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Defect: Allow bulk SC calculation to be skipped. (materialsproject#742)
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---------

Co-authored-by: Alex Ganose <[email protected]>
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@jmmshn @utf @hrushikesh-s
2 people authored and hrushikesh-s committed Nov 16, 2024
1 parent b7f20e8 commit 48e61cb
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Showing 3 changed files with 226 additions and 41 deletions.
216 changes: 177 additions & 39 deletions src/atomate2/common/flows/defect.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,15 +106,116 @@ def make(
dir2 = relax2.output.dir_name
struct1 = relax1.output.structure
struct2 = relax2.output.structure
add_info1 = {"relaxed_uuid": relax1.uuid, "distorted_uuid": relax2.uuid}
add_info2 = {"relaxed_uuid": relax2.uuid, "distorted_uuid": relax1.uuid}

deformations1, deformations2, ccd_job = self.get_deformation_and_ccd_jobs(
struct1, struct2, dir1, dir2, add_info1, add_info2
)

return Flow(
jobs=[
charged_structures,
relax1,
relax2,
deformations1,
deformations2,
ccd_job,
],
output=ccd_job.output,
name=name,
)

def make_from_relaxed_structures(
self,
structure1: Structure,
structure2: Structure,
) -> Flow:
"""
Make a job for the calculation of the configuration coordinate diagram.
Parameters
----------
structure1
The relaxed structure for charge state 1.
structure2
The relaxed structure for charge state 2.
Returns
-------
Flow
The full workflow for the calculation of the configuration coordinate
diagram.
"""
# use a more descriptive name when possible
if not isinstance(structure1, OutputReference):
name = f"{self.name}: {structure1.formula}"
if not (
isinstance(structure1, OutputReference)
or isinstance(structure2, OutputReference)
):
name = (
f"{self.name}: {structure1.formula}"
"({structure1.charge}-{structure2.charge})"
)

deformations1, deformations2, ccd_job = self.get_deformation_and_ccd_jobs(
structure1, structure2
)

return Flow(
jobs=[
deformations1,
deformations2,
ccd_job,
],
output=ccd_job.output,
name=name,
)

def get_deformation_and_ccd_jobs(
self,
struct1: Structure,
struct2: Structure,
dir1: str | None = None,
dir2: str | None = None,
add_info1: dict | None = None,
add_info2: dict | None = None,
) -> tuple[Job, Job, Job]:
"""Get the deformation and CCD jobs for the given structures.
Parameters
----------
struct1: Structure
The first structure.
struct2: Structure
The second structure.
dir1: str
The directory of the first structure.
dir2: str
The directory of the second structure.
add_info1: dict
Additional information to write
add_info2: dict
Additional information to write
Returns
-------
deformations1: Job
The deformation job for the first structure.
deformations2: Job
The deformation job for the second structure.
ccd_job: Job
The Job to construct the CCD document.
"""
deformations1 = spawn_energy_curve_calcs(
struct1,
struct2,
distortions=self.distortions,
static_maker=self.static_maker,
prev_dir=dir1,
add_name="q1",
add_info={"relaxed_uuid": relax1.uuid, "distorted_uuid": relax2.uuid},
add_info=add_info1,
)

deformations2 = spawn_energy_curve_calcs(
Expand All @@ -124,7 +225,7 @@ def make(
static_maker=self.static_maker,
prev_dir=dir2,
add_name="q2",
add_info={"relaxed_uuid": relax2.uuid, "distorted_uuid": relax1.uuid},
add_info=add_info2,
)

deformations1.append_name(" q1")
Expand All @@ -139,18 +240,7 @@ def make(
deformations1.output, deformations2.output, undistorted_index=min_abs_index
)

return Flow(
jobs=[
charged_structures,
relax1,
relax2,
deformations1,
deformations2,
ccd_job,
],
output=ccd_job.output,
name=name,
)
return deformations1, deformations2, ccd_job


