stjames 0.0.19__py3-none-any.whl → 0.0.22__py3-none-any.whl

stjames/__init__.py

@@ -10,6 +10,7 @@ from .diis_settings import *
 from .solvent_settings import *
 from .thermochem_settings import *
 from .grid_settings import *
+from .solvent_settings import *
 from .settings import *
 
 from .methods import *

stjames/_deprecated_solvent_settings.py

@@ -0,0 +1,19 @@
+import pydantic
+
+from .base import Base, LowercaseStrEnum
+
+
+class ImplicitSolventModel(LowercaseStrEnum):
+    CPCM = "cpcm"
+    ALPB = "alpb"
+    COSMO = "cosmo"
+    NONE = "none"
+
+
+class SolventSettings(Base):
+    model: ImplicitSolventModel = ImplicitSolventModel.NONE
+    epsilon: float = 78.36
+
+    grid_points_per_atom: pydantic.PositiveInt = 170
+    vdw_scale: pydantic.PositiveFloat = 1.2
+    weight_cutoff: pydantic.PositiveFloat = 1e-8

stjames/methods.py

@@ -17,10 +17,31 @@ class Method(LowercaseStrEnum):
     B97D3 = "b97-d3"
     B973C = "b97-3c"
 
+    # mGGA
+    R2SCAN = "r2scan"
+    TPSS = "tpss"
+    M06L = "m06l"
+
     # hybrid GGA
     PBE0 = "pbe0"
     B3LYP = "b3lyp"
     B3PW91 = "b3pw91"
+    B97MV = "b97m_v"
+
+    # hybrid mGGA
+    TPSS0 = "tpss0"
+    M06 = "m06"
+    M062X = "m062x"
+
+    # range-separated
+    CAMB3LYP = "camb3lyp"
+    WB97XD = "wb97x_d"
+    WB97XV = "wb97x_v"
+    WB97MV = "wb97m_v"
 
     # ML methods
     AIMNET2_WB97MD3 = "aimnet2_wb97md3"
+
+    # xTB methods
+    GFN1_XTB = "gfn1_xtb"
+    GFN2_XTB = "gfn2_xtb"

stjames/scf_settings.py

@@ -5,7 +5,6 @@ from .base import Base, LowercaseStrEnum
 from .int_settings import IntSettings
 from .grid_settings import GridSettings
 from .diis_settings import DIISSettings
-from .solvent_settings import SolventSettings
 
 
 class SCFInitMethod(LowercaseStrEnum):
@@ -29,7 +28,6 @@ class SCFSettings(Base):
     int_settings: IntSettings = IntSettings()
     grid_settings: GridSettings = GridSettings()
     diis_settings: DIISSettings = DIISSettings()
-    solvent_settings: SolventSettings = SolventSettings()
 
     #### orthonormalization
     orthonormalization: OrthonormalizationMethod = OrthonormalizationMethod.CANONICAL

stjames/settings.py

@@ -10,16 +10,19 @@ from .scf_settings import SCFSettings
 from .basis_set import BasisSet
 from .opt_settings import OptimizationSettings
 from .thermochem_settings import ThermochemistrySettings
+from .solvent_settings import SolventSettings
 
 
 class Settings(Base):
     method: Method = Method.HARTREE_FOCK
-    basis_set: Optional[BasisSet] = BasisSet(name="STO-3G")
+    basis_set: Optional[BasisSet] = None
     tasks: UniqueList[Task] = [Task.ENERGY, Task.CHARGE, Task.DIPOLE]
     corrections: UniqueList[Correction] = []
 
     mode: Mode = Mode.AUTO
 
+    solvent_settings: Optional[SolventSettings] = None
+
     # scf/opt settings will be set automatically based on mode, but can be overridden manually
     scf_settings: SCFSettings = SCFSettings()
     opt_settings: OptimizationSettings = OptimizationSettings()
@@ -30,8 +33,8 @@ class Settings(Base):
     def level_of_theory(self) -> str:
         if self.method in [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3] or self.basis_set is None:
             return self.method.value
-        elif (len(self.corrections)) == 0 or (self.method in [Method.B97D3]):
-            return f"{self.method.value}/{self.basis_set.name.lower()}"
+        #        elif (len(self.corrections)) == 0 or (self.method in [Method.B97D3]):
+        #            return f"{self.method.value}/{self.basis_set.name.lower()}"
         else:
             return f"{self.method.value}-{'-'.join([c.value for c in self.corrections])}/{self.basis_set.name.lower()}"
 
