Skip to content

Algorithm

Bases: UUIDBaseNode

Definition

An algorithm sub-object is a set of instructions that define a computational process. An algorithm consists of parameters that are used in the computation and the computational process itself.

Attributes

Keys Type Example Description Required Vocab
key str ensemble, thermo-barostat system configuration, algorithms used in a computation True True
type str NPT for ensemble, Nose-Hoover for thermostat specific type of configuration, algorithm True
parameter list[Parameter] setup associated parameters
citation Citation reference to a book, paper, or scholarly work

JSON Representation

{
    "node": ["Algorithm"],
    "key": "mc_barostat",
    "type": "barostat",
    "parameter": {
        "node": ["Parameter"],
        "key": "update_frequency",
        "value": 1000.0,
        "unit": "1/second"
    },
    "citation": {
        "node": ["Citation"],
        "type": "reference"
        "reference": {
                "node": ["Reference"],
                "type": "journal_article",
                "title": "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: SOft coarse grained Monte-Carlo Acceleration (SOMA)",
                "author": ["Ludwig Schneider", "Marcus Müller"],
                "journal": "Computer Physics Communications",
                "publisher": "Elsevier",
                "year": 2019,
                "pages": [463, 476],
                "doi": "10.1016/j.cpc.2018.08.011",
                "issn": "0010-4655",
                "website": "https://www.sciencedirect.com/science/article/pii/S0010465518303072",
        },
    },
}

Valid Parent Nodes

Valid Sub-objects

Source code in cript/nodes/subobjects/algorithm.py 
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
class Algorithm(UUIDBaseNode):
    """
    ## Definition
    An [algorithm sub-object](https://pubs.acs.org/doi/suppl/10.1021/acscentsci.3c00011/suppl_file/oc3c00011_si_001.pdf#page=25)
    is a set of instructions that define a computational process.
    An algorithm consists of parameters that are used in the computation and the computational process itself.

    ## Attributes
    | Keys      | Type            | Example                                      | Description                                            | Required | Vocab |
    |-----------|-----------------|----------------------------------------------|--------------------------------------------------------|----------|-------|
    | key       | str             | ensemble, thermo-barostat                    | system configuration, algorithms used in a computation | True     | True  |
    | type      | str             | NPT for ensemble, Nose-Hoover for thermostat | specific type of configuration, algorithm              | True     |       |
    | parameter | list[Parameter] |                                              | setup associated parameters                            |          |       |
    | citation  | Citation        |                                              | reference to a book, paper, or scholarly work          |          |       |

    ## JSON Representation
    ```json
    {
        "node": ["Algorithm"],
        "key": "mc_barostat",
        "type": "barostat",
        "parameter": {
            "node": ["Parameter"],
            "key": "update_frequency",
            "value": 1000.0,
            "unit": "1/second"
        },
        "citation": {
            "node": ["Citation"],
            "type": "reference"
            "reference": {
                    "node": ["Reference"],
                    "type": "journal_article",
                    "title": "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: SOft coarse grained Monte-Carlo Acceleration (SOMA)",
                    "author": ["Ludwig Schneider", "Marcus Müller"],
                    "journal": "Computer Physics Communications",
                    "publisher": "Elsevier",
                    "year": 2019,
                    "pages": [463, 476],
                    "doi": "10.1016/j.cpc.2018.08.011",
                    "issn": "0010-4655",
                    "website": "https://www.sciencedirect.com/science/article/pii/S0010465518303072",
            },
        },
    }
    ```

    ---
    ## Valid Parent Nodes
    * [SoftwareConfiguration](../software_configuration)

    ## Valid Sub-objects
    * [Parameter](../parameter)
    * [Citation](../citation)

    ---
    """

    @dataclass(frozen=True)
    class JsonAttributes(UUIDBaseNode.JsonAttributes):
        key: str = ""
        type: str = ""

        parameter: List[Parameter] = field(default_factory=list)
        citation: List[Citation] = field(default_factory=list)

    _json_attrs: JsonAttributes = JsonAttributes()

    def __init__(self, key: str, type: str, parameter: Optional[List[Parameter]] = None, citation: Optional[List[Citation]] = None, **kwargs):  # ignored
        """
        Create algorithm sub-object

        Parameters
        ----------
        key : str
            algorithm key must come from
            [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/algorithm_key)
        type : str
            algorithm type must come from
            [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/algorithm_type)
        parameter : List[Parameter], optional
            parameter sub-object, by default None
        citation : List[Citation], optional
            citation sub-object, by default None

        Examples
        --------
        >>> import cript
        >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")

        Returns
        -------
        None
            instantiate an algorithm node
        """
        if parameter is None:
            parameter = []
        if citation is None:
            citation = []
        super().__init__(**kwargs)
        self._json_attrs = replace(self._json_attrs, key=key, type=type, parameter=parameter)
        self.validate()

    @property
    def key(self) -> str:
        """
        Algorithm key

        Algorithm key must come from [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/algorithm_key)

        Examples
        --------
        >>> import cript
        >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
        >>> my_algorithm.key = "amorphous_cell_module"

