Interface with the Community Ocean and Vertical Mixing (CVMix) project

    Community Ocean Vertical Mixing (CVMix) is a software package that aims to provide transparent, robust, flexible, well documented, shared Fortran source code for use in parameterizing vertical mixing processes in numerical ocean models.

    This header file provides a C-language interface for Basilisk (and other projects, since the interface does not depend on Basilisk itself).


    CVMix needs to be installed first and its source code must be accessible, since the C interface is generated automatically from the Fortran sources.

    Once this done the C interface can be built using this Makefile and the correct location for the sources and/or Fortran compiler. For example:

    cd $BASILISK/src/cvmix/
    CVMIX=$HOME/local/cvmix F90=gfortran FCFLAGS="-Wall -O2" make

    Interoperability with Fortran 90

    Aside from standard considerations on compatibility of different types between C and Fortran (as documented here for example), the main difficulty is interoperability of “assumed size arrays”.

    The approach taken here is a bit of a hack and should be replaced with a more portable way of doing things when it becomes available.

    For the moment, it relies on the assumption that the “shaped array descriptor” works in a similar manner to that of gfortran. These assumptions are:

    1. The first element of the array descriptor is a pointer to the data stored in the array.

    2. The size occupied by the array descriptor is smaller than or equal to the size of the data structure below (i.e. sizeof(cvmix_1d)).

    3. The only types used by CVMix are integer, cvmix_r8, character, logical and derived types composed of these.

    4. Fortran derived types never use more memory than the corresponding C structure.

    If any of these assumptions is violated, the most likely result will be a low-level memory fault (i.e. segmentation fault, stack smashing etc.).

    #pragma autolink -L$BASILISK/cvmix -lcvmixc -lgfortran

    We define a data structure describing the array descriptor of gfortran as documented here. Note that the goal is only to define a cvmix_1d structure which occupies the right amount of memory so that conditions 2 and 4 above are verified. The actual members are never used, with the exception of gfc_array_descriptor.a which corresponds to assumption 1 above.

    typedef int indexing;
    struct dtype_type
      size_t elem_len;
      int version;
      signed char rank;
      signed char type;
      signed short attribute;
    struct descriptor_dimension
      indexing stride;
      indexing lbound;
      indexing ubound;
    struct gfc_array_descriptor
      double * a;
      indexing offset;
      struct dtype_type dtype;
      struct descriptor_dimension dim[1];
      int padding[2]; // this seems necessary!!!
    typedef double cvmix_r8;
    typedef int logical;
    typedef int integer;
    typedef struct gfc_array_descriptor cvmix_1d;
    typedef cvmix_1d cvmix_nd; // for n-rank arrays (not used)
    typedef struct {
      double * a;
      indexing offset;
      struct dtype_type dtype;
      struct descriptor_dimension dim[2];
      int padding[2]; // this seems necessary!!!
    } cvmix_2d;
    cvmix_r8 cvmix_zero = 0., cvmix_one = 1.;
    #define strlencheck(s) (s != NULL ? strlen(s) : 0)
    #include "kinds_and_types.h"
    #include "put_get.h"
    extern void cvmix_redirect_stdout_ (void);
    extern void allocate1d_ (const int * len, cvmix_1d * mem);
    extern void deallocate1d_ (cvmix_1d * mem);
    extern void allocate2d_ (const int * len1, const int * len2, cvmix_2d * mem);
    extern void deallocate2d_ (cvmix_2d * mem);
    extern void sizeofall_ (void);
    extern void cvmix_deallocate_ (cvmix_data_type * CVmix_vars);
    cvmix_1d cvmix_allocate_1d (int len)
      cvmix_1d a;
      allocate1d_ (&len, &a);
      return a;
    void cvmix_deallocate_1d (cvmix_1d a)
      deallocate1d_ (&a);
    void cvmix_1d_print (cvmix_1d * a)
      fprintf (stderr, "a: %p offset: %d dtype: %ld %d %d %d %d dim: %d %d %d\n",
    	   (void *) a->a, a->offset, a->dtype.elem_len,
    	   a->dtype.version, a->dtype.rank, a->dtype.type,
    	   a->dim[0].stride, a->dim[0].lbound, a->dim[0].ubound);  
    cvmix_2d cvmix_allocate_2d (int len1, int len2)
      cvmix_2d a;
      allocate2d_ (&len1, &len2, &a);
      return a;
    void cvmix_deallocate_2d (cvmix_2d a)
      deallocate2d_ (&a);
    #define cvmix_deallocate(a) cvmix_deallocate_(a) 
    #define cvmix_2d(c,len1,i,j) (c).a[(i) + (j)*(len1)]