def export_for_atomeye(configuration, f):
"AtomEye Extended CFG format"
pbc = configuration.pbc
atoms = configuration.atoms
aux = [
# uncomment to add temperature (works if there are atom velocities
# in the input file)
#("temperature [K]", lambda a: a.get_temperature()),
# add aux value that can be used to color code atomic positions
# in unit cell, in selected direction. The coloring works with hsv
# color scale in AtomEye, or any other scale that is cyclic, i.e.
# the same color corresponds to values 0 and 1.
#("xcolor [0-1]", in_cell_pos_fun(0, pbc[0][0]/2,
# pos0=_find_pos0(atoms))),
]
# atoms from VASP POSCAR with Selective dynamics have allow_change attr
if hasattr(atoms[0], "allow_change"):
aux += [("change x", lambda a: float(a.allow_change[0])),
("change y", lambda a: float(a.allow_change[1])),
("change z", lambda a: float(a.allow_change[2]))]
if pbc is None or len(pbc) == 0:
raise ValueError("no PBC")
if not isinstance(pbc, numpy.ndarray):
pbc = numpy.array(pbc)
print >> f, "Number of particles = %i" % len(atoms)
for i in get_comment_list(configuration):
print >> f, "# " + i
print >> f, "A = 1.0 Angstrom (basic length-scale)"
for i in range(3):
for j in range(3):
print >> f, "H0(%i,%i) = %f A" % (i + 1, j + 1,
configuration.pbc[i][j])
print >> f, ".NO_VELOCITY."
print >> f, "entry_count = %i" % (3 + len(aux))
for n, a in enumerate(aux):
print >> f, "auxiliary[%i] = %s" % (n, a[0])
H_1 = linalg.inv(pbc)
previous_name = None
for i in atoms:
if previous_name != i.name:
print >> f, pse.get_atom_mass(i.name)
print >> f, i.name
previous_name = i.name
s = numpy.dot(i.pos, H_1) % 1.0
entries = [s[0], s[1], s[2]]
for aname, afunc in aux:
entries.append(afunc(i))
print >> f, " ".join("%f" % i for i in entries)
def export_for_atomeye(configuration, f):
"AtomEye Extended CFG format"
pbc = configuration.pbc
atoms = configuration.atoms
aux = [
# uncomment to add temperature (works if there are atom velocities
# in the input file)
#("temperature [K]", lambda a: a.get_temperature()),
# add aux value that can be used to color code atomic positions
# in unit cell, in selected direction. The coloring works with hsv
# color scale in AtomEye, or any other scale that is cyclic, i.e.
# the same color corresponds to values 0 and 1.
#("xcolor [0-1]", in_cell_pos_fun(0, pbc[0][0]/2,
# pos0=_find_pos0(atoms))),
]
# atoms from VASP POSCAR with Selective dynamics have allow_change attr
if hasattr(atoms[0], "allow_change"):
aux += [ ("change x", lambda a: float(a.allow_change[0])),
("change y", lambda a: float(a.allow_change[1])),
("change z", lambda a: float(a.allow_change[2])) ]
if pbc is None or len(pbc) == 0:
raise ValueError("no PBC")
if not isinstance(pbc, numpy.ndarray):
pbc = numpy.array(pbc)
print >>f, "Number of particles = %i" % len(atoms)
for i in get_comment_list(configuration):
print >>f, "# " + i
print >>f, "A = 1.0 Angstrom (basic length-scale)"
for i in range(3):
for j in range(3):
print >>f, "H0(%i,%i) = %f A" % (i+1, j+1, configuration.pbc[i][j])
print >>f, ".NO_VELOCITY."
print >>f, "entry_count = %i" % (3 + len(aux))
for n, a in enumerate(aux):
print >>f, "auxiliary[%i] = %s" % (n, a[0])
H_1 = linalg.inv(pbc)
previous_name = None
for i in atoms:
if previous_name != i.name:
print >>f, pse.get_atom_mass(i.name)
print >>f, i.name
previous_name = i.name
s = numpy.dot(i.pos, H_1) % 1.0
entries = [s[0], s[1], s[2]]
for aname, afunc in aux:
entries.append(afunc(i))
print >>f, " ".join("%f" % i for i in entries)
def get_mass(self):
return pse.get_atom_mass(self.name)
