def add_the_unit_cell(material, buffer):
name = material.get_name()
cell = material.get_cell()
atoms = material.get_atom_list()
if cell: return material # Don't do anything for now
newname = "%s_cell" % name
newmaterial = Material(newname)
if not buffer: buffer = 2. # Can still set to a small value like 0.01
xmin, xmax, ymin, ymax, zmin, zmax = bbox_atoms(atoms, buffer)
for atom in atoms:
atno = atom.get_atno()
xyz = atom.get_position()
xyznew = array((xyz[0] - xmin, xyz[1] - ymin, xyz[2] - zmin))
newmaterial.add_atom(Atom(atno, xyznew))
newmaterial.set_cell(
Cell((xmax - xmin, 0, 0), (0, ymax - ymin, 0), (0, 0, zmax - zmin)))
opts = getattr(material, "seqquest_options", {})
if opts: newmaterial.seqquest_options = opts.copy()
opts = getattr(material, "socorro_options", {})
if opts: newmaterial.socorro_options = opts.copy()
newmaterial.bonds_from_distance()
return newmaterial
def build_the_supercell(material, ass, bss, css):
if ass == 1 and bss == 1 and css == 1:
return material
name = material.get_name()
cell = material.get_cell()
atomlist = material.get_atom_list()
axyz = cell.axyz
bxyz = cell.bxyz
cxyz = cell.cxyz
newname = "%s%d%d%d" % (name, ass, bss, css)
newmaterial = Material(newname)
naxyz = ass * axyz
nbxyz = bss * bxyz
ncxyz = css * cxyz
for atom in atomlist:
atno = atom.get_atno()
sym = atom.get_symbol()
xyz = atom.get_position()
for i in range(ass):
for j in range(bss):
for k in range(css):
xyznew = xyz + i * axyz + j * bxyz + k * cxyz
newmaterial.add_atom(Atom(atno, xyznew, sym))
newmaterial.set_cell(Cell(naxyz, nbxyz, ncxyz))
opts = getattr(material, "seqquest_options", {})
if opts: newmaterial.seqquest_options = opts.copy()
opts = getattr(material, "socorro_options", {})
if opts: newmaterial.socorro_options = opts.copy()
newmaterial.bonds_from_distance()
return newmaterial
def build_the_slab(material, cleave_dir, depth, vacuum):
name = material.get_name()
cell = material.get_cell()
atomlist = material.get_atom_list()
if not cleave_dir: cleave_dir = 'C'
axyz = cell.axyz
bxyz = cell.bxyz
cxyz = cell.cxyz
if depth == 1 and vacuum == 0:
return material # do nothing
newname = "%s_slab" % name
newmaterial = Material(newname)
#
# Replace abc -> uvw (w is the cleave direction) so we can
# cleave in more general ways:
#
if cleave_dir == "C":
uxyz = axyz
vxyz = bxyz
wxyz = cxyz
idir = 2
elif cleave_dir == "B":
uxyz = cxyz
vxyz = axyz
wxyz = bxyz
idir = 1
elif cleave_dir == "A":
uxyz = bxyz
vxyz = cxyz
wxyz = axyz
idir = 0
wlength = sqrt(dot(wxyz, wxyz))
wscale = (wlength * depth + vacuum) / wlength
nwxyz = wxyz * wscale
for atom in atomlist:
atno = atom.get_atno()
xyz = atom.get_position()
for k in range(depth):
xyznew = xyz + k * wxyz
xyznew[idir] += vacuum / 2.
newmaterial.add_atom(Atom(atno, xyznew))
if abs(xyz[idir]) < 1e-2: # Periodic image of bottom:
xyznew = xyz + depth * wxyz
xyznew[idir] += vacuum / 2.
newmaterial.add_atom(Atom(atno, xyznew))
# I can't tell whether I have to do the cyclic permutations here
# i.e. output w,u,v in some cases.
newmaterial.set_cell(Cell(uxyz, vxyz, nwxyz))
opts = getattr(material, "seqquest_options", {})
if opts: newmaterial.seqquest_options = opts.copy()
opts = getattr(material, "socorro_options", {})
if opts: newmaterial.socorro_options = opts.copy()
newmaterial.center()
newmaterial.bonds_from_distance()
return newmaterial
