Computation Process

ComputationProcess

Bases: PrimaryBaseNode

Definition

A Computational_Process is a simulation that processes or changes a virtual material. Examples include simulations of chemical reactions, chain scission, cross-linking, strong shear, etc. A computational process may also encapsulate any computation that dramatically changes the materials properties, molecular topology, and physical aspects like molecular orientation, etc. The computation_forcefield of a simulation is associated with a material. As a consequence, if the forcefield changes or gets refined via a computational procedure (density functional theory, iterative Boltzmann inversion for coarse-graining etc.) this forcefield changing step must be described as a computational_process and a new material node with a different computation_forcefield needs to be created.

Attributes

attribute	type	example	description	required	vocab
type	str	general molecular dynamics simulation	category of computation	True	True
input_data	list[Data]		input data nodes	True
output_data	list[Data]		output data nodes
ingredient	list[Ingredient]		ingredients	True
software_ configurations	list[Software Configuration]		software and algorithms used
condition	list[Condition]		setup information
property	list[Property]		computation process properties
citation	list[Citation]		reference to a book, paper, or scholarly work
notes	str		additional description of the step

Available Subobjects

• ingredient
• software_configuration
• property
• condition
• citation

JSON Representation

{
   "name":"my computational process node name",
   "node":["ComputationProcess"],
   "type":"cross_linking",
   "uid":"_:b88ac0a5-b5c0-4197-a63d-b37e1fe8c6c6",
   "uuid":"b88ac0a5-b5c0-4197-a63d-b37e1fe8c6c6"
   "ingredient":[
      {
        "node":["Ingredient"],
        "uid":"_:f68d6fff-9327-48b1-9249-33ce498005e8",
         "uuid":"f68d6fff-9327-48b1-9249-33ce498005e8"
         "keyword":["catalyst"],
         "material":{
            "name":"my material name",
            "node":["Material"],
            "uid":"_:3b12f92c-2121-4520-920e-b4c5622de34a",
            "uuid":"3b12f92c-2121-4520-920e-b4c5622de34a",
            "bigsmiles":"[H]{[>][<]C(C[>])c1ccccc1[]}",
         },

         "quantity":[
            {
               "key":"mass",
               "node":["Quantity"],
               "uid":"_:07c4a6a9-9385-4505-a30a-ca3549cedcd8",
               "uuid":"07c4a6a9-9385-4505-a30a-ca3549cedcd8",
               "uncertainty":0.2,
               "uncertainty_type":"stdev",
               "unit":"kg",
               "value":11.2
            }
         ]
      }
   ],
   "input_data":[
      {
        "name":"my data name",
         "node":["Data"],
         "type":"afm_amp",
         "uid":"_:3c16bb05-ded1-4f52-9d02-c88c1a1de915",
         "uuid":"3c16bb05-ded1-4f52-9d02-c88c1a1de915"
         "file":[
            {
               "name":"my file node name",
               "node":["File"],
               "source":"https://criptapp.org",
               "type":"calibration",
                "data_dictionary":"my file's data dictionary",
               "extension":".csv",
               "uid":"_:ee8153db-4108-49e4-8c5b-ffc26d4e6f71",
               "uuid":"ee8153db-4108-49e4-8c5b-ffc26d4e6f71"
            }
         ],
      }
   ],
}

Source code in src/cript/nodes/primary_nodes/computation_process.py

class ComputationProcess(PrimaryBaseNode):
    """
    ## Definition

    A
    [Computational_Process](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=15)
    is a simulation that processes or changes a virtual material. Examples
    include simulations of chemical reactions, chain scission, cross-linking, strong shear, etc. A
    computational process may also encapsulate any computation that dramatically changes the
    materials properties, molecular topology, and physical aspects like molecular orientation, etc. The
    computation_forcefield of a simulation is associated with a material. As a consequence, if the
    forcefield changes or gets refined via a computational procedure (density functional theory,
    iterative Boltzmann inversion for coarse-graining etc.) this forcefield changing step must be
    described as a computational_process and a new material node with a different
    computation_forcefield needs to be created.

