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authoridontgetoutmuch <dominic@steinitz.org>2018-04-22 03:17:40 -0700
committerGitHub <noreply@github.com>2018-04-22 03:17:40 -0700
commitdf9980a1bc95cbe96b6766dc232c4abc8ca28c38 (patch)
tree72eae1364abfd4ef4b022f94cb126c189f5cde85
parent94db29b5d25f28708c1d430554f0c337c26172df (diff)
parent492b7e13c47bc7e42583c6a1754bdb2bb445b94f (diff)
Merge pull request #264 from idontgetoutmuch/sundials-clean
Add Sundials as an ODE Engine
Diffstat
-rw-r--r--.circleci/config.yml29
-rw-r--r--INSTALL.md11
-rw-r--r--README.md18
-rw-r--r--examples/ButcherTableau.hs47
-rw-r--r--examples/ChangeLog.md5
-rw-r--r--examples/LICENSE30
-rw-r--r--examples/Setup.hs2
-rw-r--r--examples/examples.cabal29
-rw-r--r--examples/sundials.hs56
-rw-r--r--nixpkgs.nix1
-rw-r--r--packages/base/CHANGELOG7
-rw-r--r--packages/base/src/Internal/Container.hs2
-rw-r--r--packages/base/src/Internal/Static.hs1
-rw-r--r--packages/gsl/CHANGELOG3
-rw-r--r--packages/sundials/ChangeLog.md5
-rw-r--r--packages/sundials/LICENSE30
-rw-r--r--packages/sundials/README.md8
-rw-r--r--packages/sundials/Setup.hs2
-rw-r--r--packages/sundials/diagrams/brusselator.pngbin0 -> 27362 bytes
-rw-r--r--packages/sundials/hmatrix-sundials.cabal55
-rw-r--r--packages/sundials/src/Arkode.hsc114
-rw-r--r--packages/sundials/src/Main.hs138
-rw-r--r--packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs898
-rw-r--r--packages/sundials/src/Types.hs40
-rw-r--r--packages/sundials/src/helpers.c44
-rw-r--r--packages/sundials/src/helpers.h9
-rw-r--r--shell.nix26
-rw-r--r--stack.yaml11
28 files changed, 1594 insertions, 27 deletions
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 61d0c5a..68fa538 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,33 +2,32 @@ version: 2
2jobs: 2jobs:
3 build: 3 build:
4 docker: 4 docker:
5 - image: fpco/stack-build 5 - image: terrorjack/vanilla:haskell
6 steps: 6 steps:
7 - checkout 7 - checkout
8 - restore_cache: 8 - restore_cache:
9 key: stack-deps-{{ checksum "stack.yaml" }} 9 key: stack-deps-eek-{{ checksum "stack.yaml" }}
10 - run: 10 - run:
11 name: Setup build toolchain 11 name: Update packages
12 command: stack setup 12 command: nix-channel --update
13 - run: 13 - run:
14 name: Building dependencies 14 name: Building dependencies
15 command: stack test --only-snapshot --prefetch 15 command: |
16 nix-env -f nixpkgs.nix -iA stack
17 stack --nix --no-terminal --nix build --only-snapshot --prefetch --no-haddock --test --bench --jobs=1
16 - save_cache: 18 - save_cache:
17 paths: 19 paths:
18 - "~/.stack" 20 - "~/.stack"
19 key: stack-deps-{{ checksum "stack.yaml" }} 21 key: stack-deps-eek-{{ checksum "stack.yaml" }}
20 - run:
21 name: Set up apt
22 command: apt update
23 - run:
24 name: Installing C packages
25 command: apt -y install libglpk-dev
26 - run: 22 - run:
27 name: Building 23 name: Building
28 command: stack build --pedantic 24 command: |
25 stack --nix --no-terminal --nix build --pedantic
29 - run: 26 - run:
30 name: Building tests 27 name: Building tests
31 command: stack test --pedantic --no-run-tests 28 command: |
29 stack --nix test --pedantic --no-run-tests
32 - run: 30 - run:
33 name: Running tests 31 name: Running tests
34 command: stack test 32 command: |
33 stack --nix test
diff --git a/INSTALL.md b/INSTALL.md
index 9f5761f..99ddc38 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -1,6 +1,15 @@
1# hmatrix installation 1# hmatrix installation
2 2
3This package requires [GHC 7.8](http://www.haskell.org/ghc), [cabal-install](http://www.haskell.org/haskellwiki/Cabal-Install) (available in the [Haskell Platform](http://hackage.haskell.org/platform)), and the development packages for BLAS/[LAPACK](http://www.netlib.org/lapack) and [GSL](http://www.gnu.org/software/gsl). 3*WARNING*: these instructions are now very out of date. However, there
4is a CI script which shows what does work; you are advised to look at
5that and emulate its installation steps.
6
7This package requires [GHC 7.8](http://www.haskell.org/ghc),
8[cabal-install](http://www.haskell.org/haskellwiki/Cabal-Install)
9(available in the [Haskell
10Platform](http://hackage.haskell.org/platform)), and the development
11packages for BLAS/[LAPACK](http://www.netlib.org/lapack) and
12[GSL](http://www.gnu.org/software/gsl).
4 13
5## Linux ################################################## 14## Linux ##################################################
6 15
diff --git a/README.md b/README.md
index cdbcf85..de7f523 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,22 @@
1A Haskell library for numerical computation 1A Haskell library for numerical computation
2------------------------------------------- 2-------------------------------------------
3 3
4A purely functional interface to linear algebra and other numerical algorithms, internally implemented using [LAPACK][lapack], [BLAS][blas], and [GSL][gsl]. 4A purely functional interface to linear algebra and other numerical
5algorithms, internally implemented using [LAPACK][lapack],
6[BLAS][blas], [GSL][gsl] and [SUNDIALS][sundials].
5 7
6This package includes matrix decompositions (eigensystems, singular values, Cholesky, QR, etc.), linear solvers, numeric integration, root finding, etc. 8This package includes matrix decompositions (eigensystems, singular
9values, Cholesky, QR, etc.), linear solvers, numeric integration, root
10finding, etc.
7 11
8- [What's new][changes] in version 0.17 (July 2015) 12- [What's new][changes] in version 0.19 (April 2018). This is not
13 intended to be a breaking change but a lot of modules have been
14 modified to ensure that continuous integration is green.
15
16- Support for SUNDIALS has been added. It should be possible to
17 replace Numeric.GSL.ODE with Numeric.Sundials.ARKode.ODE and have
18 your program work as before bearing in mind that the methods and
19 error control might differ (even for those with the same names!).
9 20
10- [Code examples][examples] 21- [Code examples][examples]
11 22
@@ -26,6 +37,7 @@ Contributions, suggestions, and bug reports are welcome!
26[lapack]: http://www.netlib.org/lapack/ 37[lapack]: http://www.netlib.org/lapack/
27[blas]: http://www.netlib.org/blas/ 38[blas]: http://www.netlib.org/blas/
28[gsl]: http://www.gnu.org/software/gsl/ 39[gsl]: http://www.gnu.org/software/gsl/
40[sundials]: https://computation.llnl.gov/projects/sundials
29 41
30[tutorial]: http://dis.um.es/profesores/alberto/material/hmatrix.pdf 42[tutorial]: http://dis.um.es/profesores/alberto/material/hmatrix.pdf
31[installation]: https://github.com/AlbertoRuiz/hmatrix/blob/master/INSTALL.md 43[installation]: https://github.com/AlbertoRuiz/hmatrix/blob/master/INSTALL.md
diff --git a/examples/ButcherTableau.hs b/examples/ButcherTableau.hs
new file mode 100644
index 0000000..e667ef1
--- /dev/null
+++ b/examples/ButcherTableau.hs
@@ -0,0 +1,47 @@
1{-# OPTIONS_GHC -Wall #-}
2
3import Numeric.Sundials.ARKode.ODE
4import Numeric.LinearAlgebra
5
6import Data.List (intercalate)
7
8import Text.PrettyPrint.HughesPJClass
9
10
11butcherTableauTex :: ButcherTable -> String
12butcherTableauTex (ButcherTable m c b b2) =
13 render $
14 vcat [ text ("\n\\begin{array}{c|" ++ (concat $ replicate n "c") ++ "}")
15 , us
16 , text "\\hline"
17 , text bs <+> text "\\\\"
18 , text b2s <+> text "\\\\"
19 , text "\\end{array}"
20 ]
21 where
22 n = rows m
23 rs = toLists m
24 ss = map (\r -> intercalate " & " $ map show r) rs
25 ts = zipWith (\i r -> show i ++ " & " ++ r) (toList c) ss
26 us = vcat $ map (\r -> text r <+> text "\\\\") ts
27 bs = " & " ++ (intercalate " & " $ map show $ toList b)
28 b2s = " & " ++ (intercalate " & " $ map show $ toList b2)
29
30main :: IO ()
31main = do
32
33 let res = butcherTable (SDIRK_2_1_2 undefined)
34 putStrLn $ show res
35 putStrLn $ butcherTableauTex res
36
37 let resA = butcherTable (KVAERNO_4_2_3 undefined)
38 putStrLn $ show resA
39 putStrLn $ butcherTableauTex resA
40
41 let resB = butcherTable (SDIRK_5_3_4 undefined)
42 putStrLn $ show resB
43 putStrLn $ butcherTableauTex resB
44
45 let resC = butcherTable (FEHLBERG_6_4_5 undefined)
46 putStrLn $ show resC
47 putStrLn $ butcherTableauTex resC
diff --git a/examples/ChangeLog.md b/examples/ChangeLog.md
new file mode 100644
index 0000000..a7e4c4c
--- /dev/null
+++ b/examples/ChangeLog.md
@@ -0,0 +1,5 @@
1# Revision history for hmatrix-examples
2
3## 0.1.0.0 -- YYYY-mm-dd
4
5* First version. Released on an unsuspecting world.
diff --git a/examples/LICENSE b/examples/LICENSE
new file mode 100644
index 0000000..18e5956
--- /dev/null
+++ b/examples/LICENSE
@@ -0,0 +1,30 @@
1Copyright (c) 2018, Dominic Steinitz
2
3All rights reserved.
4
5Redistribution and use in source and binary forms, with or without
6modification, are permitted provided that the following conditions are met:
7
8 * Redistributions of source code must retain the above copyright
9 notice, this list of conditions and the following disclaimer.
10
11 * Redistributions in binary form must reproduce the above
12 copyright notice, this list of conditions and the following
13 disclaimer in the documentation and/or other materials provided
14 with the distribution.
15
16 * Neither the name of Dominic Steinitz nor the names of other
17 contributors may be used to endorse or promote products derived
18 from this software without specific prior written permission.
