def _unique_coords(self, coords_in, magmoms_in=None):
"""
Generate unique coordinates using coord and symmetry positions
and also their corresponding magnetic moments, if supplied.
"""
coords = []
if magmoms_in:
magmoms = []
magmoms_in = [Magmom(magmom) for magmom in magmoms_in]
if len(magmoms_in) != len(coords_in):
raise ValueError
for tmp_coord, tmp_magmom in zip(coords_in, magmoms_in):
for op in self.symmetry_operations:
coord = op.operate(tmp_coord)
coord = np.array([i - math.floor(i) for i in coord])
if isinstance(op, MagSymmOp):
magmom = Magmom(op.operate_magmom(tmp_magmom.moment))
else:
magmom = tmp_magmom
if not in_coord_list_pbc(
coords, coord, atol=self._site_tolerance):
coords.append(coord)
magmoms.append(magmom)
return coords, magmoms
else:
for tmp_coord in coords_in:
for op in self.symmetry_operations:
coord = op.operate(tmp_coord)
coord = np.array([i - math.floor(i) for i in coord])
if not in_coord_list_pbc(
coords, coord, atol=self._site_tolerance):
coords.append(coord)
return coords, [Magmom(0)] * len(coords) # return dummy magmoms
def test_in_coord_list_pbc(self):
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
test_coord = [0.1, 0.1, 0.1]
self.assertFalse(in_coord_list_pbc(coords, test_coord))
self.assertTrue(in_coord_list_pbc(coords, test_coord, atol=0.15))
test_coord = [0.99, 0.99, 0.99]
self.assertFalse(in_coord_list_pbc(coords, test_coord, atol=0.01))
def symm_reduce(self, coords_set, threshold=1e-6):
"""
Reduces the set of adsorbate sites by finding removing
symmetrically equivalent duplicates
Args:
coords_set: coordinate set in cartesian coordinates
threshold: tolerance for distance equivalence, used
as input to in_coord_list_pbc for dupl. checking
"""
surf_sg = SpacegroupAnalyzer(self.slab, 0.1)
symm_ops = surf_sg.get_symmetry_operations()
unique_coords = []
# Convert to fractional
coords_set = [
cart_to_frac(self.slab.lattice, coords) for coords in coords_set
]
for coords in coords_set:
incoord = False
for op in symm_ops:
if in_coord_list_pbc(unique_coords,
op.operate(coords),
atol=threshold):
incoord = True
break
if not incoord:
unique_coords += [coords]
# convert back to cartesian
return [
frac_to_cart(self.slab.lattice, coords) for coords in unique_coords
]
def symm_reduce(self, coords_set, threshold = 1e-6):
"""
Reduces the set of adsorbate sites by finding removing
symmetrically equivalent duplicates
Args:
coords_set: coordinate set in cartesian coordinates
threshold: tolerance for distance equivalence, used
as input to in_coord_list_pbc for dupl. checking
"""
surf_sg = SpacegroupAnalyzer(self.slab, 0.1)
symm_ops = surf_sg.get_symmetry_operations()
unique_coords = []
# Convert to fractional
coords_set = [cart_to_frac(self.slab.lattice, coords)
for coords in coords_set]
for coords in coords_set:
incoord = False
for op in symm_ops:
if in_coord_list_pbc(unique_coords, op.operate(coords),
atol = threshold):
incoord = True
break
if not incoord:
unique_coords += [coords]
# convert back to cartesian
return [frac_to_cart(self.slab.lattice, coords)
for coords in unique_coords]
def get_kpoint_weights(self, kpoints, atol=1e-8):
"""
Calculate the weights for a list of kpoints.
Args:
kpoints (Sequence): Sequence of kpoints. np.arrays is fine. Note
that the code does not check that the list of kpoints
provided does not contain duplicates.
atol (float): Tolerance for fractional coordinates comparisons.
Returns:
List of weights, in the SAME order as kpoints.
"""
latt = self._structure.lattice.reciprocal_lattice
grid = Structure(latt, ["H"], [[0, 0, 0]])
a = SpacegroupAnalyzer(grid)
recp_ops = a.get_symmetry_operations()
weights = []
for k in kpoints:
all_k = []
for o in recp_ops:
k2 = o.operate(k)
if not in_coord_list_pbc(all_k, k2, atol=atol):
all_k.append(k2)
weights.append(len(all_k))
return weights
def _unique_coords(self, coord_in):
"""
Generate unique coordinates using coord and symmetry positions.
