Generates mono-element slabs and writes them to separate directories,
if specified.
Parameters:
| Name |
Type |
Description |
Default |
species_list |
List[str]
|
List of chemical symbols of the slabs to be built. |
required
|
crystal_structures:
Dictionary with crystal structure to be used for each species.
These will be passed on as input to ase.build.bulk. So, must be one
of sc, fcc, bcc, tetragonal, bct, hcp, rhombohedral, orthorhombic,
diamond, zincblende, rocksalt, cesiumchloride, fluorite or wurtzite.
If not specified, the default reference crystal structure for each
species from ase.data will be used.
facets:
Dictionary with the surface facets to be considered for each
species.
If not specified for a given species, the following
defaults will be used based on the crystal structure:
fcc/bcc: 100, 111, 110
hcp: 0001
supercell_dim:
List specifying the size of the supercell to be generated in the
format (nx, ny, nz).
default_lat_param_lib:
String indicating which library the lattice constants should be pulled
from if not specified in either a_dict or c_dict.
Defaults to lattice constants defined in ase.data.
Options:
pbe_fd: parameters calculated using xc=PBE and finite-difference
beefvdw_fd: parameters calculated using xc=BEEF-vdW and finite-difference
pbe_pw: parameters calculated using xc=PBE and a plane-wave basis set
beefvdw_fd: parameters calculated using xc=BEEF-vdW and a plane-wave basis set
N.B. if there is a species present in species_list that is NOT in the
reference library specified, it will be pulled from `ase.data`
a_dict:
Dictionary with lattice parameters to be used for each species.
If not specified, defaults from default_lat_param_lib are used.
c_dict:
Dictionary with lattice parameters to be used for each species.
If not specified, defaults from default_lat_param_lib are used.
set_magnetic_moments:
List of species for which magnetic moments need to be set.
If not specified, magnetic moments will be set only for Fe, Co, Ni
(the ferromagnetic elements).
magnetic_moments:
Dictionary with the magnetic moments to be set for the chemical
species listed previously.
If not specified, default ground state magnetic moments from
ase.data are used.
vacuum:
Float specifying the amount of vacuum (in Angstrom) to be added to
the slab (the slab is placed at the center of the supercell).
n_fixed_layers:
Integer giving the number of layers of the slab to be fixed
starting from the bottom up (e.g. a value of 2 will fix the
bottom 2 layers).
write_to_disk:
Boolean specifying whether the surface structures generated should be
written to disk.
Defaults to False.
write_location:
String with the location where the per-species/per-crystal structure
directories must be constructed and structure files written to disk.
In the specified write_location, the following directory structure
will be created:
[species]/[crystal_structure + facet]/substrate/input.traj
Defaults to the current working directory.
dirs_exist_ok:
Boolean specifying whether existing directories/files should be
overwritten or not. This is passed on to the os.makedirs builtin.
Defaults to False (raises an error if directories corresponding the
species and crystal structure already exist).
Returns:
| Type |
Description |
Dictionary with surface structures (as
|
|
write-location (if any) for each
|
|
each input species.
|
|
Example:
{
"Pt": {
"fcc111": {
"structure": Pt_surface_obj,
"traj_file_path": "/path/to/Pt/fcc111/surface/traj/file"
},
"fcc100": ...
,
"Cu": ...
}
}
Source code in autocat/surface.py
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268 | def generate_surface_structures(
species_list: List[str],
crystal_structures: Dict[str, str] = None,
facets: Dict[str, str] = None,
supercell_dim: List[int] = None,
default_lat_param_lib: str = None,
a_dict: Dict[str, float] = None,
c_dict: Dict[str, float] = None,
set_magnetic_moments: List[str] = None,
magnetic_moments: Dict[str, float] = None,
vacuum: float = 10.0,
n_fixed_layers: int = 0,
write_to_disk: bool = False,
write_location: str = ".",
dirs_exist_ok: bool = False,
) -> Dict[str, Dict[str, Dict[str, Any]]]:
"""
Generates mono-element slabs and writes them to separate directories,
if specified.
Parameters
----------
species_list (REQUIRED):
List of chemical symbols of the slabs to be built.
crystal_structures:
Dictionary with crystal structure to be used for each species.
These will be passed on as input to `ase.build.bulk`. So, must be one
of sc, fcc, bcc, tetragonal, bct, hcp, rhombohedral, orthorhombic,
diamond, zincblende, rocksalt, cesiumchloride, fluorite or wurtzite.
If not specified, the default reference crystal structure for each
species from `ase.data` will be used.
facets:
Dictionary with the surface facets to be considered for each
species.
If not specified for a given species, the following
defaults will be used based on the crystal structure:
fcc/bcc: 100, 111, 110
hcp: 0001
supercell_dim:
List specifying the size of the supercell to be generated in the
format (nx, ny, nz).
default_lat_param_lib:
String indicating which library the lattice constants should be pulled
from if not specified in either a_dict or c_dict.
Defaults to lattice constants defined in `ase.data`.
Options:
pbe_fd: parameters calculated using xc=PBE and finite-difference
beefvdw_fd: parameters calculated using xc=BEEF-vdW and finite-difference
pbe_pw: parameters calculated using xc=PBE and a plane-wave basis set
beefvdw_fd: parameters calculated using xc=BEEF-vdW and a plane-wave basis set
N.B. if there is a species present in species_list that is NOT in the
reference library specified, it will be pulled from `ase.data`
a_dict:
Dictionary with lattice parameters <a> to be used for each species.