19
20THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
21"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
22LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
23A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
24OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
25SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
26LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
27DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
28THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
29(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/examples/Setup.hs b/examples/Setup.hs
new file mode 100644
index 0000000..9a994af
--- /dev/null
+++ b/examples/Setup.hs
@@ -0,0 +1,2 @@
1import Distribution.Simple
2main = defaultMain
diff --git a/examples/examples.cabal b/examples/examples.cabal
new file mode 100644
index 0000000..5e85a3d
--- /dev/null
+++ b/examples/examples.cabal
@@ -0,0 +1,29 @@
1name: examples
2version: 0.1.0.0
3synopsis: Example usage of the various hmatrix packages
4homepage: https://github.com/albertoruiz/hmatrix
5license: BSD3
6license-file: LICENSE
7author: Dominic Steinitz
8maintainer: dominic@steinitz.org
9copyright: Dominic Steinitz, Novadiscovery
10category: Math
11build-type: Simple
12extra-source-files: ChangeLog.md
13cabal-version: >=1.10
14
15executable sundials
16 main-is: sundials.hs
17 build-depends: base >=4.10 && <4.11,
18 hmatrix,
19 hmatrix-sundials,
20 hmatrix-gsl
21 default-language: Haskell2010
22
23executable butcherTableau
24 main-is: ButcherTableau.hs
25 build-depends: base >=4.10 && <4.11,
26 hmatrix,
27 hmatrix-sundials,
28 pretty
29 default-language: Haskell2010
diff --git a/examples/sundials.hs b/examples/sundials.hs
new file mode 100644
index 0000000..99f662d
--- /dev/null
+++ b/examples/sundials.hs
@@ -0,0 +1,56 @@
1{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
2
3{-# LANGUAGE ViewPatterns #-}
4
5import Numeric.Sundials.ARKode.ODE
6import Numeric.LinearAlgebra
7import Graphics.Plot
8
9vanderpol mu = do
10 let xdot nu _t [x,v] = [v, -x + nu * v * (1-x*x)]
11 xdot _ _ _ = error "vanderpol RHS not defined"
12 ts = linspace 1000 (0,50)
13 sol = toColumns $ odeSolve (xdot mu) [1,0] ts
14 mplot (ts : sol)
15 mplot sol
16
17
18harmonic w d = do
19 let xdot u dd _t [x,v] = [v, a*x + b*v] where a = -u*u; b = -2*dd*u
20 xdot _ _ _ _ = error "harmonic RHS not defined"
21 ts = linspace 100 (0,20)
22 sol = odeSolve (xdot w d) [1,0] ts
23 mplot (ts : toColumns sol)
24
25
26kepler v a = mplot (take 2 $ toColumns sol) where
27 xdot _t [x,y,vx,vy] = [vx,vy,x*k,y*k]
28 where g=1
29 k=(-g)*(x*x+y*y)**(-1.5)
30 xdot _ _ = error "kepler RHS not defined"
31 ts = linspace 100 (0,30)
32 sol = odeSolve xdot [4, 0, v * cos (a*degree), v * sin (a*degree)] ts
33 degree = pi/180
34
35
36main = do
37 vanderpol 2
38 harmonic 1 0
39 harmonic 1 0.1
40 kepler 0.3 60
41 kepler 0.4 70
42 vanderpol' 2
43
44-- example of odeSolveV with jacobian
45vanderpol' mu = do
46 let xdot nu _t (toList->[x,v]) = fromList [v, -x + nu * v * (1-x*x)]
47 xdot _ _ _ = error "vanderpol' RHS not defined"
48 jac _ (toList->[x,v]) = (2><2) [ 0 , 1
49 , -1-2*x*v*mu, mu*(1-x**2) ]
50 jac _ _ = error "vanderpol' Jacobian not defined"
51 ts = linspace 1000 (0,50)
52 hi = pure $ (ts!1 - ts!0) / 100.0
53 sol = toColumns $ odeSolveV (SDIRK_5_3_4 jac) hi 1E-8 1E-8 (xdot mu) (fromList [1,0]) ts
54 mplot sol
55
56
diff --git a/nixpkgs.nix b/nixpkgs.nix
new file mode 100644
index 0000000..77c89c6
--- /dev/null
+++ b/nixpkgs.nix
@@ -0,0 +1 @@
import (fetchTarball "https://github.com/nixos/nixpkgs/archive/f93d4b6181f5c28b20d63a4d76e182511369c1bf.tar.gz")
diff --git a/packages/base/CHANGELOG b/packages/base/CHANGELOG
index 11a57dd..fd1c171 100644
--- a/packages/base/CHANGELOG
+++ b/packages/base/CHANGELOG
@@ -2,15 +2,15 @@
2-------- 2--------
3 3
4 * Many new functions and instances in the Static module 4 * Many new functions and instances in the Static module
5 5
6 * meanCov and gaussianSample use Herm type 6 * meanCov and gaussianSample use Herm type
7 7
8 * thinQR, thinRQ 8 * thinQR, thinRQ
9 9
10 * compactSVDTol 10 * compactSVDTol
11 11
12 * unitary changed to normalize, also admits Vector (Complex Double) 12 * unitary changed to normalize, also admits Vector (Complex Double)
13 13
140.17.0.0 140.17.0.0
15-------- 15--------
16 16
@@ -288,4 +288,3 @@
288 * added NFData instances for Matrix and Vector. 288 * added NFData instances for Matrix and Vector.
289 289
290 * liftVector, liftVector2 replaced by mapVector, zipVector. 290 * liftVector, liftVector2 replaced by mapVector, zipVector.
291
diff --git a/packages/base/src/Internal/Container.hs b/packages/base/src/Internal/Container.hs
index 1520489..282163e 100644
--- a/packages/base/src/Internal/Container.hs
+++ b/packages/base/src/Internal/Container.hs
@@ -5,6 +5,8 @@
5{-# LANGUAGE FunctionalDependencies #-} 5{-# LANGUAGE FunctionalDependencies #-}
6{-# LANGUAGE UndecidableInstances #-} 6{-# LANGUAGE UndecidableInstances #-}
7 7
8{-# OPTIONS_GHC -fno-warn-simplifiable-class-constraints #-}
9
8----------------------------------------------------------------------------- 10-----------------------------------------------------------------------------
9-- | 11-- |
10-- Module : Internal.Container 12-- Module : Internal.Container
diff --git a/packages/base/src/Internal/Static.hs b/packages/base/src/Internal/Static.hs
index 6ef1350..649fbb5 100644
--- a/packages/base/src/Internal/Static.hs
+++ b/packages/base/src/Internal/Static.hs
@@ -16,6 +16,7 @@
16{-# LANGUAGE DeriveGeneric #-} 16{-# LANGUAGE DeriveGeneric #-}
17 17
18{-# OPTIONS_GHC -fno-warn-missing-signatures #-} 18{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
19{-# OPTIONS_GHC -fno-warn-simplifiable-class-constraints #-}
19 20
20{- | 21{- |
21Module : Internal.Static 22Module : Internal.Static
diff --git a/packages/gsl/CHANGELOG b/packages/gsl/CHANGELOG
index 091dc0e..a2fe038 100644
--- a/packages/gsl/CHANGELOG
+++ b/packages/gsl/CHANGELOG
@@ -2,7 +2,7 @@
2-------- 2--------
3 3
4 * Added interpolation modules 4 * Added interpolation modules
5 5
6 * Added simulated annealing module 6 * Added simulated annealing module
7 7
8 * Added odeSolveVWith 8 * Added odeSolveVWith
@@ -11,4 +11,3 @@
11-------- 11--------
12 12
13 * The modules Numeric.GSL.* have been moved from hmatrix to the new package hmatrix-gsl. 13 * The modules Numeric.GSL.* have been moved from hmatrix to the new package hmatrix-gsl.
14
diff --git a/packages/sundials/ChangeLog.md b/packages/sundials/ChangeLog.md
new file mode 100644
index 0000000..7b15777
--- /dev/null
+++ b/packages/sundials/ChangeLog.md
@@ -0,0 +1,5 @@
1# Revision history for hmatrix-sundials
2
3## 0.1.0.0 -- 2018-04-21
4
5* First version. Released on an unsuspecting world. Just Runge-Kutta methods to start with.
diff --git a/packages/sundials/LICENSE b/packages/sundials/LICENSE
new file mode 100644
index 0000000..a162e98
--- /dev/null
+++ b/packages/sundials/LICENSE
@@ -0,0 +1,30 @@
1Copyright (c) 2018, Dominic Steinitz, Novadiscovery
2
3All rights reserved.
4
5Redistribution and use in source and binary forms, with or without
6modification, are permitted provided that the following conditions are met:
7
8 * Redistributions of source code must retain the above copyright
9 notice, this list of conditions and the following disclaimer.
10
11 * Redistributions in binary form must reproduce the above
12 copyright notice, this list of conditions and the following
13 disclaimer in the documentation and/or other materials provided
14 with the distribution.
15
16 * Neither the name of Dominic Steinitz nor the names of other
17 contributors may be used to endorse or promote products derived
18 from this software without specific prior written permission.
19
20THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
21"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
22LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
23A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
24OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
25SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
26LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
27DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
28THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
29(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/packages/sundials/README.md b/packages/sundials/README.md
new file mode 100644
index 0000000..2fac5c2
--- /dev/null
+++ b/packages/sundials/README.md
@@ -0,0 +1,8 @@
1Currently only an interface to the Runge-Kutta methods:
2[ARKode](https://computation.llnl.gov/projects/sundials/arkode)
3
4The interface is almost certainly going to change. Sundials gives a
5rich set of "combinators" for controlling the solution of your problem
6and reporting on how it performed. The idea is to initially mimic
7hmatrix-gsl and add extra, richer functions but ultimately upgrade the
8whole interface both for sundials and for gsl.
