Merge pull request #1 from mboes/sundials

Cleanups to Sundials PR

8 files changed, 66 insertions, 112 deletions

diff --git a/nixpkgs.nix b/nixpkgs.nix
new file mode 100644
index 0000000..b416238
--- /dev/null
+++ b/nixpkgs.nix
@@ -0,0 +1 @@
+import (fetchTarball "https://github.com/nixos/nixpkgs/archive/54ade273e7a677ec35e501174d86d253d9d8dede.tar.gz")
diff --git a/packages/sundials/LICENSE b/packages/sundials/LICENSE
index 18e5956..e0cc65d 100644
--- a/packages/sundials/LICENSE
+++ b/packages/sundials/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2018, Dominic Steinitz
+Copyright (c) 2018 Novadiscovery, Dominic Steinitz
 
 All rights reserved.
 
diff --git a/packages/sundials/hmatrix-sundials.cabal b/packages/sundials/hmatrix-sundials.cabal
index 762537e..1ddede3 100644
--- a/packages/sundials/hmatrix-sundials.cabal
+++ b/packages/sundials/hmatrix-sundials.cabal
@@ -1,23 +1,18 @@
--- Initial sundials.cabal generated by cabal init.  For further 
--- documentation, see http://haskell.org/cabal/users-guide/
-
 name:                hmatrix-sundials
 version:             0.1.0.0
--- synopsis:            
--- description:         
-homepage:            https://github.com/idontgetoutmuch/hmatrix/tree/sundials
+homepage:            https://github.com/albertoruiz/hmatrix/tree/sundials
 license:             BSD3
 license-file:        LICENSE
 author:              Dominic Steinitz
 maintainer:          dominic@steinitz.org
--- copyright:           
 category:            Math
 build-type:          Simple
 extra-source-files:  ChangeLog.md
 cabal-version:       >=1.10
 
-extra-source-files:  src/helpers.c, src/helpers.h
-
+extra-source-files:
+  src/helpers.c
+  src/helpers.h
 
 library
   build-depends:       base >=4.10 && <4.11,
@@ -41,6 +36,7 @@ executable sundials
                        template-haskell >=2.12 && <2.13,
                        containers >=0.5 && <0.6,
                        hmatrix>=0.18,
+                       lens,
                        plots,
                        diagrams-lib,
                        diagrams-rasterific
diff --git a/packages/sundials/src/Main.hs b/packages/sundials/src/Main.hs
index 5e51372..d1f6755 100644
--- a/packages/sundials/src/Main.hs
+++ b/packages/sundials/src/Main.hs
@@ -1,6 +1,5 @@
-{-# OPTIONS_GHC -Wall #-}
+module Main where
 
-import qualified Data.Vector.Storable as V
 import           Numeric.Sundials.Arkode.ODE
 import           Numeric.LinearAlgebra
 
@@ -9,11 +8,10 @@ import qualified Diagrams.Prelude as D
 import           Diagrams.Backend.Rasterific
 
 import           Control.Lens
-import           Data.List (zip4)
 
-
-brusselator _t x = [ a - (w + 1) * u + v * u^2
-                   , w * u - v * u^2
+brusselator :: a -> [Double] -> [Double]
+brusselator _t x = [ a - (w + 1) * u + v * u^(2::Int)
+                   , w * u - v * u^(2::Int)
                    , (b - w) / eps - w * u
                    ]
   where
@@ -24,6 +22,7 @@ brusselator _t x = [ a - (w + 1) * u + v * u^2
     v = x !! 1
     w = x !! 2
 