"""
coords = []
for op in self.symmetry_operations:
coord = op.operate(coord_in)
coord = np.array([i - math.floor(i) for i in coord])
if not in_coord_list_pbc(coords, coord, atol=1e-3):
coords.append(coord)
return coords
def _unique_coords(self, coord_in):
"""
Generate unique coordinates using coord and symmetry positions.
"""
coords = []
for op in self.symmetry_operations:
coord = op.operate(coord_in)
coord = np.array([i - math.floor(i) for i in coord])
if not in_coord_list_pbc(coords, coord, atol=1e-3):
coords.append(coord)
return coords
def near_reduce(self, coords_set, threshold = 1e-4):
"""
Prunes coordinate set for coordinates that are within
threshold
Args:
coords_set (Nx3 array-like): list or array of coordinates
threshold (float): threshold value for distance
"""
unique_coords = []
coords_set = [cart_to_frac(self.slab.lattice, coords)
for coords in coords_set]
for coord in coords_set:
if not in_coord_list_pbc(unique_coords, coord, threshold):
unique_coords += [coord]
return [frac_to_cart(self.slab.lattice, coords)
for coords in unique_coords]
def near_reduce(self, coords_set, threshold = 1e-4):
"""
Prunes coordinate set for coordinates that are within
threshold
Args:
coords_set (Nx3 array-like): list or array of coordinates
threshold (float): threshold value for distance
"""
unique_coords = []
coords_set = [cart_to_frac(self.slab.lattice, coords)
for coords in coords_set]
for coord in coords_set:
if not in_coord_list_pbc(unique_coords, coord, threshold):
unique_coords += [coord]
return [frac_to_cart(self.slab.lattice, coords)
for coords in unique_coords]
def find_surface_sites_by_height(self, slab, height=0.9, xy_tol=0.05):
"""
This method finds surface sites by determining which sites are within
a threshold value in height from the topmost site in a list of sites
Args:
site_list (list): list of sites from which to select surface sites
height (float): threshold in angstroms of distance from topmost
site in slab along the slab c-vector to include in surface
site determination
xy_tol (float): if supplied, will remove any sites which are
within a certain distance in the miller plane.
Returns:
list of sites selected to be within a threshold of the highest
"""
# Get projection of coordinates along the miller index
m_projs = np.array(
[np.dot(site.coords, self.mvec) for site in slab.sites])
# Mask based on window threshold along the miller index.
topmask = (m_projs - np.amax(m_projs)) >= -height
bottommask = (np.min(m_projs) - m_projs) >= -height
mask = topmask if self.top_surface else bottommask
surf_sites = [slab.sites[n] for n in np.where(mask)[0]]
if xy_tol:
# sort surface sites by height
surf_sites = [s for (h, s) in zip(m_projs[mask], surf_sites)]
surf_sites.reverse()
unique_sites, unique_perp_fracs = [], []
for site in surf_sites:
this_perp = site.coords - np.dot(site.coords, self.mvec)
this_perp_frac = cart_to_frac(slab.lattice, this_perp)
if not in_coord_list_pbc(unique_perp_fracs, this_perp_frac):
unique_sites.append(site)
unique_perp_fracs.append(this_perp_frac)
surf_sites = unique_sites
return surf_sites
def find_surface_sites_by_height(self, slab, height=0.9, xy_tol=0.05):
"""
This method finds surface sites by determining which sites are within
a threshold value in height from the topmost site in a list of sites
Args:
site_list (list): list of sites from which to select surface sites
height (float): threshold in angstroms of distance from topmost
site in slab along the slab c-vector to include in surface
site determination
xy_tol (float): if supplied, will remove any sites which are
within a certain distance in the miller plane.
Returns:
list of sites selected to be within a threshold of the highest
"""
# Get projection of coordinates along the miller index
m_projs = np.array([np.dot(site.coords, self.mvec)
for site in slab.sites])
# Mask based on window threshold along the miller index
mask = (m_projs - np.amax(m_projs)) >= -height
surf_sites = [slab.sites[n] for n in np.where(mask)[0]]
if xy_tol:
# sort surface sites by height
surf_sites = [s for (h, s) in zip(m_projs[mask], surf_sites)]
surf_sites.reverse()
unique_sites, unique_perp_fracs = [], []
for site in surf_sites:
this_perp = site.coords - np.dot(site.coords, self.mvec)
this_perp_frac = cart_to_frac(slab.lattice, this_perp)
if not in_coord_list_pbc(unique_perp_fracs, this_perp_frac):
unique_sites.append(site)
unique_perp_fracs.append(this_perp_frac)
surf_sites = unique_sites
return surf_sites
