[gmx-users] for help about reading xtc file

[Mark Abraham]

That's only worth bothering with if you'll do that re-read several
times. Is writing out the frame(s) of interest a better solution?

Mark

On Fri, Aug 16, 2013 at 6:25 PM, Xu, Yechuan <y.xu at neu.edu> wrote:
> 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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