def update_material(self):
# Convert the sites back to the material data format
info_array = []
type_array = []
U_array = []
for site in self.sites:
for atom in site['atoms']:
info_array.append(
(*site['fractional_coords'], atom['occupancy']))
type_array.append(ptable[atom['symbol']])
U_array.append(atom['U'])
mat = self.material
mat._atominfo = np.array(info_array)
mat._atomtype = np.array(type_array)
mat._U = np.array(U_array)
old_unitcell = mat.unitcell
# Re-create the unit cell from scratch. This is easier to do
# right now than setting the variables and figuring out which
# properties need to be updated and in what order...
mat.unitcell = unitcell(mat._lparms, mat.sgnum,
mat._atomtype, mat._atominfo, mat._U,
mat._dmin.getVal('nm'), mat._beamEnergy.value,
mat._sgsetting)
# Set the stiffness back on it if it existed
if hasattr(old_unitcell, 'stiffness'):
mat.unitcell.stiffness = old_unitcell.stiffness
# Update the structure factor of the PData
mat.update_structure_factor()
def __init__(self,
name=None,
material_file=None,
dmin=DFLT_DMIN,
kev=DFLT_KEV,
sgsetting=DFLT_SGSETTING):
"""Constructor for Material
name -- (str) name of crystal
material_file -- (str) name of the material file
which contains the crystal. this could be either cif
or hdf5
"""
self.name = name
self.description = ''
self._dmin = dmin
self._beamEnergy = kev
self.sgsetting = sgsetting
if material_file:
# Get values from configuration
# self._readCfg(material_file)
# >> @ date 08/20/2020 SS removing dependence on hklmax
#self._hklMax = Material.DFLT_SSMAX
# self._beamEnergy = Material.DFLT_KEV
form = Path(material_file).suffix[1:]
if (form == 'cif'):
self._readCif(material_file)
elif (form in ['h5', 'hdf5', 'xtal']):
self._readHDFxtal(fhdf=material_file, xtal=name)
else:
# Use default values
self._lparms = Material.DFLT_LPARMS
# self._hklMax = Material.DFLT_SSMAX
#
self.description = ''
#
self.sgnum = Material.DFLT_SGNUM
self._sgsetting = Material.DFLT_SGSETTING
#
self._atominfo = Material.DFLT_ATOMINFO
#
self._U = Material.DFLT_U
#
self._atomtype = Material.DFLT_ATOMTYPE
#
self.unitcell = unitcell.unitcell(self._lparms, self.sgnum,
self._atomtype, self._atominfo,
self._U, self._dmin.getVal('nm'),
self._beamEnergy.value,
self._sgsetting)
self._newPdata()
self.update_structure_factor()
def __init__(self, name=None, cfgP=None, dmin=DFLT_DMIN, kev=DFLT_KEV, sgsetting=DFLT_SGSETTING):
"""Constructor for Material
name -- (str) name of material
cfgP -- (instance) configuration file parser with
-- the material name as a section
"""
self.name = name
self.description = ''
self._dmin = dmin
self._beamEnergy = kev
self.sgsetting = sgsetting
if(self._dmin.unit == 'angstrom'):
# convert to nm
uc_dmin = self._dmin.value * 0.1
elif(self._dmin.unit == 'nm'):
uc_dmin = self._dmin.value
if cfgP:
# Get values from configuration
# self._readCfg(cfgP)
self._hklMax = Material.DFLT_SSMAX
# self._beamEnergy = Material.DFLT_KEV
n = cfgP.find('.')
form = cfgP[n+1:]
if(form == 'cif'):
self._readCif(cfgP)
elif(form in ['h5', 'hdf5', 'xtal']):
self._readHDFxtal(fhdf=cfgP, xtal=name)
else:
# Use default values
self._lparms = Material.DFLT_LPARMS
self._hklMax = Material.DFLT_SSMAX
#
self.description = ''
#
self.sgnum = Material.DFLT_SGNUM
self._sgsetting = Material.DFLT_SGSETTING
#
self._atominfo = Material.DFLT_ATOMINFO
#
self._atomtype = Material.DFLT_ATOMTYPE
#
self.unitcell = unitcell(self._lparms, self.sgnum, self._atomtype,
self._atominfo, self._U, uc_dmin,
self._beamEnergy.value, self._sgsetting)
hkls = self.planeData.getHKLs(allHKLs=True)
sf = numpy.zeros([hkls.shape[0],])
for i,g in enumerate(hkls):
sf[i] = self.unitcell.CalcXRSF(g)
self.planeData.set_structFact(sf[~self.planeData.exclusions])
return