@@ -63,12 +66,18 @@ class Settings(Base):
                 return BasisSet(name=v)
             else:
                 # "" is basically None, let's be real here...
-                return BasisSet(name="STO-3G")
+                return None
         elif v is None:
             return None
         else:
             raise ValueError(f"invalid value ``{v}`` for ``basis_set``")
 
+    @pydantic.field_validator("corrections", mode="before")
+    @classmethod
+    def remove_empty_string(cls, v: list) -> list:
+        """ Remove empty string values. """
+        return [c for c in v if c]
+
 
 def _assign_settings_by_mode(settings: Settings) -> None:
     """Modifies ``scf_settings`` and ``opt_settings`` based on preset ``mode``."""
@@ -76,7 +85,11 @@ def _assign_settings_by_mode(settings: Settings) -> None:
 
     if mode == Mode.AUTO:
         if (Task.OPTIMIZE in settings.tasks) or (Task.GRADIENT in settings.tasks) or (Task.FREQUENCIES in settings.tasks) or (Task.HESSIAN in settings.tasks):
-            mode = Mode.CAREFUL
+            # noisy gradient! struggles to converge
+            if settings.method == Method.AIMNET2_WB97MD3:
+                mode = Mode.RAPID
+            else:
+                mode = Mode.CAREFUL
         else:
             mode = Mode.RAPID
     elif mode == Mode.MANUAL:

stjames/solvent_settings.py

@@ -1,17 +1,41 @@
-import pydantic
-
 from .base import Base, LowercaseStrEnum
 
 
-class ImplicitSolventModel(LowercaseStrEnum):
+class Solvent(LowercaseStrEnum):
+    WATER = "water"
+    NITROMETHANE = "nitromethane"
+    NITROBENZENE = "nitrobenzene"
+    TOLUENE = "toluene"
+    BENZENE = "benzene"
+    CHLOROBENZENE = "chlorobenzene"
+    CARBONTETRACHLORIDE = "carbontetrachloride"
+    DICHLOROETHANE = "dichloroethane"
+    DICHLOROMETHANE = "dichloromethane"
+    CHLOROFORM = "chloroform"
+    DIETHYLETHER = "diethylether"
+    DIISOPROPYLETHER = "diisopropylether"
+    DIMETHYLSULFOXIDE = "dimethylsulfoxide"
+    TETRAHYDROFURAN = "tetrahydrofuran"
+    CYCLOHEXANE = "cyclohexane"
+    OCTANE = "octane"
+    ACETICACID = "aceticacid"
+    HEXANE = "hexane"
+    ETHYLACETATE = "ethylacetate"
+    ACETONE = "acetone"
+    ACETONITRILE = "acetonitrile"
+    METHANOL = "methanol"
+    ETHANOL = "ethanol"
+    ISOPROPANOL = "isopropanol"
+    DIMETHYLACETAMIDE = "dimethylacetamide"
+    DIMETHYLFORMAMIDE = "dimethylformamide"
+
+
+class SolventModel(LowercaseStrEnum):
     CPCM = "cpcm"
-    NONE = "none"
+    ALPB = "alpb"
+    COSMO = "cosmo"
 
 
 class SolventSettings(Base):
-    model: ImplicitSolventModel = ImplicitSolventModel.NONE
-    epsilon: float = 78.36
-
-    grid_points_per_atom: pydantic.PositiveInt = 170
-    vdw_scale: pydantic.PositiveFloat = 1.2
-    weight_cutoff: pydantic.PositiveFloat = 1e-8
+    solvent: Solvent
+    model: SolventModel

