[gmx-developers] GMX library functions and documentation

[Ondrej Marsalek]

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?

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?

There are some small things that I have encountered as well.
Inconsistent naming: output_env_t vs t_trxstatus. Inconsistent
arguments: read_first_x wants trxstatus**, while read_next_x and
close_trj want trxstatus*.

Any input welcome, thanks,
Ondrej