If not specified, defaults from `default_lat_param_lib` are used.
c_dict:
Dictionary with lattice parameters <c> to be used for each species.
If not specified, defaults from `default_lat_param_lib` are used.
set_magnetic_moments:
List of species for which magnetic moments need to be set.
If not specified, magnetic moments will be set only for Fe, Co, Ni
(the ferromagnetic elements).
magnetic_moments:
Dictionary with the magnetic moments to be set for the chemical
species listed previously.
If not specified, default ground state magnetic moments from
`ase.data` are used.
vacuum:
Float specifying the amount of vacuum (in Angstrom) to be added to
the slab (the slab is placed at the center of the supercell).
n_fixed_layers:
Integer giving the number of layers of the slab to be fixed
starting from the bottom up (e.g. a value of 2 will fix the
bottom 2 layers).
write_to_disk:
Boolean specifying whether the surface structures generated should be
written to disk.
Defaults to False.
write_location:
String with the location where the per-species/per-crystal structure
directories must be constructed and structure files written to disk.
In the specified write_location, the following directory structure
will be created:
[species]/[crystal_structure + facet]/substrate/input.traj
Defaults to the current working directory.
dirs_exist_ok:
Boolean specifying whether existing directories/files should be
overwritten or not. This is passed on to the `os.makedirs` builtin.
Defaults to False (raises an error if directories corresponding the
species and crystal structure already exist).
Returns
-------
Dictionary with surface structures (as `ase.Atoms` objects) and
write-location (if any) for each {crystal structure and facet} specified for
each input species.
Example:
{
"Pt": {
"fcc111": {
"structure": Pt_surface_obj,
"traj_file_path": "/path/to/Pt/fcc111/surface/traj/file"
},
"fcc100": ...
,
"Cu": ...
}
}
"""
lpl = {
"pbe_fd": BULK_PBE_FD,
"beefvdw_fd": BULK_BEEFVDW_FD,
"pbe_pw": BULK_PBE_PW,
"beefvdw_pw": BULK_BEEFVDW_PW,
}
ase_build_funcs = {
"fcc100": ase.build.fcc100,
"fcc110": ase.build.fcc110,
"fcc111": ase.build.fcc111,
"bcc100": ase.build.bcc100,
"bcc110": ase.build.bcc110,
"bcc111": ase.build.bcc111,
"hcp0001": ase.build.hcp0001,
}
if crystal_structures is None:
crystal_structures = {}
if facets is None:
facets = {}
if supercell_dim is None:
supercell_dim = [3, 3, 4]
if a_dict is None:
a_dict = {}
if c_dict is None:
c_dict = {}
if set_magnetic_moments is None:
set_magnetic_moments = ["Fe", "Co", "Ni"]
if magnetic_moments is None:
magnetic_moments = {}
# load crystal structure defaults from `ase.data`, override with user input
cs_library = {
species: reference_states[atomic_numbers[species]].get("symmetry")
for species in species_list
}
cs_library.update(crystal_structures)
# load lattice params <a>, <c> from reference library, override with user input
a_library = {}
c_library = {}
if default_lat_param_lib is not None:
a_library.update(
{
species: lpl[default_lat_param_lib].get(species, {}).get("a")
for species in species_list
}
)
c_library.update(
{
species: lpl[default_lat_param_lib].get(species, {}).get("c")
for species in species_list
}
)
a_library.update(a_dict)
c_library.update(c_dict)
# load magnetic moment defaults from `ase.data`, override with user input
mm_library = {
species: ground_state_magnetic_moments[atomic_numbers[species]]
for species in species_list
}
mm_library.update(magnetic_moments)
# set default facets for each crystal structure, override with user input
ft_defaults = {
"fcc": ["100", "111", "110"],
"bcc": ["100", "111", "110"],
"hcp": ["0001"],
}
ft_library = {species: ft_defaults[cs_library[species]] for species in species_list}
ft_library.update(facets)
surface_structures = {}
for species in species_list:
cs = cs_library.get(species)
a = a_library.get(species)
c = c_library.get(species)
surf = {}
for facet in ft_library[species]:
if c is not None:
struct = ase_build_funcs[f"{cs}{facet}"](
species, size=supercell_dim, vacuum=vacuum, a=a, c=c
)
else:
struct = ase_build_funcs[f"{cs}{facet}"](
species, size=supercell_dim, vacuum=vacuum, a=a
)
if n_fixed_layers > 0:
f = FixAtoms(
mask=[
atom.tag > (supercell_dim[-1] - n_fixed_layers)
for atom in struct
]
)
struct.set_constraint([f])
if species in set_magnetic_moments:
struct.set_initial_magnetic_moments([mm_library[species]] * len(struct))
traj_file_path = None
if write_to_disk:
dir_path = os.path.join(
write_location, f"{species}", f"{cs}{facet}", "substrate"
)
os.makedirs(dir_path, exist_ok=dirs_exist_ok)
traj_file_path = os.path.join(dir_path, "input.traj")
struct.write(traj_file_path)
print(f"{species}_{cs}{facet} structure written to {traj_file_path}")
surf[f"{cs}{facet}"] = {
"structure": struct,
"traj_file_path": traj_file_path,
}
surface_structures[species] = surf
return surface_structures
|