[gmx-users] C++ xtc interface

[David van der Spoel]

On 02/10/17 23:16, Adriaan Riet wrote:
> Hello,
> 
> I would like to do some work with xtc output files, but I'm having trouble.
> The documentation <http://manual.gromacs.org/online/xtc.html> has the
> following functions:
> 
> /* All functions return 1 if successful, 0 otherwise */
> 
> extern int open_xtc(XDR *xd,char *filename,char *mode);
> /* Open a file for xdr I/O */
> 
> extern void close_xtc(XDR *xd);
> /* Close the file for xdr I/O */
> 
> extern int read_first_xtc(XDR *xd,char *filename,
> 			  int *natoms,int *step,real *time,
> 			  matrix box,rvec **x,real *prec);
> 
> 
> while the header file exposes the following signatures:
> 
> struct t_fileio *open_xtc(const char *filename, const char *mode);
> /* Open a file for xdr I/O */
> 
> void close_xtc(struct t_fileio *fio);
> /* Close the file for xdr I/O */
> 
> int read_first_xtc(struct t_fileio *fio,
>                     int *natoms, gmx_int64_t *step, real *time,
>                     matrix box, rvec **x, real *prec, gmx_bool *bOK);
> /* Open xtc file, read xtc file first time, allocate memory for x */
> 
> Further, the documentation mentions that you should link to -lgmx, but the
> only library I see for gromacs >=5.1 is -lgromacs (or -lgromacs_d). I
> assumed the function signature of the header file was correct, and made a
> small test case:
> 
> #include<iostream>
> #include "gromacs/fileio/xtcio.h"
> int main(int argc, char* argv[]){
>    const char
> filename[]={"$HOME/Documents/Research/gromacs/oakley/june2017Test/2017/09-21/10-06_angle0.42impConc0T1873.xtc"};
>    const char mode[]={'r'};
>    t_fileio *xdrFile = open_xtc(filename,mode);
>    int *natoms;
>    gmx_int64_t *step;
>    real *time;
>    matrix box;
>    rvec **x;
>    real *prec;
>    gmx_bool *bOK;
>    int answer=read_first_xtc(xdrFile,natoms,step,time,box,x,prec,bOK);
>    std::cout<<filename<<'\t'<<natoms<<std::endl;
>    if(answer){
>      std::cout<<"I'm having a good day "<<std::endl;
>    }
> 
>    return 0;
> }
> 
> I'm compiling and linking fine, and make it through the "open_xtc"
> function, but I'm segfaulting at the "read_first_xtc" function (i.e. not
> having a good day). My xtc file probably doesn't fit in memory. Has anyone
> had success using this interface? Is there a defined structure for the
> t_file_io struct?

natoms should not be  an uninitialized pointer, just an int that you 
pass with &natoms.
same with coordinates x, declare as
rvec *x
and pass as &x



Checkhow it is done in simple analysis tools in src/gromacs/gmxana

> 
> Thanks,
> Adriaan Riet
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se