def __init__(self, name, *args):
'''Creates a new lattice and calculates related values.
Keyword arguments:
name -- a string
a,b,c,alpha,beta,gamma -- lengths and angles (in degrees)
'''
self._name = name
self._a1 = None
self._a2 = None
self._a3 = None
self._alpha1 = None
self._alpha2 = None
self._alpha3 = None
self._system = "Triclinic"
if allnum(args):
# Set the direct lattice parameters
a, b, c, alpha, beta, gamma = args
self._a1 = a
self._a2 = b
self._a3 = c
self._alpha1 = alpha * TORAD
self._alpha2 = beta * TORAD
self._alpha3 = gamma * TORAD
self._set_reciprocal_cell(self._a1, self._a2, self._a3,
self._alpha1, self._alpha2, self._alpha3)
else:
self._system = args[0]
self._set_cell_for_system(self._system, *args[1:])
def setlat(name=None, *args):
"""
setlat -- interactively enter lattice parameters (Angstroms and Deg)
setlat name a -- assumes cubic
setlat name a b -- assumes tetragonal
setlat name a b c -- assumes ortho
setlat name a b c gamma -- assumes mon/hex with gam not equal to 90
setlat name a b c alpha beta gamma -- arbitrary
"""
if name is None: # Interactive
name = promptForInput("crystal name")
a = promptForNumber(' a', 1)
b = promptForNumber(' b', a)
c = promptForNumber(' c', a)
alpha = promptForNumber('alpha', 90)
beta = promptForNumber('beta', 90)
gamma = promptForNumber('gamma', 90)
ubcalc.set_lattice(name, a, b, c, alpha, beta, gamma)
elif (isinstance(name, str) and len(args) in (1, 2, 3, 4, 6)
and allnum(args)):
# first arg is string and rest are numbers
ubcalc.set_lattice(name, *args)
else:
raise TypeError()
def setlat(name=None, *args):
"""
setlat -- interactively enter lattice parameters (Angstroms and Deg)
setlat name a -- assumes cubic
setlat name a b -- assumes tetragonal
setlat name a b c -- assumes ortho
setlat name a b c gamma -- assumes mon/hex with gam not equal to 90
setlat name a b c alpha beta gamma -- arbitrary
"""
if name is None: # Interactive
name = promptForInput("crystal name")
a = promptForNumber(' a', 1)
b = promptForNumber(' b', a)
c = promptForNumber(' c', a)
alpha = promptForNumber('alpha', 90)
beta = promptForNumber('beta', 90)
gamma = promptForNumber('gamma', 90)
ubcalc.set_lattice(name, a, b, c, alpha, beta, gamma)
elif (isinstance(name, str) and
len(args) in (1, 2, 3, 4, 6) and
allnum(args)):
# first arg is string and rest are numbers
ubcalc.set_lattice(name, *args)
else:
raise TypeError()
def sim(scn, hkl):
"""sim hkl scn -- simulates moving scannable (not all)
"""
if not isinstance(hkl, (tuple, list)):
raise TypeError()
if not allnum(hkl):
raise TypeError()
try:
print scn.simulateMoveTo(hkl)
except AttributeError:
raise TypeError("The first argument does not support simulated moves")
def sim(self, scn, hkl):
"""sim hkl scn -- simulates moving scannable (not all)
"""
if not isinstance(hkl, (tuple, list)):
raise TypeError
if not allnum(hkl):
raise TypeError()
try:
print scn.simulateMoveTo(hkl)
except AttributeError:
raise TypeError("The first argument does not support simulated moves")
def sim(self, scn, hkl):
"""sim hkl scn -- simulates moving scannable (not all)
"""
if not isinstance(hkl, (tuple, list)):
raise TypeError
if not allnum(hkl):
raise TypeError()
try:
print scn.simulateMoveTo(hkl)
except AttributeError:
if diffcalc.util.RAISE_EXCEPTIONS_FOR_ALL_ERRORS:
raise TypeError(
"The first argument does not support simulated moves")
else:
print "The first argument does not support simulated moves"
def set_lattice(self, name, *shortform):
"""
Converts a list shortform crystal parameter specification to a six-long
tuple. See setlat() for a description of the shortforms supported.
"""
if not shortform:
raise TypeError("Please specify unit cell parameters.")
elif allnum(shortform):
sf = shortform
if len(sf) == 1:
system = "Cubic"
elif len(sf) == 2:
system = "Tetragonal"
elif len(sf) == 3:
system = "Orthorhombic"
elif len(sf) == 4:
if abs(sf[0] - sf[1]) < SMALL and sf[3] == 120:
system = "Hexagonal"
else:
system = "Monoclinic"
elif len(sf) == 6:
system = "Triclinic"
else:
raise TypeError(
"Invalid number of input parameters to set unit lattice.")
fullform = (system, ) + shortform
else:
if not isinstance(shortform[0], basestring):
raise TypeError("Invalid unit cell parameters specified.")
fullform = shortform
if self._state.name is None:
raise DiffcalcException(
"Cannot set lattice until a UBCalcaluation has been started "
"with newubcalc")
self._state.crystal = CrystalUnderTest(name, *fullform)
# Clear U and UB if these exist
if self._U is not None: # (UB will also exist)
print(
"Warning: Setting new unit cell parameters.\n"
" The old UB calculation has been cleared.")
self.save()
def setref2(scn, hkl):
"""setref2 scn [h k l] -- setup hkloffset scannable to scan for second reflection [hkl]"""
if not isinstance(hkl, (tuple, list)):
raise DiffcalcException("Please specify hkl values for a second reference reflection to search.")
if not allnum(hkl):
raise DiffcalcException("Please specify numeric values for hkl.")
try:
hkl_ref = scn._diffcalc._ub.ubcalc.get_reflection(0)[0]
except IndexError:
raise DiffcalcException("Please add one reference reflection into the reflection list.")
pol, az, sc = scn._diffcalc._ub.ubcalc.calc_offset_for_hkl(hkl, hkl_ref)
hkl_rot = [sc * val for val in hkl_ref]
hkl_sc = hkl_rot[:]
hkl_rot.extend([pol * TODEG, az * TODEG])
hkl_sc.extend([0, 0])
print ('\nRescaled hkl reference for second reflection : %9.4f %.4f %.4f' % (hkl_sc[0], hkl_sc[1], hkl_sc[2]))
print (' polar and azimuthal rotation angles : %9.4f %.4f\n' % (pol * TODEG, az * TODEG))
sim(scn, hkl_sc)
print ('IMPORTANT: Applying subsequent polar and azimuthal rotations might fail. In this case, please manually\n'
' find accessible azimuthal rotation range to scan for second reference reflection.')
reply = getInputWithDefault('Move to rescaled hkl position', 'y')
if reply in ('y', 'Y', 'yes'):
scn.asynchronousMoveTo(hkl_sc)
else:
print 'Aborting'
return
sim(scn, hkl_rot)
reply = getInputWithDefault('Apply polar and azimuthal rotations', 'y')
if reply in ('y', 'Y', 'yes'):
scn.asynchronousMoveTo(hkl_rot)
else:
print 'Aborting'
return