4 files changed, 122 insertions, 30 deletions

diff --git a/packages/sundials/src/Arkode.hsc b/packages/sundials/src/Arkode.hsc
index 59e701e..ae2b40f 100644
--- a/packages/sundials/src/Arkode.hsc
+++ b/packages/sundials/src/Arkode.hsc
@@ -9,12 +9,31 @@ import Foreign.C.String
 
 #include <stdio.h>
 #include <sundials/sundials_nvector.h>
+#include <sundials/sundials_matrix.h>
 #include <nvector/nvector_serial.h>
+#include <sunmatrix/sunmatrix_dense.h>
 #include <arkode/arkode.h>
 
 #def typedef struct _generic_N_Vector SunVector;
 #def typedef struct _N_VectorContent_Serial SunContent;
 
+#def typedef struct _generic_SUNMatrix SunMatrix;
+#def typedef struct _SUNMatrixContent_Dense SunMatrixContent;
+
+getContentMatrixPtr ptr = (#peek SunMatrix, content) ptr
+
+getNRows :: Ptr b -> IO CInt
+getNRows ptr = (#peek SunMatrixContent, M) ptr
+putNRows :: CInt -> Ptr b -> IO ()
+putNRows nr ptr = (#poke SunMatrixContent, M) ptr nr
+
+getNCols :: Ptr b -> IO CInt
+getNCols ptr = (#peek SunMatrixContent, N) ptr
+putNCols :: CInt -> Ptr b -> IO ()
+putNCols nc ptr = (#poke SunMatrixContent, N) ptr nc
+
+getMatrixData ptr = (#peek SunMatrixContent, data) ptr
+
 getContentPtr :: Storable a => Ptr b -> IO a
 getContentPtr ptr = (#peek SunVector, content) ptr
 
diff --git a/packages/sundials/src/Main.hs b/packages/sundials/src/Main.hs
index 71bcbac..01d3595 100644
--- a/packages/sundials/src/Main.hs
+++ b/packages/sundials/src/Main.hs
@@ -27,11 +27,26 @@ brusselator _t x = [ a - (w + 1) * u + v * u^2
     v = x !! 1
     w = x !! 2
 
+brussJac _t x = (3><3) [ (-(w + 1.0)) + 2.0 * u * v, w - 2.0 * u * v, (-w)
+                       , u * u                     , (-(u * u))     , 0.0
+                       , (-u)                      , u              , (-1.0) / eps - u
+                       ]
+  where
+    y = toList x
+    u = y !! 0
+    v = y !! 1
+    w = y !! 2
+    eps = 5.0e-6
+
 stiffish t v = [ lamda * u + 1.0 / (1.0 + t * t) - lamda * atan t ]
   where
     lamda = -100.0
     u = v !! 0
 
+stiffJac _t _v = (1><1) [ lamda ]
+  where
+    lamda = -100.0
+
 lSaxis :: [[Double]] -> P.Axis B D.V2 Double
 lSaxis xs = P.r2Axis &~ do
   let ts = xs!!0
@@ -77,14 +92,14 @@ main = do
   putStrLn $ show res
   putStrLn $ butcherTableauTex res
 
-  let res = odeSolve KVAERNO_4_2_3 brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
-  putStrLn $ show res
+  let res1 = odeSolve KVAERNO_4_2_3 brussJac brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
+  putStrLn $ show res1
   renderRasterific "diagrams/brusselator.png"
                    (D.dims2D 500.0 500.0)
-                   (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res))
+                   (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res1))
 
-  let res = odeSolve KVAERNO_4_2_3 stiffish [0.0] (fromList [0.0, 0.1 .. 10.0])
-  putStrLn $ show res
+  let res2 = odeSolve KVAERNO_4_2_3 stiffJac stiffish [0.0] (fromList [0.0, 0.1 .. 10.0])
+  putStrLn $ show res2
   renderRasterific "diagrams/stiffish.png"
                    (D.dims2D 500.0 500.0)
-                   (renderAxis $ kSaxis $ zip [0.0, 0.1 .. 10.0] (concat $ toLists res))
+                   (renderAxis $ kSaxis $ zip [0.0, 0.1 .. 10.0] (concat $ toLists res2))
diff --git a/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs b/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
index 30ff4c8..5af9e41 100644
--- a/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
+++ b/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
@@ -35,6 +35,7 @@ module Numeric.Sundials.Arkode.ODE ( solveOde
                                    , getBT
                                    , btGet
                                    , ODEMethod(..)
+                                   , odeSolveV
                                    ) where
 
