eandklahn / phd_repo

A collection of Python-code that I use/have been using for my work in neutron diffraction, molecular magnetism and as a TA in physical chemistry

Emil Andreasen Klahn

[email protected]
www.eklahn.com

phd_repo's Issues

Multiple crystalStructure classes

there are multiple classes called crystalStructure under crystallography.py, crystallography_v1.0.py and cifoperations/crystalStructure.py

these should be combined

Change magnetic form factor cards for lanthanides

Make it so that the "F XXm 3 ..." card is constructed automatically when the magnetic atom is a lanthanide

Writing cry-file A-cards from crystalStucture

crystalStructure-class does not save the Uiso-value from the cif-file when the Utype is Uani

It is a problem because generating a cry-file when occupancies are not 1 requires the Uiso-value to be put into the A-card

Split the crystalStructure-class into functions for constructing an instance and the class itself

I think this will make it more intuitive and will also make it easier to allow for creating an empty class

crystalStructure unable to initialize from CIF if current working directory is not the directory containing the file

Example of problem

from cifoperations import cc
dbm = cc.crystalStructure('C:\Users\Emil\Documents\Uddannelse\PhD\pnd_susceptibility\magnetic_ellipsoids\DBM.cif')
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Emil\Documents\Uddannelse\PhD\pyLIB\cifoperations\cc.py", line 120, in init
self._read_CIF()
File "C:\Users\Emil\Documents\Uddannelse\PhD\pyLIB\cifoperations\cc.py", line 180, in _read_CIF
cf = CifFile.ReadCif(self.cifFile)
File "C:\Program Files (x86)\Python36-32\lib\site-packages\CifFile\CifFile_module.py", line 3108, in ReadCif
permissive=permissive)
File "C:\Program Files (x86)\Python36-32\lib\site-packages\CifFile\StarFile.py", line 2174, in ReadStar
filestream = urlopen(my_uri)
File "C:\Program Files (x86)\Python36-32\lib\urllib\request.py", line 223, in urlopen
return opener.open(url, data, timeout)
File "C:\Program Files (x86)\Python36-32\lib\urllib\request.py", line 526, in open
response = self._open(req, data)
File "C:\Program Files (x86)\Python36-32\lib\urllib\request.py", line 549, in _open
'unknown_open', req)
File "C:\Program Files (x86)\Python36-32\lib\urllib\request.py", line 504, in _call_chain
result = func(*args)
File "C:\Program Files (x86)\Python36-32\lib\urllib\request.py", line 1388, in unknown_open
raise URLError('unknown url type: %s' % type)
urllib.error.URLError:
import os
os.getcwd()
'C:\Users\Emil'

Symmetry cards being read wrong

it looks like the function _read_symmop in cifoperations.symmetry is reading the symmetry element wrong when the translation is given before the rotation,
i.e.
x-1/2, -y-1/2, z-1/2 is being read correctly
but for
1/2+X,1/2-Y,1/2+Z,
the translational part is being returned as (0,0,0).