def test_wf_functions(self):
# Test slab trans params generator
for slab in self.slabs:
trans_params = get_slab_trans_params(slab)
trans = SlabTransformation(**trans_params)
new_slab = trans.apply_transformation(slab.oriented_unit_cell)
self.assertTrue(np.allclose(new_slab.cart_coords, slab.cart_coords))
self.assertTrue(np.allclose(new_slab.lattice.matrix,
slab.lattice.matrix))
# Try something a bit more complicated
formulas = ['Si', 'Sn', 'SrTiO3', 'Li2O']
structs = [PymatgenTest.get_structure(s) for s in formulas]
for struct in structs:
slabs = generate_all_slabs(struct, max_index=2, min_slab_size=10,
min_vacuum_size=20)
for slab in slabs:
trans_params = get_slab_trans_params(slab)
trans = SlabTransformation(**trans_params)
new_slab = trans.apply_transformation(slab.oriented_unit_cell)
old_coords = np.around(slab.frac_coords, 10) % 1
new_coords = np.around(new_slab.frac_coords, 10) % 1
self.assertTrue(np.allclose(old_coords, new_coords))
self.assertTrue(np.allclose(new_slab.lattice.matrix,
slab.lattice.matrix))
def test_apply_transformation(self):
trans = SubstituteSurfaceSiteTransformation("Au")
pt = Structure(Lattice.cubic(5), ["Pt"], [[0, 0, 0]]) # fictitious
slab = SlabTransformation([0, 0, 1], 20, 10).apply_transformation(pt)
out = trans.apply_transformation(slab)
self.assertEqual(out.composition.reduced_formula, "Pt3Au")
def test_apply_transformation(self):
co = Molecule(["C", "O"], [[0, 0, 0], [0, 0, 1.23]])
trans = AddAdsorbateTransformation(co)
pt = Structure(Lattice.cubic(5), ["Pt"], [[0, 0, 0]]) # fictitious
slab = SlabTransformation([0, 0, 1], 20, 10).apply_transformation(pt)
out = trans.apply_transformation(slab)
self.assertEqual(out.composition.reduced_formula, "Pt4CO")
def test_apply_transformation(self):
s = self.get_structure("LiFePO4")
trans = SlabTransformation([0, 0, 1], 10, 10, shift = 0.25)
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
slab_from_gen = gen.get_slab(0.25)
slab_from_trans = trans.apply_transformation(s)
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix,
slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords,
slab_from_trans.cart_coords)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
[[0, 0, 0]])
trans = SlabTransformation([1, 1, 1], 10, 10)
slab_from_trans = trans.apply_transformation(fcc)
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab_from_gen = gen.get_slab()
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix,
slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords,
slab_from_trans.cart_coords)
def test_wf_functions(self):
# Test slab trans params generator
for slab in self.slabs:
trans_params = get_slab_trans_params(slab)
trans = SlabTransformation(**trans_params)
new_slab = trans.apply_transformation(slab.oriented_unit_cell)
self.assertTrue(np.allclose(new_slab.cart_coords,
slab.cart_coords))
self.assertTrue(
np.allclose(new_slab.lattice.matrix, slab.lattice.matrix))
# Try something a bit more complicated
formulas = ['Si', 'Sn', 'SrTiO3', 'Li2O']
structs = [PymatgenTest.get_structure(s) for s in formulas]
for struct in structs:
slabs = generate_all_slabs(struct,
max_index=2,
min_slab_size=10,
min_vacuum_size=20)
for slab in slabs:
trans_params = get_slab_trans_params(slab)
trans = SlabTransformation(**trans_params)
new_slab = trans.apply_transformation(slab.oriented_unit_cell)
old_coords = np.around(slab.frac_coords, 10) % 1
new_coords = np.around(new_slab.frac_coords, 10) % 1
self.assertTrue(np.allclose(old_coords, new_coords))
self.assertTrue(
np.allclose(new_slab.lattice.matrix, slab.lattice.matrix))
def test_apply_transformation(self):
s = self.get_structure("LiFePO4")
trans = SlabTransformation([0, 0, 1], 10, 10, shift=0.25)
gen = SlabGenerator(s, [0, 0, 1], 10, 10)
slab_from_gen = gen.get_slab(0.25)
slab_from_trans = trans.apply_transformation(s)
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix, slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords, slab_from_trans.cart_coords)
fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"], [[0, 0, 0]])
trans = SlabTransformation([1, 1, 1], 10, 10)
slab_from_trans = trans.apply_transformation(fcc)
gen = SlabGenerator(fcc, [1, 1, 1], 10, 10)
slab_from_gen = gen.get_slab()
self.assertArrayAlmostEqual(slab_from_gen.lattice.matrix, slab_from_trans.lattice.matrix)
self.assertArrayAlmostEqual(slab_from_gen.cart_coords, slab_from_trans.cart_coords)
def get_slab_fw(slab,
transmuter=False,
db_file=None,
vasp_input_set=None,
parents=None,
vasp_cmd="vasp",
name="",
add_slab_metadata=True,
user_incar_settings=None):
"""
Function to generate a a slab firework. Returns a TransmuterFW if
bulk_structure is specified, constructing the necessary transformations
from the slab and slab generator parameters, or an OptimizeFW if only a
slab is specified.
