Jon Olav Vik wrote:
> Yes, ydot is allocated by CVODE (though not initialized to zero, as I learned
> the hard way). I do need to allocate y, however.
>
> As a start, I would like Cython to compile the following line of code:
>
> y0 = N_VNew_Serial(N)
>
> However, I'm unsure how much of the C declarations I need to duplicate (with
> ctypedef?). N_VNew_Serial returns an N_Vector:
> include/nvector/nvector_serial.h:N_Vector N_VNew_Serial(long int vec_length);
>
> The generic definition of an N_Vector is here:
>
> == BEGIN include/sundials/sundials_nvector.h (excerpt) ==
> #include <sundials/sundials_types.h>
>
> /*
> * -----------------------------------------------------------------
> * Generic definition of N_Vector
> * -----------------------------------------------------------------
> */
>
> /* Forward reference for pointer to N_Vector_Ops object */
> typedef struct _generic_N_Vector_Ops *N_Vector_Ops;
>
> /* Forward reference for pointer to N_Vector object */
> typedef struct _generic_N_Vector *N_Vector;
>
> /* Define array of N_Vectors */
> typedef N_Vector *N_Vector_S;
>
> /* Structure containing function pointers to vector operations */
> struct _generic_N_Vector_Ops {
> N_Vector (*nvclone)(N_Vector);
> N_Vector (*nvcloneempty)(N_Vector);
> void (*nvdestroy)(N_Vector);
...
>
> struct _generic_N_Vector {
> void *content;
> struct _generic_N_Vector_Ops *ops;
> };
> The abovementioned realtype (and booleantype) is defined in
> include/sundials/sundials_types.h
> from which I roughly quote some conditional defines:
> #if defined(SUNDIALS_SINGLE_PRECISION)
> typedef float realtype;
> #elif defined(SUNDIALS_DOUBLE_PRECISION)
> typedef double realtype;
> #elif defined(SUNDIALS_EXTENDED_PRECISION)
> typedef long double realtype;
>
> As for the structs, I've tried and failed along these lines:
> cdef extern from "sundials/sundials_nvector.h":
> ctypedef struct _generic_N_Vector
> ctypedef struct _generic_N_Vector *N_Vector
> ^
> ------------------------------------------------------------
> /xanadu/home/jonvi/svn/trunk/cysundials/hello.pyx:8:38: Syntax error in
> struct
> or union definition
>
> Do I really have to replicate the entire struct definition?
(Trivia: This is a lot like NumPy's source code.)
No, you just have to write "enough" for Cython to know what C code to
output. Knowing what that is probably takes some C experience though;
I'll try to help.
First, the #if-s cannot be expressed in Cython, but Cython is going in
the direction of the type of external typedefs not to matter. I think
you can safely do
cdef extern from ...:
ctypedef double realtype
It should work also when Sundials is compiled with float or long double.
Then N_Vector etc. can probably be expressed like this:
cdef extern from ....:
cdef struct _generic_N_Vector:
void* content
# not necesarry to declare ops unless you will be using
# the contents of ops from Cython
ctypedef _generic_N_Vector* N_vector
N_Vector N_VNew_Serial(long int vec_length)
Then you will be able to do
cdef NVector v = N_VNew_Serial(10)
cdef realtype* v_data = <realtype*>v.content
v_data[0] = 34
--
Dag Sverre
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