diff --git a/packages/sundials/Setup.hs b/packages/sundials/Setup.hs
new file mode 100644
index 0000000..9a994af
--- /dev/null
+++ b/packages/sundials/Setup.hs
@@ -0,0 +1,2 @@
1import Distribution.Simple
2main = defaultMain
diff --git a/packages/sundials/diagrams/brusselator.png b/packages/sundials/diagrams/brusselator.png
new file mode 100644
index 0000000..740cacb
--- /dev/null
+++ b/packages/sundials/diagrams/brusselator.png
Binary files differ
diff --git a/packages/sundials/hmatrix-sundials.cabal b/packages/sundials/hmatrix-sundials.cabal
new file mode 100644
index 0000000..532e9b4
--- /dev/null
+++ b/packages/sundials/hmatrix-sundials.cabal
@@ -0,0 +1,55 @@
1name: hmatrix-sundials
2version: 0.1.0.0
3synopsis: hmatrix interface to sundials
4description: Foo bar baz
5homepage: https://github.com/idontgetoutmuch/hmatrix/tree/sundials
6license: BSD3
7license-file: LICENSE
8author: Dominic Steinitz
9maintainer: dominic@steinitz.org
10copyright: Dominic Steinitz 2018, Novadiscovery 2018
11category: Math
12build-type: Simple
13extra-source-files: ChangeLog.md, README.md, diagrams/*.png
14extra-doc-files: diagrams/*.png
15cabal-version: >=1.10
16
17
18library
19 build-depends: base >=4.10 && <4.11,
20 inline-c >=0.6 && <0.7,
21 vector >=0.12 && <0.13,
22 template-haskell >=2.12 && <2.13,
23 containers >=0.5 && <0.6,
24 hmatrix>=0.18
25 extra-libraries: sundials_arkode
26 other-extensions: QuasiQuotes
27 hs-source-dirs: src
28 exposed-modules: Numeric.Sundials.ARKode.ODE
29 other-modules: Types,
30 Arkode
31 c-sources: src/helpers.c src/helpers.h
32 default-language: Haskell2010
33
34test-suite hmatrix-sundials-testsuite
35 type: exitcode-stdio-1.0
36 main-is: Main.hs
37 other-modules: Types,
38 Numeric.Sundials.ARKode.ODE,
39 Arkode
40 build-depends: base >=4.10 && <4.11,
41 inline-c >=0.6 && <0.7,
42 vector >=0.12 && <0.13,
43 template-haskell >=2.12 && <2.13,
44 containers >=0.5 && <0.6,
45 hmatrix>=0.18,
46 plots,
47 diagrams-lib,
48 diagrams-rasterific,
49 lens,
50 hspec
51 hs-source-dirs: src
52 default-language: Haskell2010
53 extra-libraries: sundials_arkode
54 c-sources: src/helpers.c src/helpers.h
55 default-language: Haskell2010
diff --git a/packages/sundials/src/Arkode.hsc b/packages/sundials/src/Arkode.hsc
new file mode 100644
index 0000000..9db37b5
--- /dev/null
+++ b/packages/sundials/src/Arkode.hsc
@@ -0,0 +1,114 @@
1module Arkode where
2
3import Foreign
4import Foreign.C.Types
5
6
7#include <stdio.h>
8#include <sundials/sundials_nvector.h>
9#include <sundials/sundials_matrix.h>
10#include <nvector/nvector_serial.h>
11#include <sunmatrix/sunmatrix_dense.h>
12#include <arkode/arkode.h>
13
14
15#def typedef struct _generic_N_Vector SunVector;
16#def typedef struct _N_VectorContent_Serial SunContent;
17
18#def typedef struct _generic_SUNMatrix SunMatrix;
19#def typedef struct _SUNMatrixContent_Dense SunMatrixContent;
20
21getContentMatrixPtr :: Storable a => Ptr b -> IO a
22getContentMatrixPtr ptr = (#peek SunMatrix, content) ptr
23
24getNRows :: Ptr b -> IO CInt
25getNRows ptr = (#peek SunMatrixContent, M) ptr
26putNRows :: CInt -> Ptr b -> IO ()
27putNRows nr ptr = (#poke SunMatrixContent, M) ptr nr
28
29getNCols :: Ptr b -> IO CInt
30getNCols ptr = (#peek SunMatrixContent, N) ptr
31putNCols :: CInt -> Ptr b -> IO ()
32putNCols nc ptr = (#poke SunMatrixContent, N) ptr nc
33
34getMatrixData :: Storable a => Ptr b -> IO a
35getMatrixData ptr = (#peek SunMatrixContent, data) ptr
36
37getContentPtr :: Storable a => Ptr b -> IO a
38getContentPtr ptr = (#peek SunVector, content) ptr
39
40getData :: Storable a => Ptr b -> IO a
41getData ptr = (#peek SunContent, data) ptr
42
43arkSMax :: Int
44arkSMax = #const ARK_S_MAX
45
46mIN_DIRK_NUM, mAX_DIRK_NUM :: Int
47mIN_DIRK_NUM = #const MIN_DIRK_NUM
48mAX_DIRK_NUM = #const MAX_DIRK_NUM
49
50-- FIXME: We could just use inline-c instead
51
52-- Butcher table accessors -- implicit
53sDIRK_2_1_2 :: Int
54sDIRK_2_1_2 = #const SDIRK_2_1_2
55bILLINGTON_3_3_2 :: Int
56bILLINGTON_3_3_2 = #const BILLINGTON_3_3_2
57tRBDF2_3_3_2 :: Int
58tRBDF2_3_3_2 = #const TRBDF2_3_3_2
59kVAERNO_4_2_3 :: Int
60kVAERNO_4_2_3 = #const KVAERNO_4_2_3
61aRK324L2SA_DIRK_4_2_3 :: Int
62aRK324L2SA_DIRK_4_2_3 = #const ARK324L2SA_DIRK_4_2_3
63cASH_5_2_4 :: Int
64cASH_5_2_4 = #const CASH_5_2_4
65cASH_5_3_4 :: Int
66cASH_5_3_4 = #const CASH_5_3_4
67sDIRK_5_3_4 :: Int
68sDIRK_5_3_4 = #const SDIRK_5_3_4
69kVAERNO_5_3_4 :: Int
70kVAERNO_5_3_4 = #const KVAERNO_5_3_4
71aRK436L2SA_DIRK_6_3_4 :: Int
72aRK436L2SA_DIRK_6_3_4 = #const ARK436L2SA_DIRK_6_3_4
73kVAERNO_7_4_5 :: Int
74kVAERNO_7_4_5 = #const KVAERNO_7_4_5
75aRK548L2SA_DIRK_8_4_5 :: Int
76aRK548L2SA_DIRK_8_4_5 = #const ARK548L2SA_DIRK_8_4_5
77
78-- #define DEFAULT_DIRK_2 SDIRK_2_1_2
79-- #define DEFAULT_DIRK_3 ARK324L2SA_DIRK_4_2_3
80-- #define DEFAULT_DIRK_4 SDIRK_5_3_4
81-- #define DEFAULT_DIRK_5 ARK548L2SA_DIRK_8_4_5
82
83-- Butcher table accessors -- explicit
84hEUN_EULER_2_1_2 :: Int
85hEUN_EULER_2_1_2 = #const HEUN_EULER_2_1_2
86bOGACKI_SHAMPINE_4_2_3 :: Int
87bOGACKI_SHAMPINE_4_2_3 = #const BOGACKI_SHAMPINE_4_2_3
88aRK324L2SA_ERK_4_2_3 :: Int
89aRK324L2SA_ERK_4_2_3 = #const ARK324L2SA_ERK_4_2_3
90zONNEVELD_5_3_4 :: Int
91zONNEVELD_5_3_4 = #const ZONNEVELD_5_3_4
92aRK436L2SA_ERK_6_3_4 :: Int
93aRK436L2SA_ERK_6_3_4 = #const ARK436L2SA_ERK_6_3_4
94sAYFY_ABURUB_6_3_4 :: Int
95sAYFY_ABURUB_6_3_4 = #const SAYFY_ABURUB_6_3_4
96cASH_KARP_6_4_5 :: Int
97cASH_KARP_6_4_5 = #const CASH_KARP_6_4_5
98fEHLBERG_6_4_5 :: Int
99fEHLBERG_6_4_5 = #const FEHLBERG_6_4_5
100dORMAND_PRINCE_7_4_5 :: Int
101dORMAND_PRINCE_7_4_5 = #const DORMAND_PRINCE_7_4_5
102aRK548L2SA_ERK_8_4_5 :: Int
103aRK548L2SA_ERK_8_4_5 = #const ARK548L2SA_ERK_8_4_5
104vERNER_8_5_6 :: Int
105vERNER_8_5_6 = #const VERNER_8_5_6
106fEHLBERG_13_7_8 :: Int
107fEHLBERG_13_7_8 = #const FEHLBERG_13_7_8
108
109-- #define DEFAULT_ERK_2 HEUN_EULER_2_1_2
110-- #define DEFAULT_ERK_3 BOGACKI_SHAMPINE_4_2_3
111-- #define DEFAULT_ERK_4 ZONNEVELD_5_3_4
112-- #define DEFAULT_ERK_5 CASH_KARP_6_4_5
113-- #define DEFAULT_ERK_6 VERNER_8_5_6
114-- #define DEFAULT_ERK_8 FEHLBERG_13_7_8
diff --git a/packages/sundials/src/Main.hs b/packages/sundials/src/Main.hs
new file mode 100644
index 0000000..729d35a
--- /dev/null
+++ b/packages/sundials/src/Main.hs
@@ -0,0 +1,138 @@
1{-# OPTIONS_GHC -Wall #-}
2
3import Numeric.Sundials.ARKode.ODE
4import Numeric.LinearAlgebra
5
6import Plots as P
7import qualified Diagrams.Prelude as D
8import Diagrams.Backend.Rasterific
9
10import Control.Lens
11
12import Test.Hspec
13
14
15lorenz :: Double -> [Double] -> [Double]
16lorenz _t u = [ sigma * (y - x)
17 , x * (rho - z) - y
18 , x * y - beta * z
19 ]
20 where
21 rho = 28.0
22 sigma = 10.0
23 beta = 8.0 / 3.0
24 x = u !! 0
25 y = u !! 1
26 z = u !! 2
27
28_lorenzJac :: Double -> Vector Double -> Matrix Double
29_lorenzJac _t u = (3><3) [ (-sigma), rho - z, y
30 , sigma , -1.0 , x
31 , 0.0 , (-x) , (-beta)
32 ]
33 where
34 rho = 28.0
35 sigma = 10.0
36 beta = 8.0 / 3.0
37 x = u ! 0
38 y = u ! 1
39 z = u ! 2
40
41brusselator :: Double -> [Double] -> [Double]
42brusselator _t x = [ a - (w + 1) * u + v * u * u
43 , w * u - v * u * u
44 , (b - w) / eps - w * u
45 ]
46 where
47 a = 1.0
48 b = 3.5
49 eps = 5.0e-6
50 u = x !! 0
51 v = x !! 1
52 w = x !! 2
53
54_brussJac :: Double -> Vector Double -> Matrix Double
55_brussJac _t x = (3><3) [ (-(w + 1.0)) + 2.0 * u * v, w - 2.0 * u * v, (-w)
56 , u * u , (-(u * u)) , 0.0
57 , (-u) , u , (-1.0) / eps - u
58 ]
59 where
60 y = toList x
61 u = y !! 0
62 v = y !! 1
63 w = y !! 2
64 eps = 5.0e-6
65
66stiffish :: Double -> [Double] -> [Double]
67stiffish t v = [ lamda * u + 1.0 / (1.0 + t * t) - lamda * atan t ]
68 where
69 lamda = -100.0
70 u = v !! 0
71
72stiffishV :: Double -> Vector Double -> Vector Double
73stiffishV t v = fromList [ lamda * u + 1.0 / (1.0 + t * t) - lamda * atan t ]
74 where
75 lamda = -100.0
76 u = v ! 0
77
78_stiffJac :: Double -> Vector Double -> Matrix Double
79_stiffJac _t _v = (1><1) [ lamda ]
80 where
81 lamda = -100.0
82
83lSaxis :: [[Double]] -> P.Axis B D.V2 Double
84lSaxis xs = P.r2Axis &~ do
85 let ts = xs!!0
86 us = xs!!1
87 vs = xs!!2
88 ws = xs!!3
89 P.linePlot' $ zip ts us
90 P.linePlot' $ zip ts vs
91 P.linePlot' $ zip ts ws
92
93kSaxis :: [(Double, Double)] -> P.Axis B D.V2 Double
94kSaxis xs = P.r2Axis &~ do
95 P.linePlot' xs
96
97main :: IO ()
98main = do
99
100 let res1 = odeSolve brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
101 renderRasterific "diagrams/brusselator.png"
102 (D.dims2D 500.0 500.0)
103 (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res1))
104
105 let res1a = odeSolve brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
106 renderRasterific "diagrams/brusselatorA.png"
107 (D.dims2D 500.0 500.0)
108 (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res1a))
109
110 let res2 = odeSolve stiffish [0.0] (fromList [0.0, 0.1 .. 10.0])
111 renderRasterific "diagrams/stiffish.png"
112 (D.dims2D 500.0 500.0)
113 (renderAxis $ kSaxis $ zip [0.0, 0.1 .. 10.0] (concat $ toLists res2))
114
115 let res2a = odeSolveV (SDIRK_5_3_4') Nothing 1e-6 1e-10 stiffishV (fromList [0.0]) (fromList [0.0, 0.1 .. 10.0])
116
117 let res2b = odeSolveV (TRBDF2_3_3_2') Nothing 1e-6 1e-10 stiffishV (fromList [0.0]) (fromList [0.0, 0.1 .. 10.0])
118
119 let maxDiff = maximum $ map abs $
120 zipWith (-) ((toLists $ tr res2a)!!0) ((toLists $ tr res2b)!!0)
121
122 hspec $ describe "Compare results" $ do
123 it "for two different RK methods" $
124 maxDiff < 1.0e-6
125
126 let res3 = odeSolve lorenz [-5.0, -5.0, 1.0] (fromList [0.0, 0.01 .. 10.0])
127
128 renderRasterific "diagrams/lorenz.png"
129 (D.dims2D 500.0 500.0)
130 (renderAxis $ kSaxis $ zip ((toLists $ tr res3)!!0) ((toLists $ tr res3)!!1))
131
132 renderRasterific "diagrams/lorenz1.png"
133 (D.dims2D 500.0 500.0)
134 (renderAxis $ kSaxis $ zip ((toLists $ tr res3)!!0) ((toLists $ tr res3)!!2))
135
136 renderRasterific "diagrams/lorenz2.png"
137 (D.dims2D 500.0 500.0)
138 (renderAxis $ kSaxis $ zip ((toLists $ tr res3)!!1) ((toLists $ tr res3)!!2))
diff --git a/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs b/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
new file mode 100644
index 0000000..e5a2e4d
--- /dev/null
+++ b/packages/sundials/src/Numeric/Sundials/ARKode/ODE.hs
@@ -0,0 +1,898 @@
1{-# OPTIONS_GHC -Wall #-}
2
3{-# LANGUAGE QuasiQuotes #-}
4{-# LANGUAGE TemplateHaskell #-}
5{-# LANGUAGE MultiWayIf #-}
6{-# LANGUAGE OverloadedStrings #-}
7{-# LANGUAGE ScopedTypeVariables #-}
8{-# LANGUAGE DeriveGeneric #-}
9{-# LANGUAGE TypeOperators #-}
10{-# LANGUAGE KindSignatures #-}
11{-# LANGUAGE TypeSynonymInstances #-}
12{-# LANGUAGE FlexibleInstances #-}
13{-# LANGUAGE FlexibleContexts #-}
14
15-----------------------------------------------------------------------------
16-- |
17-- Module : Numeric.Sundials.ARKode.ODE
18-- Copyright : Dominic Steinitz 2018,
19-- Novadiscovery 2018
20-- License : BSD
21-- Maintainer : Dominic Steinitz
22-- Stability : provisional
23--
24-- Solution of ordinary differential equation (ODE) initial value problems.