+stiffish :: Double -> [Double] -> [Double]
 stiffish t v = [ lamda * u + 1.0 / (1.0 + t * t) - lamda * atan t ]
   where
     lamda = -100.0
@@ -45,15 +44,14 @@ kSaxis xs = P.r2Axis &~ do
 
 main :: IO ()
 main = do
-  let res = odeSolve brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
-  putStrLn $ show res
-  renderRasterific "diagrams/brusselator.png"
-                   (D.dims2D 500.0 500.0)
-                   (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res))
-
-  let res = odeSolve stiffish [0.0] (fromList [0.0, 0.1 .. 10.0])
-  putStrLn $ show res
-  renderRasterific "diagrams/stiffish.png"
-                   (D.dims2D 500.0 500.0)
-                   (renderAxis $ kSaxis $ zip [0.0, 0.1 .. 10.0] (concat $ toLists res))
-  
+  do let res = odeSolve brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
+     putStrLn $ show res
+     renderRasterific "diagrams/brusselator.png"
+                      (D.dims2D 500.0 500.0)
+                      (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res))
+
+  do let res = odeSolve stiffish [0.0] (fromList [0.0, 0.1 .. 10.0])
+     putStrLn $ show res
+     renderRasterific "diagrams/stiffish.png"
+                      (D.dims2D 500.0 500.0)
+                      (renderAxis $ kSaxis $ zip [0.0, 0.1 .. 10.0] (concat $ toLists res))
diff --git a/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs b/packages/sundials/src/Numeric/Sundials/Arkode/ODE.hs
index f432951..6d9a1b2 100644
--- a/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
+++ b/packages/sundials/src/Numeric/Sundials/Arkode/ODE.hs
@@ -1,14 +1,14 @@
-{-# OPTIONS_GHC -Wall #-}
-
-{-# LANGUAGE QuasiQuotes #-}
-{-# LANGUAGE TemplateHaskell #-}
 {-# LANGUAGE MultiWayIf #-}
 {-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE QuasiQuotes #-}
 {-# LANGUAGE ScopedTypeVariables #-}
+{-# LANGUAGE TemplateHaskell #-}
 
-module Numeric.Sundials.Arkode.ODE ( solveOde
-                                   , odeSolve
-                                   ) where
+module Numeric.Sundials.Arkode.ODE
+  ( SundialsDiagnostics(..)
+  , solveOde
+  , odeSolve
+  ) where
 
 import qualified Language.C.Inline as C
 import qualified Language.C.Inline.Unsafe as CU
@@ -40,10 +40,10 @@ 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 "<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"
 
@@ -108,7 +108,7 @@ odeSolve f y0 ts = case solveOde g (V.fromList y0) (V.fromList $ toList ts) of
     nC = length y0
     g t x0 = V.fromList $ f t (V.toList x0)
 
