Merge pull request #137 from JaGeo/main

[WIP] VASP/Phonopy Phonon Workflow

pyproject.toml

@@ -24,9 +24,9 @@ classifiers = [
     "Topic :: Scientific/Engineering",
 ]
 requires-python = '>="3.8"'
-dependencies = [
-    "pymatgen>=2022.7.8",
-    "custodian>=2019.8.24",
+dependencies =[
+    "pymatgen>=2022.8.23",
+    "custodian>=2022.5.26",
     "pydantic",
     "monty",
     "jobflow>=0.1.5",
@@ -38,7 +38,7 @@ dependencies = [
 [project.optional-dependencies]
 amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
-phonons = ["phonopy>=1.10.8"]
+phonons = ["phonopy>=1.10.8", "seekpath"]
 docs = [
     "numpydoc==1.3.1",
     "mistune==0.8.4",
@@ -62,6 +62,8 @@ strict = [
     "click==8.1.3",
     "PyYAML==6.0",
     "cclib==1.7.1",
+    "phonopy==2.15.1",
+    "seekpath==2.0.1",
     "numpy",
 ]
 

src/atomate2/common/jobs.py

@@ -6,25 +6,46 @@
 
 from atomate2 import SETTINGS
 
+__all__ = ["structure_to_primitive", "structure_to_conventional"]
+
 
 @job
-def symmetrize_structure(
-    structure: Structure, symprec: float = SETTINGS.SYMPREC
-) -> Structure:
+def structure_to_primitive(structure: Structure, symprec: float = SETTINGS.SYMPREC):
     """
-    Symmetrize a structure.
+    Job that creates a standard primitive structure.
 
     Parameters
     ----------
-    structure : .Structure
-        A structure.
-    symprec : float
-        The symmetry precision.
+    structure: Structure object
+        input structure that will be transformed
+    symprec: float
+        precision to determine symmetry
 
     Returns
     -------
     .Structure
-        A symmetrized structure
+
     """
     sga = SpacegroupAnalyzer(structure, symprec=symprec)
     return sga.get_primitive_standard_structure()
+
+
+@job
+def structure_to_conventional(structure: Structure, symprec: float = SETTINGS.SYMPREC):
+    """
+    Job hat creates a standard conventional structure.
+
+    Parameters
+    ----------
+    structure: Structure object
+        input structure that will be transformed
+    symprec: float
+        precision to determine symmetry
+
+    Returns
+    -------
+    .Structure
+
+    """
+    sga = SpacegroupAnalyzer(structure, symprec=symprec)
+    return sga.get_conventional_standard_structure()