Transition to pymatgen VASP input sets (#854)

* complete refactor to PMG input sets for vasp

* bug fixes for input set change

* linting

* move type import to type_checking block

* remove duplicated MP yaml files

* drop dict.get(key, None) -> dict.get(key)

* change inheritance slightly, install pmg from pr

* linting

* revert vis["INCAR"] --> vis.incar

* fix lobster interface

* remove lobster test file

* revert pymatgen testing install now that separate pr is merged

* try to force pip install of pymatgen in testing

* force pmg to install from git

* improve check_poscar method to account for reordering of sites in POSCAR

* linting

* remove POTCARs and replace with spec where appropriate; remove unused vaspout.h5 files which contain full POTCARs

* restore missing test file, but only header of POTCAR

* remove POTCAR.orig.spec files

* gzip test input files

* linting

* slightly refactor MP sets

* precommit

* slight matpes modification

* precommit

* revert gh workflow dependency install

* update changelog

* fix pymatgen pip version install for strict

* bump pymatgen to v2024.6.4

* refactor MP and MatPES VASP input sets to inherit directly from pymatgen equivalents

* linting

* further cleanup matpes r2scan set

* change ase to use most recent pypi release

* add missing pip install line

* revert lobster vis potcar changes

* remove version conflict

* remove version conflict

* remove version conflict

* replace lobster sets with pymatgen equivalents

* precommit

* add ispin to lobster tightstatitsetgenerator

* remove BaseVasp.yaml to rely on inheritance from MP input sets

* precommit

* remove temp test file

* move matpes jobs/flow to pymatgen sets, mark matpes sets for deprecation

* lint

* move mp sets fully to pmg, add deprecation warnings to existing atomate2 mp sets

* remove mp set dependence from tests

* precommit

* add bandgap_tol options to vasp.test_sets

* remove todo from tests.vasp.flows.test_mp

* add pytest.warns check for deprecated mp sets

* revert docstr changes

* move deprecation warnings from __post_init__ to class

warning before:
<string>:31: FutureWarning: __post_init__ is deprecated, and will be removed on 2025-01-01
Use MPRelaxSet in pymatgen.io.vasp.sets instead.

warning after:
<string>:31: FutureWarning: MPGGARelaxSetGenerator is deprecated, and will be removed on 2025-01-01
Use MPRelaxSet in pymatgen.io.vasp.sets instead.

* pin monty==2024.7.30 in deps and strict

* add kludge for monty zpath

* precommit

* extend monty fix to vasp tests

* precommit

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: esoteric-ephemera

.github/workflows/testing.yml

@@ -61,8 +61,6 @@ jobs:
           python -m pip install --upgrade pip
           mkdir -p ~/.abinit/pseudos
           cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,tests,abinit]
           pip install torch-runstats
           pip install --no-deps nequip==0.5.6
@@ -100,8 +98,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Change log
 
+## v0.0.15
+
+## New Features 🎉
+* Transition VASP calculations to use input sets defined in pymatgen by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/854
+
+### Bug Fixes 🐛
+* Increase k-point density for MP GGA static calculations to close issue https://github.com/materialsproject/atomate2/issues/844 by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/854
+* Adds missing MAGMOMs for MatPES jobs by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/854
+
 ## v0.0.14
 
 ### New Features 🎉

pyproject.toml

@@ -30,11 +30,11 @@ dependencies = [
     "custodian>=2024.4.18",
     "emmet-core==0.82.2",
     "jobflow>=0.1.11",
-    "monty>=2024.2.2",
+    "monty>=2024.7.30",
     "numpy",
     "pydantic-settings>=2.0.3",
     "pydantic>=2.0.1",
-    "pymatgen>=2024.4.13",
+    "pymatgen>=2024.6.4",
 ]
 
 [project.optional-dependencies]
@@ -50,7 +50,7 @@ defects = [
     "python-ulid",
 ]
 forcefields = [
-    "ase>=3.22.1",
+    "ase>=3.23.0",
     "calorine<=2.2.1",
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
@@ -81,9 +81,7 @@ tests = [
 ]
 strict = [
     "PyYAML==6.0.1",
-    # must use >= for ase to not uninstall main branch install in CI
-    # last known working commit: https://gitlab.com/ase/ase@2bab58f4e
-    "ase>=3.22.1",
+    "ase==3.23.0",
     "calorine==2.2.1",
     "cclib==1.8.1",
     "chgnet==0.3.8",
@@ -96,7 +94,7 @@ strict = [
     "lobsterpy==0.4.5",
     "mace-torch>=0.3.3",
     "matgl==1.1.2",
-    "monty==2024.5.24",
+    "monty==2024.7.30",
     "mp-api==0.41.2",
     "numpy",
     "phonopy==2.26.6",

