def __init__(self, infile, comment, element, speckle, trs, refined,
outmode):
# read comment & zoom from setting file first
# if not exist, read from cmd args, then default
self.cell = GeneralIO.from_file(infile)
self.comment = comment or self.cell.comment
self.element = element
# Get number and index of target element
num = self.cell.numbers
if element is None:
tgt_ele = int(num[1])
else:
tgt_ele = Specie(element).Z
tgt_ele_index = np.where(num == tgt_ele)[0]
self.n = tgt_ele_index.size
self.s1, self.s2 = speckle
# self.ele for function all-speckle-gen-of-ele in run
self.ele = Specie.from_num(tgt_ele)
# if there no restriction given then no restriction
if trs != ():
self.tr = trs[0]
else:
self.tr = None
self.refined = refined
self.outmode = outmode
def __init__(self, position, ele):
self._position = tuple(position)
if isinstance(ele, Specie):
self._element = ele
elif isinstance(ele, int):
self._element = Specie.from_num(ele)
else:
self._element = Specie(ele)
def __init__(self, settings, comment, element, speckle, nspeckle, zoom,
trs, refined, outmode, mpr):
# read comment & zoom from setting file first
# if not exist, read from cmd args, then default
if zoom is None:
try:
zoom = settings['zoom']
except:
zoom = 1
self.zoom = zoom
if comment is None:
try:
comment = settings['comment']
except:
comment = 'default'
self.comment = comment
lat = np.array(settings['lattice'])
pos = np.array(settings['positions'])
num = np.array(settings['numbers'])
self.cell = GeneralCell(lat * self.zoom, pos, num)
self.element = element
# Get number and index of target element
if element is None:
tgt_ele = int(num[1])
else:
tgt_ele = Specie(element).Z
tgt_ele_index = np.where(num == tgt_ele)[0]
self.s1, self.s2 = speckle
self.n1, self.n2 = nspeckle
# self.ele for function all-speckle-gen-of-ele in run
self.ele = Specie.from_num(tgt_ele)
# if there no restriction given then no restriction
if trs != ():
self.tr = trs[0]
else:
self.tr = None
self.refined = refined
self.outmode = outmode
self.mpr = mpr
self.n0 = tgt_ele_index.size - self.n1 - self.n2
def from_array(cls, arr):
mfunc = np.vectorize(lambda n: Specie.from_num(n))
sarr = mfunc(arr)
return cls(sarr.tolist())