def test_find_match2(self):
sm = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=True,
scale=True,
attempt_supercell=False)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Si', 'Si'], [[0, 0, 0.1], [0, 0, 0.2]])
s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [0, 0.1, -0.95]])
s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False)
match = sm._strict_match(s1,
s2,
fu,
s1_supercell=False,
use_rms=True,
break_on_match=False)
scale_matrix = match[2]
s2.make_supercell(scale_matrix)
s2.translate_sites(range(len(s2)), match[3])
self.assertAlmostEqual(np.sum(s2.frac_coords), 0.3)
self.assertAlmostEqual(np.sum(s2.frac_coords[:, :2]), 0)
def center_structure(structure: Structure) -> Structure:
structure = structure.copy()
avg_pos = np.average(structure.frac_coords, axis=0)
structure.translate_sites(
np.arange(0, structure.num_sites),
np.array([0.5, 0.5, 0.5]) - avg_pos,
frac_coords=True,
to_unit_cell=True,
)
return structure
def test_find_match2(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=True, scale=True,
attempt_supercell=False)
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Si', 'Si'], [[0, 0, 0.1], [0, 0, 0.2]])
s2 = Structure(l, ['Si', 'Si'], [[0, 0.1, 0], [0, 0.1, -0.95]])
s1, s2, fu, s1_supercell = sm._preprocess(s1, s2, False)
match = sm._strict_match(s1, s2, fu, s1_supercell=False,
use_rms=True, break_on_match=False)
scale_matrix = match[2]
s2.make_supercell(scale_matrix)
s2.translate_sites(range(len(s2)), match[3])
self.assertAlmostEqual(np.sum(s2.frac_coords) % 1, 0.3)
self.assertAlmostEqual(np.sum(s2.frac_coords[:, :2]) % 1, 0)
def get_wf_surface(slabs,
molecules=[],
bulk_structure=None,
slab_gen_params=None,
vasp_cmd="vasp",
db_file=None,
ads_structures_params={},
add_molecules_in_box=False):
"""
Args:
slabs (list of Slabs or Structures): slabs to calculate
molecules (list of Molecules): molecules to place as adsorbates
bulk_structure (Structure): bulk structure from which generate slabs
after reoptimization. If supplied, workflow will begin with
bulk structure optimization.
slab_gen_params (dict): dictionary of slab generation parameters
used to generate the slab, necessary to get the slab
that corresponds to the bulk structure if in that mode
ads_structures_params (dict): parameters to be supplied as
kwargs to AdsorbateSiteFinder.generate_adsorption_structures
add_molecules_in_box (boolean): flag to add calculation of molecule
energies to the workflow
db_file (string): path to database file
vasp_cmd (string): vasp command
Returns:
Workflow
"""
fws, parents = [], []
if bulk_structure:
vis = MVLSlabSet(bulk_structure, bulk=True)
fws.append(
OptimizeFW(bulk_structure,
vasp_input_set=vis,
vasp_cmd="vasp",
db_file=db_file))
parents = fws[0]
for slab in slabs:
name = slab.composition.reduced_formula
if getattr(slab, "miller_index", None):
name += "_{}".format(slab.miller_index)
fws.append(
get_slab_fw(slab,
bulk_structure,
slab_gen_params,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
name=name + " slab optimization"))
for molecule in molecules:
ads_slabs = AdsorbateSiteFinder(
slab).generate_adsorption_structures(molecule,
**ads_structures_params)
for n, ads_slab in enumerate(ads_slabs):
ads_name = "{}-{} adsorbate optimization {}".format(
molecule.composition.formula, name, n)
fws.append(
get_slab_fw(ads_slab,
bulk_structure,
slab_gen_params,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
name=ads_name))
if add_molecules_in_box:
for molecule in molecules:
# molecule in box
m_struct = Structure(Lattice.cubic(10),
molecule.species_and_occu,
molecule.cart_coords,
coords_are_cartesian=True)
m_struct.translate_sites(
list(range(len(m_struct))),
np.array([0.5] * 3) - np.average(m_struct.frac_coords, axis=0))
vis = MVLSlabSet(m_struct)
fws.append(
OptimizeFW(molecule,
job_type="normal",
vasp_input_set=vis,
db_file=db_file,
vasp_cmd=vasp_cmd))
# TODO: add analysis framework
return Workflow(fws, name="")