@dataclass
Expand All @@ -161,6 +251,15 @@ class FormationEnergyMaker(Maker, ABC):
this maker is the `defect_relax_maker` which contains the settings for the atomic
relaxations that each defect supercell will undergo.
This maker can be used as a stand-alone maker to calculate all of the data
needed to populate the `DefectEntry` object. However, for you can also use this
maker with `uc_bulk` set to True (also set `collect_defect_entry_data` to False
and `bulk_relax_maker` to None). This will skip the bulk supercell calculations
assuming that bulk unit cell calculations are of high enough quality to be used
directly. In these cases, the bulk SC electrostatic potentials need to be
constructed without running a separate bulk SC calculation. This is currently
implemented through the grid re-sampling tools in `mp-pyrho`.
Attributes
----------
defect_relax_maker: Maker
Expand Down Expand Up @@ -189,6 +288,10 @@ class FormationEnergyMaker(Maker, ABC):
ng_settings = dict(zip(params, ng + ngf))
relax_maker = update_user_incar_settings(relax_maker, ng_settings)
uc_bulk: bool
If True, skip the bulk supercell calculation and only perform the defect
supercell calculations. This is useful for large-scale defect databases.
name: str
The name of the flow created by this maker.
Expand Down Expand Up @@ -251,6 +354,7 @@ class FormationEnergyMaker(Maker, ABC):

defect_relax_maker: Maker
bulk_relax_maker: Maker | None = None
uc_bulk: bool = False
name: str = "formation energy"
relax_radius: float | str | None = None
perturb: float | None = None
Expand All @@ -260,8 +364,15 @@ class FormationEnergyMaker(Maker, ABC):
def __post_init__(self) -> None:
"""Apply post init updates."""
self.validate_maker()
if self.bulk_relax_maker is None:
self.bulk_relax_maker = self.defect_relax_maker
if self.uc_bulk:
if self.bulk_relax_maker is not None:
raise ValueError("bulk_relax_maker should be None when uc_bulk is True")
if self.collect_defect_entry_data:
raise ValueError(
"collect_defect_entry_data should be False when uc_bulk is True"
)
else:
self.bulk_relax_maker = self.bulk_relax_maker or self.defect_relax_maker

def make(
self,
Expand Down Expand Up @@ -296,27 +407,41 @@ def make(
The workflow to calculate the formation energy diagram.
"""
jobs = []
if bulk_supercell_dir is None:
get_sc_job = bulk_supercell_calculation(
uc_structure=defect.structure,
relax_maker=self.bulk_relax_maker,
sc_mat=supercell_matrix,
get_planar_locpot=self.get_planar_locpot,
)
sc_mat = get_sc_job.output["sc_mat"]
lattice = get_sc_job.output["sc_struct"].lattice
bulk_supercell_dir = get_sc_job.output["dir_name"]
if not self.uc_bulk:
if bulk_supercell_dir is None:
get_sc_job = bulk_supercell_calculation(
uc_structure=defect.structure,
relax_maker=self.bulk_relax_maker,
sc_mat=supercell_matrix,
get_planar_locpot=self.get_planar_locpot,
)
sc_mat = get_sc_job.output["sc_mat"]
lattice = get_sc_job.output["sc_struct"].lattice
bulk_supercell_dir = get_sc_job.output["dir_name"]
sc_uuid = get_sc_job.output["uuid"]
else:
# all additional reader functions need to be in this job
# b/c they might receive Response objects instead of data.
get_sc_job = get_supercell_from_prv_calc(
uc_structure=defect.structure,
prv_calc_dir=bulk_supercell_dir,
sc_entry_and_locpot_from_prv=self.sc_entry_and_locpot_from_prv,
sc_mat_ref=supercell_matrix,
)
sc_mat = get_sc_job.output["sc_mat"]
lattice = get_sc_job.output["lattice"]
sc_uuid = get_sc_job.output["uuid"]
jobs.append(get_sc_job)
else:
# all additional reader functions need to be in this job
# b/c they might receive Response objects instead of data.
get_sc_job = get_supercell_from_prv_calc(
uc_structure=defect.structure,
prv_calc_dir=bulk_supercell_dir,
sc_entry_and_locpot_from_prv=self.sc_entry_and_locpot_from_prv,
sc_mat_ref=supercell_matrix,
)
sc_mat = get_sc_job.output["sc_mat"]
lattice = get_sc_job.output["lattice"]
if bulk_supercell_dir is not None:
raise ValueError(
"bulk_supercell_dir should be None when uc_bulk is True."
"We will be using a uc bulk calculation, so no bulk supercell "
"is needed."
)
sc_mat = supercell_matrix
lattice = None
sc_uuid = None

spawn_output = spawn_defect_q_jobs(
defect=defect,
Expand All @@ -327,13 +452,26 @@ def make(
add_info={
"bulk_supercell_dir": bulk_supercell_dir,
"bulk_supercell_matrix": sc_mat,
"bulk_supercell_uuid": get_sc_job.uuid,
"bulk_supercell_uuid": sc_uuid,
},
relax_radius=self.relax_radius,
perturb=self.perturb,
validate_charge=self.validate_charge,
)
jobs.extend([get_sc_job, spawn_output])

if self.uc_bulk:
# run the function here so we can get the charge state
# calculations ASAP
response = spawn_output.function(
*spawn_output.function_args, **spawn_output.function_kwargs
)
jobs.append(response.replace)
output_ = response.output
else:
# execute this as job so you can string a single bulk sc with multiple
# defect scs
jobs.append(spawn_output)
output_ = spawn_output.output

if self.collect_defect_entry_data:
collection_job = get_defect_entry(
Expand All @@ -344,7 +482,7 @@ def make(

return Flow(
jobs=jobs,
output=spawn_output.output,
output=output_,
name=self.name,
)

Expand Down
5 changes: 3 additions & 2 deletions src/atomate2/common/jobs/defect.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -300,7 +300,7 @@ def get_planar_locpot(task_doc: TaskDoc) -> NDArray:
def spawn_defect_q_jobs(
defect: Defect,
relax_maker: RelaxMaker,
relaxed_sc_lattice: Lattice,
relaxed_sc_lattice: Lattice | None = None,
sc_mat: NDArray | None = None,
defect_index: int | str = "",
add_info: dict | None = None,
Expand Down Expand Up @@ -355,7 +355,8 @@ def spawn_defect_q_jobs(
sc_def_struct = defect.get_supercell_structure(
sc_mat=sc_mat, relax_radius=relax_radius, perturb=perturb
)
sc_def_struct.lattice = relaxed_sc_lattice
if relaxed_sc_lattice is not None:
sc_def_struct.lattice = relaxed_sc_lattice
if sc_mat is not None:
sc_mat = np.array(sc_mat).tolist()
for qq in defect.get_charge_states():
Expand Down
46 changes: 46 additions & 0 deletions tests/vasp/flows/test_defect.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -185,3 +185,49 @@ def _check_plnr_locpot(name):
prv_dir = test_dir / "vasp/GaN_Mg_defect/bulk_relax/outputs"
flow2 = maker.make(defects[0], bulk_supercell_dir=prv_dir, defect_index=0)
_ = run_locally(flow2, create_folders=True, ensure_success=True)


def test_formation_energy_maker_uc(mock_vasp, clean_dir, test_dir, monkeypatch):
from jobflow import run_locally

# mapping from job name to directory containing test files
ref_paths = {
"relax Mg_Ga-0 q=-2": "GaN_Mg_defect/relax_Mg_Ga-0_q=-2",
"relax Mg_Ga-0 q=-1": "GaN_Mg_defect/relax_Mg_Ga-0_q=-1",
"relax Mg_Ga-0 q=0": "GaN_Mg_defect/relax_Mg_Ga-0_q=0",
"relax Mg_Ga-0 q=1": "GaN_Mg_defect/relax_Mg_Ga-0_q=1",
}

fake_run_vasp_kwargs = {
k: {"incar_settings": ["ISIF"], "check_inputs": ["incar"]} for k in ref_paths
}

# automatically use fake VASP and write POTCAR.spec during the test
mock_vasp(ref_paths, fake_run_vasp_kwargs)

struct = Structure.from_file(test_dir / "structures" / "GaN.cif")
defects = list(
SubstitutionGenerator().get_defects(
structure=struct, substitution={"Ga": ["Mg"]}
)
)

maker = FormationEnergyMaker(
relax_radius="auto",
perturb=0.1,
collect_defect_entry_data=False,
validate_charge=False,
uc_bulk=True,
)
flow = maker.make(
defects[0],
supercell_matrix=[[2, 2, 0], [2, -2, 0], [0, 0, 1]],
defect_index=0,
)

# run the flow and ensure that it finished running successfully
_ = run_locally(
flow,
create_folders=True,
ensure_success=True,
)

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