single_point
Single point energy calculations for molecular structures.
ASESinglePoint
dataclass
Bases: PymatGenMaker[InputType, OutputType], SinglePointCalculation
flowchart TD
jfchemistry.single_point.ASESinglePoint[ASESinglePoint]
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker[PymatGenMaker]
jfchemistry.core.makers.jfchem_maker.JFChemMaker[JFChemMaker]
jfchemistry.core.makers.core_maker.CoreMaker[CoreMaker]
jfchemistry.single_point.base.SinglePointCalculation[SinglePointCalculation]
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker --> jfchemistry.single_point.ASESinglePoint
jfchemistry.core.makers.jfchem_maker.JFChemMaker --> jfchemistry.core.makers.pymatgen_maker.PymatGenMaker
jfchemistry.core.makers.core_maker.CoreMaker --> jfchemistry.core.makers.jfchem_maker.JFChemMaker
jfchemistry.single_point.base.SinglePointCalculation --> jfchemistry.single_point.ASESinglePoint
click jfchemistry.single_point.ASESinglePoint href "" "jfchemistry.single_point.ASESinglePoint"
click jfchemistry.core.makers.pymatgen_maker.PymatGenMaker href "" "jfchemistry.core.makers.pymatgen_maker.PymatGenMaker"
click jfchemistry.core.makers.jfchem_maker.JFChemMaker href "" "jfchemistry.core.makers.jfchem_maker.JFChemMaker"
click jfchemistry.core.makers.core_maker.CoreMaker href "" "jfchemistry.core.makers.core_maker.CoreMaker"
click jfchemistry.single_point.base.SinglePointCalculation href "" "jfchemistry.single_point.base.SinglePointCalculation"
Base class for single point energy calculations using ASE calculators.
Combines single point energy calculations with ASE calculator interfaces. This class provides the framework for calculating the single point energy of a structure using various ASE calculators (neural networks, machine learning , semi-empirical, etc.).
| ATTRIBUTE | DESCRIPTION |
|---|---|
name |
Name of the calculator (default: "ASE Single Point Calculator").
TYPE:
|
calculator |
The calculator to use for the calculation.
TYPE:
|
Source code in jfchemistry/single_point/ase.py
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make
make(input: InputType | list[InputType], **kwargs) -> Response[_output_model]
Create a workflow job for processing structure(s).
Automatically handles job distribution for lists of structures. Each structure in a list is processed as a separate job for parallel execution.
| PARAMETER | DESCRIPTION |
|---|---|
input
|
Single Pymatgen SiteCollection or list of SiteCollections.
TYPE:
|
**kwargs
|
Additional kwargs to pass to the operation.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
Response[_output_model]
|
Response containing: - structure: Processed structure(s) - files: XYZ format file(s) of the structure(s) - properties: Computed properties from the operation |
Examples:
>>> from jfchemistry.conformers import CRESTConformers
>>> from pymatgen.core import Molecule
>>> molecule = Molecule.from_ase_atoms(molecule("C2H6"))
>>> # Generate conformers
>>> conformer_gen = CRESTConformers(ewin=6.0)
>>> job = conformer_gen.make(input)
Source code in jfchemistry/core/makers/jfchem_maker.py
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ORCASinglePointCalculator
dataclass
Bases: SinglePointCalculation, PymatGenMaker[InputType, OutputType], ORCACalculator
flowchart TD
jfchemistry.single_point.ORCASinglePointCalculator[ORCASinglePointCalculator]
jfchemistry.single_point.base.SinglePointCalculation[SinglePointCalculation]
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker[PymatGenMaker]
jfchemistry.core.makers.jfchem_maker.JFChemMaker[JFChemMaker]
jfchemistry.core.makers.core_maker.CoreMaker[CoreMaker]
jfchemistry.calculators.orca.orca_calculator.ORCACalculator[ORCACalculator]
jfchemistry.calculators.base.WavefunctionCalculator[WavefunctionCalculator]
jfchemistry.calculators.base.Calculator[Calculator]
jfchemistry.single_point.base.SinglePointCalculation --> jfchemistry.single_point.ORCASinglePointCalculator
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker --> jfchemistry.single_point.ORCASinglePointCalculator
jfchemistry.core.makers.jfchem_maker.JFChemMaker --> jfchemistry.core.makers.pymatgen_maker.PymatGenMaker
jfchemistry.core.makers.core_maker.CoreMaker --> jfchemistry.core.makers.jfchem_maker.JFChemMaker
jfchemistry.calculators.orca.orca_calculator.ORCACalculator --> jfchemistry.single_point.ORCASinglePointCalculator
jfchemistry.calculators.base.WavefunctionCalculator --> jfchemistry.calculators.orca.orca_calculator.ORCACalculator
jfchemistry.calculators.base.Calculator --> jfchemistry.calculators.base.WavefunctionCalculator
click jfchemistry.single_point.ORCASinglePointCalculator href "" "jfchemistry.single_point.ORCASinglePointCalculator"
click jfchemistry.single_point.base.SinglePointCalculation href "" "jfchemistry.single_point.base.SinglePointCalculation"
click jfchemistry.core.makers.pymatgen_maker.PymatGenMaker href "" "jfchemistry.core.makers.pymatgen_maker.PymatGenMaker"
click jfchemistry.core.makers.jfchem_maker.JFChemMaker href "" "jfchemistry.core.makers.jfchem_maker.JFChemMaker"
click jfchemistry.core.makers.core_maker.CoreMaker href "" "jfchemistry.core.makers.core_maker.CoreMaker"
click jfchemistry.calculators.orca.orca_calculator.ORCACalculator href "" "jfchemistry.calculators.orca.orca_calculator.ORCACalculator"
click jfchemistry.calculators.base.WavefunctionCalculator href "" "jfchemistry.calculators.base.WavefunctionCalculator"
click jfchemistry.calculators.base.Calculator href "" "jfchemistry.calculators.base.Calculator"
Calculate the single point energy of a structure using ORCA DFT calculator.