25--
26-- <https://computation.llnl.gov/projects/sundials/sundials-software>
27--
28-- A simple example:
29--
30-- <<diagrams/brusselator.png#diagram=brusselator&height=400&width=500>>
31--
32-- @
33-- import Numeric.Sundials.ARKode.ODE
34-- import Numeric.LinearAlgebra
35--
36-- import Plots as P
37-- import qualified Diagrams.Prelude as D
38-- import Diagrams.Backend.Rasterific
39--
40-- brusselator :: Double -> [Double] -> [Double]
41-- brusselator _t x = [ a - (w + 1) * u + v * u * u
42-- , w * u - v * u * u
43-- , (b - w) / eps - w * u
44-- ]
45-- where
46-- a = 1.0
47-- b = 3.5
48-- eps = 5.0e-6
49-- u = x !! 0
50-- v = x !! 1
51-- w = x !! 2
52--
53-- lSaxis :: [[Double]] -> P.Axis B D.V2 Double
54-- lSaxis xs = P.r2Axis &~ do
55-- let ts = xs!!0
56-- us = xs!!1
57-- vs = xs!!2
58-- ws = xs!!3
59-- P.linePlot' $ zip ts us
60-- P.linePlot' $ zip ts vs
61-- P.linePlot' $ zip ts ws
62--
63-- main = do
64-- let res1 = odeSolve brusselator [1.2, 3.1, 3.0] (fromList [0.0, 0.1 .. 10.0])
65-- renderRasterific "diagrams/brusselator.png"
66-- (D.dims2D 500.0 500.0)
67-- (renderAxis $ lSaxis $ [0.0, 0.1 .. 10.0]:(toLists $ tr res1))
68-- @
69--
70-- KVAERNO_4_2_3
71--
72-- \[
73-- \begin{array}{c|cccc}
74-- 0.0 & 0.0 & 0.0 & 0.0 & 0.0 \\
75-- 0.871733043 & 0.4358665215 & 0.4358665215 & 0.0 & 0.0 \\
76-- 1.0 & 0.490563388419108 & 7.3570090080892e-2 & 0.4358665215 & 0.0 \\
77-- 1.0 & 0.308809969973036 & 1.490563388254106 & -1.235239879727145 & 0.4358665215 \\
78-- \hline
79-- & 0.308809969973036 & 1.490563388254106 & -1.235239879727145 & 0.4358665215 \\
80-- & 0.490563388419108 & 7.3570090080892e-2 & 0.4358665215 & 0.0 \\
81-- \end{array}
82-- \]
83--
84-- SDIRK_2_1_2
85--
86-- \[
87-- \begin{array}{c|cc}
88-- 1.0 & 1.0 & 0.0 \\
89-- 0.0 & -1.0 & 1.0 \\
90-- \hline
91-- & 0.5 & 0.5 \\
92-- & 1.0 & 0.0 \\
93-- \end{array}
94-- \]
95--
96-- SDIRK_5_3_4
97--
98-- \[
99-- \begin{array}{c|ccccc}
100-- 0.25 & 0.25 & 0.0 & 0.0 & 0.0 & 0.0 \\
101-- 0.75 & 0.5 & 0.25 & 0.0 & 0.0 & 0.0 \\
102-- 0.55 & 0.34 & -4.0e-2 & 0.25 & 0.0 & 0.0 \\
103-- 0.5 & 0.2727941176470588 & -5.036764705882353e-2 & 2.7573529411764705e-2 & 0.25 & 0.0 \\
104-- 1.0 & 1.0416666666666667 & -1.0208333333333333 & 7.8125 & -7.083333333333333 & 0.25 \\
105-- \hline
106-- & 1.0416666666666667 & -1.0208333333333333 & 7.8125 & -7.083333333333333 & 0.25 \\
107-- & 1.2291666666666667 & -0.17708333333333334 & 7.03125 & -7.083333333333333 & 0.0 \\
108-- \end{array}
109-- \]
110-----------------------------------------------------------------------------
111module Numeric.Sundials.ARKode.ODE ( odeSolve
112 , odeSolveV
113 , odeSolveVWith
114 , odeSolveVWith'
115 , ButcherTable(..)
116 , butcherTable
117 , ODEMethod(..)
118 , StepControl(..)
119 , Jacobian
120 , SundialsDiagnostics(..)
121 ) where
122
123import qualified Language.C.Inline as C
124import qualified Language.C.Inline.Unsafe as CU
125
126import Data.Monoid ((<>))
127import Data.Maybe (isJust)
128
129import Foreign.C.Types
130import Foreign.Ptr (Ptr)
131import Foreign.ForeignPtr (newForeignPtr_)
132import Foreign.Storable (Storable)
133
134import qualified Data.Vector.Storable as V
135import qualified Data.Vector.Storable.Mutable as VM
136
137import Data.Coerce (coerce)
138import System.IO.Unsafe (unsafePerformIO)
139import GHC.Generics
140
141import Numeric.LinearAlgebra.Devel (createVector)
142
143import Numeric.LinearAlgebra.HMatrix (Vector, Matrix, toList, (><),
144 subMatrix, rows, cols, toLists,
145 size, subVector)
146
147import qualified Types as T
148import Arkode
149import qualified Arkode as B
150
151
152C.context (C.baseCtx <> C.vecCtx <> C.funCtx <> T.sunCtx)
153
154C.include "<stdlib.h>"
155C.include "<stdio.h>"
156C.include "<math.h>"
157C.include "<arkode/arkode.h>" -- prototypes for ARKODE fcts., consts.
