mat3ra-esse 2024.4.8.post1__py3-none-any.whl → 2024.4.8.post3__py3-none-any.whl

mat3ra/esse/models/software_directory/ml/unit/processing/feature_selection/__init__.py

@@ -0,0 +1,180 @@
+# generated by datamodel-codegen:
+#   filename:  software_directory/ml/unit/processing/feature_selection.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, ConfigDict, Field, RootModel
+
+
+class Operation(Enum):
+    feature_selection = "feature_selection"
+
+
+class OperationType(Enum):
+    filter_based = "filter_based"
+
+
+class Algorithm(Enum):
+    f_regression = "f_regression"
+
+
+class InputData(BaseModel):
+    nFeatures: float
+    """
+    number of features to select for model training. If equal to 0, will use all available features
+    """
+    algorithm: Algorithm
+    """
+    feature selection algorithm following sklearn.feature_selection
+    """
+
+
+class Type(Enum):
+    processing = "processing"
+
+
+class Status(Enum):
+    idle = "idle"
+    active = "active"
+    warning = "warning"
+    error = "error"
+    finished = "finished"
+
+
+class Name(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class ConsistencyCheck(BaseModel):
+    key: str
+    """
+    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+    """
+    name: Name
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    severity: Severity
+    """
+    Severity level of the problem, which is used in UI to differentiate.
+    """
+    message: str
+    """
+    Message generated by the consistency check describing the problem.
+    """
+
+
+class NameResultSchema(BaseModel):
+    name: str
+    """
+    The name of this item. e.g. scf_accuracy
+    """
+
+
+class StatusTrackItem(BaseModel):
+    trackedAt: float
+    status: str
+    repetition: Optional[float] = None
+
+
+class FilterBasedFeatureSelectionUnitSchema(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    operation: Operation
+    """
+    Contains information about the operation used.
+    """
+    operationType: OperationType
+    """
+    Contains information about the specific type of the operation used.
+    """
+    inputData: InputData
+    """
+    unit input (type to be specified by the child units)
+    """
+    type: Type
+    """
+    type of the unit
+    """
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    isDraft: Optional[bool] = None
+    name: Optional[str] = None
+    """
+    name of the unit. e.g. pw_scf
+    """
+    status: Optional[Status] = None
+    """
+    Status of the unit.
+    """
+    head: Optional[bool] = None
+    """
+    Whether this unit is the first one to be executed.
+    """
+    flowchartId: str
+    """
+    Identity of the unit in the workflow. Used to trace the execution flow of the workflow.
+    """
+    next: Optional[str] = None
+    """
+    Next unit's flowchartId. If empty, the current unit is the last.
+    """
+    enableRender: Optional[bool] = None
+    """
+    Whether Rupy should attempt to use Jinja templating to add context variables into the unit
+    """
+    context: Optional[Dict[str, Any]] = None
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    consistencyChecks: Optional[List[ConsistencyCheck]] = None
+    schemaVersion: Optional[str] = "2022.8.16"
+    """
+    entity's schema version. Used to distinct between different schemas.
+    """
+    isDefault: Optional[bool] = False
+    """
+    Identifies that entity is defaultable
+    """
+    preProcessors: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the pre-processors for this calculation
+    """
+    postProcessors: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the post-processors for this calculation
+    """
+    monitors: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the monitors for this calculation
+    """
+    results: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the results for this calculation
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """
+    statusTrack: Optional[List[StatusTrackItem]] = None
+
+
+class ESSE(RootModel[FilterBasedFeatureSelectionUnitSchema]):
+    root: FilterBasedFeatureSelectionUnitSchema

mat3ra/esse/models/software_directory/ml/unit/processing/feature_selection/filter_based.py

