Electrode Workflow

pyproject.toml

@@ -43,7 +43,7 @@ cclib = ["cclib"]
 mp = ["mp-api>=0.37.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
 lobster = ["ijson>=3.2.2", "lobsterpy>=0.3.7"]
-defects = ["dscribe>=1.2.0", "pymatgen-analysis-defects>=2022.11.30"]
+defects = ["dscribe>=1.2.0", "pymatgen-analysis-defects>=2022.11.30", "python-ulid"]
 forcefields = [
  "ase>=3.22.1",
  "chgnet>=0.2.2",
@@ -92,6 +92,7 @@ strict = [
  "quippy-ase==0.9.14",
  "seekpath==2.1.0",
  "typing-extensions==4.10.0",
+ "python-ulid==2.2.0"
 ]
 
 [project.scripts]

src/atomate2/cli/dev.py

@@ -17,13 +17,31 @@
 
 
 @dev.command(context_settings={"help_option_names": ["-h", "--help"]})
-@click.argument("test_dir")
-def vasp_test_data(test_dir: Path) -> None:
+@click.argument(
+ "test_dir",
+)
+@click.option(
+ "--additional_file",
+ "-a",
+ multiple=True,
+ help="list of additional files to copy from each completed VASP directory. "
+ "Example: `--additional_file CHGCAR --additional_file LOCPOT`",
+)
+def vasp_test_data(test_dir: str | Path, additional_file: list[str]) -> None:
  """Generate test data for VASP unit tests.
 
  This script expects there is an outputs.json file and job folders in the current
  directory. Please refer to the atomate2 documentation on writing unit tests for more
  information.
+
+ Parameters
+ ----------
+ test_dir
+ The directory to write the test data to.
+ Should not contain spaces or punctuation.
+ additional_files
+ list of additional files to copy from each completed VASP directory.
+ Example: `--additional_file CHGCAR --additional_file LOCPOT`,
  """
  import warnings
  from pathlib import Path
@@ -110,6 +128,7 @@
  "vasprun*",
  "OUTCAR*",
  "*.json*",
+ *additional_file,
  ],
  allow_missing=True,
  )

