stjames 0.0.10__py3-none-any.whl → 0.0.12__py3-none-any.whl

stjames/basis_set.py

@@ -1,11 +1,27 @@
 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...

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/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/settings.py

@@ -57,7 +57,7 @@ class Settings(Base):
         if isinstance(v, (BasisSet, dict)):
             return v
         elif isinstance(v, str):
-            if len(str):
+            if len(v):
                 return BasisSet(name=v)
             else:
                 # "" is basically None, let's be real here...

{stjames-0.0.10.dist-info → stjames-0.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.10
+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-0.0.10.dist-info → stjames-0.0.12.dist-info}/RECORD

@@ -1,6 +1,6 @@
 stjames/__init__.py,sha256=Ug7W5de-chl5pK1KU5StVUReJAnw2G1g6zJpoBywmVY,407
 stjames/base.py,sha256=ww8aRYBC1w1mga90QVOSdtQO8Dh3mPFn4oP0woQ_9qQ,1069
-stjames/basis_set.py,sha256=l-K9yepRHE3mA_0eY3MVbtQQNxU8xoYkXL4Ap_EELS0,319
+stjames/basis_set.py,sha256=uax7wOv7C9640TMDOkFqTQvgZ5UxvyWx1Fp8-IGzils,935
 stjames/calculation.py,sha256=H2YubnWeWCg62MSdih4PT1jBqFosT8QZ1ioljOHvvTE,784
 stjames/corrections.py,sha256=vVO0CEBxWveCsWGd2Fa9D9eFeteFYB_bpa56T2f8S-Y,268
 stjames/diis_settings.py,sha256=vplTXRf_noJYJM3Qfre1aHsb9ZTfSrQAL7_zA41zvMg,546
@@ -9,14 +9,14 @@ stjames/int_settings.py,sha256=9B3Np7cV2A2C2PqUoxITHlJ2J90558thqkX2JDNxk-U,635
 stjames/methods.py,sha256=7cs5aaz1khuY1E9ozCYQvwkWdjhAMhfBIXc0pd6rU9w,369
 stjames/modes.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=cOtSI0pxyQeVLqR0E0owx4MU4HUor0c36kwUP9564wE,2820
-stjames/opt_settings.py,sha256=7qpMGq8dPLKLaZ7N-KAeal_VoEl40okfH9AvNCKXVuA,722
-stjames/scf_settings.py,sha256=17NwifBfbbnflVQQ2d3Fa1V6dd3eh4S1fTAAe5QbSM4,1854
-stjames/settings.py,sha256=eZ82WJklNLxa0dAUOaVDe4Lvu4eA3YTwc4f0S9IpIKQ,7150
+stjames/opt_settings.py,sha256=qhmhodrk0d3tGlBEl5RVCWvTYBzOKZTLdOqmkmRoF0I,735
+stjames/scf_settings.py,sha256=rsXk19OQmOLsiYT3vREEia4RMU89uMUQceVA1UsvlY0,2104
+stjames/settings.py,sha256=uMtILIxJ3dF1UI_V6Z-_bZr81j3fLAhoZx_796NBsJ8,7148
 stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/tasks.py,sha256=TTl-iTdvDNCZTdPsyS6bYmxzY0ez9PgYlL62fztayXQ,307
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
-stjames-0.0.10.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.10.dist-info/METADATA,sha256=Q4urDtTOVhxGXOa-i7Vp8vUzaN_XIfwg9Px-VpL3-GI,1605
-stjames-0.0.10.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-stjames-0.0.10.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.10.dist-info/RECORD,,
+stjames-0.0.12.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.12.dist-info/METADATA,sha256=9_RxJtFnM7V9LPwsvJsh3v7hN_rM2ytvtFD6i1Exv_I,1605
+stjames-0.0.12.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+stjames-0.0.12.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.12.dist-info/RECORD,,