@@ -0,0 +1,176 @@
+# generated by datamodel-codegen:
+#   filename:  software_directory/ml/unit/processing/feature_selection/filter_based.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Any, Dict, List, Optional, Union
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class Operation(Enum):
+    feature_selection = "feature_selection"
+
+
+class OperationType(Enum):
+    filter_based = "filter_based"
+
+
+class Algorithm(Enum):
+    f_regression = "f_regression"
+
+
+class InputData(BaseModel):
+    nFeatures: float
+    """
+    number of features to select for model training. If equal to 0, will use all available features
+    """
+    algorithm: Algorithm
+    """
+    feature selection algorithm following sklearn.feature_selection
+    """
+
+
+class Type(Enum):
+    processing = "processing"
+
+
+class Status(Enum):
+    idle = "idle"
+    active = "active"
+    warning = "warning"
+    error = "error"
+    finished = "finished"
+
+
+class Name(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class ConsistencyCheck(BaseModel):
+    key: str
+    """
+    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+    """
+    name: Name
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    severity: Severity
+    """
+    Severity level of the problem, which is used in UI to differentiate.
+    """
+    message: str
+    """
+    Message generated by the consistency check describing the problem.
+    """
+
+
+class NameResultSchema(BaseModel):
+    name: str
+    """
+    The name of this item. e.g. scf_accuracy
+    """
+
+
+class StatusTrackItem(BaseModel):
+    trackedAt: float
+    status: str
+    repetition: Optional[float] = None
+
+
+class FilterBasedFeatureSelectionUnitSchema(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    operation: Operation
+    """
+    Contains information about the operation used.
+    """
+    operationType: OperationType
+    """
+    Contains information about the specific type of the operation used.
+    """
+    inputData: InputData
+    """
+    unit input (type to be specified by the child units)
+    """
+    type: Type
+    """
+    type of the unit
+    """
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    isDraft: Optional[bool] = None
+    name: Optional[str] = None
+    """
+    name of the unit. e.g. pw_scf
+    """
+    status: Optional[Status] = None
+    """
+    Status of the unit.
+    """
+    head: Optional[bool] = None
+    """
+    Whether this unit is the first one to be executed.
+    """
+    flowchartId: str
+    """
+    Identity of the unit in the workflow. Used to trace the execution flow of the workflow.
+    """
+    next: Optional[str] = None
+    """
+    Next unit's flowchartId. If empty, the current unit is the last.
+    """
+    enableRender: Optional[bool] = None
+    """
+    Whether Rupy should attempt to use Jinja templating to add context variables into the unit
+    """
+    context: Optional[Dict[str, Any]] = None
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    consistencyChecks: Optional[List[ConsistencyCheck]] = None
+    schemaVersion: Optional[str] = "2022.8.16"
+    """
+    entity's schema version. Used to distinct between different schemas.
+    """
+    isDefault: Optional[bool] = False
+    """
+    Identifies that entity is defaultable
+    """
+    preProcessors: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the pre-processors for this calculation
+    """
+    postProcessors: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the post-processors for this calculation
+    """
+    monitors: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the monitors for this calculation
+    """
+    results: Optional[List[Union[NameResultSchema, str]]] = None
+    """
+    names of the results for this calculation
+    """
+    tags: Optional[List[str]] = None
+    """
+    entity tags
+    """
+    statusTrack: Optional[List[StatusTrackItem]] = None

mat3ra/esse/models/software_directory/modeling/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5

mat3ra/esse/models/software_directory/modeling/deepmd.py

@@ -0,0 +1,112 @@
+# generated by datamodel-codegen:
+#   filename:  software_directory/modeling/deepmd.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import List, Optional
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class Name(Enum):
+    deepmd = "deepmd"
+
+
+class Summary(Enum):
+    DeePMD_is_a_deep_learning_package_that_is_based_on_neural_network_fitted_first_principles_data_for_many_body_potential_energy_representation_and_molecular_dynamics = "DeePMD is a deep learning package that is based on neural network fitted first-principles data for many-body potential energy representation and molecular dynamics"
+
+
+class Version(Enum):
+    field_2_0_2 = "2.0.2"
+
+
+class Exec(Enum):
+    dp = "dp"
+    lmp = "lmp"
+    python = "python"
+
+
+class Name24(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class ConsistencyCheck(BaseModel):
+    key: str
+    """
+    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+    """
+    name: Name24
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    severity: Severity
+    """
+    Severity level of the problem, which is used in UI to differentiate.
+    """
+    message: str
+    """
+    Message generated by the consistency check describing the problem.
+    """
+
+
+class DeePMDAppSchema(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    name: Optional[Name] = None
+    """
+    entity name
+    """
+    summary: Optional[Summary] = None
+    """
+    Application's short description.
+    """
+    version: Optional[Version] = None
+    """
+    Application version. e.g. 5.3.5
+    """
+    exec: Optional[Exec] = None
+    shortName: Optional[str] = None
+    """
+    The short name of the application. e.g. qe
+    """
+    build: Optional[str] = None
+    """
+    Application build. e.g. VTST
+    """
+    hasAdvancedComputeOptions: Optional[bool] = None
+    """
+    Whether advanced compute options are present
+    """
+    isLicensed: Optional[bool] = None
+    """
+    Whether licensing is present
+    """
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    consistencyChecks: Optional[List[ConsistencyCheck]] = None
+    schemaVersion: Optional[str] = "2022.8.16"
+    """
+    entity's schema version. Used to distinct between different schemas.
+    """
+    isDefault: Optional[bool] = False
+    """
+    Identifies that entity is defaultable
+    """

mat3ra/esse/models/software_directory/modeling/espresso/__init__.py

@@ -0,0 +1,39 @@
+# generated by datamodel-codegen:
+#   filename:  software_directory/modeling/espresso.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import Optional
+
+from pydantic import BaseModel
+
+
+class Name(Enum):
+    espresso = "espresso"
+
+
+class Summary(Enum):
+    Quantum_Espresso = "Quantum Espresso"
+
+
+class Version(Enum):
+    field_5_2_1 = "5.2.1"
+    field_5_4_0 = "5.4.0"
+    field_6_0_0 = "6.0.0"
+    field_6_3 = "6.3"
+    field_6_4_1 = "6.4.1"
+    field_6_5_0 = "6.5.0"
+    field_6_6_0 = "6.6.0"
+    field_6_7_0 = "6.7.0"
+    field_6_8_0 = "6.8.0"
+    field_7_0 = "7.0"
+    field_7_2 = "7.2"
+    field_7_3 = "7.3"
+
+
+class EspressoAppSchema(BaseModel):
+    name: Optional[Name] = None
+    summary: Optional[Summary] = None
+    version: Optional[Version] = None

