The start of a library

1 files changed, 265 insertions, 0 deletions

diff --git a/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs b/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
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+++ b/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
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+{-# OPTIONS_GHC -Wall #-}
+
+{-# LANGUAGE QuasiQuotes #-}
+{-# LANGUAGE TemplateHaskell #-}
+{-# LANGUAGE MultiWayIf #-}
+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE ScopedTypeVariables #-}
+
+module Numeric.Sundials.Arkode.ODE ( solveOdeC ) where
+
+import qualified Language.C.Inline as C
+import qualified Language.C.Inline.Unsafe as CU
+import           Data.Monoid ((<>))
+import           Foreign.C.Types
+import           Foreign.Ptr (Ptr)
+import qualified Data.Vector.Storable as V
+
+import           Data.Coerce (coerce)
+import qualified Data.Vector.Storable.Mutable as VM
+import           Foreign.ForeignPtr (newForeignPtr_)
+import           Foreign.Storable (Storable)
+import           System.IO.Unsafe (unsafePerformIO)
+
+import           Foreign.Storable (peekByteOff)
+
+import           Numeric.LinearAlgebra.HMatrix (Vector, Matrix)
+
+import qualified Types as T
+
+C.context (C.baseCtx <> C.vecCtx <> C.funCtx <> T.sunCtx)
+
+-- C includes
+C.include "<stdio.h>"
+C.include "<math.h>"
+C.include "<arkode/arkode.h>"                 -- prototypes for ARKODE fcts., consts.
+C.include "<nvector/nvector_serial.h>"        -- serial N_Vector types, fcts., macros
+C.include "<sunmatrix/sunmatrix_dense.h>"     -- access to dense SUNMatrix           
+C.include "<sunlinsol/sunlinsol_dense.h>"     -- access to dense SUNLinearSolver     
+C.include "<arkode/arkode_direct.h>"          -- access to ARKDls interface          
+C.include "<sundials/sundials_types.h>"       -- definition of type realtype         
+C.include "<sundials/sundials_math.h>"
+C.include "../../../helpers.h"
+
+
+-- These were semi-generated using hsc2hs with Bar.hsc as the
+-- template. They are probably very fragile and could easily break on
+-- different architectures and / or changes in the sundials package.
+
+getContentPtr :: Storable a => Ptr b -> IO a
+getContentPtr ptr = ((\hsc_ptr -> peekByteOff hsc_ptr 0)) ptr
+
+getData :: Storable a => Ptr b -> IO a
+getData ptr = ((\hsc_ptr -> peekByteOff hsc_ptr 16)) ptr
+
+getDataFromContents :: Storable b => Int -> Ptr a -> IO (V.Vector b)
+getDataFromContents len ptr = do
+  qtr <- getContentPtr ptr
+  rtr <- getData qtr
+  vectorFromC len rtr
+
+putDataInContents :: Storable a => V.Vector a -> Int -> Ptr b -> IO ()
+putDataInContents vec len ptr = do
+  qtr <- getContentPtr ptr
+  rtr <- getData qtr
+  vectorToC vec len rtr
+
+-- Utils
+
+vectorFromC :: Storable a => Int -> Ptr a -> IO (V.Vector a)
+vectorFromC len ptr = do
+  ptr' <- newForeignPtr_ ptr
+  V.freeze $ VM.unsafeFromForeignPtr0 ptr' len
+
+vectorToC :: Storable a => V.Vector a -> Int -> Ptr a -> IO ()
+vectorToC vec len ptr = do
+  ptr' <- newForeignPtr_ ptr
+  V.copy (VM.unsafeFromForeignPtr0 ptr' len) vec
+
+stiffish :: Double -> V.Vector Double -> V.Vector Double
+stiffish t v = V.fromList [ lamda * u + 1.0 / (1.0 + t * t) - lamda * atan t ]
+  where
+    u = v V.! 0
+    lamda = -100.0
+
+brusselator :: Double -> V.Vector Double -> V.Vector Double
+brusselator _t x = V.fromList [ a - (w + 1) * u + v * u^2
+                              , w * u - v * u^2
+                              , (b - w) / eps - w * u
+                              ]
+  where
+    a = 1.0
+    b = 3.5
+    eps = 5.0e-6
+    u = x V.! 0
+    v = x V.! 1
+    w = x V.! 2
+
+
+odeSolve :: (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 = undefined
+
+solveOdeC ::
+  (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)         -- ^ Error code or solution
+solveOdeC fun f0 ts = unsafePerformIO $ do
+  let dim = V.length f0
+      nEq :: CLong
+      nEq = fromIntegral dim
+  fMut <- V.thaw f0
+  -- We need the types that sundials expects. These are tied together
+  -- in 'Types'. The Haskell type is currently empty!
+  let funIO :: CDouble -> Ptr T.BarType -> Ptr T.BarType -> Ptr () -> IO CInt
+      funIO x y f _ptr = do
+        -- Convert the pointer we get from C (y) to a vector, and then
+        -- apply the user-supplied function.
+        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
+        -- 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 */
+                         N_Vector y = NULL;              /* empty vector for storing solution */
+                         SUNMatrix A = NULL;             /* empty matrix for linear solver */
+                         SUNLinearSolver LS = NULL;      /* empty linear solver object */
+                         void *arkode_mem = NULL;        /* empty ARKode memory structure */
+                         FILE *UFID;
+                         realtype t, tout;
+                         long int nst, nst_a, nfe, nfi, nsetups, nje, nfeLS, nni, ncfn, netf;
+
+                         /* general problem parameters */
+                         realtype T0 = RCONST(0.0);    /* initial time */
+                         realtype Tf = RCONST(10.0);   /* final time */
+                         realtype dTout = RCONST(1.0); /* time between outputs */
+                         sunindextype NEQ = $(sunindextype nEq); /* number of dependent vars. */
+                         realtype reltol = 1.0e-6;     /* tolerances */
+                         realtype abstol = 1.0e-10;
+
+                         /* Initial diagnostics output */
+                         printf("\nAnalytical ODE test problem:\n");
+                         printf("   reltol = %.1"ESYM"\n",  reltol);
+                         printf("   abstol = %.1"ESYM"\n\n",abstol);
+
+                         /* Initialize data structures */
+                         y = N_VNew_Serial(NEQ);      /* Create serial vector for solution */
+                         if (check_flag((void *)y, "N_VNew_Serial", 0)) return 1;
+                         int i;
+                         for (i = 0; i < NEQ; i++) {
+                           NV_Ith_S(y,i) = ($vec-ptr:(double *fMut))[i];
+                         }; /* Specify initial condition */
+                         arkode_mem = ARKodeCreate(); /* Create the solver memory */
+                         if (check_flag((void *)arkode_mem, "ARKodeCreate", 0)) return 1;
+
+                         /* Call ARKodeInit to initialize the integrator memory and specify the */
+                         /*    right-hand side function in y'=f(t,y), the inital time T0, and */
+                         /*    the initial dependent variable vector y.  Note: since this */
+                         /*    problem is fully implicit, we set f_E to NULL and f_I to f. */
+
+                         /* Here we use the C types defined in helpers.h which tie up with */
+                         /* the Haskell types defined in Types                             */
+                         flag = ARKodeInit(arkode_mem, NULL, $fun:(int (* funIO) (double t, BarType y[], BarType dydt[], void * params)), T0, y);
+                         if (check_flag(&flag, "ARKodeInit", 1)) return 1;
+
+                         /* Set routines */
+                         flag = ARKodeSStolerances(arkode_mem, reltol, abstol);  /* Specify tolerances */
+                         if (check_flag(&flag, "ARKodeSStolerances", 1)) return 1;
+
+                         /* Initialize dense matrix data structure and solver */
+                         A = SUNDenseMatrix(NEQ, NEQ);
+                         if (check_flag((void *)A, "SUNDenseMatrix", 0)) return 1;
+                         LS = SUNDenseLinearSolver(y, A);
+                         if (check_flag((void *)LS, "SUNDenseLinearSolver", 0)) return 1;
+
+                         /* Linear solver interface */
+                         flag = ARKDlsSetLinearSolver(arkode_mem, LS, A);        /* Attach matrix and linear solver */
+                         /* Open output stream for results, output comment line */
+                         UFID = fopen("solution.txt","w");
+                         fprintf(UFID,"# t u\n");
+
+                         /* output initial condition to disk */
+                         fprintf(UFID," %.16"ESYM" %.16"ESYM"\n", T0, NV_Ith_S(y,0));  
+
+                         /* Main time-stepping loop: calls ARKode to perform the integration, then
+                            prints results.  Stops when the final time has been reached */
