Merge branch 'main' into trigger-atomate2-ci-on-pmg-master-push

materialsproject · May 11, 2024 · 06c4444 · 06c4444
2 parents 0fa6356 + df7c769
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diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -43,13 +43,6 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        # ERROR: Cannot install atomate2 and atomate2[strict,tests]==0.0.1 because these package versions have conflicting dependencies.
-        # The conflict is caused by:
-        #   atomate2[strict,tests] 0.0.1 depends on pymatgen>=2023.10.4
-        #   atomate2[strict,tests] 0.0.1 depends on pymatgen==2023.10.4; extra == "strict"
-        # ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
-        #   chgnet 0.2.1 depends on pymatgen>=2023.5.31
-        #   emmet-core 0.70.0 depends on pymatgen>=2023.10.11
         run: |
           python -m pip install --upgrade pip
           mkdir -p ~/.abinit/pseudos

diff --git a/docs/about/contributors.md b/docs/about/contributors.md
@@ -90,8 +90,8 @@ Lawrence Berkeley National Laboratory
 [0000-0003-3439-4856]: https://orcid.org/0000-0003-3439-4856
 
 **Matthew McDermott** [![gh]][mattmcdermott] [![orc]][0000-0002-4071-3000] \
-PhD student \
-University of California, Berkeley
+Postdoctoral Researcher \
+Lawrence Berkeley National Laboratory
 
 [mattmcdermott]: https://github.com/mattmcdermott
 [0000-0002-4071-3000]: https://orcid.org/0000-0002-4071-3000

diff --git a/docs/dev/workflow_tutorial.md b/docs/dev/workflow_tutorial.md
@@ -2,14 +2,14 @@
 
 ## Anatomy of an `atomate2` computational workflow (i.e., what do I need to write?)
 
-Every `atomate2` workflow is an instance of jobflow's `Flow ` class, which is a collection of Job and/or other `Flow` objects. So your end goal is to produce a `Flow `.
+Every `atomate2` workflow is an instance of jobflow's `Flow` class, which is a collection of Job and/or other `Flow` objects. So your end goal is to produce a `Flow`.
 
-In the context of computational materials science, `Flow ` objects are most easily created by a `Maker`, which contains a factory method make() that produces a `Flow `, given certain inputs. Typically, the input to `Maker`.make() includes atomic coordinate information in the form of a `pymatgen` `Structure` or `Molecule` object. So the basic signature looks like this:
+In the context of computational materials science, `Flow` objects are most easily created by a `Maker`, which contains a factory method make() that produces a `Flow`, given certain inputs. Typically, the input to `Maker`.make() includes atomic coordinate information in the form of a `pymatgen` `Structure` or `Molecule` object. So the basic signature looks like this:
 
 ```py
 class ExampleMaker(Maker):
     def make(self, coordinates: Structure) -> Flow:
-        # take the input coordinates and return a `Flow `
+        # take the input coordinates and return a `Flow`
         return Flow(...)
 ```
 
@@ -49,15 +49,16 @@ Finally, most `atomate2` workflows return structured output in the form of "Task
 **TODO - extend code block above to illustrate TaskDoc usage**
 
 In summary, a new `atomate2` workflow consists of the following components:
- - A `Maker` that actually generates the workflow
- - One or more `Job` and/or `Flow ` classes that define the discrete steps in the workflow
- - (optionally) an `InputGenerator` that produces a `pymatgen` `InputSet` for writing calculation input files
- - (optionally) a `TaskDocument` that defines a schema for storing the output data
+
+- A `Maker` that actually generates the workflow
+- One or more `Job` and/or `Flow` classes that define the discrete steps in the workflow
+- (optionally) an `InputGenerator` that produces a `pymatgen` `InputSet` for writing calculation input files
+- (optionally) a `TaskDocument` that defines a schema for storing the output data
 
 ## Where do I put my code?
 
 Because of the distributed design of the MP Software Ecosystem, writing a complete new workflow may involve making contributions to more than one GitHub repository. The following guidelines should help you understand where to put your contribution.
 