 import qualified Language.C.Inline as C
@@ -45,7 +46,7 @@ import           Data.Monoid ((<>))
 import           Foreign.C.Types
 import           Foreign.Ptr (Ptr)
 import           Foreign.ForeignPtr (newForeignPtr_)
-import           Foreign.Storable (Storable, peekByteOff)
+import           Foreign.Storable (Storable)
 
 import qualified Data.Vector.Storable as V
 import qualified Data.Vector.Storable.Mutable as VM
@@ -55,7 +56,8 @@ import           System.IO.Unsafe (unsafePerformIO)
 
 import           Numeric.LinearAlgebra.Devel (createVector)
 
-import           Numeric.LinearAlgebra.HMatrix (Vector, Matrix, toList, (><), subMatrix)
+import           Numeric.LinearAlgebra.HMatrix (Vector, Matrix, toList, (><),
+                                                subMatrix, rows, cols, toLists)
 
 import qualified Types as T
 import           Arkode (sDIRK_2_1_2, kVAERNO_4_2_3)
@@ -78,12 +80,34 @@ C.include "../../../helpers.h"
 C.include "Arkode_hsc.h"
 
 
-getDataFromContents :: Storable b => Int -> Ptr a -> IO (V.Vector b)
+getDataFromContents :: Int -> Ptr T.SunVector -> IO (V.Vector CDouble)
 getDataFromContents len ptr = do
   qtr <- B.getContentPtr ptr
   rtr <- B.getData qtr
   vectorFromC len rtr
 
+-- FIXME: Potentially an instance of Storable
+getMatrixDataFromContents :: Ptr T.SunMatrix -> IO T.SunMatrix
+getMatrixDataFromContents ptr = do
+  qtr <- B.getContentMatrixPtr ptr
+  rs  <- B.getNRows qtr
+  cs  <- B.getNCols qtr
+  rtr <- B.getMatrixData qtr
+  vs  <- vectorFromC (fromIntegral $ rs * cs) rtr
+  return $ T.SunMatrix { T.rows = rs, T.cols = cs, T.vals = vs }
+
+putMatrixDataFromContents :: T.SunMatrix -> Ptr T.SunMatrix -> IO ()
+putMatrixDataFromContents mat ptr = do
+  let rs = T.rows mat
+      cs = T.cols mat
+      vs = T.vals mat
+  qtr <- B.getContentMatrixPtr ptr
+  B.putNRows rs qtr
+  B.putNCols cs qtr
+  rtr <- B.getMatrixData qtr
+  vectorToC vs (fromIntegral $ rs * cs) rtr
+-- FIXME: END
+
 putDataInContents :: Storable a => V.Vector a -> Int -> Ptr b -> IO ()
 putDataInContents vec len ptr = do
   qtr <- B.getContentPtr ptr
@@ -103,16 +127,16 @@ vectorToC vec len ptr = do
   V.copy (VM.unsafeFromForeignPtr0 ptr' len) vec
 
 data SundialsDiagnostics = SundialsDiagnostics {
-    aRKodeGetNumSteps               :: Int
-  , aRKodeGetNumStepAttempts        :: Int
-  , aRKodeGetNumRhsEvals_fe         :: Int
-  , aRKodeGetNumRhsEvals_fi         :: Int
-  , aRKodeGetNumLinSolvSetups       :: Int
-  , aRKodeGetNumErrTestFails        :: Int
-  , aRKodeGetNumNonlinSolvIters     :: Int
-  , aRKodeGetNumNonlinSolvConvFails :: Int
-  , aRKDlsGetNumJacEvals            :: Int
-  , aRKDlsGetNumRhsEvals            :: Int
+    _aRKodeGetNumSteps               :: Int
+  , _aRKodeGetNumStepAttempts        :: Int
+  , _aRKodeGetNumRhsEvals_fe         :: Int
+  , _aRKodeGetNumRhsEvals_fi         :: Int
+  , _aRKodeGetNumLinSolvSetups       :: Int
+  , _aRKodeGetNumErrTestFails        :: Int
+  , _aRKodeGetNumNonlinSolvIters     :: Int
+  , _aRKodeGetNumNonlinSolvConvFails :: Int
+  , _aRKDlsGetNumJacEvals            :: Int
+  , _aRKDlsGetNumRhsEvals            :: Int
   } deriving Show
 
