def create_hkl_surface(lattice,
hkl,
layers,
vacuum=1.0,
center=False,
pbc=True):
"""
Use ase.build.surface to build a surface with surface normal (hkl).
Args:
lattice (pyiron.atomistics.structure.atoms.Atoms/str): bulk Atoms
instance or str, e.g. "Fe", from which to build the surface
hkl (list): miller indices of surface to be created
layers (int): # of atomic layers in the surface
vacuum (float): vacuum spacing
center (bool): shift all positions to center the surface
in the cell
Returns:
pyiron.atomistics.structure.atoms.Atoms instance: Required surface
"""
# https://gitlab.com/ase/ase/blob/master/ase/lattice/surface.py
s.publication_add(publication_ase())
surface = ase_surf(lattice, hkl, layers)
z_max = np.max(surface.positions[:, 2])
surface.cell[2, 2] = z_max + vacuum
if center:
surface.positions += 0.5 * surface.cell[2] - [0, 0, z_max / 2]
surface.pbc = pbc
return ase_to_pyiron(surface)
def db_entry(self):
"""
Generate the initial database entry
Returns:
(dict): db_dict
"""
db_dict = super(InteractiveWrapper, self).db_entry()
if self.structure:
if isinstance(self.structure, PAtoms):
parent_structure = self.structure.get_parent_basis()
else:
parent_structure = ase_to_pyiron(
self.structure).get_parent_basis()
db_dict["ChemicalFormula"] = parent_structure.get_chemical_formula(
)
return db_dict
def create_ase_bulk(
name,
crystalstructure=None,
a=None,
c=None,
covera=None,
u=None,
orthorhombic=False,
cubic=False,
):
"""
Creating bulk systems using ASE bulk module. Crystal structure and lattice constant(s) will be guessed if not
provided.
name (str): Chemical symbol or symbols as in 'MgO' or 'NaCl'.
crystalstructure (str): Must be one of sc, fcc, bcc, hcp, diamond, zincblende,
rocksalt, cesiumchloride, fluorite or wurtzite.
a (float): Lattice constant.
c (float): Lattice constant.
c_over_a (float): c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3).
u (float): Internal coordinate for Wurtzite structure.
orthorhombic (bool): Construct orthorhombic unit cell instead of primitive cell which is the default.
cubic (bool): Construct cubic unit cell if possible.
Returns:
pyiron.atomistics.structure.atoms.Atoms: Required bulk structure
"""
s.publication_add(publication_ase())
return ase_to_pyiron(
bulk(
name=name,
crystalstructure=crystalstructure,
a=a,
c=c,
covera=covera,
u=u,
orthorhombic=orthorhombic,
cubic=cubic,
))
def poly_fit(self, fit_order=3, vol_erg_dic=None):
self._set_fit_module(vol_erg_dic=vol_erg_dic)
fit_dict = self.fit_module.fit_polynomial(fit_order=fit_order)
if fit_dict is None:
self._logger.warning("Minimum could not be found!")
else:
self.input["fit_type"] = fit_dict["fit_type"]
self.input["fit_order"] = fit_dict["fit_order"]
with self.project_hdf5.open("input") as hdf5_input:
self.input.to_hdf(hdf5_input)
with self.project_hdf5.open("output") as hdf5:
hdf5["equilibrium_energy"] = fit_dict["energy_eq"]
hdf5["equilibrium_volume"] = fit_dict["volume_eq"]
hdf5["equilibrium_bulk_modulus"] = fit_dict["bulkmodul_eq"]
hdf5["equilibrium_b_prime"] = fit_dict["b_prime_eq"]
with self._hdf5.open("output") as hdf5:
structure = self.get_structure(iteration_step=-1)
if not isinstance(structure, Atoms):
structure = ase_to_pyiron(structure)
structure.to_hdf(hdf5)
self.fit_dict = fit_dict
return fit_dict
def pymatgen_to_pyiron(structure):
return ase_to_pyiron(AseAtomsAdaptor.get_atoms(structure))
def _final_struct_to_hdf(self):
with self._hdf5.open("output") as hdf5:
structure = self.get_structure(iteration_step=-1)
if not isinstance(structure, Atoms):
structure = ase_to_pyiron(structure)
structure.to_hdf(hdf5)
def create_surface(element,
surface_type,
size=(1, 1, 1),
vacuum=1.0,
center=False,
pbc=True,
**kwargs):
"""
Generate a surface based on the ase.build.surface module.
Args:
element (str): Element name
surface_type (str): The string specifying the surface type generators available through ase (fcc111,
hcp0001 etc.)
size (tuple): Size of the surface
vacuum (float): Length of vacuum layer added to the surface along the z direction
center (bool): Tells if the surface layers have to be at the center or at one end along the z-direction
pbc (list/numpy.ndarray): List of booleans specifying the periodic boundary conditions along all three
directions.
**kwargs: Additional, arguments you would normally pass to the structure generator like 'a', 'b',
'orthogonal' etc.
Returns:
pyiron.atomistics.structure.atoms.Atoms instance: Required surface
"""
# https://gitlab.com/ase/ase/blob/master/ase/lattice/surface.py
if pbc is None:
pbc = True
s.publication_add(publication_ase())
for surface_class in [
add_adsorbate,
add_vacuum,
bcc100,
bcc110,
bcc111,
diamond100,
diamond111,
fcc100,
fcc110,
fcc111,
fcc211,
hcp0001,
hcp10m10,
mx2,
hcp0001_root,
fcc111_root,
bcc111_root,
root_surface,
root_surface_analysis,
ase_surf,
]:
if surface_type == surface_class.__name__:
surface_type = surface_class
break
if isinstance(surface_type, types.FunctionType):
if center:
surface = surface_type(symbol=element,
size=size,
vacuum=vacuum,
**kwargs)
else:
surface = surface_type(symbol=element, size=size, **kwargs)
z_max = np.max(surface.positions[:, 2])
surface.cell[2, 2] = z_max + vacuum
surface.pbc = pbc
return ase_to_pyiron(surface)
else:
return None