stjames 0.0.37__tar.gz → 0.0.39__tar.gz

{stjames-0.0.37/stjames.egg-info → stjames-0.0.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.37
+Version: 0.0.39
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.37 → stjames-0.0.39}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.37"
+version = "0.0.39"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"

{stjames-0.0.37 → stjames-0.0.39}/stjames/base.py

@@ -18,13 +18,13 @@ class Base(pydantic.BaseModel):
 
 
 class LowercaseStrEnum(str, Enum):
-    """Enum where hyphens and case are ignored."""
+    """Enum where hyphens, underscores, and case are ignored."""
 
     @classmethod
     def _missing_(cls, value: str) -> str | None:  # type: ignore
         # Type note: technically breaking Liskov, value: object in Enum
         for member in cls:
-            if member.lower().replace("-", "") == value.lower().replace("-", ""):
+            if member.lower().replace("-", "").replace("_", "") == value.lower().replace("-", "").replace("_", ""):
                 return member
         return None
 

{stjames-0.0.37 → stjames-0.0.39}/stjames/method.py

@@ -2,48 +2,37 @@ from .base import LowercaseStrEnum
 
 
 class Method(LowercaseStrEnum):
-    #### Hartree–Fock:
     HARTREE_FOCK = "hf"
-    HF3C = "hf-3c"
+    HF3C = "hf_3c"
 
-    #### DFT:
-    # LDA
-    LSDA = "lsda"
-
-    # local GGA
     PBE = "pbe"
-    BLYP = "blyp"
-    BP86 = "bp86"
-    B97D3 = "b97-d3"
-    B973C = "b97-3c"
-
-    # mGGA
+    B973C = "b97_3c"
     R2SCAN = "r2scan"
+    R2SCAN3C = "r2scan_3c"
     TPSS = "tpss"
     M06L = "m06l"
 
-    # hybrid GGA
     PBE0 = "pbe0"
     B3LYP = "b3lyp"
-    B3PW91 = "b3pw91"
-    B97MV = "b97m_v"
-
-    # hybrid mGGA
-    TPSS0 = "tpss0"
+    TPSSH = "tpssh"
     M06 = "m06"
     M062X = "m062x"
 
-    # range-separated
     CAMB3LYP = "camb3lyp"
-    WB97XD = "wb97x_d"
     WB97XD3 = "wb97x_d3"
     WB97XV = "wb97x_v"
     WB97MV = "wb97m_v"
+    WB97MD3BJ = "wb97m_d3bj"
+    WB97X3C = "wb97x_3c"
+
+    DSDBLYPD3BJ = "dsd_blyp_d3bj"
 
-    # ML methods
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
-    AIMNET2_B973C = "aimnet2_b973c"
 
-    # xTB methods
+    GFN0_XTB = "gfn0_xtb"
     GFN1_XTB = "gfn1_xtb"
     GFN2_XTB = "gfn2_xtb"
+    GFN_FF = "gfn_ff"
+
+    # this was going to be removed, but Jonathon wrote such a nice basis set test... it's off the front end.
+    BP86 = "bp86"

{stjames-0.0.37 → stjames-0.0.39}/stjames/molecule.py

@@ -10,7 +10,7 @@ from .base import Base
 
 
 class VibrationalMode(Base):
-    frequency: float
+    frequency: float  # in cm-1
     reduced_mass: float
     force_constant: float
     displacements: list[list[float]]
@@ -18,7 +18,7 @@ class VibrationalMode(Base):
 
 class Atom(Base):
     atomic_number: NonNegativeInt
-    position: list[float]
+    position: list[float]  # in Å
 
 
 class Molecule(Base):
@@ -26,10 +26,10 @@ class Molecule(Base):
     multiplicity: PositiveInt
     atoms: list[Atom]
 
-    energy: Optional[float] = None
+    energy: Optional[float] = None  # in Hartree
     scf_iterations: Optional[NonNegativeInt] = None
     scf_completed: Optional[bool] = None
-    elapsed: Optional[float] = None
+    elapsed: Optional[float] = None  # in seconds
 
     homo_lumo_gap: Optional[float] = None  # in eV
 
@@ -37,7 +37,7 @@ class Molecule(Base):
 
     mulliken_charges: Optional[list[float]] = None
     mulliken_spin_densities: Optional[list[float]] = None
-    dipole: Optional[list[float]] = None
+    dipole: Optional[list[float]] = None  # in Debye
 
     vibrational_modes: Optional[list[VibrationalMode]] = None
 

{stjames-0.0.37 → stjames-0.0.39}/stjames/settings.py

@@ -16,18 +16,20 @@ from .thermochem_settings import ThermochemistrySettings
 PREPACKAGED_METHODS = [
     Method.HF3C,
     Method.B973C,
+    Method.R2SCAN3C,
     Method.AIMNET2_WB97MD3,
-    Method.AIMNET2_B973C,
     Method.GFN2_XTB,
     Method.GFN1_XTB,
+    Method.GFN0_XTB,
+    Method.GFN_FF,
 ]
 
 METHODS_WITH_CORRECTION = [
-    Method.B97D3,
-    Method.WB97XD,
     Method.WB97XD3,
     Method.WB97XV,
     Method.WB97MV,
+    Method.WB97MD3BJ,
+    Method.DSDBLYPD3BJ,
 ]
 
 T = TypeVar("T")
@@ -48,15 +50,17 @@ class Settings(Base):
     opt_settings: OptimizationSettings = OptimizationSettings()
     thermochem_settings: ThermochemistrySettings = ThermochemistrySettings()
 
+    # mypy has this dead wrong (https://docs.pydantic.dev/2.0/usage/computed_fields/)
+    @pydantic.computed_field  # type: ignore[misc]
     @property
-    @pydantic.computed_field
     def level_of_theory(self) -> str:
+        corrections = list(filter(lambda x: x not in (None, ""), self.corrections))
+
         if self.method in PREPACKAGED_METHODS or self.basis_set is None:
             method = self.method.value
-        elif self.method in METHODS_WITH_CORRECTION:
+        elif self.method in METHODS_WITH_CORRECTION or len(corrections) == 0:
             method = f"{self.method.value}/{self.basis_set.name.lower()}"
         else:
-            corrections = list(filter(lambda x: x not in (None, ""), self.corrections))
             method = f"{self.method.value}-{'-'.join([c.value for c in corrections])}/{self.basis_set.name.lower()}"
 
         if self.solvent_settings is not None:

{stjames-0.0.37 → stjames-0.0.39}/stjames/solvent.py

@@ -31,6 +31,7 @@ class Solvent(LowercaseStrEnum):
 
 
 class SolventModel(LowercaseStrEnum):
+    PCM = "pcm"
     CPCM = "cpcm"
     ALPB = "alpb"
     COSMO = "cosmo"

{stjames-0.0.37 → stjames-0.0.39}/stjames/workflows/conformer.py

@@ -48,7 +48,7 @@ class ConformerWorkflow(Workflow):
         self.settings = csearch_settings_by_mode(self.mode, self.settings)
 
 
-def csearch_settings_by_mode(mode: Mode, old_settings: Optional[ConformerSettings]) -> ConformerSettings:
+def csearch_settings_by_mode(mode: Mode, old_settings: Optional[ConformerSettings] = None) -> ConformerSettings:
     if mode == Mode.MANUAL:
         assert old_settings is not None
         return old_settings

{stjames-0.0.37 → stjames-0.0.39/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.37
+Version: 0.0.39
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames