Merge pull request #90 from gpetretto/abinit2

Abinit workflows

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(src/atomate2/vasp/schemas/calc_types/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.256
+  rev: v0.0.259
   hooks:
   - id: ruff
     args: [--fix]

docs/user/codes/vasp.md

@@ -260,7 +260,41 @@ VASP_CMD: <<VASP_CMD>>
 LOBSTER_CMD: <<LOBSTER_CMD>>
 ```
 
+Outputs from the automatic analysis with LobsterPy can easily be extracted from the database and also plotted:
 
+```python
+from jobflow import SETTINGS
+from pymatgen.electronic_structure.cohp import Cohp
+from pymatgen.electronic_structure.plotter import CohpPlotter
+
+store = SETTINGS.JOB_STORE
+store.connect()
+
+result = store.query_one(
+    {"name": "lobster_run_0"},
+    properties=[
+        "output.lobsterpy_data.cohp_plot_data",
+        "output.lobsterpy_data_cation_anion.cohp_plot_data",
+    ],
+    load=True,
+)
+
+for number, (key, cohp) in enumerate(
+    result["output"]["lobsterpy_data"]["cohp_plot_data"].items()
+):
+    plotter = CohpPlotter()
+    cohp = Cohp.from_dict(cohp)
+    plotter.add_cohp(key, cohp)
+    plotter.save_plot("plots_all_bonds" + str(number) + ".pdf")
+
+for number, (key, cohp) in enumerate(
+    result["output"]["lobsterpy_data_cation_anion"]["cohp_plot_data"].items()
+):
+    plotter = CohpPlotter()
+    cohp = Cohp.from_dict(cohp)
+    plotter.add_cohp(key, cohp)
+    plotter.save_plot("plots_cation_anion_bonds" + str(number) + ".pdf")
+```
 
 (modifying_input_sets)=
 Modifying input sets

pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-abinit = ["abipy @ git+https://github.com/abinit/abipy.git@develop"]
+abinit = ["abipy>=0.9.3"]
 amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
 mp = ["mp-api>=0.27.5"]
@@ -46,31 +46,31 @@ lobster = ["lobsterpy"]
 defects = ["pymatgen-analysis-defects>=2022.11.30", "dscribe>=1.2.0"]
 docs = [
     "numpydoc==1.5.0",
-    "ipython==8.11.0",
+    "ipython==8.12.0",
     "FireWorks==2.0.3",
     "autodoc_pydantic==1.8.0",
     "jupyter-book==0.14.0",
     "jsonschema[format]",
 ]
 dev = ["pre-commit>=2.12.1"]
-tests = ["pytest==7.2.2", "pytest-cov==4.0.0", "FireWorks==2.0.3", "pytest-mock==3.6.1"]
+tests = ["pytest==7.3.0", "pytest-cov==4.0.0", "FireWorks==2.0.3", "pytest-mock==3.10.0"]
 strict = [
-    "pydantic==1.10.6",
-    "pymatgen==2023.3.10",
+    "pydantic==1.10.7",
+    "pymatgen==2023.3.23",
     "custodian==2023.3.10",
     "monty==2022.9.9",
     "jobflow==0.1.11",
     "click==8.1.3",
     "PyYAML==6.0",
     "cclib==1.7.2",
-    "phonopy==2.17.2",
+    "phonopy==2.18.0",
     "seekpath==2.0.1",
     "numpy",
     "mp-api==0.30.10",
     "dscribe==1.2.2",
-    "pymatgen-analysis-defects==2023.3.3",
-    "lobsterpy==0.2.8",
-    "emmet-core==0.51.0"
+    "pymatgen-analysis-defects==2023.4.5",
+    "lobsterpy==0.2.9",
+    "emmet-core==0.51.6"
 ]
 
 [project.scripts]

src/atomate2/abinit/flows/core.py

@@ -1,14 +1,19 @@
 """Core abinit flow makers."""
+from __future__ import annotations
 
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import List, Optional, Union
 
 from jobflow import Flow, Maker
 from pymatgen.core.structure import Structure
 
 from atomate2.abinit.jobs.base import BaseAbinitMaker
-from atomate2.abinit.jobs.core import NonSCFMaker, RelaxMaker, StaticMaker
+from atomate2.abinit.jobs.core import (
+    LineNonSCFMaker,
+    RelaxMaker,
+    StaticMaker,
+    UniformNonSCFMaker,
+)
 
 
 @dataclass
@@ -29,15 +34,15 @@ class BandStructureMaker(Maker):
         The maker to use for the non-self-consistent field calculations.
     """
 
-    name: str = "band structure"
-    bandstructure_type: str = "both"
+    name: str = "band structure - dos"
     static_maker: BaseAbinitMaker = field(default_factory=StaticMaker)
-    bs_maker: BaseAbinitMaker = field(default_factory=NonSCFMaker)
+    bs_maker: BaseAbinitMaker | None = field(default_factory=LineNonSCFMaker)
+    dos_maker: BaseAbinitMaker | None = field(default_factory=UniformNonSCFMaker)
 
     def make(
         self,