 -- | Stepping functions
@@ -134,15 +158,16 @@ odeSolveV
     -> Vector Double     -- ^ initial conditions
     -> Vector Double     -- ^ desired solution times
     -> Matrix Double     -- ^ solution
-odeSolveV meth hi epsAbs epsRel = undefined
+odeSolveV _meth _hi _epsAbs _epsRel = undefined
 
 odeSolve :: ODEMethod
+         -> (Double -> Vector Double -> Matrix Double)
          -> (Double -> [Double] -> [Double]) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
          -> [Double]                         -- ^ initial conditions
          -> Vector Double                    -- ^ desired solution times
          -> Matrix Double                    -- ^ solution
-odeSolve method f y0 ts =
-  case solveOde method 1.0e-6 1.0e-10 g (V.fromList y0) (V.fromList $ toList ts) of
+odeSolve method jac f y0 ts =
+  case solveOde method jac' 1.0e-6 1.0e-10 g (V.fromList y0) (V.fromList $ toList ts) of
     Left c -> error $ show c -- FIXME
     Right (v, _) -> (nR >< nC) (V.toList v)
   where
@@ -150,30 +175,40 @@ odeSolve method f y0 ts =
     nR = length us
     nC = length y0
     g t x0 = V.fromList $ f t (V.toList x0)
+    jac' t v = foo $ jac t (V.fromList $ toList v)
+    foo m = T.SunMatrix { T.rows = nr, T.cols = nc, T.vals = vs }
+      where
+        nr = fromIntegral $ rows m
+        nc = fromIntegral $ cols m
+        vs = V.fromList $ map coerce $ concat $ toLists m
 
 solveOde ::
   ODEMethod
+  -> (Double -> V.Vector Double -> T.SunMatrix)
   -> Double
   -> Double
   -> (Double -> V.Vector Double -> V.Vector Double) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
   -> V.Vector Double                     -- ^ Initial conditions
   -> V.Vector Double                     -- ^ Desired solution times
   -> Either Int ((V.Vector Double), SundialsDiagnostics) -- ^ Error code or solution
-solveOde method relTol absTol f y0 tt =
-  case solveOdeC (fromIntegral $ fromEnum method) (CDouble relTol) (CDouble absTol)
+solveOde method jac relTol absTol f y0 tt =
+  case solveOdeC (fromIntegral $ fromEnum method) jacH (CDouble relTol) (CDouble absTol)
                  (coerce f) (coerce y0) (coerce tt) of
     Left c -> Left $ fromIntegral c
     Right (v, d) -> Right (coerce v, d)
+  where
+    jacH t v = jac (coerce t) (coerce v)
 