158C.include "<nvector/nvector_serial.h>" -- serial N_Vector types, fcts., macros
159C.include "<sunmatrix/sunmatrix_dense.h>" -- access to dense SUNMatrix
160C.include "<sunlinsol/sunlinsol_dense.h>" -- access to dense SUNLinearSolver
161C.include "<arkode/arkode_direct.h>" -- access to ARKDls interface
162C.include "<sundials/sundials_types.h>" -- definition of type realtype
163C.include "<sundials/sundials_math.h>"
164C.include "../../../helpers.h"
165C.include "Arkode_hsc.h"
166
167
168getDataFromContents :: Int -> Ptr T.SunVector -> IO (V.Vector CDouble)
169getDataFromContents len ptr = do
170 qtr <- B.getContentPtr ptr
171 rtr <- B.getData qtr
172 vectorFromC len rtr
173
174-- FIXME: Potentially an instance of Storable
175_getMatrixDataFromContents :: Ptr T.SunMatrix -> IO T.SunMatrix
176_getMatrixDataFromContents ptr = do
177 qtr <- B.getContentMatrixPtr ptr
178 rs <- B.getNRows qtr
179 cs <- B.getNCols qtr
180 rtr <- B.getMatrixData qtr
181 vs <- vectorFromC (fromIntegral $ rs * cs) rtr
182 return $ T.SunMatrix { T.rows = rs, T.cols = cs, T.vals = vs }
183
184putMatrixDataFromContents :: T.SunMatrix -> Ptr T.SunMatrix -> IO ()
185putMatrixDataFromContents mat ptr = do
186 let rs = T.rows mat
187 cs = T.cols mat
188 vs = T.vals mat
189 qtr <- B.getContentMatrixPtr ptr
190 B.putNRows rs qtr
191 B.putNCols cs qtr
192 rtr <- B.getMatrixData qtr
193 vectorToC vs (fromIntegral $ rs * cs) rtr
194-- FIXME: END
195
196putDataInContents :: Storable a => V.Vector a -> Int -> Ptr b -> IO ()
197putDataInContents vec len ptr = do
198 qtr <- B.getContentPtr ptr
199 rtr <- B.getData qtr
200 vectorToC vec len rtr
201
202-- Utils
203
204vectorFromC :: Storable a => Int -> Ptr a -> IO (V.Vector a)
205vectorFromC len ptr = do
206 ptr' <- newForeignPtr_ ptr
207 V.freeze $ VM.unsafeFromForeignPtr0 ptr' len
208
209vectorToC :: Storable a => V.Vector a -> Int -> Ptr a -> IO ()
210vectorToC vec len ptr = do
211 ptr' <- newForeignPtr_ ptr
212 V.copy (VM.unsafeFromForeignPtr0 ptr' len) vec
213
214data SundialsDiagnostics = SundialsDiagnostics {
215 aRKodeGetNumSteps :: Int
216 , aRKodeGetNumStepAttempts :: Int
217 , aRKodeGetNumRhsEvals_fe :: Int
218 , aRKodeGetNumRhsEvals_fi :: Int
219 , aRKodeGetNumLinSolvSetups :: Int
220 , aRKodeGetNumErrTestFails :: Int
221 , aRKodeGetNumNonlinSolvIters :: Int
222 , aRKodeGetNumNonlinSolvConvFails :: Int
223 , aRKDlsGetNumJacEvals :: Int
224 , aRKDlsGetNumRhsEvals :: Int
225 } deriving Show
226
227type Jacobian = Double -> Vector Double -> Matrix Double
228
229-- | Stepping functions
230data ODEMethod = SDIRK_2_1_2 Jacobian
231 | SDIRK_2_1_2'
232 | BILLINGTON_3_3_2 Jacobian
233 | BILLINGTON_3_3_2'
234 | TRBDF2_3_3_2 Jacobian
235 | TRBDF2_3_3_2'
236 | KVAERNO_4_2_3 Jacobian
237 | KVAERNO_4_2_3'
238 | ARK324L2SA_DIRK_4_2_3 Jacobian
239 | ARK324L2SA_DIRK_4_2_3'
240 | CASH_5_2_4 Jacobian
241 | CASH_5_2_4'
242 | CASH_5_3_4 Jacobian
243 | CASH_5_3_4'
244 | SDIRK_5_3_4 Jacobian
245 | SDIRK_5_3_4'
246 | KVAERNO_5_3_4 Jacobian
247 | KVAERNO_5_3_4'
248 | ARK436L2SA_DIRK_6_3_4 Jacobian
249 | ARK436L2SA_DIRK_6_3_4'
250 | KVAERNO_7_4_5 Jacobian
251 | KVAERNO_7_4_5'
252 | ARK548L2SA_DIRK_8_4_5 Jacobian
253 | ARK548L2SA_DIRK_8_4_5'
254 | HEUN_EULER_2_1_2 Jacobian
255 | HEUN_EULER_2_1_2'
256 | BOGACKI_SHAMPINE_4_2_3 Jacobian
257 | BOGACKI_SHAMPINE_4_2_3'
258 | ARK324L2SA_ERK_4_2_3 Jacobian
259 | ARK324L2SA_ERK_4_2_3'
260 | ZONNEVELD_5_3_4 Jacobian
261 | ZONNEVELD_5_3_4'
262 | ARK436L2SA_ERK_6_3_4 Jacobian
263 | ARK436L2SA_ERK_6_3_4'
264 | SAYFY_ABURUB_6_3_4 Jacobian
265 | SAYFY_ABURUB_6_3_4'
266 | CASH_KARP_6_4_5 Jacobian
267 | CASH_KARP_6_4_5'
268 | FEHLBERG_6_4_5 Jacobian
269 | FEHLBERG_6_4_5'
270 | DORMAND_PRINCE_7_4_5 Jacobian
271 | DORMAND_PRINCE_7_4_5'
272 | ARK548L2SA_ERK_8_4_5 Jacobian
273 | ARK548L2SA_ERK_8_4_5'
274 | VERNER_8_5_6 Jacobian
275 | VERNER_8_5_6'
276 | FEHLBERG_13_7_8 Jacobian
277 | FEHLBERG_13_7_8'
278 deriving Generic
279
280constrName :: (HasConstructor (Rep a), Generic a)=> a -> String
281constrName = genericConstrName . from
282
283class HasConstructor (f :: * -> *) where
284 genericConstrName :: f x -> String
285
286instance HasConstructor f => HasConstructor (D1 c f) where
287 genericConstrName (M1 x) = genericConstrName x
288
289instance (HasConstructor x, HasConstructor y) => HasConstructor (x :+: y) where
290 genericConstrName (L1 l) = genericConstrName l
291 genericConstrName (R1 r) = genericConstrName r
292
293instance Constructor c => HasConstructor (C1 c f) where
294 genericConstrName x = conName x
295
296instance Show ODEMethod where
297 show x = constrName x
298
299-- FIXME: We can probably do better here with generics
300getMethod :: ODEMethod -> Int
301getMethod (SDIRK_2_1_2 _) = sDIRK_2_1_2
302getMethod (SDIRK_2_1_2') = sDIRK_2_1_2
303getMethod (BILLINGTON_3_3_2 _) = bILLINGTON_3_3_2
304getMethod (BILLINGTON_3_3_2') = bILLINGTON_3_3_2
305getMethod (TRBDF2_3_3_2 _) = tRBDF2_3_3_2
306getMethod (TRBDF2_3_3_2') = tRBDF2_3_3_2
307getMethod (KVAERNO_4_2_3 _) = kVAERNO_4_2_3
308getMethod (KVAERNO_4_2_3') = kVAERNO_4_2_3
309getMethod (ARK324L2SA_DIRK_4_2_3 _) = aRK324L2SA_DIRK_4_2_3
310getMethod (ARK324L2SA_DIRK_4_2_3') = aRK324L2SA_DIRK_4_2_3
311getMethod (CASH_5_2_4 _) = cASH_5_2_4
312getMethod (CASH_5_2_4') = cASH_5_2_4
313getMethod (CASH_5_3_4 _) = cASH_5_3_4
314getMethod (CASH_5_3_4') = cASH_5_3_4
315getMethod (SDIRK_5_3_4 _) = sDIRK_5_3_4
316getMethod (SDIRK_5_3_4') = sDIRK_5_3_4
317getMethod (KVAERNO_5_3_4 _) = kVAERNO_5_3_4
318getMethod (KVAERNO_5_3_4') = kVAERNO_5_3_4
319getMethod (ARK436L2SA_DIRK_6_3_4 _) = aRK436L2SA_DIRK_6_3_4
320getMethod (ARK436L2SA_DIRK_6_3_4') = aRK436L2SA_DIRK_6_3_4
321getMethod (KVAERNO_7_4_5 _) = kVAERNO_7_4_5
322getMethod (KVAERNO_7_4_5') = kVAERNO_7_4_5
323getMethod (ARK548L2SA_DIRK_8_4_5 _) = aRK548L2SA_DIRK_8_4_5
324getMethod (ARK548L2SA_DIRK_8_4_5') = aRK548L2SA_DIRK_8_4_5
325getMethod (HEUN_EULER_2_1_2 _) = hEUN_EULER_2_1_2
326getMethod (HEUN_EULER_2_1_2') = hEUN_EULER_2_1_2
327getMethod (BOGACKI_SHAMPINE_4_2_3 _) = bOGACKI_SHAMPINE_4_2_3
328getMethod (BOGACKI_SHAMPINE_4_2_3') = bOGACKI_SHAMPINE_4_2_3
329getMethod (ARK324L2SA_ERK_4_2_3 _) = aRK324L2SA_ERK_4_2_3
330getMethod (ARK324L2SA_ERK_4_2_3') = aRK324L2SA_ERK_4_2_3
331getMethod (ZONNEVELD_5_3_4 _) = zONNEVELD_5_3_4
332getMethod (ZONNEVELD_5_3_4') = zONNEVELD_5_3_4
333getMethod (ARK436L2SA_ERK_6_3_4 _) = aRK436L2SA_ERK_6_3_4
334getMethod (ARK436L2SA_ERK_6_3_4') = aRK436L2SA_ERK_6_3_4
335getMethod (SAYFY_ABURUB_6_3_4 _) = sAYFY_ABURUB_6_3_4
336getMethod (SAYFY_ABURUB_6_3_4') = sAYFY_ABURUB_6_3_4
337getMethod (CASH_KARP_6_4_5 _) = cASH_KARP_6_4_5
338getMethod (CASH_KARP_6_4_5') = cASH_KARP_6_4_5
339getMethod (FEHLBERG_6_4_5 _) = fEHLBERG_6_4_5
340getMethod (FEHLBERG_6_4_5' ) = fEHLBERG_6_4_5
341getMethod (DORMAND_PRINCE_7_4_5 _) = dORMAND_PRINCE_7_4_5
342getMethod (DORMAND_PRINCE_7_4_5') = dORMAND_PRINCE_7_4_5
343getMethod (ARK548L2SA_ERK_8_4_5 _) = aRK548L2SA_ERK_8_4_5
344getMethod (ARK548L2SA_ERK_8_4_5') = aRK548L2SA_ERK_8_4_5
345getMethod (VERNER_8_5_6 _) = vERNER_8_5_6
346getMethod (VERNER_8_5_6') = vERNER_8_5_6
347getMethod (FEHLBERG_13_7_8 _) = fEHLBERG_13_7_8
348getMethod (FEHLBERG_13_7_8') = fEHLBERG_13_7_8
349
350getJacobian :: ODEMethod -> Maybe Jacobian
351getJacobian (SDIRK_2_1_2 j) = Just j
352getJacobian (BILLINGTON_3_3_2 j) = Just j
353getJacobian (TRBDF2_3_3_2 j) = Just j
354getJacobian (KVAERNO_4_2_3 j) = Just j
355getJacobian (ARK324L2SA_DIRK_4_2_3 j) = Just j
356getJacobian (CASH_5_2_4 j) = Just j
357getJacobian (CASH_5_3_4 j) = Just j
358getJacobian (SDIRK_5_3_4 j) = Just j
359getJacobian (KVAERNO_5_3_4 j) = Just j
360getJacobian (ARK436L2SA_DIRK_6_3_4 j) = Just j
361getJacobian (KVAERNO_7_4_5 j) = Just j
362getJacobian (ARK548L2SA_DIRK_8_4_5 j) = Just j
363getJacobian (HEUN_EULER_2_1_2 j) = Just j
364getJacobian (BOGACKI_SHAMPINE_4_2_3 j) = Just j
365getJacobian (ARK324L2SA_ERK_4_2_3 j) = Just j
366getJacobian (ZONNEVELD_5_3_4 j) = Just j
367getJacobian (ARK436L2SA_ERK_6_3_4 j) = Just j
368getJacobian (SAYFY_ABURUB_6_3_4 j) = Just j
369getJacobian (CASH_KARP_6_4_5 j) = Just j
370getJacobian (FEHLBERG_6_4_5 j) = Just j
371getJacobian (DORMAND_PRINCE_7_4_5 j) = Just j
372getJacobian (ARK548L2SA_ERK_8_4_5 j) = Just j
373getJacobian (VERNER_8_5_6 j) = Just j
374getJacobian (FEHLBERG_13_7_8 j) = Just j
375getJacobian _ = Nothing
376
377-- | A version of 'odeSolveVWith' with reasonable default step control.
