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Musite: use of crystal descriptors and lattice sums to identify muon sites
This is the white paper for a suite of matlab programs to identify muons sites.
Requirements:
- A CIF or CIF-like extension to describe lattices with a
magnetic base, i.e. the standard for a file containing the information
- An easy way of producing this file from the knowledge of the crystal symmetry and
atom cell positions; this is provided at least
- by hand, through the Bilbao server which lists e.g.
the Wyckoff positions of any crystal group and the instructions
to generate a CIF file, visualize, and then save it.
This is a simple interactive procedure, where a standard CIF for BaTiO3
can be edited and modified into the crystal of choice.
- by the Computational Crystallography Toolbox cctbx, in python
- by the Atomic Simulation Environment [[https://wiki.fysik.dtu.dk/ase/|ASE] in python
The cctbx and ASE solution offer lattice visualization. When proceeding by hand
- A local visualization program for CIF, e.g. the free software Jmol.
- When you launch Jmol and open the saved CIF file, you will probably see only the
unit cell in wireframe, plus the base. In order to see the full cell (i.e. to loop
on the Wyckoff positions) you must left-click on the image to get a menu, and select
Load/Load full unit cell from it.
The minimal plan may be then developed in matlab or in python. It includes
- A loading matlab routine to read the magnetic CIF file (the python equivalent is already there)
- Generation of a suitable finite magnetic and charge lattice
- A dipolar sum routine for chosen sets of positions
- A visualization routine for the field intensity and direction at these positions
- A constrained search routine for electrostatic energy minima on surfaces.
Initial implementation by cctbx and ipython, numpy, scipy, matplotlib
- cctbx provides
- the full capabilities of the International Tables of Crystallography for generating unit cells of any lattice, from the input of a CIF file
- the python scripting for performing this standard task simply
- a python web interface for generating forms to give free access to such standard scripts from a web server
(e.g. http://fis.unipr.it)
- how to handle distribution is an open question, maybe through browser interface cgi
- ASE provides
- superior documentation with respect to cctbx
- all the symmetry groups
- a simple visualization interface
- an all-python solution
- access to DFT calculations
- distribution implies: installing python (probably ipython), which is documented; installing ASE (also well documented), maybe including dipsum in ASE?
Questions:
- how does the web interface work? See examples in cctbx_bundle/cctbx_sources/cctbx/web
- include magnetic structure by its q vector
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