 solveOdeC ::
   CInt ->
+  (CDouble -> V.Vector CDouble -> T.SunMatrix) ->
   CDouble ->
   CDouble ->
   (CDouble -> V.Vector CDouble -> V.Vector CDouble) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
   -> V.Vector CDouble -- ^ Initial conditions
   -> V.Vector CDouble -- ^ Desired solution times
   -> Either CInt ((V.Vector CDouble), SundialsDiagnostics) -- ^ Error code or solution
-solveOdeC method relTol absTol fun f0 ts = unsafePerformIO $ do
+solveOdeC method jacH relTol absTol fun f0 ts = unsafePerformIO $ do
   let dim = V.length f0
       nEq :: CLong
       nEq = fromIntegral dim
@@ -197,9 +232,19 @@ solveOdeC method relTol absTol fun f0 ts = unsafePerformIO $ do
         fImm <- fun x <$> getDataFromContents dim y
         -- Fill in the provided pointer with the resulting vector.
         putDataInContents fImm dim f
-        -- I don't understand what this comment means
+        -- FIXME: I don't understand what this comment means
+        -- Unsafe since the function will be called many times.
+        [CU.exp| int{ 0 } |]
+  let jacIO :: CDouble -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr T.SunMatrix ->
+               Ptr () -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr T.SunVector ->
+               IO CInt
+      jacIO t y _fy jacS _ptr _tmp1 _tmp2 _tmp3 = do
+        foo <- jacH t <$> getDataFromContents dim y
+        putMatrixDataFromContents foo jacS
+        -- FIXME: I don't understand what this comment means
         -- Unsafe since the function will be called many times.
         [CU.exp| int{ 0 } |]
+
   res <- [C.block| int {
                          /* general problem variables */
                          int flag;                       /* reusable error-checking flag */
@@ -246,6 +291,11 @@ solveOdeC method relTol absTol fun f0 ts = unsafePerformIO $ do
 
                          /* Linear solver interface */
                          flag = ARKDlsSetLinearSolver(arkode_mem, LS, A);        /* Attach matrix and linear solver */
+
+                         flag = ARKDlsSetJacFn(arkode_mem, $fun:(int (* jacIO) (double t, SunVector y[], SunVector fy[], SunMatrix Jac[], void * params, SunVector tmp1[], SunVector tmp2[], SunVector tmp3[])));
+                         if (check_flag(&flag, "ARKDlsSetJacFn", 1)) return 1;
+
+
                          /* Store initial conditions */
                          for (j = 0; j < NEQ; j++) {
                            ($vec-ptr:(double *qMatMut))[0 * $(int nTs) + j] = NV_Ith_S(y,j);
@@ -340,7 +390,8 @@ btGet :: ODEMethod -> Matrix Double
 btGet method = case getBT method of
                  Left c -> error $ show c -- FIXME
                  -- FIXME
-                 Right (v, sqp) -> subMatrix (0, 0) (2, 2) $ (B.arkSMax >< B.arkSMax) (V.toList v)
+                 Right (v, _sqp) -> subMatrix (0, 0) (2, 2) $
+                                    (B.arkSMax >< B.arkSMax) (V.toList v)
 
 getBT :: ODEMethod -> Either Int (V.Vector Double, V.Vector Int)
 getBT method = case getButcherTable method of
@@ -352,9 +403,9 @@ getButcherTable method = unsafePerformIO $ do
   -- arkode seems to want an ODE in order to set and then get the
   -- Butcher tableau so here's one to keep it happy
   let fun :: CDouble -> V.Vector CDouble -> V.Vector CDouble
-      fun t ys = V.fromList [ ys V.! 0 ]
-      f0       = V.fromList [ 1.0 ]
-      ts       = V.fromList [ 0.0 ]
+      fun _t ys = V.fromList [ ys V.! 0 ]
+      f0        = V.fromList [ 1.0 ]
+      ts        = V.fromList [ 0.0 ]
       dim = V.length f0
       nEq :: CLong
       nEq = fromIntegral dim
diff --git a/packages/sundials/src/Types.hs b/packages/sundials/src/Types.hs
index e910c57..04e4280 100644
--- a/packages/sundials/src/Types.hs
+++ b/packages/sundials/src/Types.hs
@@ -15,8 +15,14 @@ import qualified Language.C.Types as CT
 import qualified Data.Map as Map
 import           Language.C.Inline.Context
 
+import qualified Data.Vector.Storable as V
+
 
 data SunVector
+data SunMatrix = SunMatrix { rows :: CInt
+                           , cols :: CInt
+                           , vals :: V.Vector CDouble
+                           }
 
 -- FIXME: Is this true?
 type SunIndexType = CLong
@@ -26,6 +32,7 @@ sunTypesTable = Map.fromList
   [
     (CT.TypeName "sunindextype", [t| SunIndexType |] )
   , (CT.TypeName "SunVector", [t| SunVector |] )
+  , (CT.TypeName "SunMatrix", [t| SunMatrix |] )
   ]
 
 sunCtx :: Context