378odeSolveV
379 :: ODEMethod
380 -> Maybe Double -- ^ initial step size - by default, ARKode
381 -- estimates the initial step size to be the
382 -- solution \(h\) of the equation
383 -- \(\|\frac{h^2\ddot{y}}{2}\| = 1\), where
384 -- \(\ddot{y}\) is an estimated value of the
385 -- second derivative of the solution at \(t_0\)
386 -> Double -- ^ absolute tolerance for the state vector
387 -> Double -- ^ relative tolerance for the state vector
388 -> (Double -> Vector Double -> Vector Double) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
389 -> Vector Double -- ^ initial conditions
390 -> Vector Double -- ^ desired solution times
391 -> Matrix Double -- ^ solution
392odeSolveV meth hi epsAbs epsRel f y0 ts =
393 case odeSolveVWith meth (X epsAbs epsRel) hi g y0 ts of
394 Left c -> error $ show c -- FIXME
395 -- FIXME: Can we do better than using lists?
396 Right (v, _d) -> (nR >< nC) (V.toList v)
397 where
398 us = toList ts
399 nR = length us
400 nC = size y0
401 g t x0 = coerce $ f t x0
402
403-- | A version of 'odeSolveV' with reasonable default parameters and
404-- system of equations defined using lists. FIXME: we should say
405-- something about the fact we could use the Jacobian but don't for
406-- compatibility with hmatrix-gsl.
407odeSolve :: (Double -> [Double] -> [Double]) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
408 -> [Double] -- ^ initial conditions
409 -> Vector Double -- ^ desired solution times
410 -> Matrix Double -- ^ solution
411odeSolve f y0 ts =
412 -- FIXME: These tolerances are different from the ones in GSL
413 case odeSolveVWith SDIRK_5_3_4' (XX' 1.0e-6 1.0e-10 1 1) Nothing g (V.fromList y0) (V.fromList $ toList ts) of
414 Left c -> error $ show c -- FIXME
415 Right (v, _d) -> (nR >< nC) (V.toList v)
416 where
417 us = toList ts
418 nR = length us
419 nC = length y0
420 g t x0 = V.fromList $ f t (V.toList x0)
421
422odeSolveVWith' ::
423 ODEMethod
424 -> StepControl
425 -> Maybe Double -- ^ initial step size - by default, ARKode
426 -- estimates the initial step size to be the
427 -- solution \(h\) of the equation
428 -- \(\|\frac{h^2\ddot{y}}{2}\| = 1\), where
429 -- \(\ddot{y}\) is an estimated value of the second
430 -- derivative of the solution at \(t_0\)
431 -> (Double -> V.Vector Double -> V.Vector Double) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
432 -> V.Vector Double -- ^ Initial conditions
433 -> V.Vector Double -- ^ Desired solution times
434 -> Matrix Double -- ^ Error code or solution
435odeSolveVWith' method control initStepSize f y0 tt =
436 case odeSolveVWith method control initStepSize f y0 tt of
437 Left c -> error $ show c -- FIXME
438 Right (v, _d) -> (nR >< nC) (V.toList v)
439 where
440 nR = V.length tt
441 nC = V.length y0
442
443odeSolveVWith ::
444 ODEMethod
445 -> StepControl
446 -> Maybe Double -- ^ initial step size - by default, ARKode
447 -- estimates the initial step size to be the
448 -- solution \(h\) of the equation
449 -- \(\|\frac{h^2\ddot{y}}{2}\| = 1\), where
450 -- \(\ddot{y}\) is an estimated value of the second
451 -- derivative of the solution at \(t_0\)
452 -> (Double -> V.Vector Double -> V.Vector Double) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
453 -> V.Vector Double -- ^ Initial conditions
454 -> V.Vector Double -- ^ Desired solution times
455 -> Either Int ((V.Vector Double), SundialsDiagnostics) -- ^ Error code or solution
456odeSolveVWith method control initStepSize f y0 tt =
457 case solveOdeC (fromIntegral $ getMethod method) (coerce initStepSize) jacH (scise control)
458 (coerce f) (coerce y0) (coerce tt) of
459 Left c -> Left $ fromIntegral c
460 Right (v, d) -> Right (coerce v, d)
461 where
462 l = size y0
463 scise (X absTol relTol) = coerce (V.replicate l absTol, relTol)
464 scise (X' absTol relTol) = coerce (V.replicate l absTol, relTol)
465 scise (XX' absTol relTol yScale _yDotScale) = coerce (V.replicate l absTol, yScale * relTol)
466 -- FIXME; Should we check that the length of ss is correct?
467 scise (ScXX' absTol relTol yScale _yDotScale ss) = coerce (V.map (* absTol) ss, yScale * relTol)
468 jacH = fmap (\g t v -> matrixToSunMatrix $ g (coerce t) (coerce v)) $
469 getJacobian method
470 matrixToSunMatrix m = T.SunMatrix { T.rows = nr, T.cols = nc, T.vals = vs }
471 where
472 nr = fromIntegral $ rows m
473 nc = fromIntegral $ cols m
474 -- FIXME: efficiency
475 vs = V.fromList $ map coerce $ concat $ toLists m
476
477solveOdeC ::
478 CInt ->
479 Maybe CDouble ->
480 (Maybe (CDouble -> V.Vector CDouble -> T.SunMatrix)) ->
481 (V.Vector CDouble, CDouble) ->
482 (CDouble -> V.Vector CDouble -> V.Vector CDouble) -- ^ The RHS of the system \(\dot{y} = f(t,y)\)
483 -> V.Vector CDouble -- ^ Initial conditions
484 -> V.Vector CDouble -- ^ Desired solution times
485 -> Either CInt ((V.Vector CDouble), SundialsDiagnostics) -- ^ Error code or solution
486solveOdeC method initStepSize jacH (absTols, relTol) fun f0 ts = unsafePerformIO $ do
487
488 let isInitStepSize :: CInt
489 isInitStepSize = fromIntegral $ fromEnum $ isJust initStepSize
490 ss :: CDouble
491 ss = case initStepSize of
492 -- It would be better to put an error message here but
493 -- inline-c seems to evaluate this even if it is never
494 -- used :(
495 Nothing -> 0.0
496 Just x -> x
497 let dim = V.length f0
498 nEq :: CLong
499 nEq = fromIntegral dim
500 nTs :: CInt
501 nTs = fromIntegral $ V.length ts
502 -- FIXME: fMut is not actually mutatated
503 fMut <- V.thaw f0
504 tMut <- V.thaw ts
505 -- FIXME: I believe this gets taken from the ghc heap and so should
506 -- be subject to garbage collection.
507 quasiMatrixRes <- createVector ((fromIntegral dim) * (fromIntegral nTs))
508 qMatMut <- V.thaw quasiMatrixRes
509 diagnostics :: V.Vector CLong <- createVector 10 -- FIXME
510 diagMut <- V.thaw diagnostics
511 -- We need the types that sundials expects. These are tied together
512 -- in 'Types'. FIXME: The Haskell type is currently empty!
513 let funIO :: CDouble -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr () -> IO CInt
514 funIO x y f _ptr = do
515 -- Convert the pointer we get from C (y) to a vector, and then
516 -- apply the user-supplied function.
517 fImm <- fun x <$> getDataFromContents dim y
518 -- Fill in the provided pointer with the resulting vector.
519 putDataInContents fImm dim f
520 -- FIXME: I don't understand what this comment means
521 -- Unsafe since the function will be called many times.
522 [CU.exp| int{ 0 } |]
523 let isJac :: CInt
524 isJac = fromIntegral $ fromEnum $ isJust jacH
525 jacIO :: CDouble -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr T.SunMatrix ->
526 Ptr () -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr T.SunVector ->
527 IO CInt
528 jacIO t y _fy jacS _ptr _tmp1 _tmp2 _tmp3 = do
529 case jacH of
530 Nothing -> error "Numeric.Sundials.ARKode.ODE: Jacobian not defined"
531 Just jacI -> do j <- jacI t <$> getDataFromContents dim y
532 putMatrixDataFromContents j jacS
533 -- FIXME: I don't understand what this comment means
534 -- Unsafe since the function will be called many times.
535 [CU.exp| int{ 0 } |]
536
537 res <- [C.block| int {
538 /* general problem variables */
539
540 int flag; /* reusable error-checking flag */
541 int i, j; /* reusable loop indices */
542 N_Vector y = NULL; /* empty vector for storing solution */
543 N_Vector tv = NULL; /* empty vector for storing absolute tolerances */
544 SUNMatrix A = NULL; /* empty matrix for linear solver */
545 SUNLinearSolver LS = NULL; /* empty linear solver object */
546 void *arkode_mem = NULL; /* empty ARKode memory structure */
547 realtype t;
548 long int nst, nst_a, nfe, nfi, nsetups, nje, nfeLS, nni, ncfn, netf;
549
550 /* general problem parameters */
551
552 realtype T0 = RCONST(($vec-ptr:(double *tMut))[0]); /* initial time */
553 sunindextype NEQ = $(sunindextype nEq); /* number of dependent vars. */
554
555 /* Initialize data structures */
556
557 y = N_VNew_Serial(NEQ); /* Create serial vector for solution */
558 if (check_flag((void *)y, "N_VNew_Serial", 0)) return 1;
559 /* Specify initial condition */
560 for (i = 0; i < NEQ; i++) {
561 NV_Ith_S(y,i) = ($vec-ptr:(double *fMut))[i];
562 };
563
564 tv = N_VNew_Serial(NEQ); /* Create serial vector for absolute tolerances */
565 if (check_flag((void *)tv, "N_VNew_Serial", 0)) return 1;
566 /* Specify tolerances */
567 for (i = 0; i < NEQ; i++) {
568 NV_Ith_S(tv,i) = ($vec-ptr:(double *absTols))[i];
569 };
570
571 arkode_mem = ARKodeCreate(); /* Create the solver memory */
572 if (check_flag((void *)arkode_mem, "ARKodeCreate", 0)) return 1;