    ## Attributes
    | attribute                | type                          | example                               | description                                   | required | vocab |
    |--------------------------|-------------------------------|---------------------------------------|-----------------------------------------------|----------|-------|
    | type                     | str                           | general molecular dynamics simulation | category of computation                       | True     | True  |
    | input_data               | list[Data]                    |                                       | input data nodes                              | True     |       |
    | output_data              | list[Data]                    |                                       | output data nodes                             |          |       |
    | ingredient               | list[Ingredient]              |                                       | ingredients                                   | True     |       |
    | software_ configurations | list[Software  Configuration] |                                       | software and algorithms used                  |          |       |
    | condition                | list[Condition]               |                                       | setup information                             |          |       |
    | property                 | list[Property]                |                                       | computation process properties                |          |       |
    | citation                 | list[Citation]                |                                       | reference to a book, paper, or scholarly work |          |       |
    | notes                    | str                           |                                       | additional description of the step            |          |       |


    ## Available Subobjects
    * [ingredient](../../subobjects/ingredient)
    * [software_configuration](../../subobjects/software_configuration)
    * [property](../../subobjects/property)
    * [condition](../../subobjects/condition)
    * [citation](../../subobjects/citation)

    ## JSON Representation
    ```json
    {
       "name":"my computational process node name",
       "node":["ComputationProcess"],
       "type":"cross_linking",
       "uid":"_:b88ac0a5-b5c0-4197-a63d-b37e1fe8c6c6",
       "uuid":"b88ac0a5-b5c0-4197-a63d-b37e1fe8c6c6"
       "ingredient":[
          {
            "node":["Ingredient"],
            "uid":"_:f68d6fff-9327-48b1-9249-33ce498005e8",
             "uuid":"f68d6fff-9327-48b1-9249-33ce498005e8"
             "keyword":["catalyst"],
             "material":{
                "name":"my material name",
                "node":["Material"],
                "uid":"_:3b12f92c-2121-4520-920e-b4c5622de34a",
                "uuid":"3b12f92c-2121-4520-920e-b4c5622de34a",
                "bigsmiles":"[H]{[>][<]C(C[>])c1ccccc1[]}",
             },

             "quantity":[
                {
                   "key":"mass",
                   "node":["Quantity"],
                   "uid":"_:07c4a6a9-9385-4505-a30a-ca3549cedcd8",
                   "uuid":"07c4a6a9-9385-4505-a30a-ca3549cedcd8",
                   "uncertainty":0.2,
                   "uncertainty_type":"stdev",
                   "unit":"kg",
                   "value":11.2
                }
             ]
          }
       ],
       "input_data":[
          {
            "name":"my data name",
             "node":["Data"],
             "type":"afm_amp",
             "uid":"_:3c16bb05-ded1-4f52-9d02-c88c1a1de915",
             "uuid":"3c16bb05-ded1-4f52-9d02-c88c1a1de915"
             "file":[
                {
                   "name":"my file node name",
                   "node":["File"],
                   "source":"https://criptapp.org",
                   "type":"calibration",
                    "data_dictionary":"my file's data dictionary",
                   "extension":".csv",
                   "uid":"_:ee8153db-4108-49e4-8c5b-ffc26d4e6f71",
                   "uuid":"ee8153db-4108-49e4-8c5b-ffc26d4e6f71"
                }
             ],
          }
       ],
    }
    ```

    """

    @dataclass(frozen=True)
    class JsonAttributes(PrimaryBaseNode.JsonAttributes):
        """
        all computational_process nodes attributes
        """

        type: str = ""
        # TODO add proper typing in future, using Any for now to avoid circular import error
        input_data: List[Union[Any, UIDProxy]] = field(default_factory=list)
        output_data: List[Union[Any, UIDProxy]] = field(default_factory=list)
        ingredient: List[Union[Any, UIDProxy]] = field(default_factory=list)
        software_configuration: List[Union[Any, UIDProxy]] = field(default_factory=list)
        condition: List[Union[Any, UIDProxy]] = field(default_factory=list)
        property: List[Union[Any, UIDProxy]] = field(default_factory=list)
        citation: List[Union[Any, UIDProxy]] = field(default_factory=list)

    _json_attrs: JsonAttributes = JsonAttributes()

    @beartype
    def __init__(
        self,
        name: str,
        type: str,
        input_data: List[Union[Any, UIDProxy]],
        ingredient: List[Union[Any, UIDProxy]],
        output_data: Optional[List[Union[Any, UIDProxy]]] = None,
        software_configuration: Optional[List[Union[Any, UIDProxy]]] = None,
        condition: Optional[List[Union[Any, UIDProxy]]] = None,
        property: Optional[List[Union[Any, UIDProxy]]] = None,
        citation: Optional[List[Union[Any, UIDProxy]]] = None,
        notes: str = "",
        **kwargs
    ):
        """
        create a computational_process node

