stjames 0.0.14__tar.gz → 0.0.17__tar.gz

{stjames-0.0.14/stjames.egg-info → stjames-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.14
+Version: 0.0.17
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.14 → stjames-0.0.17}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.14"
+version = "0.0.17"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"

{stjames-0.0.14 → stjames-0.0.17}/stjames/__init__.py

@@ -7,6 +7,7 @@ from .scf_settings import *
 from .int_settings import *
 from .opt_settings import *
 from .diis_settings import *
+from .solvent_settings import *
 from .thermochem_settings import *
 from .grid_settings import *
 from .settings import *

{stjames-0.0.14 → stjames-0.0.17}/stjames/diis_settings.py

@@ -15,7 +15,7 @@ class DIISStrategy(LowercaseStrEnum):
 
 
 class DIISSettings(Base):
-    strategy: DIISStrategy = DIISStrategy.DIIS
+    strategy: DIISStrategy = DIISStrategy.ADIIS_DIIS
     subspace_size: pydantic.PositiveInt = 12
 
     # if it's a hybrid strategy, where do we transition?

{stjames-0.0.14 → stjames-0.0.17}/stjames/grid_settings.py

@@ -14,7 +14,7 @@ class GridSettings(Base):
     radial_grid_type: RadialGridType = RadialGridType.LMG
     angular_num_points: pydantic.PositiveInt = 434
 
-    weight_cutoff: pydantic.PositiveFloat = 1e-14
+    weight_cutoff: pydantic.PositiveFloat = 1e-11
 
     # for LMG
     radial_precision: pydantic.PositiveFloat = 1e-11

{stjames-0.0.14 → stjames-0.0.17}/stjames/int_settings.py

@@ -27,5 +27,5 @@ class IntSettings(Base):
 
     @property
     def resolution_of_the_identity(self) -> bool:
-        """ Abstracting in case we add RIJCOSX, etc later """
+        """Abstracting in case we add RIJCOSX, etc later"""
         return self.strategy == ERIStrategy.RIJK

{stjames-0.0.14 → stjames-0.0.17}/stjames/methods.py

@@ -21,3 +21,6 @@ class Method(LowercaseStrEnum):
     PBE0 = "pbe0"
     B3LYP = "b3lyp"
     B3PW91 = "b3pw91"
+
+    # ML methods
+    AIMNET2_WB97MD3 = "aimnet2_wb97md3"

{stjames-0.0.14 → stjames-0.0.17}/stjames/molecule.py

@@ -84,7 +84,7 @@ class Molecule(Base):
         if (num_electrons - num_unpaired_electrons) % 2 != 0:
             raise ValueError(
                 f"The combination of {num_electrons} electrons, charge {self.charge}, and multiplicity {self.multiplicity} is impossible. "
-                "Double-check the charge and multiplicity values given and verify that it's correct."
+                "Double-check the charge and multiplicity values given and verify that they are correct."
             )
 
         return self

{stjames-0.0.14 → stjames-0.0.17}/stjames/opt_settings.py

@@ -19,7 +19,7 @@ class Constraint(Base):
 
 
 class OptimizationSettings(Base):
-    max_steps: pydantic.PositiveInt = 100
+    max_steps: pydantic.PositiveInt = 250
     transition_state: bool = False
 
     # when are we converged?

{stjames-0.0.14 → stjames-0.0.17}/stjames/scf_settings.py

@@ -5,6 +5,7 @@ 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):
@@ -28,6 +29,7 @@ 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-0.0.14 → stjames-0.0.17}/stjames/settings.py

@@ -28,7 +28,7 @@ class Settings(Base):
     @pydantic.computed_field
     @property
     def level_of_theory(self) -> str:
-        if self.method in [Method.HF3C, Method.B973C]:
+        if self.method in [Method.HF3C, Method.B973C, Method.AIMNET2_WB97MD3]:
             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()}"
@@ -117,8 +117,8 @@ def _assign_settings_by_mode(settings: Settings) -> None:
         scf_settings.rms_error_threshold = 1e-8
         scf_settings.max_error_threshold = 1e-6
         scf_settings.rebuild_frequency = 20
-        scf_settings.int_settings.eri_threshold = 1e-8
-        scf_settings.int_settings.csam_multiplier = 5.0
+        scf_settings.int_settings.eri_threshold = 1e-9
+        scf_settings.int_settings.csam_multiplier = 1.0
         scf_settings.int_settings.pair_overlap_threshold = 1e-9
     elif mode == Mode.CAREFUL:
         scf_settings.energy_threshold = 1e-6
@@ -149,17 +149,20 @@ def _assign_settings_by_mode(settings: Settings) -> None:
 
     opt_settings = settings.opt_settings
 
+    # constrained optimizations warrant loosening the settings a bit
+    has_constraints = len(opt_settings.constraints) > 0
+
     # cf. DLFIND manual, and https://www.cup.uni-muenchen.de/ch/compchem/geom/basic.html
     # and the discussion at https://geometric.readthedocs.io/en/latest/how-it-works.html
     if mode == Mode.RECKLESS:
         opt_settings.energy_threshold = 1e-5
         opt_settings.max_gradient_threshold = 4.5e-3
         opt_settings.rms_gradient_threshold = 3e-3
-    elif mode == Mode.RAPID:
-        opt_settings.energy_threshold = 1e-6
+    elif (mode == Mode.RAPID) or (mode == Mode.CAREFUL and has_constraints):
+        opt_settings.energy_threshold = 5e-5
         opt_settings.max_gradient_threshold = 2.5e-3
         opt_settings.rms_gradient_threshold = 1.7e-3
-    elif mode == Mode.CAREFUL:
+    elif mode == Mode.CAREFUL or (mode == mode.METICULOUS and has_constraints):
         opt_settings.energy_threshold = 1e-6
         opt_settings.max_gradient_threshold = 4.5e-4
         opt_settings.rms_gradient_threshold = 3e-4

stjames-0.0.17/stjames/solvent_settings.py

@@ -0,0 +1,17 @@
+import pydantic
+
+from .base import Base, LowercaseStrEnum
+
+
+class ImplicitSolventModel(LowercaseStrEnum):
+    CPCM = "cpcm"
+    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-0.0.14 → stjames-0.0.17/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.14
+Version: 0.0.17
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.14 → stjames-0.0.17}/stjames.egg-info/SOURCES.txt

@@ -15,6 +15,7 @@ stjames/molecule.py
 stjames/opt_settings.py
 stjames/scf_settings.py
 stjames/settings.py
+stjames/solvent_settings.py
 stjames/status.py
 stjames/tasks.py
 stjames/thermochem_settings.py