Merge pull request #46 from rveltz/syntax

update for new diffeq syntax

REQUIRE

@@ -2,4 +2,4 @@ julia 0.6
 BinDeps 0.4.3
 Compat 0.17.0
 Parameters 0.5.0
-DiffEqBase 1.5.1
+DiffEqBase 3.0.0

src/common.jl

@@ -1,5 +1,18 @@
 ## Common Interface Solve Functions
 
+type CommonFunction{F,P}
+    func::F
+    p::P
+    neq::Cint
+end
+
+function commonfun(t::T1,y::T2,yp::T3,comfun::CommonFunction) where {T1,T2,T3}
+  y_ = unsafe_wrap(Array,y,comfun.neq)
+  ydot_ = unsafe_wrap(Array,yp,comfun.neq)
+  comfun.func(ydot_,y_,comfun.p,t)
+  return Int32(0)
+end
+
 function solve{uType,tType,isinplace}(
     prob::AbstractODEProblem{uType,tType,isinplace},
     alg::LSODAAlgorithm,
@@ -84,14 +97,13 @@ function solve{uType,tType,isinplace}(
 
     ### Fix the more general function to Sundials allowed style
     if !isinplace && (typeof(prob.u0)<:Vector{Float64} || typeof(prob.u0)<:Number)
-        f! = (t,u,du,userdata) -> (du[:] = prob.f(t,u); nothing)
+        f! = (du,u,p,t) -> (du[:] = prob.f(u,p,t); nothing)
     elseif !isinplace && typeof(prob.u0)<:AbstractArray
-        f! = (t,u,du,userdata) -> (du[:] = vec(prob.f(t,reshape(u,sizeu))); nothing)
+        f! = (du,u,p,t) -> (du[:] = vec(prob.f(reshape(u,sizeu),p,t)); nothing)
     elseif typeof(prob.u0)<:Vector{Float64}
-        f! = (t,u,du,userdata) -> prob.f(t,u,du)
+        f! = prob.f
     else # Then it's an in-place function on an abstract array
-        f! = (t,u,du,userdata) -> (prob.f(t,reshape(u,sizeu),reshape(du,sizeu));
-                          u = vec(u); du=vec(du); nothing)
+        f! = (du,u,p,t) -> (prob.f(reshape(du,sizeu),reshape(u,sizeu),p,t); nothing)
     end
 
     ures = Vector{Vector{Float64}}()
@@ -104,7 +116,7 @@ function solve{uType,tType,isinplace}(
     save_start ? ts = [t0] : ts = Vector{typeof(t0)}(0)
 
     neq = Int32(length(u0))
-    userfun = UserFunctionAndData(f!, userdata,neq)
+    comfun = CommonFunction(f!,prob.p,neq)
 
     atol = ones(Float64,neq)
     rtol = ones(Float64,neq)
@@ -132,13 +144,13 @@ function solve{uType,tType,isinplace}(
     end
     opt.itask = itask_tmp
 
-    const fex_c = cfunction(lsodafun,Cint,(Cdouble,Ptr{Cdouble},Ptr{Cdouble},Ref{typeof(userfun)}))
+    const fex_c = cfunction(commonfun,Cint,(Cdouble,Ptr{Cdouble},Ptr{Cdouble},Ref{typeof(comfun)}))
 
     ctx = lsoda_context_t()
     ctx.function_ = fex_c
     ctx.neq = neq
     ctx.state = 1
-    ctx.data = pointer_from_objref(userfun)
+    ctx.data = pointer_from_objref(comfun)
     ch = ContextHandle(ctx)
 
     lsoda_prepare(ctx,opt)

src/solver.jl

@@ -110,7 +110,7 @@ function lsoda(f::Function, y0::Vector{Float64}, tspan::Vector{Float64}; userdat
 		@assert (ctx_ptr.state >0) string("LSODA error istate = ", ctx_ptr.state, ", error = ",unsafe_string(ctx_ptr.error))
 		yres[k,:] = copy(y)
   end
-  
+
   lsoda_free(ctx_ptr)
   return yres
 end
@@ -127,7 +127,7 @@ function lsoda_evolve!(ctx::lsoda_context_t,y::Vector{Float64},tspan::Vector{Flo
 # 		# ctx.data.data = userdata
 # 		# unsafe_pointer_to_objref(ctx.data).data = userdata
 # 	end
-	
+
 	t    = Array{Float64}(1)
 	tout = Array{Float64}(1)
 	t[1] = tspan[1]