfoNoReturn,
-  appendCurrSol, populateSolList, assignArrayIndex, assignSolFromObj,
+  appendCurrSol, populateSolList, populateSolList', assignArrayIndex, assignSolFromObj,
   initSolListFromArray, initSolListWithVal, solveAndPopulateWhile,
   returnExprList, fixedReturn, fixedReturn', initSolWithVal,
   ExternalLibraryCall, StepGroupFill(..), StepFill(..), FunctionIntFill(..),
@@ -67,7 +67,7 @@ import Language.Drasil.Code.ExternalLibrary (ExternalLibrary, Step,
   inlineArg, inlineNamedArg, preDefinedArg, preDefinedNamedArg, functionArg,
   customObjArg, recordArg, lockedParam, unnamedParam, customClass,
   implementation, constructorInfo, methodInfo, methodInfoNoReturn,
-  appendCurrSol, populateSolList, assignArrayIndex, assignSolFromObj,
+  appendCurrSol, populateSolList, populateSolList', assignArrayIndex, assignSolFromObj,
   initSolListFromArray, initSolListWithVal, solveAndPopulateWhile,
   returnExprList, fixedReturn, fixedReturn', initSolWithVal)
 import Language.Drasil.Code.ExternalLibraryCall (ExternalLibraryCall,

code/drasil-code/lib/Language/Drasil/Code/ExternalLibrary.hs

@@ -9,7 +9,7 @@ module Language.Drasil.Code.ExternalLibrary (ExternalLibrary, Step(..),
   lockedNamedArg, inlineArg, inlineNamedArg, preDefinedArg, preDefinedNamedArg,
   functionArg, customObjArg, recordArg, lockedParam, unnamedParam, customClass,
   implementation, constructorInfo, methodInfo, methodInfoNoReturn,
-  appendCurrSol, populateSolList, assignArrayIndex, assignSolFromObj,
+  appendCurrSol, populateSolList, populateSolList', assignArrayIndex, assignSolFromObj,
   initSolListFromArray, initSolListWithVal, solveAndPopulateWhile,
   returnExprList, fixedReturn, fixedReturn', initSolWithVal
 ) where
@@ -260,6 +260,17 @@ populateSolList arr el fld = [statementStep (\cdchs es -> case (cdchs, es) of
     (_,_) -> error popErr)]
   where popErr = "Fill for populateSolList should provide one CodeChunk and no Exprs"
 
+-- | Specifies a statement where a solution list is populated by iterating
+--   through a solution array.
+populateSolList' :: CodeVarChunk -> CodeVarChunk -> [Step]
+populateSolList' arr el = [statementStep (\cdchs es -> case (cdchs, es) of
+    ([s], []) -> FAsg s (Matrix [[]])
+    (_,_) -> error popErr),
+  statementStep (\cdchs es -> case (cdchs, es) of
+    ([s], []) -> FForEach el (sy arr) [FAppend (sy s) (sy el)]
+    (_,_) -> error popErr)]
+  where popErr = "Fill for populateSolList' should provide one CodeChunk and no Exprs"
+
 -- | Specifies statements where every index of an array is assigned a value.
 assignArrayIndex :: Step
 assignArrayIndex = statementStep (\cdchs es -> case (cdchs, es) of

code/drasil-example/swhsnopcm/lib/Drasil/SWHSNoPCM/Body.hs

@@ -25,7 +25,7 @@ import Data.Drasil.Concepts.Thermodynamics (heatCapSpec, htFlux, phaseChange,
   temp, thermalAnalysis, thermalConduction, thermocon)
 
 import Data.Drasil.ExternalLibraries.ODELibraries (scipyODESymbols, osloSymbols,
-  arrayVecDepVar, apacheODESymbols, odeintSymbols)
+  arrayVecDepVar, apacheODESymbols, odeintSymbols, jlODESymbols)
 
 import qualified Data.Drasil.Quantities.Thermodynamics as QT (temp,
   heatCapSpec, htFlux, sensHeat)
@@ -94,8 +94,9 @@ symbolsAll :: [QuantityDict] --FIXME: Why is PCM (swhsSymbolsAll) here?
                                --FOUND LOC OF ERROR: Instance Models
 symbolsAll = map qw symbols ++ map qw specParamValList ++
   [qw coilSAMax, qw tauW] ++ map qw [absTol, relTol] ++
-  scipyODESymbols ++ osloSymbols ++ apacheODESymbols ++ odeintSymbols
-  ++ map qw [listToArray $ quantvar tempW, arrayVecDepVar noPCMODEInfo]
+  scipyODESymbols ++ jlODESymbols ++ osloSymbols ++ apacheODESymbols ++
+  odeintSymbols ++
+  map qw [listToArray $ quantvar tempW, arrayVecDepVar noPCMODEInfo]
 