-solveOde :: 
+solveOde ::
   (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
@@ -116,7 +116,7 @@ solveOde ::
 solveOde f y0 tt = case solveOdeC (coerce f) (coerce y0) (coerce tt) of
                      Left c -> Left $ fromIntegral c
                      Right (v, d) -> Right (coerce v, d)
-                        
+
 solveOdeC ::
   (CDouble -> V.Vector CDouble -> V.Vector CDouble) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
           -> V.Vector CDouble -- ^ Initial conditions
@@ -285,13 +285,13 @@ solveOdeC fun f0 ts = unsafePerformIO $ do
                          flag = ARKDlsGetNumRhsEvals(arkode_mem, &nfeLS);
                          check_flag(&flag, "ARKDlsGetNumRhsEvals", 1);
                          ($vec-ptr:(long int *diagMut))[9] = ncfn;
-                         
+
                          /* 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
@@ -311,4 +311,3 @@ solveOdeC fun f0 ts = unsafePerformIO $ do
       return $ Right (m, d)
     else do
       return $ Left res
-
diff --git a/packages/sundials/stack.yaml b/packages/sundials/stack.yaml
deleted file mode 100644
index 9c6b17c..0000000
--- a/packages/sundials/stack.yaml
+++ /dev/null
@@ -1,66 +0,0 @@
-# This file was automatically generated by 'stack init'
-#
-# Some commonly used options have been documented as comments in this file.
-# For advanced use and comprehensive documentation of the format, please see:
-# https://docs.haskellstack.org/en/stable/yaml_configuration/
-
-# Resolver to choose a 'specific' stackage snapshot or a compiler version.
-# A snapshot resolver dictates the compiler version and the set of packages
-# to be used for project dependencies. For example:
-#
-# resolver: lts-3.5
-# resolver: nightly-2015-09-21
-# resolver: ghc-7.10.2
-# resolver: ghcjs-0.1.0_ghc-7.10.2
-# resolver:
-#  name: custom-snapshot
-#  location: "./custom-snapshot.yaml"
-resolver: lts-10.9
-
-# User packages to be built.
-# Various formats can be used as shown in the example below.
-#
-# packages:
-# - some-directory
-# - https://example.com/foo/bar/baz-0.0.2.tar.gz
-# - location:
-#    git: https://github.com/commercialhaskell/stack.git
-#    commit: e7b331f14bcffb8367cd58fbfc8b40ec7642100a
-# - location: https://github.com/commercialhaskell/stack/commit/e7b331f14bcffb8367cd58fbfc8b40ec7642100a
-#   extra-dep: true
-#  subdirs:
-#  - auto-update
-#  - wai
-#
-# A package marked 'extra-dep: true' will only be built if demanded by a
-# non-dependency (i.e. a user package), and its test suites and benchmarks
-# will not be run. This is useful for tweaking upstream packages.
-packages:
-- .
-# Dependency packages to be pulled from upstream that are not in the resolver
-# (e.g., acme-missiles-0.3)
-# extra-deps: []
-
-# Override default flag values for local packages and extra-deps
-# flags: {}
-
-# Extra package databases containing global packages
-# extra-package-dbs: []
-
-# Control whether we use the GHC we find on the path
-# system-ghc: true
-#
-# Require a specific version of stack, using version ranges
-# require-stack-version: -any # Default
-# require-stack-version: ">=1.6"
-#
-# Override the architecture used by stack, especially useful on Windows
-# arch: i386
-# arch: x86_64
-#
-# Extra directories used by stack for building
-# extra-include-dirs: [/path/to/dir]
-# extra-lib-dirs: [/path/to/dir]
-#
-# Allow a newer minor version of GHC than the snapshot specifies
-# compiler-check: newer-minor
\ No newline at end of file
diff --git a/shell.nix b/shell.nix
new file mode 100644
index 0000000..c034dde
--- /dev/null
+++ b/shell.nix
@@ -0,0 +1,20 @@
+{ghc}:
+
+with import <nixpkgs> {};
+
+let
+  gfortranlibdir = "${gfortran7.cc.lib}";
+  # XXX Workaround https://ghc.haskell.org/trac/ghc/ticket/11042.
+  libHack = if stdenv.isDarwin then {
+      DYLD_LIBRARY_PATH = [gfortranlibdir];
+    } else {
+      LD_LIBRARY_PATH = [gfortranlibdir];
+    };
+in
+haskell.lib.buildStackProject ({
+  name = "haskell-sundials";
+  buildInputs = [blas liblapack sundials zlib];
+  inherit ghc;
+  # XXX Workaround https://ghc.haskell.org/trac/ghc/ticket/11042.
+  extraArgs = ["--extra-lib-dirs=${gfortranlibdir}"];
+} // libHack)
diff --git a/stack.yaml b/stack.yaml
index 1198e57..04bbfb6 100644
--- a/stack.yaml
+++ b/stack.yaml
@@ -13,5 +13,11 @@ packages:
 - packages/gsl/
 - packages/glpk/
 - packages/base/
-extra-deps: []
-resolver: lts-8.15
+- packages/sundials/
+extra-deps:
+- diagrams-rasterific-1.4
+- plots-0.1.0.2
+resolver: lts-10.9
+nix:
+  path: [nixpkgs=./nixpkgs.nix]
+  shell-file: shell.nix