- - All workflow code (`Job`, `Flow `, `Maker`) belongs in `atomate2`
- - `InputSet` and `InputGenerator` code belongs in `pymatgen`. However, if you need to create these classes from scratch (i.e., you are working with a code that is not already supported in`pymatgen`), then it is recommended to include them in `atomate2` at first to facilitate rapid iteration. Once mature, they can be moved to `pymatgen` or to a `pymatgen` [addon package](https://pymatgen.org/addons).
- - `TaskDocument` schemas should generally be developed in `atomate2` alongside the workflow code. We recommend that you first check emmet to see if there is an existing schema that matches what you need. If so, you can import it. If not, check [`cclib`](https://cclib.github.io/). `cclib` output can be imported via [`atomate2.common.schemas.TaskDocument`](https://github.com/materialsproject/atomate2/blob/main/src/atomate2/common/schemas/cclib.py). If neither code has what you need, then new schemas should be developed within `atomate2` (or `cclib`).
+- All workflow code (`Job`, `Flow`, `Maker`) belongs in `atomate2`
+- `InputSet` and `InputGenerator` code belongs in `pymatgen`. However, if you need to create these classes from scratch (i.e., you are working with a code that is not already supported in`pymatgen`), then it is recommended to include them in `atomate2` at first to facilitate rapid iteration. Once mature, they can be moved to `pymatgen` or to a `pymatgen` [addon package](https://pymatgen.org/addons).
+- `TaskDocument` schemas should generally be developed in `atomate2` alongside the workflow code. We recommend that you first check emmet to see if there is an existing schema that matches what you need. If so, you can import it. If not, check [`cclib`](https://cclib.github.io/). `cclib` output can be imported via [`atomate2.common.schemas.TaskDocument`](https://github.com/materialsproject/atomate2/blob/main/src/atomate2/common/schemas/cclib.py). If neither code has what you need, then new schemas should be developed within `atomate2` (or `cclib`).
diff --git a/docs/user/codes/vasp.md b/docs/user/codes/vasp.md
@@ -247,7 +247,7 @@ adjust them if necessary. The default might not be strict enough
 for your specific case.
 ```
 
-### Lobster
+### LOBSTER
 
 Perform bonding analysis with [LOBSTER](http://cohp.de/) and [LobsterPy](https://github.com/jageo/lobsterpy)
 
@@ -367,6 +367,43 @@ for number, (key, cohp) in enumerate(
     plotter.add_cohp(key, cohp)
     plotter.save_plot(f"plots_cation_anion_bonds{number}.pdf")
 ```
+# Running the LOBSTER workflow without database and with one job script only
+
+It is also possible to run the VASP-LOBSTER workflow with a minimal setup.
+In this case, you will run the VASP calculations on the same node as the LOBSTER calculations.
+In between, the different computations you will switch from MPI to OpenMP parallelization.
+
+For example, for a node with 48 cores, you could use an adapted version of the following SLURM script:
+
+```bash
+#!/bin/bash
+#SBATCH -J vasplobsterjob
+#SBATCH -o ./%x.%j.out
+#SBATCH -e ./%x.%j.err
+#SBATCH -D ./
+#SBATCH --mail-type=END
+#SBATCH [email protected]
+#SBATCH --time=24:00:00
+#SBATCH --nodes=1
+#This needs to be adapted if you run with different cores
+#SBATCH --ntasks=48
+
+# ensure you load the modules to run VASP, e.g., module load vasp
+module load my_vasp_module
+# please activate the required conda environment
+conda activate my_environment
+cd my_folder
+# the following script needs to contain the workflow
+python xyz.py
+```
+
+The `LOBSTER_CMD` now needs an additional export of the number of threads.
+
+```yaml
+VASP_CMD: <<VASP_CMD>>
+LOBSTER_CMD: OMP_NUM_THREADS=48 <<LOBSTER_CMD>>
+```
+
 