        Examples
        --------
        >>> import cript
        >>> data_files = cript.File(
        ...     name="my file node name",
        ...     source="https://criptapp.org",
        ...     type="calibration",
        ...     extension=".csv",
        ...     data_dictionary="my file's data dictionary"
        ... )
        >>> input_data = cript.Data(name="my data name", type="afm_amp", file=[data_files])
        >>> my_material = cript.Material(
        ...     name="my material",
        ...     names = ["my material alternative name"]
        ... )
        >>> my_quantity = cript.Quantity(key="mass", value=1.23, unit="kg")
        >>> ingredient = cript.Ingredient(
        ...     material=my_material,
        ...     quantity=[my_quantity],
        ... )
        >>> my_computation_process = cript.ComputationProcess(
        ...     name="my computational process name",
        ...     type="cross_linking",
        ...     input_data=[input_data],
        ...     ingredient=[ingredient],
        ... )


        Parameters
        ----------
        name: str
            computational process name
        type: str
            type of computation process from CRIPT controlled vocabulary
        input_data: List[Data]
            list of input data for computational process
        ingredient: List[Ingredient]
            list of ingredients for this computational process node
        output_data: List[Data] default=None
            list of output data for this computational process node
        software_configuration: List[SoftwareConfiguration] default=None
            list of software configurations for this computational process node
        condition: List[Condition] default=None
            list of condition for this computational process node
        property: List[Property] default=None
            list of properties for this computational process node
        citation: List[Citation] default=None
            list of citation for this computational process node
        notes: str default=""
            optional notes for the computational process node

        Returns
        -------
        None
            instantiate computationalProcess node
        """
        super().__init__(name=name, notes=notes, **kwargs)

        if input_data is None:
            input_data = []

        if ingredient is None:
            ingredient = []

        if output_data is None:
            output_data = []

        if software_configuration is None:
            software_configuration = []

        if condition is None:
            condition = []

        if property is None:
            property = []

        if citation is None:
            citation = []

        new_json_attrs = replace(
            self._json_attrs,
            type=type,
            input_data=input_data,
            ingredient=ingredient,
            output_data=output_data,
            software_configuration=software_configuration,
            condition=condition,
            property=property,
            citation=citation,
        )
        self._update_json_attrs_if_valid(new_json_attrs)

    @property
    @beartype
    def type(self) -> str:
        """
        The [computational process type](https://app.criptapp.org/vocab/computational_process_type)
        must come from CRIPT Controlled vocabulary

        Examples
        --------
        >>> import cript
        >>> my_computation_process.type = "DPD"   # doctest: +SKIP

        Returns
        -------
        str
            computational process type
        """
        return self._json_attrs.type

    @type.setter
    @beartype
    def type(self, new_type: str) -> None:
        """
        set the computational_process type

        computational_process type must come from CRIPT controlled vocabulary

        Parameters
        ----------
        new_type: str
            new computational process type.
            computational process type must come from CRIPT controlled vocabulary

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, type=new_type)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def input_data(self) -> List[Any]:
        """
        List of input data for the computational process node

        Examples
        --------
        >>> import cript
        >>> my_file = cript.File(
        ...     name="my file node name",
        ...     source="https://criptapp.org",
        ...     type="calibration",
        ...     data_dictionary="my file's data dictionary",
        ...     extension=".csv",
        ... )
        >>> my_input_data = cript.Data(name="my input data name", type="afm_amp", file=[my_file])
        >>> my_computation_process.input_data = [my_input_data]     # doctest: +SKIP

        Returns
        -------
        List[Data]
            list of input data for this computational process node
        """
        return self._json_attrs.input_data.copy()

    @input_data.setter
    @beartype
    def input_data(self, new_input_data_list: List[Any]) -> None:
        """
        set the input data for this computational process

        Parameters
        ----------
        new_input_data_list: List[Data]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, input_data=new_input_data_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def output_data(self) -> List[Any]:
        """
        List of the output data for the computational_process

