[gmx-users] for help about reading xtc file

[Xu, Yechuan]

Yes, I realized that it is a opaque structure.
I just want to read a certain frame from the
xtc file. For example, last time I read the xtc
file to a certain frame, I want to recorde the
position and next time I can read the xtc file
from there, not from beginning.

Did anybody do that?

Thanks,
YC

On Aug 16, 2013, at 4:39 AM, Mark Abraham wrote:

> 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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