+                         t = T0;
+                         tout = T0+dTout;
+                         printf("        t           u\n");
+                         printf("   ---------------------\n");
+                         while (Tf - t > 1.0e-15) {
+
+                           flag = ARKode(arkode_mem, tout, y, &t, ARK_NORMAL);      /* call integrator */
+                           if (check_flag(&flag, "ARKode", 1)) break;
+                           printf("  %10.6"FSYM"  %10.6"FSYM"\n", t, NV_Ith_S(y,0));          /* access/print solution */
+                           fprintf(UFID," %.16"ESYM" %.16"ESYM"\n", t, NV_Ith_S(y,0));  
+                           if (flag >= 0) {                                         /* successful solve: update time */
+                             tout += dTout;
+                             tout = (tout > Tf) ? Tf : tout;
+                           } else {                                                 /* unsuccessful solve: break */
+                             fprintf(stderr,"Solver failure, stopping integration\n");
+                             break;
+                           }
+                         }
+                         printf("   ---------------------\n");
+                         fclose(UFID);
+
+                         for (i = 0; i < NEQ; i++) {
+                           ($vec-ptr:(double *fMut))[i] = NV_Ith_S(y,i);
+                         };
+
+                         /* Get/print some final statistics on how the solve progressed */
+                         flag = ARKodeGetNumSteps(arkode_mem, &nst);
+                         check_flag(&flag, "ARKodeGetNumSteps", 1);
+                         flag = ARKodeGetNumStepAttempts(arkode_mem, &nst_a);
+                         check_flag(&flag, "ARKodeGetNumStepAttempts", 1);
+                         flag = ARKodeGetNumRhsEvals(arkode_mem, &nfe, &nfi);
+                         check_flag(&flag, "ARKodeGetNumRhsEvals", 1);
+                         flag = ARKodeGetNumLinSolvSetups(arkode_mem, &nsetups);
+                         check_flag(&flag, "ARKodeGetNumLinSolvSetups", 1);
+                         flag = ARKodeGetNumErrTestFails(arkode_mem, &netf);
+                         check_flag(&flag, "ARKodeGetNumErrTestFails", 1);
+                         flag = ARKodeGetNumNonlinSolvIters(arkode_mem, &nni);
+                         check_flag(&flag, "ARKodeGetNumNonlinSolvIters", 1);
+                         flag = ARKodeGetNumNonlinSolvConvFails(arkode_mem, &ncfn);
+                         check_flag(&flag, "ARKodeGetNumNonlinSolvConvFails", 1);
+                         flag = ARKDlsGetNumJacEvals(arkode_mem, &nje);
+                         check_flag(&flag, "ARKDlsGetNumJacEvals", 1);
+                         flag = ARKDlsGetNumRhsEvals(arkode_mem, &nfeLS);
+                         check_flag(&flag, "ARKDlsGetNumRhsEvals", 1);
+                       
+                         printf("\nFinal Solver Statistics:\n");
+                         printf("   Internal solver steps = %li (attempted = %li)\n", nst, nst_a);
+                         printf("   Total RHS evals:  Fe = %li,  Fi = %li\n", nfe, nfi);
+                         printf("   Total linear solver setups = %li\n", nsetups);
+                         printf("   Total RHS evals for setting up the linear system = %li\n", nfeLS);
+                         printf("   Total number of Jacobian evaluations = %li\n", nje);
+                         printf("   Total number of Newton iterations = %li\n", nni);
+                         printf("   Total number of linear solver convergence failures = %li\n", ncfn);
+                         printf("   Total number of error test failures = %li\n\n", netf);
+
+                         /* Clean up and return */
+                         N_VDestroy(y);            /* Free y vector */
+                         ARKodeFree(&arkode_mem);  /* Free integrator memory */
+                         SUNLinSolFree(LS);        /* Free linear solver */
+                         SUNMatDestroy(A);         /* Free A matrix */
+ 
+                         return flag;
+                       } |]
+  if res ==0
+    then do
+      v <- V.freeze fMut
+      return $ Right v
+    else do
+      return $ Left res
+
+main :: IO ()
+main = do
+  let res = solveOdeC (coerce brusselator) (V.fromList [1.2, 3.1, 3.0]) undefined
+  putStrLn $ show res