mat3ra/esse/models/software_directory/modeling/espresso/arguments.py

@@ -0,0 +1,35 @@
+# generated by datamodel-codegen:
+#   filename:  software_directory/modeling/espresso/arguments.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from typing import Optional
+
+from pydantic import BaseModel, ConfigDict, conint
+
+
+class QuantumEspressoArgumentsSchema(BaseModel):
+    model_config = ConfigDict(
+        extra="forbid",
+    )
+    nimage: Optional[conint(ge=1, le=100)] = 1
+    """
+    Processors can be divided into different `images`, each corresponding to a different self-consistent or linear-response calculation, loosely coupled to others.
+    """
+    npools: Optional[conint(ge=1, le=100)] = 1
+    """
+    Each image can be subpartitioned into `pools`, each taking care of a group of k-points.
+    """
+    nband: Optional[conint(ge=1, le=100)] = 1
+    """
+    Each pool is subpartitioned into `band groups`, each taking care of a group of Kohn-Sham orbitals (also called bands, or wavefunctions).
+    """
+    ntg: Optional[conint(ge=1, le=100)] = 1
+    """
+    In order to allow good parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes, FFTs on Kohn-Sham states are redistributed to `task` groups so that each group can process several wavefunctions at the same time.
+    """
+    ndiag: Optional[conint(ge=1, le=100)] = 1
+    """
+    A further level of parallelization, independent on PW or k-point parallelization, is the parallelization of subspace diagonalization / iterative orthonormalization. Both operations required the diagonalization of arrays whose dimension is the number of Kohn-Sham states (or a small multiple of it). All such arrays are distributed block-like across the `linear-algebra group`, a subgroup of the pool of processors, organized in a square 2D grid. As a consequence the number of processors in the linear-algebra group is given by n2, where n is an integer; n2 must be smaller than the number of processors in the PW group. The diagonalization is then performed in parallel using standard linear algebra operations.
+    """

mat3ra/esse/models/software_directory/modeling/nwchem.py

@@ -0,0 +1,113 @@
+# generated by datamodel-codegen:
+#   filename:  software_directory/modeling/nwchem.json
+#   version:   0.25.5
+
+from __future__ import annotations
+
+from enum import Enum
+from typing import List, Optional
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class Name(Enum):
+    NWChem = "NWChem"
+
+
+class Summary(Enum):
+    NWChem__a_comprehensive_and_scalable_open_source_solution_for_large_scale_molecular_simulations = (
+        "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations"
+    )
+
+
+class Version(Enum):
+    field_6_6 = "6.6"
+    field_7_0_2 = "7.0.2"
+
+
+class Exec(Enum):
+    nwchem = "nwchem"
+
+
+class Name146(Enum):
+    default = "default"
+    atomsTooClose = "atomsTooClose"
+    atomsOverlap = "atomsOverlap"
+
+
+class Severity(Enum):
+    info = "info"
+    warning = "warning"
+    error = "error"
+
+
+class ConsistencyCheck(BaseModel):
+    key: str
+    """
+    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
+    """
+    name: Name146
+    """
+    Name of the consistency check that is performed, which is listed in an enum.
+    """
+    severity: Severity
+    """
+    Severity level of the problem, which is used in UI to differentiate.
+    """
+    message: str
+    """
+    Message generated by the consistency check describing the problem.
+    """
+
+
+class NWChem(BaseModel):
+    model_config = ConfigDict(
+        extra="allow",
+    )
+    name: Optional[Name] = None
+    """
+    entity name
+    """
+    summary: Optional[Summary] = None
+    """
+    Application's short description.
+    """
+    version: Optional[Version] = None
+    """
+    Application version. e.g. 5.3.5
+    """
+    exec: Optional[Exec] = None
+    shortName: Optional[str] = None
+    """
+    The short name of the application. e.g. qe
+    """
+    build: Optional[str] = None
+    """
+    Application build. e.g. VTST
+    """
+    hasAdvancedComputeOptions: Optional[bool] = None
+    """
+    Whether advanced compute options are present
+    """
+    isLicensed: Optional[bool] = None
+    """
+    Whether licensing is present
+    """
+    field_id: Optional[str] = Field(None, alias="_id")
+    """
+    entity identity
+    """
+    slug: Optional[str] = None
+    """
+    entity slug
+    """
+    systemName: Optional[str] = None
+    consistencyChecks: Optional[List[ConsistencyCheck]] = None
+    schemaVersion: Optional[str] = "2022.8.16"
+    """
+    entity's schema version. Used to distinct between different schemas.
+    """
+    isDefault: Optional[bool] = False
+    """
+    Identifies that entity is defaultable
+    """

mat3ra/esse/models/software_directory/modeling/unit/__init__.py

@@ -0,0 +1,3 @@
+# generated by datamodel-codegen:
+#   filename:  schema
+#   version:   0.25.5