Args:
slab (Slab or Structure): structure or slab corresponding
to the slab to be calculated
transmuter (bool): whether or not to use a TransmuterFW based
on slab params, if this option is selected, input slab must
be a Slab object (as opposed to Structure)
vasp_input_set (VaspInputSet): vasp_input_set corresponding to
the slab calculation
parents (Fireworks or list of ints): parent FWs
db_file (string): path to database file
vasp_cmd (string): vasp command
name (string): name of firework
add_slab_metadata (bool): whether to add slab metadata to task doc
Returns:
Firework corresponding to slab calculation
"""
vasp_input_set = vasp_input_set or MPSurfaceSet(
slab, user_incar_settings=user_incar_settings)
# If a bulk_structure is specified, generate the set of transformations,
# else just create an optimize FW with the slab
if transmuter:
if not isinstance(slab, Slab):
raise ValueError(
"transmuter mode requires slab to be a Slab object")
# Get transformation from oriented bulk and slab
oriented_bulk = slab.oriented_unit_cell
slab_trans_params = get_slab_trans_params(slab)
trans_struct = SlabTransformation(**slab_trans_params)
slab_from_bulk = trans_struct.apply_transformation(oriented_bulk)
# Ensures supercell construction
supercell_trans = SupercellTransformation.from_scaling_factors(
round(slab.lattice.a / slab_from_bulk.lattice.a),
round(slab.lattice.b / slab_from_bulk.lattice.b))
# Get site properties, set velocities to zero if not set to avoid
# custodian issue
site_props = slab.site_properties
if 'velocities' not in site_props:
site_props['velocities'] = [0. for s in slab]
# Get adsorbates for InsertSitesTransformation
if "adsorbate" in slab.site_properties.get("surface_properties", ""):
ads_sites = [
site for site in slab
if site.properties["surface_properties"] == "adsorbate"
]
else:
ads_sites = []
transformations = [
"SlabTransformation", "SupercellTransformation",
"InsertSitesTransformation", "AddSitePropertyTransformation"
]
trans_params = [
slab_trans_params, {
"scaling_matrix": supercell_trans.scaling_matrix
}, {
"species": [site.species_string for site in ads_sites],
"coords": [site.frac_coords for site in ads_sites]
}, {
"site_properties": site_props
}
]
fw = TransmuterFW(name=name,
structure=oriented_bulk,
transformations=transformations,
transformation_params=trans_params,
copy_vasp_outputs=True,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
vasp_input_set=vasp_input_set)
else:
fw = OptimizeFW(name=name,
structure=slab,
vasp_input_set=vasp_input_set,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=parents,
job_type="normal")
# Add slab metadata
if add_slab_metadata:
parent_structure_metadata = get_meta_from_structure(
slab.oriented_unit_cell)
fw.tasks[-1]["additional_fields"].update({
"slab":
slab,
"parent_structure":
slab.oriented_unit_cell,
"parent_structure_metadata":
parent_structure_metadata
})
return fw
def get_slab_fw(slab,
bulk_structure=None,
slab_gen_params={},
db_file=None,
vasp_input_set=None,
parents=None,
vasp_cmd="vasp",
name=""):
"""
Function to generate a a slab firework. Returns a TransmuterFW if bulk_structure is specified,
constructing the necessary transformations from the slab and slab generator parameters,
or an OptimizeFW if only a slab is specified.
Args:
slab (Slab or Structure): structure or slab corresponding
to the slab to be calculated
bulk_structure (Structure): bulk structure corresponding to slab, if
provided, slab firework is constructed as a TransmuterFW using
the necessary transformations to get the slab from the bulk
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
vasp_input_set (VaspInputSet): vasp_input_set corresponding to
the slab calculation
parents (Fireworks or list of ints): parent FWs
db_file (string): path to database file
vasp_cmd (string): vasp command
Returns:
Firework
"""
vasp_input_set = vasp_input_set or MVLSlabSet(slab)
# If a bulk_structure is specified, generate the set of transformations, else
# just create an optimize FW with the slab
if bulk_structure:
if not isinstance(slab, Slab):
raise ValueError(
"structure input to get_slab_fw requires slab to be a slab object!"
