Dear Jure, I got the crystallographic database from http://pmsl.planet.sci.kobe-u.ac.jp/~seto/?page_id=37&lang=en .
A) I'm not very familiar with C language. For example how should I do? "R 3 -2=c " --> "R 3 -2\"c\0 " is a safe way in C? B) The symmetry database assumes the crystal structure is set with one of standard origins and one of sets of axes, i.e., numerical symmetry operations change by the choices of them. The crystal structure a user defines may not follow a good crystallographic manner. How do you use the database in this case? C) I saw this. https://github.com/openbabel/openbabel/blob/master/data/space-groups.txt#L6 You say "They have 6 entries for P1", but this sounds for me crystallographically very strange. Table 1 in [1] just gives cetring information, but there is no cetring for P1. Best regards, Togo On Wed, Feb 5, 2014 at 7:56 PM, Jure Varlec <jure.var...@ki.si> wrote: > 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(tm) 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 >> > > ------------------------------------------------------------------------------ > Managing the Performance of Cloud-Based Applications > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. > Read the Whitepaper. > http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk > _______________________________________________ > Avogadro-devel mailing list > Avogadro-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Atsushi Togo http://atztogo.github.com/ atz.t...@gmail.com ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