        Examples
        --------
        >>> import cript
        >>> my_file = cript.File(
        ...     name="my file node name",
        ...     source="https://criptapp.org",
        ...     type="calibration",
        ...     extension=".csv",
        ...     data_dictionary="my file's data dictionary"
        ... )
        >>> my_output_data = cript.Data(name="my output data name", type="afm_amp", file=[my_file])
        >>> my_computation_process.output_data = [my_output_data]    # doctest: +SKIP

        Returns
        -------
        List[Data]
            list of output data from this computational process node
        """
        return self._json_attrs.output_data.copy()

    @output_data.setter
    @beartype
    def output_data(self, new_output_data_list: List[Any]) -> None:
        """
        set the output_data list for the computational_process

        Parameters
        ----------
        new_output_data_list: List[Data]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, output_data=new_output_data_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def ingredient(self) -> List[Any]:
        """
        List of ingredients for the computational_process

        Examples
        --------
        >>> import cript
        >>> my_material = cript.Material(name="my material", bigsmiles = "my bigsmiles")
        >>> my_quantity = cript.Quantity(
        ...     key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"
        ... )
        >>> my_ingredient = cript.Ingredient(
        ...     material=my_material, quantity=[my_quantity], keyword=["catalyst"]
        ... )
        >>> my_computation_process.ingredient = [my_ingredient]   # doctest: +SKIP

        Returns
        -------
        List[Ingredient]
            list of ingredients for this computational process
        """
        return self._json_attrs.ingredient.copy()

    @ingredient.setter
    @beartype
    def ingredient(self, new_ingredient_list: List[Any]) -> None:
        """
        set the ingredients list for this computational process

        Parameters
        ----------
        new_ingredient_list: List[Ingredient]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, ingredient=new_ingredient_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def software_configuration(self) -> List[Any]:
        """
        List of software_configuration for the computational process

        Examples
        --------
        >>> import cript
        >>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
        >>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)
        >>> my_computation_process.software_configuration = [my_software_configuration]   # doctest: +SKIP

        Returns
        -------
        List[SoftwareConfiguration]
            List of software configurations used for this computational process node
        """
        return self._json_attrs.software_configuration.copy()

    @software_configuration.setter
    @beartype
    def software_configuration(self, new_software_configuration_list: List[Any]) -> None:
        """
        set the list of software_configuration for the computational process

        Parameters
        ----------
        new_software_configuration_list: List[SoftwareConfiguration]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, software_configuration=new_software_configuration_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def condition(self) -> List[Any]:
        """
        List of condition for the computational process

        Examples
        --------
        >>> import cript
        >>> my_condition = cript.Condition(key="atm", type="min", value=1)
        >>> my_computation_process.condition = [my_condition]     # doctest: +SKIP

        Returns
        -------
        List[Condition]
            list of condition for this computational process node
        """
        return self._json_attrs.condition.copy()

    @condition.setter
    @beartype
    def condition(self, new_condition: List[Any]) -> None:
        """
        set the condition for the computational process

        Parameters
        ----------
        new_condition: List[Condition]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, condition=new_condition)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def citation(self) -> List[Any]:
        """
        List of citation for the computational process

        Examples
        --------
        >>> import cript
        >>> my_reference = cript.Reference(type="journal_article", title="'Living' Polymers")
        >>> my_citation = cript.Citation(type="derived_from", reference=my_reference)
        >>> my_computation_process.citation = [my_citation]     # doctest: +SKIP

        Returns
        -------
        List[Citation]
            list of citation for this computational process
        """
        return self._json_attrs.citation.copy()

    @citation.setter
    @beartype
    def citation(self, new_citation_list: List[Any]) -> None:
        """
        set the citation list for the computational process node

        Parameters
        ----------
        new_citation_list: List[Citation]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, citation=new_citation_list)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    @beartype
    def property(self) -> List[Any]:
        """
        List of properties

        Examples
        --------
        >>> import cript
        >>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
        >>> my_computation_process.property = [my_property]     # doctest: +SKIP

        Returns
        -------
        List[Property]
            list of properties for this computational process node
        """
        return self._json_attrs.property.copy()

    @property.setter
    @beartype
    def property(self, new_property_list: List[Any]) -> None:
        """
        set the properties list for the computational process

        Parameters
        ----------
        new_property_list: List[Property]

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, property=new_property_list)
        self._update_json_attrs_if_valid(new_attrs)

citation: List[Any] property writable

List of citation for the computational process

Examples:

>>> import cript
>>> my_reference = cript.Reference(type="journal_article", title="'Living' Polymers")
>>> my_citation = cript.Citation(type="derived_from", reference=my_reference)
>>> my_computation_process.citation = [my_citation]

Returns:

Type	Description
List[Citation]	list of citation for this computational process

condition: List[Any] property writable

List of condition for the computational process

Examples:

>>> import cript
>>> my_condition = cript.Condition(key="atm", type="min", value=1)
>>> my_computation_process.condition = [my_condition]

Returns:

Type	Description
List[Condition]	list of condition for this computational process node

ingredient: List[Any] property writable

List of ingredients for the computational_process

Examples:

>>> import cript
>>> my_material = cript.Material(name="my material", bigsmiles = "my bigsmiles")
>>> my_quantity = cript.Quantity(
...     key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"
... )
>>> my_ingredient = cript.Ingredient(
...     material=my_material, quantity=[my_quantity], keyword=["catalyst"]
... )
>>> my_computation_process.ingredient = [my_ingredient]

Returns:

Type	Description
List[Ingredient]	list of ingredients for this computational process

input_data: List[Any] property writable

List of input data for the computational process node

Examples:

>>> import cript
>>> my_file = cript.File(
...     name="my file node name",
...     source="https://criptapp.org",
...     type="calibration",
...     data_dictionary="my file's data dictionary",
...     extension=".csv",
... )
>>> my_input_data = cript.Data(name="my input data name", type="afm_amp", file=[my_file])
>>> my_computation_process.input_data = [my_input_data]

Returns:

Type	Description
List[Data]	list of input data for this computational process node

output_data: List[Any] property writable

List of the output data for the computational_process

Examples:

>>> import cript
>>> my_file = cript.File(
...     name="my file node name",
...     source="https://criptapp.org",
...     type="calibration",
...     extension=".csv",
...     data_dictionary="my file's data dictionary"
... )
>>> my_output_data = cript.Data(name="my output data name", type="afm_amp", file=[my_file])
>>> my_computation_process.output_data = [my_output_data]

Returns:

Type	Description
List[Data]	list of output data from this computational process node

property: List[Any] property writable

List of properties

Examples:

>>> import cript
>>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
>>> my_computation_process.property = [my_property]

Returns:

Type	Description
List[Property]	list of properties for this computational process node

software_configuration: List[Any] property writable

List of software_configuration for the computational process

Examples:

>>> import cript
>>> my_software = cript.Software(name="LAMMPS", version="23Jun22", source="lammps.org")
>>> my_software_configuration = cript.SoftwareConfiguration(software=my_software)
>>> my_computation_process.software_configuration = [my_software_configuration]

Returns:

Type	Description
List[SoftwareConfiguration]	List of software configurations used for this computational process node

type: str property writable

The computational process type must come from CRIPT Controlled vocabulary

Examples:

>>> import cript
>>> my_computation_process.type = "DPD"

Returns:

Type	Description
str	computational process type

JsonAttributes dataclass

Bases: JsonAttributes

all computational_process nodes attributes

Source code in src/cript/nodes/primary_nodes/computation_process.py

@dataclass(frozen=True)
class JsonAttributes(PrimaryBaseNode.JsonAttributes):
    """
    all computational_process nodes attributes
    """

    type: str = ""
    # TODO add proper typing in future, using Any for now to avoid circular import error
    input_data: List[Union[Any, UIDProxy]] = field(default_factory=list)
    output_data: List[Union[Any, UIDProxy]] = field(default_factory=list)
    ingredient: List[Union[Any, UIDProxy]] = field(default_factory=list)
    software_configuration: List[Union[Any, UIDProxy]] = field(default_factory=list)
    condition: List[Union[Any, UIDProxy]] = field(default_factory=list)
    property: List[Union[Any, UIDProxy]] = field(default_factory=list)
    citation: List[Union[Any, UIDProxy]] = field(default_factory=list)

__init__(name, type, input_data, ingredient, output_data=None, software_configuration=None, condition=None, property=None, citation=None, notes='', **kwargs)

create a computational_process node

Examples:

>>> import cript
>>> data_files = cript.File(
...     name="my file node name",
...     source="https://criptapp.org",
...     type="calibration",
...     extension=".csv",
...     data_dictionary="my file's data dictionary"
... )
>>> input_data = cript.Data(name="my data name", type="afm_amp", file=[data_files])
>>> my_material = cript.Material(
...     name="my material",
...     names = ["my material alternative name"]
... )
>>> my_quantity = cript.Quantity(key="mass", value=1.23, unit="kg")
>>> ingredient = cript.Ingredient(
...     material=my_material,
...     quantity=[my_quantity],
... )
>>> my_computation_process = cript.ComputationProcess(
...     name="my computational process name",
...     type="cross_linking",
...     input_data=[input_data],
...     ingredient=[ingredient],
... )

Parameters:

Name	Type	Description	Default
name	str	computational process name	required
type	str	type of computation process from CRIPT controlled vocabulary	required
input_data	List[Union[Any, UIDProxy]]	list of input data for computational process	required
ingredient	List[Union[Any, UIDProxy]]	list of ingredients for this computational process node	required
output_data	Optional[List[Union[Any, UIDProxy]]]	list of output data for this computational process node	None
software_configuration	Optional[List[Union[Any, UIDProxy]]]	list of software configurations for this computational process node	None
condition	Optional[List[Union[Any, UIDProxy]]]	list of condition for this computational process node	None
property	Optional[List[Union[Any, UIDProxy]]]	list of properties for this computational process node	None
citation	Optional[List[Union[Any, UIDProxy]]]	list of citation for this computational process node	None
notes	str	optional notes for the computational process node	''

Returns:

Type	Description
None	instantiate computationalProcess node

Source code in src/cript/nodes/primary_nodes/computation_process.py

@beartype
def __init__(
    self,
    name: str,
    type: str,
    input_data: List[Union[Any, UIDProxy]],
    ingredient: List[Union[Any, UIDProxy]],
    output_data: Optional[List[Union[Any, UIDProxy]]] = None,
    software_configuration: Optional[List[Union[Any, UIDProxy]]] = None,
    condition: Optional[List[Union[Any, UIDProxy]]] = None,
    property: Optional[List[Union[Any, UIDProxy]]] = None,
    citation: Optional[List[Union[Any, UIDProxy]]] = None,
    notes: str = "",
    **kwargs
):
    """
    create a computational_process node

    Examples
    --------
    >>> import cript
    >>> data_files = cript.File(
    ...     name="my file node name",
    ...     source="https://criptapp.org",
    ...     type="calibration",
    ...     extension=".csv",
    ...     data_dictionary="my file's data dictionary"
    ... )
    >>> input_data = cript.Data(name="my data name", type="afm_amp", file=[data_files])
    >>> my_material = cript.Material(
    ...     name="my material",
    ...     names = ["my material alternative name"]
    ... )
    >>> my_quantity = cript.Quantity(key="mass", value=1.23, unit="kg")
    >>> ingredient = cript.Ingredient(
    ...     material=my_material,
    ...     quantity=[my_quantity],
    ... )
    >>> my_computation_process = cript.ComputationProcess(
    ...     name="my computational process name",
    ...     type="cross_linking",
    ...     input_data=[input_data],
    ...     ingredient=[ingredient],
    ... )


    Parameters
    ----------
    name: str
        computational process name
    type: str
        type of computation process from CRIPT controlled vocabulary
    input_data: List[Data]
        list of input data for computational process
    ingredient: List[Ingredient]
        list of ingredients for this computational process node
    output_data: List[Data] default=None
        list of output data for this computational process node
    software_configuration: List[SoftwareConfiguration] default=None
        list of software configurations for this computational process node
    condition: List[Condition] default=None
        list of condition for this computational process node
    property: List[Property] default=None
        list of properties for this computational process node
    citation: List[Citation] default=None
        list of citation for this computational process node
    notes: str default=""
        optional notes for the computational process node

    Returns
    -------
    None
        instantiate computationalProcess node
    """
    super().__init__(name=name, notes=notes, **kwargs)

    if input_data is None:
        input_data = []

    if ingredient is None:
        ingredient = []

    if output_data is None:
        output_data = []

    if software_configuration is None:
        software_configuration = []

    if condition is None:
        condition = []

    if property is None:
        property = []

    if citation is None:
        citation = []

    new_json_attrs = replace(
        self._json_attrs,
        type=type,
        input_data=input_data,
        ingredient=ingredient,
        output_data=output_data,
        software_configuration=software_configuration,
        condition=condition,
        property=property,
        citation=citation,
    )
    self._update_json_attrs_if_valid(new_json_attrs)