def add_atom_data(atom, atom2):
"""
Creates atom specific lines for equivalent atoms of different models.
:param atom: Atom object from model 1.
:param atom2: Atom object from model 2.
:return: String ready to be written to a peanut input file.
"""
n = atom.get_name().lstrip(atom.get_element())
frac = atom.get_frac()
adp = cart2frac_ADP(atom.adp[use], atom.molecule.get_cell())
eq = Uiso(adp)
atomlines = '\n' \
' ATCO {el:2s}{n:<6}{x:8.5f}{y:8.5f}{z:8.5f}{eq:8.5f}{oc:8.5f}{ox:8.5f}{s:>10}\n'\
.format(el=atom.get_element(),
n=n,
x=frac[0],
y=frac[1],
z=frac[2],
eq=eq,
oc=1,
ox=0,
s=2)
atomlines += ' UIJ CAL {el:2s}{n:<6}{u11:8.5f}{u22:8.5f}{u33:8.5f}{u12:8.5f}{u13:8.5f}{u23:8.5f}\n'\
.format(el=atom.get_element(),
n=n,
u11=adp[0],
u22=adp[1],
u33=adp[2],
u12=adp[3],
u13=adp[4],
u23=adp[5])
try:
adp = atom2.adp['frac_meas']
except KeyError:
adp = cart2frac_ADP(atom2.adp['cart_meas'], atom.molecule.get_cell())
atomlines += ' UIJ {el:2s}{n:<6}{u11:8.5f}{u22:8.5f}{u33:8.5f}{u12:8.5f}{u13:8.5f}{u23:8.5f}\n'\
.format(el=atom.get_element(),
n=n,
u11=adp[0],
u22=adp[1],
u33=adp[2],
u12=adp[3],
u13=adp[4],
u23=adp[5])
atomlines += ' UIJE {el:2s}{n:<6}{u11:8.5f}{u22:8.5f}{u33:8.5f}{u12:8.5f}{u13:8.5f}{u23:8.5f}\n'\
.format(el=atom.get_element(),
n=n,
u11=0,
u22=0,
u33=0,
u12=0,
u13=0,
u23=0)
return atomlines
def set_adp_cart(self, value):
if not value is None:
value = cart2frac_ADP(value, self.cell)
# ===================================================================
# if self.get_element()=='H':
# value=[10+i for i in value]
#===================================================================
self.adp_frac = [value[0], value[1], value[2],
value[5], value[4], value[3]]
self.adp_updated = True
else:
self.adp_updated = False
def set_adp_cart(self, value):
if not None is value:
self.adp_frac = cart2frac_ADP(value, self.cell)
def set_adp_cart(self, name, value):
self.adp_cart[name] = value
frac = cart2frac_ADP(value, self.cell)
self.adp_frac[name] = frac
