stjames 0.0.11__tar.gz → 0.0.12__tar.gz

{stjames-0.0.11/stjames.egg-info → stjames-0.0.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.11
+Version: 0.0.12
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.11 → stjames-0.0.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.11"
+version = "0.0.12"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"

stjames-0.0.12/stjames/basis_set.py

@@ -0,0 +1,28 @@
+import pydantic
+from typing import Optional, Self
+
+from .base import Base
+
+
+class BasisSetOverride(Base):
+    name: str
+    atomic_numbers: Optional[list[pydantic.PositiveInt]] = None
+    atoms: Optional[list[pydantic.PositiveInt]] = None  # 1-indexed
+
+    @pydantic.model_validator(mode="after")
+    def check_override(self) -> Self:
+        # ^ is xor
+        assert (self.atomic_numbers is not None) ^ (self.atoms is not None), "Exactly one of ``atomic_numbers`` or ``atoms`` must be specified!"
+        return self
+
+
+class BasisSet(Base):
+    name: str
+
+    # do we want to override the default basis set for specific atoms or elements?
+    overrides: Optional[list[BasisSetOverride]] = []
+
+    # value below which a basis function can be ignored
+    # (for improving DFT grid calcs, as per Stratmann/Scuseria/Frisch CPL 1996)
+    # this shouldn't really need to be modified...
+    cutoff_threshold: pydantic.PositiveFloat = 1e-10

{stjames-0.0.11 → stjames-0.0.12}/stjames/opt_settings.py

@@ -15,7 +15,7 @@ class Constraint(Base):
     """Represents a single constraint."""
 
     constraint_type: ConstraintType
-    atoms: list[int]
+    atoms: list[int]  # 1-indexed
 
 
 class OptimizationSettings(Base):

{stjames-0.0.11 → stjames-0.0.12}/stjames/scf_settings.py

@@ -15,6 +15,12 @@ class SCFInitMethod(LowercaseStrEnum):
     READ = "read"
 
 
+class OrthonormalizationMethod(LowercaseStrEnum):
+    SYMMETRIC = "symmetric"
+    CANONICAL = "canonical"
+    # cholesky, in future?
+
+
 class SCFSettings(Base):
     max_iters: int = 100
     init_method: SCFInitMethod = SCFInitMethod.SAD
@@ -23,6 +29,9 @@ class SCFSettings(Base):
     grid_settings: GridSettings = GridSettings()
     diis_settings: DIISSettings = DIISSettings()
 
+    #### orthonormalization
+    orthonormalization: OrthonormalizationMethod = OrthonormalizationMethod.CANONICAL
+
     #### damping
     do_damping: bool = True
     # when should we stop damping?

{stjames-0.0.11 → stjames-0.0.12/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.11
+Version: 0.0.12
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

stjames-0.0.11/stjames/basis_set.py

@@ -1,12 +0,0 @@
-import pydantic
-
-from .base import Base
-
-
-class BasisSet(Base):
-    name: str
-
-    # value below which a basis function can be ignored
-    # (for improving DFT grid calcs, as per Stratmann/Scuseria/Frisch CPL 1996)
-    # this shouldn't really need to be modified...
-    cutoff_threshold: pydantic.PositiveFloat = 1e-10