 (modifying_input_sets)=
 Modifying input sets

diff --git a/pyproject.toml b/pyproject.toml
@@ -27,14 +27,14 @@ requires-python = ">=3.9"
 dependencies = [
     "PyYAML",
     "click",
-    "custodian>=2024.2.15",
-    "emmet-core>=0.78.0rc4",
+    "custodian>=2024.4.18",
+    "emmet-core==0.82.2",
     "jobflow>=0.1.11",
     "monty>=2024.2.2",
     "numpy",
     "pydantic-settings>=2.0.3",
     "pydantic>=2.0.1",
-    "pymatgen>=2024.3.1",
+    "pymatgen>=2024.4.13",
 ]
 
 [project.optional-dependencies]
@@ -43,19 +43,19 @@ amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
 mp = ["mp-api>=0.37.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
-lobster = ["ijson>=3.2.2", "lobsterpy>=0.3.7"]
+lobster = ["ijson>=3.2.2", "lobsterpy>=0.3.8"]
 defects = [
     "dscribe>=1.2.0",
-    "pymatgen-analysis-defects>=2022.11.30",
+    "pymatgen-analysis-defects>=2024.5.11",
     "python-ulid",
 ]
 forcefields = [
     "ase>=3.22.1",
-    "torch<=2.2.1", # incompatibility with dgl if newer versions are used
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
-    "matgl>=1.0.0",
+    "matgl>=1.1.1",
     "quippy-ase>=0.9.14",
+    "torch<=2.2.1",       # incompatibility with dgl if newer versions are used
 ]
 docs = [
     "FireWorks==2.0.3",
@@ -70,35 +70,40 @@ docs = [
     "sphinx_design==0.5.0",
 ]
 dev = ["pre-commit>=2.12.1"]
-tests = ["FireWorks==2.0.3", "pytest-cov==5.0.0", "pytest==8.0.2", "pytest-mock==3.14.0"]
+tests = [
+    "FireWorks==2.0.3",
+    "pytest-cov==5.0.0",
+    "pytest-mock==3.14.0",
+    "pytest==8.0.2",
+]
 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",
-    "torch==2.2.1",
     "cclib==1.8.1",
     "chgnet==0.3.5",
     "click==8.1.7",
-    "custodian==2024.3.12",
+    "custodian==2024.4.18",
     "dscribe==2.1.0",
     "emmet-core==0.82.2",
     "ijson==3.2.3",
     "jobflow==0.1.17",
-    "lobsterpy==0.3.8",
+    "lobsterpy==0.4.0",
     "mace-torch>=0.3.3",
-    "matgl==1.0.0",
+    "matgl==1.1.1",
     "monty==2024.3.31",
     "mp-api==0.41.2",
     "numpy",
     "phonopy==2.22.1",
     "pydantic-settings==2.2.1",
     "pydantic==2.7.1",
-    "pymatgen-analysis-defects==2024.4.23",
-    "pymatgen==2024.3.1",
+    "pymatgen-analysis-defects==2024.5.11",
+    "pymatgen==2024.5.1",
     "python-ulid==2.5.0",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",
+    "torch==2.2.1",
     "typing-extensions==4.11.0",
 ]
 
@@ -126,7 +131,7 @@ ignore_missing_imports = true
 no_strict_optional = true
 
 [tool.pytest.ini_options]
-addopts = "-p no:warnings --import-mode=importlib"
+addopts = "-p no:warnings --import-mode=importlib --cov-config=pyproject.toml"
 filterwarnings = [
     "ignore:.*POTCAR.*:UserWarning",
     "ignore:.*input structure.*:UserWarning",
@@ -154,8 +159,10 @@ exclude_lines = [
 
 [tool.ruff]
 target-version = "py39"
-lint.select = ["ALL"]
-lint.ignore = [
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
     "ANN002",
     "ANN003",
     "ANN101",  # missing self type annotation
@@ -188,9 +195,12 @@ lint.ignore = [
     "TD",      # TODOs
     "TRY003",  # long message outside exception class
 ]
-lint.pydocstyle.convention = "numpy"
-lint.isort.known-first-party = ["atomate2"]
-lint.isort.split-on-trailing-comma = false
+pydocstyle.convention = "numpy"
+isort.known-first-party = ["atomate2"]
+isort.split-on-trailing-comma = false
+
+[tool.ruff.format]
+docstring-code-format = true
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]

diff --git a/src/atomate2/abinit/flows/core.py b/src/atomate2/abinit/flows/core.py
@@ -50,8 +50,7 @@ def make(
         structure: Structure,
         restart_from: str | Path | None = None,
     ) -> Flow:
-        """
-        Create a band structure flow.
+        """Create a band structure flow.
 