{stjames-0.0.19.dist-info → stjames-0.0.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.19
+Version: 0.0.22
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.19.dist-info → stjames-0.0.22.dist-info}/RECORD

@@ -1,4 +1,5 @@
-stjames/__init__.py,sha256=7uBcI929i2iKK96sEC6V59WII3TRgYWpvMbGGg6Gx0k,439
+stjames/__init__.py,sha256=yQF57YFNAXtZ7vqG89cRf1Pk4hKRCYlaTNzX4JkhHoo,471
+stjames/_deprecated_solvent_settings.py,sha256=ALUZeQoxDS11EvZexT1J2SDAlLTiXe-x4jV8tenDqMc,445
 stjames/base.py,sha256=ww8aRYBC1w1mga90QVOSdtQO8Dh3mPFn4oP0woQ_9qQ,1069
 stjames/basis_set.py,sha256=uax7wOv7C9640TMDOkFqTQvgZ5UxvyWx1Fp8-IGzils,935
 stjames/calculation.py,sha256=H2YubnWeWCg62MSdih4PT1jBqFosT8QZ1ioljOHvvTE,784
@@ -6,18 +7,18 @@ stjames/corrections.py,sha256=vVO0CEBxWveCsWGd2Fa9D9eFeteFYB_bpa56T2f8S-Y,268
 stjames/diis_settings.py,sha256=QHc7L-hktkbOWBYr29byTdqL8lWJzKJiY9XW8ha4Qzo,552
 stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
 stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
-stjames/methods.py,sha256=gYf5NLbWdmbwy4yvpRpCUVMKokwAXPXGV1Yrr9LED08,427
+stjames/methods.py,sha256=pevOgDxVrPFfw51E8avaxNtcyoMjIe_sx_HkW1FrboQ,782
 stjames/modes.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=2_cBc-00dM7I6J9_TFZTaomyUXlYHA4fP0Erb3zGVdM,2824
 stjames/opt_settings.py,sha256=RwXikvwW6fTODK3FK8Xvyqy4DY-qMVtZHndWirBxujk,735
-stjames/scf_settings.py,sha256=mk1wWmGnjcmEEifo1aNKIAGeOeOEaPHDPCvFOLvBIYE,2492
-stjames/settings.py,sha256=NbPIM9YMCM3T-Dtu76l0gkhagQao2lXvTaP9l6D4VeM,7533
-stjames/solvent_settings.py,sha256=UaR_klyQiXhB8D8Pa0-7p62N-p_JPzjdbMlfTggKXxk,407
+stjames/scf_settings.py,sha256=e31f1mWRmcFkMnc-loQak_2037L-l4AYpnl-glchrCc,2388
+stjames/settings.py,sha256=VgIHvyNoTuf26eLg-OdGxKoKw3WOSq14frKgI2Y63MQ,7989
+stjames/solvent_settings.py,sha256=3ssY-vQCCa071srfJbwCYEKDpWos8Mgvmg_dTpAnbJw,1104
 stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/tasks.py,sha256=TTl-iTdvDNCZTdPsyS6bYmxzY0ez9PgYlL62fztayXQ,307
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
-stjames-0.0.19.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.19.dist-info/METADATA,sha256=2sGnZA_j4314nl38t7cVdWTh8Dl6-dWRuKXEULvhkV0,1605
-stjames-0.0.19.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-stjames-0.0.19.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.19.dist-info/RECORD,,
+stjames-0.0.22.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.22.dist-info/METADATA,sha256=BAjMIYp4hBGY723lKFcoA5zg7aHYrnodsCifjTRBeD8,1605
+stjames-0.0.22.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+stjames-0.0.22.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.22.dist-info/RECORD,,