Inherits all attributes from ORCACalculator.
| ATTRIBUTE | DESCRIPTION |
|---|---|
name |
Name of the calculator (default: "ORCA Single Point Calculator").
TYPE:
|
basename |
Basename of the calculator (default: "orca_single_point").
TYPE:
|
Source code in jfchemistry/single_point/orca.py
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make
make(input: InputType | list[InputType], **kwargs) -> Response[_output_model]
Create a workflow job for processing structure(s).
Automatically handles job distribution for lists of structures. Each structure in a list is processed as a separate job for parallel execution.
| PARAMETER | DESCRIPTION |
|---|---|
input
|
Single Pymatgen SiteCollection or list of SiteCollections.
TYPE:
|
**kwargs
|
Additional kwargs to pass to the operation.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
Response[_output_model]
|
Response containing: - structure: Processed structure(s) - files: XYZ format file(s) of the structure(s) - properties: Computed properties from the operation |
Examples:
>>> from jfchemistry.conformers import CRESTConformers
>>> from pymatgen.core import Molecule
>>> molecule = Molecule.from_ase_atoms(molecule("C2H6"))
>>> # Generate conformers
>>> conformer_gen = CRESTConformers(ewin=6.0)
>>> job = conformer_gen.make(input)
Source code in jfchemistry/core/makers/jfchem_maker.py
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PySCFGPUSinglePoint
dataclass
Bases: PySCFCalculator, PymatGenMaker[InputType, OutputType], SinglePointCalculation
flowchart TD
jfchemistry.single_point.PySCFGPUSinglePoint[PySCFGPUSinglePoint]
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker[PymatGenMaker]
jfchemistry.core.makers.jfchem_maker.JFChemMaker[JFChemMaker]
jfchemistry.core.makers.core_maker.CoreMaker[CoreMaker]
jfchemistry.single_point.base.SinglePointCalculation[SinglePointCalculation]
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker --> jfchemistry.single_point.PySCFGPUSinglePoint
jfchemistry.core.makers.jfchem_maker.JFChemMaker --> jfchemistry.core.makers.pymatgen_maker.PymatGenMaker
jfchemistry.core.makers.core_maker.CoreMaker --> jfchemistry.core.makers.jfchem_maker.JFChemMaker
jfchemistry.single_point.base.SinglePointCalculation --> jfchemistry.single_point.PySCFGPUSinglePoint
click jfchemistry.single_point.PySCFGPUSinglePoint href "" "jfchemistry.single_point.PySCFGPUSinglePoint"
click jfchemistry.core.makers.pymatgen_maker.PymatGenMaker href "" "jfchemistry.core.makers.pymatgen_maker.PymatGenMaker"
click jfchemistry.core.makers.jfchem_maker.JFChemMaker href "" "jfchemistry.core.makers.jfchem_maker.JFChemMaker"
click jfchemistry.core.makers.core_maker.CoreMaker href "" "jfchemistry.core.makers.core_maker.CoreMaker"
click jfchemistry.single_point.base.SinglePointCalculation href "" "jfchemistry.single_point.base.SinglePointCalculation"
PySCF GPU Calculator with full type support.
This calculator wraps the PySCF GPU package to provide DFT calculation capabilities.
| ATTRIBUTE | DESCRIPTION |
|---|---|
name |
Name of the calculator (default: "PySCF GPU").
TYPE:
|
cores |
Number of CPU cores to use for parallel calculations (default: 1).
TYPE:
|
basis_set |
Basis set to use for the calculation (488 options available).
TYPE:
|
xc_functional |
Exchange-correlation functional to use (195 options available).
TYPE:
|
Source code in jfchemistry/single_point/pyscfgpu.py
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make
make(input: InputType | list[InputType], **kwargs) -> Response[_output_model]
Create a workflow job for processing structure(s).