573
574 /* Call ARKodeInit to initialize the integrator memory and specify the */
575 /* right-hand side function in y'=f(t,y), the inital time T0, and */
576 /* the initial dependent variable vector y. Note: we treat the */
577 /* problem as fully implicit and set f_E to NULL and f_I to f. */
578
579 /* Here we use the C types defined in helpers.h which tie up with */
580 /* the Haskell types defined in Types */
581 if ($(int method) < MIN_DIRK_NUM) {
582 flag = ARKodeInit(arkode_mem, $fun:(int (* funIO) (double t, SunVector y[], SunVector dydt[], void * params)), NULL, T0, y);
583 if (check_flag(&flag, "ARKodeInit", 1)) return 1;
584 } else {
585 flag = ARKodeInit(arkode_mem, NULL, $fun:(int (* funIO) (double t, SunVector y[], SunVector dydt[], void * params)), T0, y);
586 if (check_flag(&flag, "ARKodeInit", 1)) return 1;
587 }
588
589 /* FIXME: A hack for initial testing */
590 flag = ARKodeSetMinStep(arkode_mem, 1.0e-12);
591 if (check_flag(&flag, "ARKodeSetMinStep", 1)) return 1;
592 flag = ARKodeSetMaxNumSteps(arkode_mem, 10000);
593 if (check_flag(&flag, "ARKodeSetMaxNumSteps", 1)) return 1;
594
595 /* Set routines */
596 flag = ARKodeSVtolerances(arkode_mem, $(double relTol), tv);
597 if (check_flag(&flag, "ARKodeSVtolerances", 1)) return 1;
598
599 /* Initialize dense matrix data structure and solver */
600 A = SUNDenseMatrix(NEQ, NEQ);
601 if (check_flag((void *)A, "SUNDenseMatrix", 0)) return 1;
602 LS = SUNDenseLinearSolver(y, A);
603 if (check_flag((void *)LS, "SUNDenseLinearSolver", 0)) return 1;
604
605 /* Attach matrix and linear solver */
606 flag = ARKDlsSetLinearSolver(arkode_mem, LS, A);
607 if (check_flag(&flag, "ARKDlsSetLinearSolver", 1)) return 1;
608
609 /* Set the initial step size if there is one */
610 if ($(int isInitStepSize)) {
611 /* FIXME: We could check if the initial step size is 0 */
612 /* or even NaN and then throw an error */
613 flag = ARKodeSetInitStep(arkode_mem, $(double ss));
614 if (check_flag(&flag, "ARKodeSetInitStep", 1)) return 1;
615 }
616
617 /* Set the Jacobian if there is one */
618 if ($(int isJac)) {
619 flag = ARKDlsSetJacFn(arkode_mem, $fun:(int (* jacIO) (double t, SunVector y[], SunVector fy[], SunMatrix Jac[], void * params, SunVector tmp1[], SunVector tmp2[], SunVector tmp3[])));
620 if (check_flag(&flag, "ARKDlsSetJacFn", 1)) return 1;
621 }
622
623 /* Store initial conditions */
624 for (j = 0; j < NEQ; j++) {
625 ($vec-ptr:(double *qMatMut))[0 * $(int nTs) + j] = NV_Ith_S(y,j);
626 }
627
628 /* Explicitly set the method */
629 if ($(int method) >= MIN_DIRK_NUM) {
630 flag = ARKodeSetIRKTableNum(arkode_mem, $(int method));
631 if (check_flag(&flag, "ARKodeSetIRKTableNum", 1)) return 1;
632 } else {
633 flag = ARKodeSetERKTableNum(arkode_mem, $(int method));
634 if (check_flag(&flag, "ARKodeSetERKTableNum", 1)) return 1;
635 }
636
637 /* Main time-stepping loop: calls ARKode to perform the integration */
638 /* Stops when the final time has been reached */
639 for (i = 1; i < $(int nTs); i++) {
640
641 flag = ARKode(arkode_mem, ($vec-ptr:(double *tMut))[i], y, &t, ARK_NORMAL); /* call integrator */
642 if (check_flag(&flag, "ARKode", 1)) break;
643
644 /* Store the results for Haskell */
645 for (j = 0; j < NEQ; j++) {
646 ($vec-ptr:(double *qMatMut))[i * NEQ + j] = NV_Ith_S(y,j);
647 }
648
649 /* unsuccessful solve: break */
650 if (flag < 0) {
651 fprintf(stderr,"Solver failure, stopping integration\n");
652 break;
653 }
654 }
655
656 /* Get some final statistics on how the solve progressed */
657
658 flag = ARKodeGetNumSteps(arkode_mem, &nst);
659 check_flag(&flag, "ARKodeGetNumSteps", 1);
660 ($vec-ptr:(long int *diagMut))[0] = nst;
661
662 flag = ARKodeGetNumStepAttempts(arkode_mem, &nst_a);
663 check_flag(&flag, "ARKodeGetNumStepAttempts", 1);
664 ($vec-ptr:(long int *diagMut))[1] = nst_a;
665
666 flag = ARKodeGetNumRhsEvals(arkode_mem, &nfe, &nfi);
667 check_flag(&flag, "ARKodeGetNumRhsEvals", 1);
668 ($vec-ptr:(long int *diagMut))[2] = nfe;
669 ($vec-ptr:(long int *diagMut))[3] = nfi;
670
671 flag = ARKodeGetNumLinSolvSetups(arkode_mem, &nsetups);
672 check_flag(&flag, "ARKodeGetNumLinSolvSetups", 1);
673 ($vec-ptr:(long int *diagMut))[4] = nsetups;
674
675 flag = ARKodeGetNumErrTestFails(arkode_mem, &netf);
676 check_flag(&flag, "ARKodeGetNumErrTestFails", 1);
677 ($vec-ptr:(long int *diagMut))[5] = netf;
678
679 flag = ARKodeGetNumNonlinSolvIters(arkode_mem, &nni);
680 check_flag(&flag, "ARKodeGetNumNonlinSolvIters", 1);
681 ($vec-ptr:(long int *diagMut))[6] = nni;
682
683 flag = ARKodeGetNumNonlinSolvConvFails(arkode_mem, &ncfn);
684 check_flag(&flag, "ARKodeGetNumNonlinSolvConvFails", 1);
685 ($vec-ptr:(long int *diagMut))[7] = ncfn;
686
687 flag = ARKDlsGetNumJacEvals(arkode_mem, &nje);
688 check_flag(&flag, "ARKDlsGetNumJacEvals", 1);
689 ($vec-ptr:(long int *diagMut))[8] = ncfn;
690
691 flag = ARKDlsGetNumRhsEvals(arkode_mem, &nfeLS);
692 check_flag(&flag, "ARKDlsGetNumRhsEvals", 1);
693 ($vec-ptr:(long int *diagMut))[9] = ncfn;
694
695 /* Clean up and return */
696 N_VDestroy(y); /* Free y vector */
697 N_VDestroy(tv); /* Free tv vector */
698 ARKodeFree(&arkode_mem); /* Free integrator memory */
699 SUNLinSolFree(LS); /* Free linear solver */
700 SUNMatDestroy(A); /* Free A matrix */
701
702 return flag;
703 } |]
704 if res == 0
705 then do
706 preD <- V.freeze diagMut
707 let d = SundialsDiagnostics (fromIntegral $ preD V.!0)
708 (fromIntegral $ preD V.!1)
709 (fromIntegral $ preD V.!2)
710 (fromIntegral $ preD V.!3)
711 (fromIntegral $ preD V.!4)
712 (fromIntegral $ preD V.!5)
713 (fromIntegral $ preD V.!6)
714 (fromIntegral $ preD V.!7)
715 (fromIntegral $ preD V.!8)
716 (fromIntegral $ preD V.!9)
717 m <- V.freeze qMatMut
718 return $ Right (m, d)
719 else do
720 return $ Left res
721
722data ButcherTable = ButcherTable { am :: Matrix Double
723 , cv :: Vector Double
724 , bv :: Vector Double
725 , b2v :: Vector Double
726 }
727 deriving Show
728
729data ButcherTable' a = ButcherTable' { am' :: V.Vector a
730 , cv' :: V.Vector a
731 , bv' :: V.Vector a
732 , b2v' :: V.Vector a
733 }
734 deriving Show
735
736butcherTable :: ODEMethod -> ButcherTable
737butcherTable method =
738 case getBT method of
739 Left c -> error $ show c -- FIXME
740 Right (ButcherTable' v w x y, sqp) ->
741 ButcherTable { am = subMatrix (0, 0) (s, s) $ (B.arkSMax >< B.arkSMax) (V.toList v)
742 , cv = subVector 0 s w
743 , bv = subVector 0 s x
744 , b2v = subVector 0 s y
745 }
746 where
747 s = fromIntegral $ sqp V.! 0
748
749getBT :: ODEMethod -> Either Int (ButcherTable' Double, V.Vector Int)
750getBT method = case getButcherTable method of
751 Left c ->
752 Left $ fromIntegral c
753 Right (ButcherTable' a b c d, sqp) ->
754 Right $ ( ButcherTable' (coerce a) (coerce b) (coerce c) (coerce d)
755 , V.map fromIntegral sqp )
756
757getButcherTable :: ODEMethod
758 -> Either CInt (ButcherTable' CDouble, V.Vector CInt)
759getButcherTable method = unsafePerformIO $ do
760 -- ARKode seems to want an ODE in order to set and then get the
761 -- Butcher tableau so here's one to keep it happy
762 let funI :: CDouble -> V.Vector CDouble -> V.Vector CDouble
763 funI _t ys = V.fromList [ ys V.! 0 ]
764 let funE :: CDouble -> V.Vector CDouble -> V.Vector CDouble
765 funE _t ys = V.fromList [ ys V.! 0 ]
766 f0 = V.fromList [ 1.0 ]
767 ts = V.fromList [ 0.0 ]
768 dim = V.length f0
769 nEq :: CLong
770 nEq = fromIntegral dim
771 mN :: CInt
772 mN = fromIntegral $ getMethod method
773
774 btSQP :: V.Vector CInt <- createVector 3
775 btSQPMut <- V.thaw btSQP
776 btAs :: V.Vector CDouble <- createVector (B.arkSMax * B.arkSMax)
777 btAsMut <- V.thaw btAs
778 btCs :: V.Vector CDouble <- createVector B.arkSMax
779 btBs :: V.Vector CDouble <- createVector B.arkSMax
780 btB2s :: V.Vector CDouble <- createVector B.arkSMax
781 btCsMut <- V.thaw btCs
782 btBsMut <- V.thaw btBs
783 btB2sMut <- V.thaw btB2s
784 let funIOI :: CDouble -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr () -> IO CInt
785 funIOI x y f _ptr = do
786 fImm <- funI x <$> getDataFromContents dim y
787 putDataInContents fImm dim f
788 -- FIXME: I don't understand what this comment means
789 -- Unsafe since the function will be called many times.
790 [CU.exp| int{ 0 } |]
791 let funIOE :: CDouble -> Ptr T.SunVector -> Ptr T.SunVector -> Ptr () -> IO CInt
792 funIOE x y f _ptr = do
793 fImm <- funE x <$> getDataFromContents dim y
794 putDataInContents fImm dim f
795 -- FIXME: I don't understand what this comment means
796 -- Unsafe since the function will be called many times.
