def __repr__(self):
"""Represent the Poscar class."""
header = (str(self.comment) + str("\n1.0\n") +
str(self.atoms.lattice_mat[0][0]) + " " +
str(self.atoms.lattice_mat[0][1]) + " " +
str(self.atoms.lattice_mat[0][2]) + "\n" +
str(self.atoms.lattice_mat[1][0]) + " " +
str(self.atoms.lattice_mat[1][1]) + " " +
str(self.atoms.lattice_mat[1][2]) + "\n" +
str(self.atoms.lattice_mat[2][0]) + " " +
str(self.atoms.lattice_mat[2][1]) + " " +
str(self.atoms.lattice_mat[2][2]) + "\n")
order = np.argsort(self.atoms.elements)
coords = self.atoms.frac_coords
coords_ordered = np.array(coords)[order]
elements_ordered = np.array(self.atoms.elements)[order]
props_ordered = np.array(self.atoms.props)[order]
# check_selective_dynamics = False
counts = get_counts(elements_ordered)
if "T" in "".join(map(str, self.atoms.props[0])):
middle = (" ".join(map(str, counts.keys())) + "\n" +
" ".join(map(str, counts.values())) +
"\nSelective dynamics\n" + "Direct\n")
else:
middle = (" ".join(map(str, counts.keys())) + "\n" +
" ".join(map(str, counts.values())) + "\ndirect\n")
rest = ""
# print ('repr',self.frac_coords, self.frac_coords.shape)
for ii, i in enumerate(coords_ordered):
p_ordered = str(props_ordered[ii])
rest = rest + " ".join(map(str, i)) + " " + str(p_ordered) + "\n"
result = header + middle + rest
return result
def write_file(self, filename):
"""Write the Poscar object to a file."""
f = open(filename, "w")
header = (str(self.comment) + str("\n1.0\n") +
str(self.atoms.lattice_mat[0][0]) + " " +
str(self.atoms.lattice_mat[0][1]) + " " +
str(self.atoms.lattice_mat[0][2]) + "\n" +
str(self.atoms.lattice_mat[1][0]) + " " +
str(self.atoms.lattice_mat[1][1]) + " " +
str(self.atoms.lattice_mat[1][2]) + "\n" +
str(self.atoms.lattice_mat[2][0]) + " " +
str(self.atoms.lattice_mat[2][1]) + " " +
str(self.atoms.lattice_mat[2][2]) + "\n")
# order = np.argsort(self.atoms.elements)
coords = self.atoms.frac_coords
# DO NOT USE ORDER
coords_ordered = np.array(coords) # [order]
elements_ordered = np.array(self.atoms.elements) # [order]
props_ordered = np.array(self.atoms.props) # [order]
# check_selective_dynamics = False
counts = get_counts(elements_ordered)
if "T" in "".join(map(str, self.atoms.props[0])):
middle = (" ".join(map(str, counts.keys())) + "\n" +
" ".join(map(str, counts.values())) +
"\nSelective dynamics\n" + "Direct\n")
else:
middle = (" ".join(map(str, counts.keys())) + "\n" +
" ".join(map(str, counts.values())) + "\ndirect\n")
rest = ""
# print ('repr',self.frac_coords, self.frac_coords.shape)
for ii, i in enumerate(coords_ordered):
p_ordered = str(props_ordered[ii])
rest = rest + " ".join(map(str, i)) + " " + str(p_ordered) + "\n"
result = header + middle + rest
f.write(result)
f.close()
def get_string(self, cart=True, sort_order="X"):
"""
Convert Atoms to string.
Optional arguments below.
Args:
cart:True/False for cartesian/fractional coords.
sort_order: sort by chemical properties of
elements. Default electronegativity.
"""
system = str(self.composition.formula)
header = (str(system) + str("\n1.0\n") + str(self.lattice_mat[0][0]) +
" " + str(self.lattice_mat[0][1]) + " " +
str(self.lattice_mat[0][2]) + "\n" +
str(self.lattice_mat[1][0]) + " " +
str(self.lattice_mat[1][1]) + " " +
str(self.lattice_mat[1][2]) + "\n" +
str(self.lattice_mat[2][0]) + " " +
str(self.lattice_mat[2][1]) + " " +
str(self.lattice_mat[2][2]) + "\n")
if sort_order is None:
order = np.argsort(self.elements)
else:
order = np.argsort([
Specie(i).element_property(sort_order) for i in self.elements
])
if cart:
coords = self.cart_coords
else:
coords = self.frac_coords
coords_ordered = np.array(coords)[order]
elements_ordered = np.array(self.elements)[order]
props_ordered = np.array(self.props)[order]
# check_selective_dynamics = False # TODO
counts = get_counts(elements_ordered)
cart_frac = ""
if cart:
cart_frac = "\nCartesian\n"
else:
cart_frac = "\nDirect\n"
if "T" in "".join(map(str, self.props[0])):
middle = (" ".join(map(str, counts.keys())) + "\n" +
" ".join(map(str, counts.values())) +
"\nSelective dynamics\n" + cart_frac)
else:
middle = (" ".join(map(str, counts.keys())) + "\n" +
" ".join(map(str, counts.values())) + cart_frac)
rest = ""
for ii, i in enumerate(coords_ordered):
if self.show_props:
rest = (rest + " ".join(map(str, i)) + " " +
str(props_ordered[ii]) + "\n")
else:
rest = rest + " ".join(map(str, i)) + "\n"
result = header + middle + rest
return result
