def fetch(self):
"""Creates a cell initializer object.
Note that the cell can be initialized from the lengths of the sides and
the angles between them instead of by a vector, as specified by the
'abc' or 'abcABC' modes.
"""
mode = self.mode.fetch()
ibase = super(InputInitCell, self).fetch()
if mode == "abc" or mode == "abcABC":
h = io_xml.read_array(np.float, ibase.value)
if mode == "abc":
if h.size != 3:
raise ValueError(
"If you are initializing cell from cell side lengths you must pass the 'cell' tag an array of 3 floats."
)
else:
h = mt.abc2h(h[0], h[1], h[2], np.pi / 2, np.pi / 2,
np.pi / 2)
elif mode == "abcABC":
if h.size != 6:
raise ValueError(
"If you are initializing cell from cell side lengths and angles you must pass the 'cell' tag an array of 6 floats."
)
else:
h = mt.abc2h(
h[0],
h[1],
h[2],
h[3] * np.pi / 180.0,
h[4] * np.pi / 180.0,
h[5] * np.pi / 180.0,
)
h.shape = (9, )
ibase.value = h
mode = "manual"
if mode == "manual":
h = ibase.value
if h.size != 9:
raise ValueError(
"Cell objects must contain a 3x3 matrix describing the cell vectors."
)
if not (h[3] == 0.0 and h[6] == 0.0 and h[7] == 0.0):
warning(
"Cell vector matrix must be upper triangular, all elements below the diagonal being set to zero.",
verbosity.low,
)
h[3] = h[6] = h[7] = 0
ibase.value = h
return self._initclass(value=ibase.value,
mode=mode,
units=self.units.fetch())
def getval(self):
"""Calculates the value from the data supplied in the xml file.
Either reads the string from the input file as an array of numbers,
or as a string specifying either a file name or a single value.
"""
value = super(InputInitBase, self).fetch()
if self.mode.fetch() == "manual":
if "[" in value and "]" in value: # value appears to be a list
if self._storageclass is float:
value = io_xml.read_array(np.float, value)
else:
value = io_xml.read_list(value)
else:
value = io_xml.read_type(self._storageclass, value)
else:
value = str(value) # typically this will be a no-op
return value
def getval(self):
"""Calculates the value from the data supplied in the xml file.
Either reads the string from the input file as an array of numbers,
or as a string specifying either a file name or a single value.
"""
value = super(InputInitBase, self).fetch()
if self.mode.fetch() == "manual":
if '[' in value and ']' in value: # value appears to be a list
if self._storageclass is float:
value = io_xml.read_array(np.float, value)
else:
value = io_xml.read_list(value)
else:
value = io_xml.read_type(self._storageclass, value)
else:
value = str(value) # typically this will be a no-op
return value
def fetch(self):
"""Creates a cell initializer object.
Note that the cell can be initialized from the lengths of the sides and
the angles between them instead of by a vector, as specified by the
'abc' or 'abcABC' modes.
"""
mode = self.mode.fetch()
ibase = super(InputInitCell, self).fetch()
if mode == "abc" or mode == "abcABC":
h = io_xml.read_array(np.float, ibase.value)
if mode == "abc":
if h.size != 3:
raise ValueError("If you are initializing cell from cell side lengths you must pass the 'cell' tag an array of 3 floats.")
else:
h = mt.abc2h(h[0], h[1], h[2], np.pi / 2, np.pi / 2, np.pi / 2)
elif mode == "abcABC":
if h.size != 6:
raise ValueError("If you are initializing cell from cell side lengths and angles you must pass the 'cell' tag an array of 6 floats.")
else:
h = mt.abc2h(h[0], h[1], h[2], h[3] * np.pi / 180.0, h[4] * np.pi / 180.0, h[5] * np.pi / 180.0)
h.shape = (9,)
ibase.value = h
mode = "manual"
if mode == "manual":
h = ibase.value
if h.size != 9:
raise ValueError("Cell objects must contain a 3x3 matrix describing the cell vectors.")
if not (h[3] == 0.0 and h[6] == 0.0 and h[7] == 0.0):
warning("Cell vector matrix must be upper triangular, all elements below the diagonal being set to zero.", verbosity.low)
h[3] = h[6] = h[7] = 0
ibase.value = h
return self._initclass(value=ibase.value, mode=mode, units=self.units.fetch())