Generates bulk crystal structures and writes them to separate
directories, if specified.
Parameters:
| Name |
Type |
Description |
Default |
species_list |
List[str]
|
List of chemical symbols of the bulk structures to be constructed. |
required
|
cystal_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.
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.
write_to_disk:
Boolean specifying whether the bulk 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_1]_bulk_[crystal_structure_1]/input.traj
[species_1]_bulk_[crystal_structure_2]/input.traj
...
[species_2]_bulk_[crystal_structure_2]/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 bulk structures (as
|
|
write-location (if any) for each input species.
|
|
Example:
{
"Pt": {"structure": Pt_ase_obj, "traj_file_path": "/path/to/Pt/traj/file"},
"Cr": ...
}
Source code in autocat/bulk.py
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193 | def generate_bulk_structures(
species_list: List[str],
crystal_structures: Dict[str, str] = 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,
write_to_disk: bool = False,
write_location: str = ".",
dirs_exist_ok: bool = False,
) -> Dict[str, Dict[str, Any]]:
"""
Generates bulk crystal structures and writes them to separate
directories, if specified.
Parameters
----------
species_list (REQUIRED):
List of chemical symbols of the bulk structures to be constructed.
cystal_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.
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.
write_to_disk:
Boolean specifying whether the bulk 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_1]_bulk_[crystal_structure_1]/input.traj
[species_1]_bulk_[crystal_structure_2]/input.traj
...
[species_2]_bulk_[crystal_structure_2]/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 bulk structures (as `ase.Atoms` objects) and
write-location (if any) for each input species.
Example:
{
"Pt": {"structure": Pt_ase_obj, "traj_file_path": "/path/to/Pt/traj/file"},
"Cr": ...
}
"""
lpl = {
"pbe_fd": BULK_PBE_FD,
"beefvdw_fd": BULK_BEEFVDW_FD,
"pbe_pw": BULK_PBE_PW,
"beefvdw_pw": BULK_BEEFVDW_PW,
}
if crystal_structures is None:
crystal_structures = {}
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)
bulk_structures = {}
for species in species_list:
cs = cs_library.get(species)
a = a_library.get(species)
c = c_library.get(species)
bs = bulk(species, crystalstructure=cs, a=a, c=c)
if species in set_magnetic_moments:
bs.set_initial_magnetic_moments([mm_library[species]] * len(bs))
traj_file_path = None
if write_to_disk:
dir_path = os.path.join(write_location, f"{species}_bulk_{cs}")
os.makedirs(dir_path, exist_ok=dirs_exist_ok)
traj_file_path = os.path.join(dir_path, "input.traj")
bs.write(traj_file_path)
print(f"{species}_bulk_{cs} structure written to {traj_file_path}")
bulk_structures[species] = {
"structure": bs,
"traj_file_path": traj_file_path,
}
return bulk_structures
|