Re: [Avogadro-devel] Avogadro and SPGLIB

[Albert D. <de...@pi...>]

David,

After some playing around I was able to determine that SPGlib will generate the primitive lattice and basis atoms correctly for use in PWScf.  The avospg method reduceToPrimitive appears to work correctly only when I disable spg_refine_cell.  So far I have been unable to figure out what might be wrong between OBUnitCell::SetData and the Avogadro display.

What I would like to do is use the spglib and avospg (crystallography extension) methods to determine the primitive lattice from my PWScf input generator.  The goal is have a button that will generate the PWScf input using either the generated primitive cell or take the displayed cell verbatim without changing the display.  Is it possible to connect the crystallography extension with a quantum input generator or should I re-implement the necessary methods in the PWScf input generator?


Thanks,
Albert


On Mar 15, 2012, at 12:20 PM, David Lonie wrote:

> Hi Albert,
> 
> On Wed, Mar 14, 2012 at 1:40 PM, Albert DeFusco <de...@pi...> wrote:
>> I am working on writing an input generator for PWScf.  The input requires that user knows the atomic lattice basis and the Bravais lattice or the exact primitive lattice vectors. I have been playing with SPGLIB in Avogadro to be able to convert unit cell atoms and lattice vectors into the primitive lattice and the atomic basis and I am having trouble getting it to work correctly.  Is SPGLIB a good library for this or should I look elsewhere?
> 
> SPGlib should work well for this. The other alternative would be to
> interface with Stokes' FINDSYM code in the ISOTROPY package, but it
> does not provide a library interface and cannot be included with
> Avogadro:
> 
> http://stokes.byu.edu/iso/findsym.html
> 
>> I have found that when I run a simple C program linked to Avogardo's libspglib.a, where I use the same atom positions and cell matrix, different results are obtained from those I can print during Avogadro's call to the spglib routines.  Further, the Cell Matrix reported back to the gui is very different.
> 
> The code that the crystallography extension uses is in avospglib.h/cpp
> in the crystallography extension's subdirectory. I've been able to
> reproduce your issue -- I've tracked it to the
> OpenBabel::OBUnitCell::SetData call, for instance:
> 
>    cell->SetData(Avogadro::Eigen2OB(cellMatrix));
> 
>    OpenBabel::matrix3x3 setCellMat = cell->GetCellMatrix();
> 
> in the "applyToMolecule" method ends up with:
> 
> cellMatrix   = 1.5, -1.5, 0 || -1.5, 0, -1.5 || 1.5 1.5 0
> setCellMat = 1.5, -1.5, 0 || -1.5, 0, -1.5 || 1.5 1.5 -2.22044604
> 
> when I reduce a Fd-3m 3 angstrom cubic cell as in your example.
> 
> This has worked well in the past for a number of different structures,
> so I suspect that there is something specific about this structure
> that is confusing the OBUnitCell::SetData method. I spent some time
> looking at it, but couldn't track it down. I may have time to work on
> this later, but it may be a while.
> 
> Feel free to poke around in the OBUnitCell code to track this down and
> I'll answer any questions you have to the best of my ability.
> 
> Hope this helps,
> 
> Dave
> 
>> For example, the silicon diamond crystal unit cell is a cubic lattice with 8 atoms and has Fd-3m (227) space group symmetry.  The 8 atoms in fractional coordinates are listed below.
>> 
>> Si   0.00000   0.00000   0.00000
>> Si   0.00000   0.50000   0.50000
>> Si   0.50000   0.50000   0.00000
>> Si   0.50000   0.00000   0.50000
>> Si   0.75000   0.25000   0.75000
>> Si   0.25000   0.25000   0.25000
>> Si   0.25000   0.75000   0.75000
>> Si   0.75000   0.75000   0.25000
>> 
>> In order to make a usable PWScf input I have to generate the primitive lattice and the atomic basis.  A correct PWScf input is show below where PWScf identifies 48 symmetry operations.
>> 
>> ATOMIC_POSITIONS
>>  Si 0.00 0.00 0.00
>>  Si 0.25 0.25 0.25
>> CELL_PARAMETERS cubic
>> -0.500000   0.000000   0.500000
>>  0.000000   0.500000   0.500000
>> -0.500000   0.500000   0.000000
>> 
>> Here "CELL_PARAMETERS" refers to the primitive lattice vectors in fractional coordinates.
>> 
>> Since primitive lattice vectors are not unique, there are other possible solutions.  All attempts I have made to generate primitive lattice vectors and the atomic basis with SPGLIB do not work in PWScf. At best I have been able make input files that have 8 of the expected 48 symmetry operations.
>> 
>> 
>> Thanks,
>> Albert
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> Avogadro-devel mailing list
>> Avo...@li...
>> https://lists.sourceforge.net/lists/listinfo/avogadro-devel