 concepts :: [UnitalChunk]
 concepts = map ucw [density, tau, inSA, outSA,

code/drasil-example/swhsnopcm/lib/Drasil/SWHSNoPCM/Choices.hs

@@ -8,7 +8,7 @@ import Language.Drasil.Code (Choices(..), CodeSpec, codeSpec, Comments(..),
   ExtLib(..))
 
 import Data.Drasil.ExternalLibraries.ODELibraries (scipyODEPckg, osloPckg,
-  apacheODEPckg, odeintPckg)
+  apacheODEPckg, odeintPckg, jlODEPckg)
 import Drasil.SWHSNoPCM.Body (noPCMODEInfo, fullSI)
 
 code :: CodeSpec
@@ -17,13 +17,14 @@ code = codeSpec fullSI choices []
 
 choices :: Choices
 choices = defaultChoices {
-  lang = [Python, Cpp, CSharp, Java],
+  lang = [Python, Cpp, CSharp, Java, Julia],
   architecture = makeArchit Modular Program,
-  dataInfo = makeData Unbundled (Store Bundled) Const,
+  dataInfo = makeData Unbundled (Store Unbundled) Const,
   optFeats = makeOptFeats
     (makeDocConfig [CommentFunc, CommentClass, CommentMod] Quiet Hide)
     (makeLogConfig [] "log.txt")
     [SampleInput "../../datafiles/swhsnopcm/sampleInput.txt", ReadME],
   srsConstraints = makeConstraints Warning Warning,
-  extLibs = [Math (makeODE [noPCMODEInfo] [scipyODEPckg, osloPckg, apacheODEPckg, odeintPckg])]
+  extLibs = [Math (makeODE [noPCMODEInfo] [scipyODEPckg, osloPckg,
+    apacheODEPckg, odeintPckg, jlODEPckg])]
 }

code/drasil-gool/lib/Drasil/GOOL/InterfaceCommon.hs

@@ -502,7 +502,7 @@ convType (Func ps r) = funcType (map convType ps) (convType r)
 convType Void = void
 convType InFile = infile
 convType OutFile = outfile
-convType (Object _) = error "Objects not supported"
+convType (Object n) = error $ "convType: Objects not supported (name: '" ++ n ++ "')"
 
 convScope :: (ScopeSym r) => ScopeData -> r (Scope r)
 convScope (SD {scopeTag = Global}) = global

code/drasil-gool/lib/Drasil/GOOL/LanguageRenderer/CommonPseudoOO.hs

@@ -418,7 +418,7 @@ multiReturn f vs = do
   returnStmt $ mkStateVal IC.void $ f $ valueList vs'
 
 listDec :: (CommonRenderSym r) => SVariable r -> r (Scope r) -> MSStatement r
-listDec v scp = IC.varDecDef v scp $ IC.litList (onStateValue variableType v) []
+listDec v scp = listDecDef v scp []
 
 funcDecDef :: (OORenderSym r) => SVariable r -> r (Scope r) -> [SVariable r] ->
   MSBody r -> MSStatement r

