[gmx-users] some questions about gmx_density.c

Yang Ye leafyoung at yahoo.com
Tue Aug 5 15:56:14 CEST 2008


Perhaps gmx-devel is a better place for this mail.

t_filenm does nothing with the algorithm flow. It's a struct to hold
various input/output file names. The definition is found in some file
under include/.

Most analysis program follow a template as shown in
share/template/template.c. What the template does, in simple words, is:
it reads the trajectory frame by frame, for each frame, perform some
calculation. If you want to write your own analysis program, start from
one analysis program (for g_density, modify function calc_density shall
only involve the real algorithm of calculating density) or the template.

To understand some development work for Gromacs (not only analysis
tools), I recommend Erik's talk in CSC2007.

"Thursday 1.3. Workshop day 3" *Gromacs development.*

Yang Ye

beibei wrote:
> Hi, all
> Maybe since I am a newer with programming in C, I felt very difficult
> in reading codes of GROMACS. I want to know the arithmetic flow of
> gmx_density.c. I read many times but have no idea about it. Could
> anybody tell me the arithmetic flow of gmx_density.c? And where is the
> definition of t_filenm? Many thanks.
> Beibei
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