src/atomate2/common/flows/electrode.py

@@ -0,0 +1,183 @@
+"""Flow for electrode analysis."""
+
+from __future__ import annotations
+
+import logging
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from jobflow import Flow, Maker
+from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
+
+from atomate2.common.jobs.electrode import (
+ RelaxJobSummary,
+ get_computed_entries,
+ get_insertion_electrode_doc,
+ get_stable_inserted_results,
+ get_structure_group_doc,
+)
+
+if TYPE_CHECKING:
+ from pathlib import Path
+
+ from pymatgen.alchemy import ElementLike
+ from pymatgen.core.structure import Structure
+ from pymatgen.entries.computed_entries import ComputedEntry
+ from pymatgen.io.vasp.outputs import VolumetricData
+
+logger = logging.getLogger(__name__)
+
+__author__ = "Jimmy Shen"
+__email__ = "jmmshn@gmail.com"
+
+
+@dataclass
+class ElectrodeInsertionMaker(Maker, ABC):
+ """Attempt ion insertion into a structure.
+
+ The basic unit for cation insertion is:
+ [get_stable_inserted_structure]:
+ (static) -> (chgcar analysis) ->
+ N x (relax) -> (return best structure)
+
+ The workflow is:
+ [relax structure]
+ [get_stable_inserted_structure]
+ [get_stable_inserted_structure]
+ [get_stable_inserted_structure]
+ ... until the insertion is no longer topotactic.
+
+ This workflow requires the users to provide the following functions:
+ self.get_charge_density(task_doc: TaskDoc):
+ Get the charge density of a TaskDoc output from a calculation.
+ self.update_static_maker():
+ Ensure that the static maker will store the desired data.
+
+ If you use this workflow please cite the following paper:
+ Shen, J.-X., Horton, M., & Persson, K. A. (2020).
+ A charge-density-based general cation insertion algorithm for
+ generating new Li-ion cathode materials.
+ npj Computational Materials, 6(161), 1—7.
+ doi: 10.1038/s41524-020-00422-3
+
+ Attributes
+ ----------
+ name: str
+ The name of the flow created by this maker.
+ relax_maker: RelaxMaker
+ A maker to perform relaxation calculations.
+ bulk_relax_maker: Maker
+ A separate maker to perform the first bulk relaxation calculation.
+ If None, the relax_maker will be used.
+ static_maker: Maker
+ A maker to perform static calculations.
+ structure_matcher: StructureMatcher
+ The structure matcher to use to determine if additional insertion is needed.
+ """
+
+ relax_maker: Maker
+ static_maker: Maker
+ bulk_relax_maker: Maker | None = None
+ name: str = "ion insertion"
+ structure_matcher: StructureMatcher = field(
+ default_factory=lambda: StructureMatcher(
+ comparator=ElementComparator(),
+ )
+ )
+
+ def __post_init__(self) -> None:
+ """Ensure that the static maker will store the desired data."""
+ self.update_static_maker()
+
+ def make(
+ self,
+ structure: Structure,
+ inserted_element: ElementLike,
+ n_steps: int | None,
+ insertions_per_step: int = 4,
+ working_ion_entry: ComputedEntry | None = None,
+ ) -> Flow:
+ """Make the flow.
+
+ Parameters
+ ----------
+ structure:
+ Structure to insert ion into.
+ inserted_species:
+ Species to insert.
+ n_steps: int
+ The maximum number of sequential insertion steps to attempt.
+ insertions_per_step: int
+ The maximum number of ion insertion sites to attempt.
+
+ Returns
+ -------
+ Flow for ion insertion.
+ """
+ # First relax the structure
+ if self.bulk_relax_maker:
+ relax = self.bulk_relax_maker.make(structure)
+ else:
+ relax = self.relax_maker.make(structure)
+ # add ignored_species to the structure matcher
+ sm = _add_ignored_species(self.structure_matcher, inserted_element)
+ # Get the inserted structure
+ new_entries_job = get_stable_inserted_results(
+ structure=relax.output.structure,
+ inserted_element=inserted_element,
+ structure_matcher=sm,
+ static_maker=self.static_maker,
+ relax_maker=self.relax_maker,
+ get_charge_density=self.get_charge_density,
+ n_steps=n_steps,
+ insertions_per_step=insertions_per_step,
+ )
+ relaxed_summary = RelaxJobSummary(
+ structure=relax.output.structure,
+ entry=relax.output.entry,
+ dir_name=relax.output.dir_name,
+ uuid=relax.output.uuid,
+ )
+ get_entries_job = get_computed_entries(new_entries_job.output, relaxed_summary)
+ structure_group_job = get_structure_group_doc(
+ get_entries_job.output, ignored_species=str(inserted_element)
+ )
+ jobs = [relax, new_entries_job, get_entries_job, structure_group_job]
+ output = structure_group_job.output
+ if working_ion_entry:
+ insertion_electrode_job = get_insertion_electrode_doc(
+ get_entries_job.output, working_ion_entry
+ )
+ jobs.append(insertion_electrode_job)
+ output = insertion_electrode_job.output
+ return Flow(jobs=jobs, output=output)
+
+ @abstractmethod
+ def get_charge_density(self, prev_dir: Path | str) -> VolumetricData:
+ """Get the charge density of a structure.
+
+ Parameters
+ ----------
+ prev_dir:
+ The previous directory where the static calculation was performed.
+
+ Returns
+ -------
+ The charge density.
+ """
+
+ @abstractmethod
+ def update_static_maker(self) -> None:
+ """Ensure that the static maker will store the desired data."""
+
+
+def _add_ignored_species(
+ structure_matcher: StructureMatcher, species: ElementLike
+) -> StructureMatcher:
+ """Add an ignored species to a structure matcher."""
+ sm_dict = structure_matcher.as_dict()
+ ignored_species = set(sm_dict.get("ignored_species", set()))
+ ignored_species.add(str(species))
+ sm_dict["ignored_species"] = list(ignored_species)
+ return StructureMatcher.from_dict(sm_dict)