Dear Togo,
Good to see you here!
I spent the last two days groveling through spglib source looking for the best
way to fix Avogadro's spacegroup support. There I learned about Hall symbols,
which I didn't know about because The Big Giant Book of Spacegroups™ I have
here does not mention them. According to [1], it's because I only have Volume
A. Oh well, not being a crystallographer I learn as I go :)
Looking at OpenBabel source, it turns out it's not as limited as I first
thought, it has a complete database, but very underdocumented API. Therefore,
fixing the bug I wrote about in the is easily doable by enhancing spglib API.
I updated the bundled spglib to version 1.5.2 which includes spg_get_dataset()
function. Having access to the Hall symbol, it is now possible to tell
OpenBabel the exact spacegroup. Well, almost.
I propose the following changes to spglib:
A) Sanitizing string fields in SpglibDataset
The string fields in the database contain padding at the end. A null character
should terminate the useful part of the string. For compatibility with
OpenBabel, [1], and, possibly, other software, the '=' character in the Hall
symbol should be replaced with '"'. After these two changes,
OpenBabel::SpaceGroup::GetSpaceGroup() successfully returns the correct
spacegroup object. In the long term, should spglib be compatible with [2]?
B) Allow access to the spglib data without knowing the full unit cell.
We need this in order to get symmetry operations when the unit cell is still
incomplete and to provide more detailed choices in the GUI. There should be a
function to fetch data given a Hall symbol, and an interface allowing
iteration through all spacegroups. The data returned should include symmetry
operations. One option is keeping SpglibDataset with cell-specific fields
zeroed out, or maybe something like
struct {
SpacegroupType info;
int n_operations;
int (*rotations)[3][3];
double (*translations)[3];
};
C) There is additional data to take into account.
Please take a look at table 1 in [1]. OpenBabel uses these symbols in their
data explicitly. Look at the space-groups.txt file installed with OpenBabel.
They have 6 entries for P1, unlike spglib or, for that matter, table 6 in [1].
While I'm not sure what this means for spacegroup perception (does it have
something to do with the origin_shift field?), I do know that spglib cannot
return the Hall symbols required to identify those spacegroups to OpenBabel.
What do you think?
[1] http://cci.lbl.gov/sginfo/hall_symbols.html
[2] http://cci.lbl.gov/sginfo/itvb_2001_table_a1427_hall_symbols.html
Regards,
Jure
On Wednesday 05 of February 2014 10:45:27 Atsushi Togo wrote:
> Dear Albert,
>
> I'm a developer of spglib. Please let me know If you have some request
> or need some modification on spglib side for your convenience.
>
> Best,
>
> Togo
>
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