def write_xsf(file_name, atoms):
"""
For the given AtomsSystem instance, write an .xsf file.
Usage:
>>> write_xsf(file_name, atoms)
"""
xsf = open(file_name, 'w')
# Molecular structure...
if atoms.get_cell() is None:
xsf.write('ATOMS\n')
i = 0
for atom in atoms._atoms:
x,y,z = atom.get_position()
info = atomic_number(atom.get_symbol()), x, y, z
xsf.write('%2d %12.6f %12.6f %12.6f\n' % info)
i += 1
xsf.close()
else:
xsf.write('CRYSTAL\n')
# Primitive lattice vectors (in Angstroms)
xsf.write('PRIMVEC\n')
va,vb,vc = atoms.get_cell()[0],atoms.get_cell()[1],atoms.get_cell()[2]
#va, vb, vc = convert_abc2xyz(cell[0], cell[1], cell[2],
# cell[3], cell[4], cell[5])
xsf.write('%12.6f %12.6f %12.6f\n' % tuple(va))
xsf.write('%12.6f %12.6f %12.6f\n' % tuple(vb))
xsf.write('%12.6f %12.6f %12.6f\n' % tuple(vc))
# Conventional lattice vectors (in Angstroms)
xsf.write('CONVVEC\n')
xsf.write('%12.6f %12.6f %12.6f\n' % tuple(va))
xsf.write('%12.6f %12.6f %12.6f\n' % tuple(vb))
xsf.write('%12.6f %12.6f %12.6f\n' % tuple(vc))
# Atomic coord. in a primitive unit cell (in Angstroms)
xsf.write('PRIMCOORD\n')
xsf.write('%s 1\n' % str(len(atoms)))
i = 0
for atom in atoms._atoms:
x,y,z = atom.get_position()
info = atomic_number(atom.get_symbol()), x, y, z
xsf.write('%2d %12.6f %12.6f %12.6f\n' % info)
i += 1
xsf.close()
def set_mass(self, mass):
if mass == None:
self._mass = float(atomic_weight[atomic_number(self._symbol)])
elif mass < 0:
raise ValueError, "Negative mass is not allowed."
elif type(mass) != float and type(mass) != int:
raise ValueError, "Invaild mass value : %s" % str(mass)
else: self._mass = mass
def find_lattice_parameters(symb):
info = reference_states[atomic_number(symb)]
if info == None:
raise ValueError, 'Can`t guess lattice.'
lattice = info['symmetry']
# type, lattice constant
if lattice == 'fcc' or lattice =='BCC' or lattice == 'Diamond' or lattice == 'Cubic':
return lattice, info['a']
# type, length of a, c/a ratio
elif lattice == 'hcp' or lattice == 'Tetragonal':
return lattice, info['a'], info['c/a']
# type, c/a, length of a, b/a
elif lattice == 'Orthorhombic':
return lattice, info['c/a'], info['a'], info['b/a']
# type, length of a, alpha
elif lattice == 'Rhombohedral':
return lattice, info['a'], info['alpha']
# type, interatomic distance
elif lattice == 'diatom':
return lattice, info['d']