Automatically handles job distribution for lists of structures. Each structure in a list is processed as a separate job for parallel execution.
| PARAMETER | DESCRIPTION |
|---|---|
input
|
Single Pymatgen SiteCollection or list of SiteCollections.
TYPE:
|
**kwargs
|
Additional kwargs to pass to the operation.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
Response[_output_model]
|
Response containing: - structure: Processed structure(s) - files: XYZ format file(s) of the structure(s) - properties: Computed properties from the operation |
Examples:
>>> from jfchemistry.conformers import CRESTConformers
>>> from pymatgen.core import Molecule
>>> molecule = Molecule.from_ase_atoms(molecule("C2H6"))
>>> # Generate conformers
>>> conformer_gen = CRESTConformers(ewin=6.0)
>>> job = conformer_gen.make(input)
Source code in jfchemistry/core/makers/jfchem_maker.py
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TorchSimSinglePoint
dataclass
Bases: SinglePointCalculation, PymatGenMaker[InputType, OutputType], TorchSimCalculator
flowchart TD
jfchemistry.single_point.TorchSimSinglePoint[TorchSimSinglePoint]
jfchemistry.single_point.base.SinglePointCalculation[SinglePointCalculation]
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker[PymatGenMaker]
jfchemistry.core.makers.jfchem_maker.JFChemMaker[JFChemMaker]
jfchemistry.core.makers.core_maker.CoreMaker[CoreMaker]
jfchemistry.calculators.torchsim.torchsim_calculator.TorchSimCalculator[TorchSimCalculator]
jfchemistry.calculators.base.Calculator[Calculator]
jfchemistry.single_point.base.SinglePointCalculation --> jfchemistry.single_point.TorchSimSinglePoint
jfchemistry.core.makers.pymatgen_maker.PymatGenMaker --> jfchemistry.single_point.TorchSimSinglePoint
jfchemistry.core.makers.jfchem_maker.JFChemMaker --> jfchemistry.core.makers.pymatgen_maker.PymatGenMaker
jfchemistry.core.makers.core_maker.CoreMaker --> jfchemistry.core.makers.jfchem_maker.JFChemMaker
jfchemistry.calculators.torchsim.torchsim_calculator.TorchSimCalculator --> jfchemistry.single_point.TorchSimSinglePoint
jfchemistry.calculators.base.Calculator --> jfchemistry.calculators.torchsim.torchsim_calculator.TorchSimCalculator
click jfchemistry.single_point.TorchSimSinglePoint href "" "jfchemistry.single_point.TorchSimSinglePoint"
click jfchemistry.single_point.base.SinglePointCalculation href "" "jfchemistry.single_point.base.SinglePointCalculation"
click jfchemistry.core.makers.pymatgen_maker.PymatGenMaker href "" "jfchemistry.core.makers.pymatgen_maker.PymatGenMaker"
click jfchemistry.core.makers.jfchem_maker.JFChemMaker href "" "jfchemistry.core.makers.jfchem_maker.JFChemMaker"
click jfchemistry.core.makers.core_maker.CoreMaker href "" "jfchemistry.core.makers.core_maker.CoreMaker"
click jfchemistry.calculators.torchsim.torchsim_calculator.TorchSimCalculator href "" "jfchemistry.calculators.torchsim.torchsim_calculator.TorchSimCalculator"
click jfchemistry.calculators.base.Calculator href "" "jfchemistry.calculators.base.Calculator"
Base class for single point energy calculations using TorchSim calculators.
Combines single point energy calculations with TorchSim calculator interfaces. This class provides the framework for calculating the single point energy of a structure using various TorchSim calculators (neural networks, machine learning , semi-empirical, etc.).
| ATTRIBUTE | DESCRIPTION |
|---|---|
name |
Name of the calculator (default: "ASE Single Point Calculator").
TYPE:
|
Source code in jfchemistry/single_point/torchsim.py
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make
make(input: InputType | list[InputType], **kwargs) -> Response[_output_model]
Create a workflow job for processing structure(s).
Automatically handles job distribution for lists of structures. Each structure in a list is processed as a separate job for parallel execution.
| PARAMETER | DESCRIPTION |
|---|---|
input
|
Single Pymatgen SiteCollection or list of SiteCollections.
TYPE:
|
**kwargs
|
Additional kwargs to pass to the operation.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
Response[_output_model]
|
Response containing: - structure: Processed structure(s) - files: XYZ format file(s) of the structure(s) - properties: Computed properties from the operation |
Examples:
>>> from jfchemistry.conformers import CRESTConformers
>>> from pymatgen.core import Molecule
>>> molecule = Molecule.from_ase_atoms(molecule("C2H6"))
>>> # Generate conformers
>>> conformer_gen = CRESTConformers(ewin=6.0)
>>> job = conformer_gen.make(input)
Source code in jfchemistry/core/makers/jfchem_maker.py
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