[gmx-users] for help about reading xtc file

[Mark Abraham]

On Thu, Aug 15, 2013 at 11:33 PM, Xu, Yechuan <y.xu at neu.edu> wrote:
> Thank you for your reply. after I read the xdrfile.c,
>
> I changed the sentence as
> pos=xdr_getpos((XDR*) (xtc->xdr));
>
> like that in the file of xdrfile.c. I also copy the definition
> for XDR and xdr_op to my own code.

You can see those functions, but the fact that there's an opaque
struct is a clue you're not supposed to want to use them. Your code
has already read the frame using the public interface in
xdrfile_xtc.h. What else are you trying to achieve?

Mark

> But I still got the errors:
> seekxtc.c:61:33: error: dereferencing pointer to incomplete type
>        pos=xdr_getpos((XDR *)(xtc->xdr));
>                                                         ^
>
> here are my code:
> #include <stdio.h>
> #include <stdlib.h>
> #include <math.h>
> #include <xdrfile_xtc.h>
>
> enum xdr_op
> {
>    XDR_ENCODE = 0,
>    XDR_DECODE = 1,
>    XDR_FREE   = 2
> };
>
> typedef struct XDR XDR;
>
> struct XDR
> {
>    enum xdr_op x_op;
>    struct xdr_ops
>    {
>       int (*x_getlong) (XDR *__xdrs, int32_t *__lp);
>       int (*x_putlong) (XDR *__xdrs, int32_t *__lp);
>       int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
>       int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);
>       /* two next routines are not 64-bit IO safe - don't use! */
>       unsigned int (*x_getpostn) (XDR *__xdrs);
>       int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);
>       void (*x_destroy) (XDR *__xdrs);
>    }
>    *x_ops;
>    char *x_private;
> };
>
>
> int main(int argc, char *argv[])
> {
>    int i;
>    int step, read_return, result;
>    int natoms;
>    float time,prec=1000.;
>    matrix box;
>    rvec *x;
>    XDRFILE *xtc;
>    char *fname;
>    unsigned int pos;
>
>    printf("begin, argc=%d\n",argc);
>    if(argc==2){
>       fname=argv[1];
>    }
>
>    xtc=xdrfile_open (fname,"r");
>    read_xtc_natoms (fname,&natoms);
>    printf("number of atoms: %d\n",natoms);
>
>    x = calloc(natoms, sizeof (x[0]));
>
>    while(1){
>       read_return=read_xtc(xtc,natoms,&step,&time,box,x,&prec);
>       if (read_return!=0) break;
>
>       pos=xdr_getpos((XDR *)(xtc->xdr));
>       printf("%d\n",pos);
>
>    }
>
>    xdrfile_close (xtc);
> }
> Thanks,
> YC
>
>
> On Aug 15, 2013, at 3:09 PM, Mark Abraham wrote:
>
>> Right, because a pointer to an XDRFILE is neither a struct nor a union
>> :-) Look at how these routines are used, and consult the header files
>> for the right types to give them.
>>
>> Mark
>>
>> On Thu, Aug 15, 2013 at 7:29 PM, Xu, Yechuan <y.xu at neu.edu> wrote:
>>> Hi Everyone,
>>>
>>> I want to read a certain frame in a xtc file. How can I do that?
>>> I see there are xdr_getpos() and xdr_setpos(). How should I use
>>> these functions?
>>>
>>> I tried:
>>>
>>> XDRFILE *xtc;
>>> unsigned int pos;
>>>
>>> pos=xdr_getpos(xtc.xdr);
>>>
>>> but I got:
>>> error: request for member ‘xdr’ in something not a structure or union
>>>
>>> Thanks in advance.
>>> YC--
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