         structure: Structure,
-        restart_from: Optional[Union[str, Path]] = None,
+        restart_from: str | Path | None = None,
     ):
         """
         Create a band structure flow.
@@ -54,85 +59,24 @@ def make(
         Flow
             A band structure flow.
         """
-        if self.bandstructure_type not in ("both", "line", "uniform"):
-            raise ValueError(
-                f"Unrecognised bandstructure type {self.bandstructure_type}"
-            )
-
         static_job = self.static_maker.make(structure, restart_from=restart_from)
         jobs = [static_job]
 
-        if self.bandstructure_type in ("both", "uniform"):
-            uniform_job = self.bs_maker.make(
+        if self.dos_maker:
+            uniform_job = self.dos_maker.make(
                 prev_outputs=static_job.output.dir_name,
-                mode="uniform",
             )
-            uniform_job.name += " uniform"
             jobs.append(uniform_job)
 
-        if self.bandstructure_type in ("both", "line"):
+        if self.bs_maker:
             line_job = self.bs_maker.make(
                 prev_outputs=static_job.output.dir_name,
-                mode="line",
             )
-            line_job.name += " line"
             jobs.append(line_job)
 
         return Flow(jobs, name=self.name)
 
 
-@dataclass
-class LineBandStructureMaker(Maker):
-    # TODO: make this more similar to Vasp
-    """
-    Maker to generate line abinit band structure.
-
-    This is a static calculation followed by a non-self-consistent field
-    calculations.
-
-    Parameters
-    ----------
-    name : str
-        Name of the flows produced by this maker.
-    scf_maker : .BaseAbinitMaker
-        The maker to use for the static calculation.
-    bs_maker : .BaseAbinitMaker
-        The maker to use for the non-self-consistent field calculations.
-    """
-
-    name: str = "line band structure"
-    scf_maker: BaseAbinitMaker = field(default_factory=StaticMaker)
-    bs_maker: BaseAbinitMaker = field(default_factory=NonSCFMaker)
-
-    def make(
-        self,
-        structure: Structure,
-        restart_from: Optional[Union[str, Path]] = None,
-    ):
-        """
-        Create a line mode band structure flow.
-
-        Parameters
-        ----------
-        structure : Structure
-            A pymatgen structure object.
-        restart_from : str or Path or None
-            One previous directory to restart from.
-
-        Returns
-        -------
-        Flow
-            A line mode band structure flow.
-        """
-        scf_job = self.scf_maker.make(structure, restart_from=restart_from)
-        line_job = self.bs_maker.make(
-            prev_outputs=scf_job.output.dir_name,
-            mode="line",
-        )
-        jobs = [scf_job, line_job]
-        return Flow(jobs, line_job.output, name=self.name)
-
-
 @dataclass
 class RelaxFlowMaker(Maker):
     """
@@ -147,7 +91,7 @@ class RelaxFlowMaker(Maker):
     """
 
     name: str = "relaxation"
-    relaxation_makers: List[Maker] = field(
+    relaxation_makers: list[Maker] = field(
         default_factory=lambda: [
             RelaxMaker.ionic_relaxation(),
             RelaxMaker.full_relaxation(),
@@ -156,8 +100,8 @@ class RelaxFlowMaker(Maker):
 
     def make(
         self,
-        structure: Optional[Structure] = None,
-        restart_from: Optional[Union[str, Path]] = None,
+        structure: Structure | None = None,
+        restart_from: str | Path | None = None,
     ):
         """
         Create a relaxation flow.
@@ -190,5 +134,5 @@ def make(
     def ion_ioncell_relaxation(cls, *args, **kwargs):
         """Create a double relaxation (ionic relaxation + full relaxation)."""
         ion_rlx_maker = RelaxMaker.ionic_relaxation(*args, **kwargs)
-        ioncell_rlx_maker = RelaxMaker.from_prev_maker(ion_rlx_maker, relax_cell=True)
+        ioncell_rlx_maker = RelaxMaker.full_relaxation(*args, **kwargs)
         return cls(relaxation_makers=[ion_rlx_maker, ioncell_rlx_maker])