797 [CU.exp| int{ 0 } |]
798 res <- [C.block| int {
799 /* general problem variables */
800
801 int flag; /* reusable error-checking flag */
802 N_Vector y = NULL; /* empty vector for storing solution */
803 void *arkode_mem = NULL; /* empty ARKode memory structure */
804 int i, j; /* reusable loop indices */
805
806 /* general problem parameters */
807
808 realtype T0 = RCONST(($vec-ptr:(double *ts))[0]); /* initial time */
809 sunindextype NEQ = $(sunindextype nEq); /* number of dependent vars */
810
811 /* Initialize data structures */
812
813 y = N_VNew_Serial(NEQ); /* Create serial vector for solution */
814 if (check_flag((void *)y, "N_VNew_Serial", 0)) return 1;
815 /* Specify initial condition */
816 for (i = 0; i < NEQ; i++) {
817 NV_Ith_S(y,i) = ($vec-ptr:(double *f0))[i];
818 };
819 arkode_mem = ARKodeCreate(); /* Create the solver memory */
820 if (check_flag((void *)arkode_mem, "ARKodeCreate", 0)) return 1;
821
822 flag = ARKodeInit(arkode_mem, $fun:(int (* funIOE) (double t, SunVector y[], SunVector dydt[], void * params)), $fun:(int (* funIOI) (double t, SunVector y[], SunVector dydt[], void * params)), T0, y);
823 if (check_flag(&flag, "ARKodeInit", 1)) return 1;
824
825 if ($(int mN) >= MIN_DIRK_NUM) {
826 flag = ARKodeSetIRKTableNum(arkode_mem, $(int mN));
827 if (check_flag(&flag, "ARKodeSetIRKTableNum", 1)) return 1;
828 } else {
829 flag = ARKodeSetERKTableNum(arkode_mem, $(int mN));
830 if (check_flag(&flag, "ARKodeSetERKTableNum", 1)) return 1;
831 }
832
833 int s, q, p;
834 realtype *ai = (realtype *)malloc(ARK_S_MAX * ARK_S_MAX * sizeof(realtype));
835 realtype *ae = (realtype *)malloc(ARK_S_MAX * ARK_S_MAX * sizeof(realtype));
836 realtype *ci = (realtype *)malloc(ARK_S_MAX * sizeof(realtype));
837 realtype *ce = (realtype *)malloc(ARK_S_MAX * sizeof(realtype));
838 realtype *bi = (realtype *)malloc(ARK_S_MAX * sizeof(realtype));
839 realtype *be = (realtype *)malloc(ARK_S_MAX * sizeof(realtype));
840 realtype *b2i = (realtype *)malloc(ARK_S_MAX * sizeof(realtype));
841 realtype *b2e = (realtype *)malloc(ARK_S_MAX * sizeof(realtype));
842 flag = ARKodeGetCurrentButcherTables(arkode_mem, &s, &q, &p, ai, ae, ci, ce, bi, be, b2i, b2e);
843 if (check_flag(&flag, "ARKode", 1)) return 1;
844 $vec-ptr:(int *btSQPMut)[0] = s;
845 $vec-ptr:(int *btSQPMut)[1] = q;
846 $vec-ptr:(int *btSQPMut)[2] = p;
847 for (i = 0; i < s; i++) {
848 for (j = 0; j < s; j++) {
849 /* FIXME: double should be realtype */
850 ($vec-ptr:(double *btAsMut))[i * ARK_S_MAX + j] = ai[i * ARK_S_MAX + j];
851 }
852 }
853
854 for (i = 0; i < s; i++) {
855 ($vec-ptr:(double *btCsMut))[i] = ci[i];
856 ($vec-ptr:(double *btBsMut))[i] = bi[i];
857 ($vec-ptr:(double *btB2sMut))[i] = b2i[i];
858 }
859
860 /* Clean up and return */
861 N_VDestroy(y); /* Free y vector */
862 ARKodeFree(&arkode_mem); /* Free integrator memory */
863
864 return flag;
865 } |]
866 if res == 0
867 then do
868 x <- V.freeze btAsMut
869 y <- V.freeze btSQPMut
870 z <- V.freeze btCsMut
871 u <- V.freeze btBsMut
872 v <- V.freeze btB2sMut
873 return $ Right (ButcherTable' { am' = x, cv' = z, bv' = u, b2v' = v }, y)
874 else do
875 return $ Left res
876
877-- | Adaptive step-size control
878-- functions.
879--
880-- [GSL](https://www.gnu.org/software/gsl/doc/html/ode-initval.html#adaptive-step-size-control)
881-- allows the user to control the step size adjustment using
882-- \(D_i = \epsilon^{abs}s_i + \epsilon^{rel}(a_{y} |y_i| + a_{dy/dt} h |\dot{y}_i|)\) where
883-- \(\epsilon^{abs}\) is the required absolute error, \(\epsilon^{rel}\)
884-- is the required relative error, \(s_i\) is a vector of scaling
885-- factors, \(a_{y}\) is a scaling factor for the solution \(y\) and
886-- \(a_{dydt}\) is a scaling factor for the derivative of the solution \(dy/dt\).
887--
888-- [ARKode](https://computation.llnl.gov/projects/sundials/arkode)
889-- allows the user to control the step size adjustment using
890-- \(\eta^{rel}|y_i| + \eta^{abs}_i\). For compatibility with
891-- [hmatrix-gsl](https://hackage.haskell.org/package/hmatrix-gsl),
892-- tolerances for \(y\) and \(\dot{y}\) can be specified but the latter have no
893-- effect.
894data StepControl = X Double Double -- ^ absolute and relative tolerance for \(y\); in GSL terms, \(a_{y} = 1\) and \(a_{dy/dt} = 0\); in ARKode terms, the \(\eta^{abs}_i\) are identical
895 | X' Double Double -- ^ absolute and relative tolerance for \(\dot{y}\); in GSL terms, \(a_{y} = 0\) and \(a_{dy/dt} = 1\); in ARKode terms, the latter is treated as the relative tolerance for \(y\) so this is the same as specifying 'X' which may be entirely incorrect for the given problem
896 | XX' Double Double Double Double -- ^ include both via relative tolerance
897 -- scaling factors \(a_y\), \(a_{{dy}/{dt}}\); in ARKode terms, the latter is ignored and \(\eta^{rel} = a_{y}\epsilon^{rel}\)
898 | ScXX' Double Double Double Double (Vector Double) -- ^ scale absolute tolerance of \(y_i\); in ARKode terms, \(a_{{dy}/{dt}}\) is ignored, \(\eta^{abs}_i = s_i \epsilon^{abs}\) and \(\eta^{rel} = a_{y}\epsilon^{rel}\)
diff --git a/packages/sundials/src/Types.hs b/packages/sundials/src/Types.hs
new file mode 100644
index 0000000..04e4280
--- /dev/null
+++ b/packages/sundials/src/Types.hs
@@ -0,0 +1,40 @@
1{-# OPTIONS_GHC -Wall #-}
2
3{-# LANGUAGE QuasiQuotes #-}
4{-# LANGUAGE TemplateHaskell #-}
5{-# LANGUAGE MultiWayIf #-}
6{-# LANGUAGE OverloadedStrings #-}
7{-# LANGUAGE EmptyDataDecls #-}
8
9module Types where
10
11import Foreign.C.Types
12
13import qualified Language.Haskell.TH as TH
14import qualified Language.C.Types as CT
15import qualified Data.Map as Map
16import Language.C.Inline.Context
17
18import qualified Data.Vector.Storable as V
19
20
21data SunVector
22data SunMatrix = SunMatrix { rows :: CInt
23 , cols :: CInt
24 , vals :: V.Vector CDouble
25 }
26
27-- FIXME: Is this true?
28type SunIndexType = CLong
29
30sunTypesTable :: Map.Map CT.TypeSpecifier TH.TypeQ
31sunTypesTable = Map.fromList
32 [
33 (CT.TypeName "sunindextype", [t| SunIndexType |] )
34 , (CT.TypeName "SunVector", [t| SunVector |] )
35 , (CT.TypeName "SunMatrix", [t| SunMatrix |] )
36 ]
37
38sunCtx :: Context
39sunCtx = mempty {ctxTypesTable = sunTypesTable}
40
diff --git a/packages/sundials/src/helpers.c b/packages/sundials/src/helpers.c
new file mode 100644
index 0000000..f0ca592
--- /dev/null
+++ b/packages/sundials/src/helpers.c
@@ -0,0 +1,44 @@
1#include <stdio.h>
2#include <math.h>
3#include <arkode/arkode.h> /* prototypes for ARKODE fcts., consts. */
4#include <nvector/nvector_serial.h> /* serial N_Vector types, fcts., macros */
5#include <sunmatrix/sunmatrix_dense.h> /* access to dense SUNMatrix */
6#include <sunlinsol/sunlinsol_dense.h> /* access to dense SUNLinearSolver */
7#include <arkode/arkode_direct.h> /* access to ARKDls interface */
8#include <sundials/sundials_types.h> /* definition of type realtype */
9#include <sundials/sundials_math.h>
10
11/* Check function return value...
12 opt == 0 means SUNDIALS function allocates memory so check if
13 returned NULL pointer
14 opt == 1 means SUNDIALS function returns a flag so check if
15 flag >= 0
16 opt == 2 means function allocates memory so check if returned
17 NULL pointer
18*/
19int check_flag(void *flagvalue, const char *funcname, int opt)
20{
21 int *errflag;
22
23 /* Check if SUNDIALS function returned NULL pointer - no memory allocated */
24 if (opt == 0 && flagvalue == NULL) {
25 fprintf(stderr, "\nSUNDIALS_ERROR: %s() failed - returned NULL pointer\n\n",
26 funcname);
27 return 1; }
28
29 /* Check if flag < 0 */
30 else if (opt == 1) {
31 errflag = (int *) flagvalue;
32 if (*errflag < 0) {
33 fprintf(stderr, "\nSUNDIALS_ERROR: %s() failed with flag = %d\n\n",
34 funcname, *errflag);
35 return 1; }}
36
37 /* Check if function returned NULL pointer - no memory allocated */
38 else if (opt == 2 && flagvalue == NULL) {
39 fprintf(stderr, "\nMEMORY_ERROR: %s() failed - returned NULL pointer\n\n",
40 funcname);
41 return 1; }
42
43 return 0;
44}
diff --git a/packages/sundials/src/helpers.h b/packages/sundials/src/helpers.h
new file mode 100644
index 0000000..3d8fbc0
--- /dev/null
+++ b/packages/sundials/src/helpers.h
@@ -0,0 +1,9 @@
1/* Check function return value...
2 opt == 0 means SUNDIALS function allocates memory so check if
3 returned NULL pointer
4 opt == 1 means SUNDIALS function returns a flag so check if
5 flag >= 0
6 opt == 2 means function allocates memory so check if returned
7 NULL pointer
8*/
9int check_flag(void *flagvalue, const char *funcname, int opt);
diff --git a/shell.nix b/shell.nix
new file mode 100644
index 0000000..42bbe08
--- /dev/null
+++ b/shell.nix
@@ -0,0 +1,26 @@
1{ nixpkgs ? import <nixpkgs> {} }:
2let p = nixpkgs; in
3
4 let
5 myStack = p.writeShellScriptBin "stack" ''
6 exec ${p.stack}/bin/stack --no-nix --no-docker --system-ghc $STACK_IN_NIX_EXTRA_ARGS "$@"
7 '';
8in
9p.haskell.lib.buildStackProject {
10 name = "hmatrix";
11
12 buildInputs = [
13 p.zlib
14 p.sundials
15 p.blas
16 p.gfortran.cc
17 p.liblapack
18 p.gsl
19 p.glpk
20 p.pkgconfig
21 p.stack
22 p.sundials
23 myStack
24 ] ++ (if p.stdenv.isDarwin then [p.darwin.apple_sdk.frameworks.Accelerate] else [])
25 ++ (if p.stdenv.isDarwin then [p.darwin.apple_sdk.frameworks.Cocoa] else []);
26}
diff --git a/stack.yaml b/stack.yaml
index 1198e57..9b858c0 100644
--- a/stack.yaml
+++ b/stack.yaml
@@ -13,5 +13,12 @@ packages:
13- packages/gsl/ 13- packages/gsl/
14- packages/glpk/ 14- packages/glpk/
15- packages/base/ 15- packages/base/
16extra-deps: [] 16- packages/sundials/
17resolver: lts-8.15 17- examples/
18extra-deps:
19- diagrams-rasterific-1.4
20- plots-0.1.0.2
21resolver: lts-10.9
22nix:
23 path: [nixpkgs=./nixpkgs.nix]
24 shell-file: shell.nix
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-01 04:33:10 +0000