xtc file format
Description
The xtc format is a portable format for trajectories.
It uses the xdr routines for writing and reading
data which was created for the Unix NFS system. The trajectories
are written using a reduced precision algorithm which works
in the following way: the coordinates (in nm) are multiplied by a scale
factor, typically 1000, so that you have coordinates in pm.
These are rounded to integer values. Then several other tricks are
performed, for instance making use of the fact that atoms close
in sequence are usually close in space too (e.g. a water molecule).
To this end, the xdr library is extended with a special routine
to write 3-D float coordinates. This routine was written by Frans van Hoesel
as part of an Europort project, and can be obtained through this link.
All the data is stored using calls to xdr routines.
- int magic
- A magic number, for the current file version its value is 1995.
- int natoms
- The number of atoms in the trajectory.
- int step
- The simulation step.
- float time
- The simulation time.
- float box[3][3]
- The computational box which is stored as a set of three basis
vectors, to allow for triclinic PBC. For a rectangular box the
box edges are stored on the diagonal of the matrix.
- 3dfcoord x[natoms]
- The coordinates themselves stored in reduced precision.
Please note that when the number of atoms is smaller than 9
no reduced precision is used.
Using xtc in your "C" programs
To read and write these files the following "C" routines are available:
/* 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);
/* Open xtc file, read xtc file first time, allocate memory for x */
extern int read_next_xtc(XDR *xd,
int *natoms,int *step,real *time,
matrix box,rvec *x,real *prec);
/* Read subsequent frames */
extern int write_xtc(XDR *xd,
int natoms,int step,real time,
matrix box,rvec *x,real prec);
/* Write a frame to xtc file */
To use the library function include "xtcio.h"
in your file and link with -lgmx.$(CPU)
Using xtc in your FORTRAN programs
To read and write these in a FORTRAN program use the calls to
readxtc and writextc as in the following sample program
which reads and xtc file and copies it to a new one:
program testxtc
parameter (maxatom=10000,maxx=3*maxatom)
integer xd,xd2,natoms,step,ret,i
real time,box(9),x(maxx)
call xdrfopen(xd,"test.xtc","r",ret)
print *,'opened test.xtc, ret=',ret
call xdrfopen(xd2,"testout.xtc","w",ret)
print *,'opened testout.xtc, ret=',ret
10 call readxtc(xd,natoms,step,time,box,x,prec,ret)
if ( ret .eq. 1 ) then
call writextc(xd2,natoms,step,time,box,x,prec,ret)
else
print *,'Error reading xtc'
endif
stop
end
To link your program use -L$(GMXHOME)/lib/$(CPU) -lxtcf
on your linker command line.
The source for this test can be found in file
$(GMXHOME)/src/gmxlib/testxtcf.f.