Jochen Hub wrote:
Jelger Risselada wrote:
Finally had a look through the gromacs 4.0 source code.
Don't know if this bug/points already have been reported and changed in
4.0.2:
1) There is never memory allocated for the pointers to the user defined
groups:
mdatoms->cU1 etc.
I'm not sure, but there is a
/* The user should fix this */
if (FALSE)
srenew(md->cU1,md->nalloc);
if (FALSE)
srenew(md->cU2,md->nalloc);
in ./src/mdlib/mdatom.c.
You can remove the FALSE and get the memory allocation, I guess.
Jochen
A hardcoded if(FALSE) in the middle of no where with the command /*The
user should fix this */ .
How flexible.. ;-)
greetings
Jelger
These pointers will stay NULL when a user defined group is defined in
the mdp file.
I find these groups normally a pretty useful interface for simple fast
implementations.
2) The pull code has indeed completely changed, however to me the
questionable factor 0.5 remained the same:
In pull.c:
/* Add the pull contribution to the virial */
vir[j][m] += 0.5*f[j]*r_ij[g][m];
I do agree with the positive sign of the summation, but why is there a
factor 0.5 to correct for double counting included in the summation. The
summation is already ordered as r_ij and f[j] is the distance vector and
force between the particle and the equilibrium position of the spring
and therefore double counting cannot occur. Ofcourse it's possible that
this factor 0.5 is not meant as a double counting correction factor, but
then I don't see where it does come from. If this factor is indeed
incorrect it might affect the pressure significantly in case a large
pulling group is used.
greetings
Jelger
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