Merge branch 'main' into abinit_scf

.gitignore

@@ -61,3 +61,5 @@ docs/src/reference/atomate2.*
 docs/reference/atomate2.*
 
 .vscode/
+
+.DS_Store

.pre-commit-config.yaml

@@ -53,7 +53,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.961
+  rev: v0.971
   hooks:
   - id: mypy
     files: ^src/

README.md

@@ -37,9 +37,9 @@ It is easy to customise and compose any of the above workflows.
 
 ## Quick start
 
-Workflows in atomate2 written using the [jobflow] library. Workflows are generated using
-`Maker` objects, that have a consistent API for modifying input settings and chaining
-workflows together.  Below, we demonstrate how to run a band structure workflow
+Workflows in atomate2 are written using the [jobflow] library. Workflows are generated using
+`Maker` objects which have a consistent API for modifying input settings and chaining
+workflows together. Below, we demonstrate how to run a band structure workflow
 (see the [documentation][RelaxBandStructure] for more details). In total, 4 VASP
 calculations will be performed:
 

pyproject.toml

@@ -25,7 +25,7 @@ classifiers = [
 ]
 requires-python = '>="3.8"'
 dependencies = [
-    'pymatgen>=2022.3.22',
+    'pymatgen>=2022.7.8',
     'custodian>=2019.8.24',
     "pydantic",
     "monty",
@@ -57,7 +57,7 @@ tests = [
 ]
 strict = [
     "pydantic==1.9.0",
-    "pymatgen==2022.5.17",
+    "pymatgen==2022.7.8",
     "custodian==2022.2.13",
     "monty==2022.4.26",
     "jobflow==0.1.8",

src/atomate2/vasp/jobs/base.py

@@ -10,6 +10,7 @@
 from monty.serialization import dumpfn
 from monty.shutil import gzip_dir
 from pymatgen.core import Structure
+from pymatgen.core.trajectory import Trajectory
 from pymatgen.electronic_structure.bandstructure import (
     BandStructure,
     BandStructureSymmLine,
@@ -34,6 +35,7 @@
     Locpot,
     Chgcar,
     Wavecar,
+    Trajectory,
     "force_constants",
     "normalmode_eigenvecs",
 ]

src/atomate2/vasp/jobs/core.py

@@ -6,6 +6,15 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from custodian.vasp.handlers import (
+    FrozenJobErrorHandler,
+    IncorrectSmearingHandler,
+    LargeSigmaHandler,
+    MeshSymmetryErrorHandler,
+    PositiveEnergyErrorHandler,
+    StdErrHandler,
+    VaspErrorHandler,
+)
 from pymatgen.alchemy.materials import TransformedStructure
 from pymatgen.alchemy.transmuters import StandardTransmuter
 from pymatgen.core.structure import Structure
@@ -17,6 +26,7 @@
     HSERelaxSetGenerator,
     HSEStaticSetGenerator,
     HSETightRelaxSetGenerator,
+    MDSetGenerator,
     NonSCFSetGenerator,
     RelaxSetGenerator,
     StaticSetGenerator,
@@ -36,6 +46,7 @@
     "TightRelaxMaker",
     "HSETightRelaxMaker",
     "TransmuterMaker",
+    "MDMaker",
 ]
 
 
@@ -519,6 +530,62 @@ def make(
         return super().make.original(self, structure, prev_vasp_dir)
 
 
+@dataclass
+class MDMaker(BaseVaspMaker):
+    """
+    Maker to create VASP molecular dynamics jobs.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputSetGenerator
+        A generator used to make the input set.
+    write_input_set_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
+    copy_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
+    run_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.run_vasp`.
+    task_document_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.TaskDocument.from_directory`.
+    stop_children_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.should_stop_children`.
+    write_additional_data : dict
+        Additional data to write to the current directory. Given as a dict of
+        {filename: data}. Note that if using FireWorks, dictionary keys cannot contain
+        the "." character which is typically used to denote file extensions. To avoid
+        this, use the ":" character, which will automatically be converted to ".". E.g.
+        ``{"my_file:txt": "contents of the file"}``.
+    """
+
+    name: str = "molecular dynamics"
+
+    input_set_generator: VaspInputGenerator = field(default_factory=MDSetGenerator)
+
+    # Explicitly pass the handlers to not use the default ones. Some default handlers
+    # such as PotimErrorHandler do not apply to MD runs.
+    run_vasp_kwargs: dict = field(
+        default_factory=lambda: {
+            "handlers": (
+                VaspErrorHandler(),
+                MeshSymmetryErrorHandler(),
+                PositiveEnergyErrorHandler(),
+                FrozenJobErrorHandler(),
+                StdErrHandler(),
+                LargeSigmaHandler(),
+                IncorrectSmearingHandler(),
+            )
+        }
+    )
+
+    # Store ionic steps info in a pymatgen Trajectory object instead of in the output
+    # document.
+    task_document_kwargs: dict = field(
+        default_factory=lambda: {"store_trajectory": True}
+    )
+
+
 def _get_transformations(
     transformations: tuple[str, ...], params: tuple[dict, ...] | None
 ):

src/atomate2/vasp/schemas/calc_types/_generate.py

@@ -16,6 +16,7 @@
     "Static",
     "Structure Optimization",
     "Deformation",
+    "MD",
     "Unrecognized",
 ]