)
slab_trans_params = {
"miller_index": slab.miller_index,
"shift": slab.shift
}
slab_trans_params.update(slab_gen_params)
# Get supercell parameters
trans_struct = SlabTransformation(**slab_trans_params)
slab_from_bulk = trans_struct.apply_transformation(bulk_structure)
supercell_trans = SupercellTransformation.from_scaling_factors(
round(slab.lattice.a / slab_from_bulk.lattice.a),
round(slab.lattice.b / slab_from_bulk.lattice.b))
# Get adsorbates for InsertSitesTransformation
if "adsorbate" in slab.site_properties.get("surface_properties",
[None]):
ads_sites = [
site for site in slab
if site.properties["surface_properties"] == "adsorbate"
]
else:
ads_sites = []
transformations = [
"SlabTransformation", "SupercellTransformation",
"InsertSitesTransformation", "AddSitePropertyTransformation"
]
trans_params = [
slab_trans_params, {
"scaling_matrix": supercell_trans.scaling_matrix
}, {
"species": [site.species_string for site in ads_sites],
"coords": [site.frac_coords for site in ads_sites]
}, {
"site_properties": slab.site_properties
}
]
return TransmuterFW(name=name,
structure=bulk_structure,
transformations=transformations,
transformation_params=trans_params,
copy_vasp_outputs=True,
db_file=db_file,
vasp_cmd=vasp_cmd,
parents=parents,
vasp_input_set=vasp_input_set)
else:
return OptimizeFW(name=name,
structure=slab,
vasp_input_set=vasp_input_set,
vasp_cmd=vasp_cmd,
db_file=db_file,
parents=parents,
job_type="normal")
def get_slab_fw(slab, transmuter=False, db_file=None, vasp_input_set=None,
parents=None, vasp_cmd="vasp", name="", add_slab_metadata=True):
"""
Function to generate a a slab firework. Returns a TransmuterFW if
bulk_structure is specified, constructing the necessary transformations
from the slab and slab generator parameters, or an OptimizeFW if only a
slab is specified.
Args:
slab (Slab or Structure): structure or slab corresponding
to the slab to be calculated
transmuter (bool): whether or not to use a TransmuterFW based
on slab params, if this option is selected, input slab must
be a Slab object (as opposed to Structure)
vasp_input_set (VaspInputSet): vasp_input_set corresponding to
the slab calculation
parents (Fireworks or list of ints): parent FWs
db_file (string): path to database file
vasp_cmd (string): vasp command
name (string): name of firework
add_slab_metadata (bool): whether to add slab metadata to task doc
Returns:
Firework corresponding to slab calculation
"""
vasp_input_set = vasp_input_set or MPSurfaceSet(slab)
# If a bulk_structure is specified, generate the set of transformations,
# else just create an optimize FW with the slab
if transmuter:
if not isinstance(slab, Slab):
raise ValueError("transmuter mode requires slab to be a Slab object")
# Get transformation from oriented bulk and slab
oriented_bulk = slab.oriented_unit_cell
slab_trans_params = get_slab_trans_params(slab)
trans_struct = SlabTransformation(**slab_trans_params)
slab_from_bulk = trans_struct.apply_transformation(oriented_bulk)
# Ensures supercell construction
supercell_trans = SupercellTransformation.from_scaling_factors(
round(slab.lattice.a / slab_from_bulk.lattice.a),
round(slab.lattice.b / slab_from_bulk.lattice.b))
# Get site properties, set velocities to zero if not set to avoid
# custodian issue
site_props = slab.site_properties
if 'velocities' not in site_props:
site_props['velocities'] = [0. for s in slab]
# Get adsorbates for InsertSitesTransformation
if "adsorbate" in slab.site_properties.get("surface_properties", ""):
ads_sites = [site for site in slab
if site.properties["surface_properties"] == "adsorbate"]
else:
ads_sites = []
transformations = [
"SlabTransformation", "SupercellTransformation",
"InsertSitesTransformation", "AddSitePropertyTransformation"]
trans_params = [slab_trans_params,
{"scaling_matrix": supercell_trans.scaling_matrix},
{"species": [site.species_string for site in ads_sites],
"coords": [site.frac_coords for site in ads_sites]},
{"site_properties": site_props}]
fw = TransmuterFW(name=name, structure=oriented_bulk,
transformations=transformations,
transformation_params=trans_params,
copy_vasp_outputs=True, db_file=db_file,
vasp_cmd=vasp_cmd, parents=parents,
vasp_input_set=vasp_input_set)
else:
fw = OptimizeFW(name=name, structure=slab,
vasp_input_set=vasp_input_set, vasp_cmd=vasp_cmd,
db_file=db_file, parents=parents, job_type="normal")
# Add slab metadata
if add_slab_metadata:
parent_structure_metadata = get_meta_from_structure(
slab.oriented_unit_cell)
fw.tasks[-1]["additional_fields"].update(
{"slab": slab, "parent_structure": slab.oriented_unit_cell,
"parent_structure_metadata": parent_structure_metadata})
return fw