code/drasil-gool/lib/Drasil/GOOL/LanguageRenderer/JuliaRenderer.hs

@@ -43,7 +43,8 @@ import Drasil.GOOL.RendererClassesProc (ProcRenderSym, RenderFile(..),
   RenderMod(..), ModuleElim, ProcRenderMethod(..))
 import qualified Drasil.GOOL.RendererClassesProc as RC (module')
 import Drasil.GOOL.LanguageRenderer (printLabel, listSep, listSep',
-  variableList, parameterList, forLabel, inLabel, tryLabel, catchLabel)
+  variableList, parameterList, forLabel, inLabel, tryLabel, catchLabel,
+  valueList)
 import qualified Drasil.GOOL.LanguageRenderer as R (sqrt, abs, log10, log,
   exp, sin, cos, tan, asin, acos, atan, floor, ceil, multiStmt, body,
   addComments, blockCmt, docCmt, commentedMod, listSetFunc, commentedItem,
@@ -60,7 +61,7 @@ import qualified Drasil.GOOL.LanguageRenderer.LanguagePolymorphic as G (
   emptyStmt, print, comment, valStmt, returnStmt, param, docFunc, throw, arg,
   argsList, ifCond, smartAdd, local, var)
 import qualified Drasil.GOOL.LanguageRenderer.CommonPseudoOO as CP (bool,
-  boolRender, extVar, funcType, litArray, listDec, listDecDef, listAccessFunc,
+  boolRender, extVar, funcType, listDec, listDecDef, listAccessFunc,
   listSetFunc, notNull, extFuncAppMixedArgs, functionDoc, listSize, listAdd,
   listAppend, intToIndex', indexToInt', inOutFunc, docInOutFunc', forLoopError,
   varDecDef, openFileR', openFileW', openFileA', multiReturn, multiAssign,
@@ -138,10 +139,11 @@ instance RenderFile JuliaCode where
 instance ImportSym JuliaCode where
   type Import JuliaCode = Doc
   langImport n = let modName = text n
-                     fileName = text $ n ++ '.' : jlExt
+    in toCode $ importLabel <+> modName
+  modImport n = let modName = text n
+                    fileName = text $ n ++ '.' : jlExt
     in toCode $ vcat [includeLabel <> parens (doubleQuotes fileName),
-      importLabel <+> text "." <> modName] -- TODO: we want a dot only when the import is locally defined.
-  modImport = langImport
+                      importLabel <+> text "." <> modName]
 
 instance ImportElim JuliaCode where
   import' = unJLC
@@ -257,7 +259,7 @@ instance ScopeElim JuliaCode where
 instance VariableSym JuliaCode where
   type Variable JuliaCode = VarData
   var = G.var
-  constant = var -- TODO: add `const` keyword in global scope, and follow Python for local
+  constant = var
   extVar l n t = modify (addModuleImportVS l) >> CP.extVar l n t
   arrayElem i = A.arrayElem (litInt i)
 
@@ -289,8 +291,8 @@ instance Literal JuliaCode where
   litFloat = jlLitFloat
   litInt = G.litInt
   litString = G.litString
-  litArray = CP.litArray brackets
-  litList = litArray
+  litArray = litList
+  litList = jlLitList
 
 instance MathConstant JuliaCode where
   pi :: SValue JuliaCode
@@ -661,6 +663,14 @@ jlClassError = "Classes are not supported in Julia"
 jlLitFloat :: (CommonRenderSym r) => Float -> SValue r
 jlLitFloat f = mkStateVal float (text jlFloatConc <> parens (D.float f))
 
+jlLitList :: (CommonRenderSym r) => VSType r -> [SValue r] -> SValue r
+jlLitList t' es = do
+  t <- t'
+  let lt' = listType t'
+  elems <- sequence es
+  let typeDec = if null es then RC.type' t else empty
+  mkStateVal lt' (typeDec <> brackets (valueList elems))
+
 jlCast :: (CommonRenderSym r) => VSType r -> SValue r -> SValue r
 jlCast t' v' = do
   t <- t'
@@ -962,7 +972,7 @@ jlModStart n = jlMod <+> text n
 using :: Doc
 using = text "using"
 
-usingModule :: Label -> Doc -- TODO: see if you need to add context for package vs file
+usingModule :: Label -> Doc
 usingModule n = using <+> text n
 
 -- IO

code/drasil-lang/lib/Language/Drasil/CodeExpr/Class.hs

@@ -5,7 +5,6 @@ import Language.Drasil.UID (HasUID(..))
 import Language.Drasil.Symbol (HasSymbol)
 import Language.Drasil.Space (Space(Actor), HasSpace(..))
 import Language.Drasil.Chunk.CodeVar (CodeIdea, CodeVarChunk)
-import Language.Drasil.Expr.Class (ExprC(..))
 import Language.Drasil.CodeExpr.Lang (CodeExpr(FCall, New, Message, Field))
 
 import Control.Lens ( (^.) )
@@ -57,6 +56,5 @@ instance CodeExprC CodeExpr where
             "Actor space"
 
   -- | Similar to 'apply', but takes a relation to apply to 'FCall'.
-  applyWithNamedArgs f [] [] = sy f
   applyWithNamedArgs f ps ns = FCall (f ^. uid) ps (zip (map ((^. uid) . fst) ns) 
     (map snd ns))