src/atomate2/abinit/sets/base.py

@@ -326,11 +326,10 @@ def get_input_set(
         structure : Structure
             Pymatgen Structure object.
         restart_from : str or Path or list or tuple
-            Directory (as a str or Path) or list/tuple of 1 directory (as a str
-            or Path) to restart from.
+            Directory or list/tuple of 1 directory to restart from.
         prev_outputs : str or Path or list or tuple
-            Directory (as a str or Path) or list/tuple of directories (as a str
-            or Path) needed as dependencies for the AbinitInputSet generated.
+            Directory or list/tuple of directories needed as dependencies for the
+                AbinitInputSet generated.
         """
         # Get the pseudos as a PseudoTable
         pseudos = as_pseudo_table(self.pseudos) if self.pseudos else None

src/atomate2/abinit/utils/history.py

@@ -195,7 +195,7 @@ def get_total_run_time(self) -> Any:
         """Get the total run time based summing the abinit stop event run times."""
         total_run_time = 0
         for te in self.get_events_by_types(JobEvent.ABINIT_STOP):
-            run_time = te.details.get("run_time", None)
+            run_time = te.details.get("run_time")
             if run_time:
                 total_run_time += run_time
 

src/atomate2/common/files.py

@@ -97,11 +97,11 @@ def delete_files(
         The hostname used to specify a remote filesystem. Can be given as either
         "username@host" or just "host" in which case the username will be
         inferred from the current user. If ``None``, the local filesystem will be used.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str or .Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all files
         in the directory will be deleted.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str or .Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     allow_missing : bool
         Whether to error if a file in ``include_files`` is not present in the directory.
@@ -188,11 +188,11 @@ def gzip_files(
         The hostname used to specify a remote filesystem. Can be given as either
         "username@host" or just "host" in which case the username will be
         inferred from the current user. If ``None``, the local filesystem will be used.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str or .Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all files
         in the directory will be gzipped.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str or .Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     allow_missing : bool
         Whether to error if a file in ``include_files`` is not present in the directory.
@@ -241,11 +241,11 @@ def gunzip_files(
         The hostname used to specify a remote filesystem. Can be given as either
         "username@host" or just "host" in which case the username will be
         inferred from the current user. If ``None``, the local filesystem will be used.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str or .Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all
         gzipped files in the directory will be gunzipped.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str or .Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     allow_missing : bool
         Whether to error if a file in ``include_files`` is not present in the directory.
@@ -287,11 +287,11 @@ def find_and_filter_files(
         A file client.
     directory : str or Path
         A directory in which to find files.
-    include_files : None or list of (str or Path)
+    include_files : None or list of (str or .Path)
         Filenames to include as a list of str or Path objects given relative to
         directory. Glob file paths are supported, e.g. "\*.dat". If ``None``, all files
         in the source directory will be returned.
-    exclude_files : None or list of (str or Path)
+    exclude_files : None or list of (str or .Path)
         Filenames to exclude. Supports glob file matching, e.g., "\*.dat".
     host : str or None
         A hostname used to specify a remote filesystem. Can be given as either

src/atomate2/common/jobs/defect.py

@@ -460,7 +460,7 @@ def get_defect_entry(charge_state_summary: dict, bulk_summary: dict) -> list[dic
                 "bulk_dir_name": bulk_dir_name,
                 "bulk_locpot": bulk_locpot,
                 "bulk_uuid": bulk_summary.get("uuid"),
-                "defect_uuid": qq_summary.get("uuid", None),
+                "defect_uuid": qq_summary.get("uuid"),
             }
         )
     return defect_ent_res

src/atomate2/cp2k/jobs/base.py

@@ -92,7 +92,7 @@ class BaseCp2kMaker(Maker):
     ----------
     name : str
         The job name.
-    input_set_generator : .VaspInputGenerator
+    input_set_generator : .Cp2kInputGenerator
         A generator used to make the input set.
     write_input_set_kwargs : dict
         Keyword arguments that will get passed to :obj:`.write_cp2k_input_set`.

src/atomate2/lobster/schemas.py

@@ -11,7 +11,9 @@
 from emmet.core.structure import StructureMetadata
 from monty.dev import requires
 from monty.json import MontyDecoder, jsanitize
-from monty.os.path import zpath
+
+# TODO: remove this kludge when monty is fixed
+from monty.os.path import zpath as monty_zpath
 from pydantic import BaseModel, Field
 from pymatgen.core import Structure
 from pymatgen.electronic_structure.cohp import Cohp, CompleteCohp
@@ -45,6 +47,11 @@
 logger = logging.getLogger(__name__)
 
 
+def zpath(pathname: Union[str, Path]) -> str:
+    """Kludge to fix monty zpath bug."""
+    return monty_zpath(str(pathname))
+
+
 class LobsteroutModel(BaseModel):
     """Definition of computational settings from the LOBSTER computation."""
 

src/atomate2/vasp/files.py

@@ -201,4 +201,4 @@ def write_vasp_input_set(
                 Path(filename).unlink()
 
     logger.info("Writing VASP input set.")
-    vis.write_input(directory, potcar_spec=potcar_spec, **kwargs)
+    vis.write_input(directory, **kwargs)