[gmx-developers] GMX library functions and documentation

[Roland Schulz]

On Fri, Sep 14, 2012 at 10:39 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 15/09/2012 12:14 AM, Ondrej Marsalek wrote:
> > Hi,
> >
> > I am writing an analysis tool and I am having some trouble using the
> > GMX library functions or finding documentation for them. I am
> > currently working against 4.5.3. Is there some kind of comprehensive
> > documentation? It seems that the Doxygen documentation make targets
> > mentioned on the web do not exist in 4.5.3. Should I just read the
> > code?
>
> Unfortunately the best approach available is to look around at what
> existing tools do and pick one/several that have a similar mode of
> operation and derive from that. Hopefully things will improve a lot in
> the transition to GROMACS 5, but that is some (man-)years away yet.
>

The Gromacs 5 analysis tool framework is already documented very well (
http://jenkins.gromacs.org/job/Doxygen_Nightly_master/javadoc/html-user/group__module__trajectoryanalysis.html)
and
the parts I'm using work very well. I personally would write new analysis
tools for Gromacs 5. If you want to try it out, you can get it from git.

Roland


>
> > One specific problem that I have is with output_env_t. I have found
> > these two functions:
> >
> > output_env_init
> > output_env_init_default
> >
> > and as I have no specific requirements, I just wanted to use the
> > second one, at the very beginning of my program. However, it
> > segfaults:
> >
> > ==21076== Process terminating with default action of signal 11 (SIGSEGV)
> > ==21076==  Bad permissions for mapped region at address 0x4096E0
> > ==21076==    at 0x56B4C85: output_env_init (oenv.c:96)
> > ==21076==    by 0x56B4E92: output_env_init_default (oenv.c:143)
> > ==21076==    by 0x403049: main (ctcf.c:483)
> >
> > Checking all the analysis tools, I don't see a single use of any of
> > these two functions, although the output environment is used. Should I
> > just use it uninitialized?
>
> I've never needed to know. I suggest you copy the kind of thing that
> other tools do.
>
> > There are some small things that I have encountered as well.
> > Inconsistent naming: output_env_t vs t_trxstatus.
>
> These do different things. Not sure what you mean.
>
> >   Inconsistent
> > arguments: read_first_x wants trxstatus**, while read_next_x and
> > close_trj want trxstatus*.
>
> Generally, functions with names matching *first* might allocate memory,
> so they need the address of a pointer to store. Later functions just
> need the pointer to use.
>
> Mark
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