Dear Jure,
A) OK. Thanks.
B) I'm fine to make a spglib interface to access the database. I will
work on that. Then, even if you have database, the design of GUI would
be e not easy. At least the designer should know the basic of
crystallography, then you have to very restrict the possible inputs of
lattice parameters and atomic positions to the standard settings. Most
users don't know those crystallographic standard, so if you offer too
much freedoms to users, you may get a lot of questions from those
users. If you ignore crystallographic definitions and conventions, the
computer program breaks down mathematically.
C) My English skill is not enough to understand that you wrote. Hall
symbol proposes possible sets of symmetry operations with respect to
the choices of standard origins and axes. What I meant was, for
example No. 5 shown below, that there are 9 different ways to
represent it and you can recover 9 different sets of symmetry
operations from those Hall symbols following information of tables in
http://cci.lbl.gov/sginfo/hall_symbols.html , i.e. Hall symbols are
very condensed way to represent matrix representations, and those
tables are just necessary to recover the matrix representations
following the recipe but not to generate the matrix representations by
multiplying all the information in the tables. But for P1, there is
only one.
5:b1 C 1 2 1 C 2y
5:b2 A 1 2 1 A 2y
5:b3 I 1 2 1 I 2y
5:c1 A 1 1 2 A 2
5:c2 B 1 1 2 B 2
5:c3 I 1 1 2 I 2
5:a1 B 2 1 1 B 2x
5:a2 C 2 1 1 C 2x
5:a3 I 2 1 1 I 2x
Best regards,
Togo
On Thu, Feb 6, 2014 at 1:08 AM, Jure Varlec <jure.var...@ki.si> wrote:
> Dear Togo,
>
> A) Correct, C strings are null-terminated, meaning that string methods stop on
> the first null character regardless of buffer size.
>
> B) You are right, of course. Shows I'm a newbie :) . But anyway, there should
> be a way to get at the data. It's up to the user to specify the needed
> information. The current Set Spacegroup dialog in Avogadro is simply
> inadequate. For an example, look at the screenshot from VESTA[1]. The GUI has
> to present available options, therefore it must know about them. What do you
> propose we do? Have Avogadro know about all possibilities, generate an
> archetypal unit cell and pass it to spglib? Or have spglib generate possible
> options and have Avogadro simply wrap them in a GUI? I haven't thought this
> through yet (it's not my immediate concern), but I'm willing to implement a
> GUI if someone helps me with a crystallographic point of view.
>
> C) *scratches head* Well, you know this stuff way better than I do, so if
> there's no way to get a Hall symbol that's not in spglib's database, I'm OK.
>
> [1]https://oblak.varlec.si/public.php?service=files&t=d431f5fb77db6a2e106ecc95eebf3b73
>
> PS: what's the attachment policy on this list?
>
> Regards,
>
> Jure
>
> On Wednesday 05 of February 2014 23:19:37 Atsushi Togo wrote:
>> 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
>>
>
>
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--
Atsushi Togo
http://atztogo.github.com/
atz.t...@gmail.com
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