         Parameters
         ----------
@@ -109,8 +108,7 @@ def make(
         structure: Structure | None = None,
         restart_from: str | Path | None = None,
     ) -> Flow:
-        """
-        Create a relaxation flow.
+        """Create a relaxation flow.
 
         Parameters
         ----------

diff --git a/src/atomate2/abinit/jobs/base.py b/src/atomate2/abinit/jobs/base.py
@@ -144,8 +144,7 @@ def make(
         restart_from: str | Path | list[str] | None = None,
         history: JobHistory | None = None,
     ) -> jobflow.Job:
-        """
-        Return an ABINIT jobflow.Job.
+        """Get an ABINIT jobflow.Job.
 
         Parameters
         ----------

diff --git a/src/atomate2/abinit/jobs/core.py b/src/atomate2/abinit/jobs/core.py
@@ -123,8 +123,7 @@ def make(
         history: JobHistory | None = None,
         mode: str = "uniform",
     ) -> Job:
-        """
-        Run a non-scf ABINIT job.
+        """Run a non-scf ABINIT job.
 
         Parameters
         ----------

diff --git a/src/atomate2/abinit/schemas/calculation.py b/src/atomate2/abinit/schemas/calculation.py
@@ -6,10 +6,7 @@
 import os
 from datetime import datetime
 from pathlib import Path
-from typing import TYPE_CHECKING, Optional, Union
-
-if TYPE_CHECKING:
-    pass
+from typing import Optional, Union
 
 from abipy.electrons.gsr import GsrFile
 from abipy.flowtk import events
@@ -18,6 +15,7 @@
 from jobflow.utils import ValueEnum
 from pydantic import BaseModel, Field
 from pymatgen.core import Structure
+from typing_extensions import Self
 
 from atomate2.abinit.utils.common import LOG_FILE_NAME, MPIABORTFILE, get_event_report
 
@@ -110,9 +108,8 @@ class CalculationOutput(BaseModel):
     def from_abinit_gsr(
         cls,
         output: GsrFile,  # Must use auto_load kwarg when passed
-    ) -> CalculationOutput:
-        """
-        Create an Abinit output document from Abinit outputs.
+    ) -> Self:
+        """Create an Abinit output document from Abinit outputs.
 
         Parameters
         ----------
@@ -211,9 +208,8 @@ def from_abinit_files(
         abinit_gsr_file: Path | str = "out_GSR.nc",
         abinit_log_file: Path | str = LOG_FILE_NAME,
         abinit_abort_file: Path | str = MPIABORTFILE,
-    ) -> tuple[Calculation, dict[AbinitObject, dict]]:
-        """
-        Create an Abinit calculation document from a directory and file paths.
+    ) -> tuple[Self, dict[AbinitObject, dict]]:
+        """Create an Abinit calculation document from a directory and file paths.
 
         Parameters
         ----------
@@ -263,15 +259,14 @@ def from_abinit_files(
             msg = f"{cls} exception while parsing event_report:\n{exc}"
             logger.critical(msg)
 
-        return (
-            cls(
-                dir_name=str(dir_name),
-                task_name=task_name,
-                abinit_version=abinit_gsr.abinit_version,
-                has_abinit_completed=has_abinit_completed,
-                completed_at=completed_at,
-                output=output_doc,
-                event_report=report,
-            ),
-            None,  # abinit_objects,
+        instance = cls(
+            dir_name=str(dir_name),
+            task_name=task_name,
+            abinit_version=abinit_gsr.abinit_version,
+            has_abinit_completed=has_abinit_completed,
+            completed_at=completed_at,
+            output=output_doc,
+            event_report=report,
         )
+
+        return instance, None  # abinit_objects,