        Returns
        -------
        str
            algorithm key
        """
        return self._json_attrs.key

    @key.setter
    def key(self, new_key: str) -> None:
        """
        set the algorithm key

        > Algorithm key must come from
        [CRIPT Controlled Vocabulary](https://app.criptapp.org/vocab/algorithm_key)

        Parameters
        ----------
        new_key : str
            algorithm key
        """
        new_attrs = replace(self._json_attrs, key=new_key)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    def type(self) -> str:
        """
        Algorithm type

        > Algorithm type must come from
        [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/algorithm_type)

        Examples
        --------
        >>> import cript
        >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
        >>> my_algorithm.type = "integration"

        Returns
        -------
        str
            algorithm type
        """
        return self._json_attrs.type

    @type.setter
    def type(self, new_type: str) -> None:
        new_attrs = replace(self._json_attrs, type=new_type)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    def parameter(self) -> List[Parameter]:
        """
        list of [Parameter](../parameter) sub-objects for the algorithm sub-object

        Examples
        --------
        >>> import cript
        >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
        >>> my_parameters = [
        ...     cript.Parameter("update_frequency", 1000.0, "1/second"),
        ...     cript.Parameter("damping_time", 1.0, "second"),
        ... ]
        >>> my_algorithm.parameter = my_parameters

        Returns
        -------
        List[Parameter]
            list of parameters for the algorithm sub-object
        """
        return self._json_attrs.parameter.copy()

    @parameter.setter
    def parameter(self, new_parameter: List[Parameter]) -> None:
        """
        set a list of cript.Parameter sub-objects

        Parameters
        ----------
        new_parameter : List[Parameter]
            list of Parameter sub-objects for the algorithm sub-object

        Returns
        -------
        None
        """
        new_attrs = replace(self._json_attrs, parameter=new_parameter)
        self._update_json_attrs_if_valid(new_attrs)

    @property
    def citation(self) -> Citation:
        """
        [citation](../citation) sub-object for algorithm sub-object

        Examples
        --------
        >>> import cript
        >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
        >>> title = (
        ...     "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: "
        ...     "Soft coarse grained Monte-Carlo Acceleration (SOMA)"
        ... )
        >>> my_reference = cript.Reference(
        ...     type="journal_article",
        ...     title=title,
        ...     author=["Ludwig Schneider", "Marcus Müller"],
        ...     journal="Computer Physics Communications",
        ...     publisher="Elsevier",
        ...     year=2019,
        ...     pages=[463, 476],
        ...     doi="10.1016/j.cpc.2018.08.011",
        ...     issn="0010-4655",
        ...     website="https://www.sciencedirect.com/science/article/pii/S0010465518303072",
        ... )
        >>> my_citation = cript.Citation(type="reference", reference=my_reference)
        >>> my_algorithm.citation = [my_citation]


        Returns
        -------
        citation node: Citation
            get the algorithm citation node
        """
        return self._json_attrs.citation.copy()  # type: ignore

    @citation.setter
    def citation(self, new_citation: List[Citation]) -> None:
        """
        set the algorithm citation sub-object

        Parameters
        ----------
        new_citation : Citation
            new citation sub-object to replace the current

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

citation: Citation property writable

citation sub-object for algorithm sub-object

Examples:

>>> import cript
>>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
>>> title = (
...     "Multi-architecture Monte-Carlo (MC) simulation of soft coarse-grained polymeric materials: "
...     "Soft coarse grained Monte-Carlo Acceleration (SOMA)"
... )
>>> my_reference = cript.Reference(
...     type="journal_article",
...     title=title,
...     author=["Ludwig Schneider", "Marcus Müller"],
...     journal="Computer Physics Communications",
...     publisher="Elsevier",
...     year=2019,
...     pages=[463, 476],
...     doi="10.1016/j.cpc.2018.08.011",
...     issn="0010-4655",
...     website="https://www.sciencedirect.com/science/article/pii/S0010465518303072",
... )
>>> my_citation = cript.Citation(type="reference", reference=my_reference)
>>> my_algorithm.citation = [my_citation]

Returns:

Type Description
citation node

get the algorithm citation node

key: str property writable

Algorithm key

Algorithm key must come from CRIPT controlled vocabulary

Examples:

>>> import cript
>>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
>>> my_algorithm.key = "amorphous_cell_module"

Returns:

Type Description
str

algorithm key

parameter: List[Parameter] property writable

list of Parameter sub-objects for the algorithm sub-object

Examples:

>>> import cript
>>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
>>> my_parameters = [
...     cript.Parameter("update_frequency", 1000.0, "1/second"),
...     cript.Parameter("damping_time", 1.0, "second"),
... ]
>>> my_algorithm.parameter = my_parameters

Returns:

Type Description
List[Parameter]

list of parameters for the algorithm sub-object

type: str property writable

Algorithm type

Algorithm type must come from CRIPT controlled vocabulary

Examples:

>>> import cript
>>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")
>>> my_algorithm.type = "integration"

Returns:

Type Description
str

algorithm type

__init__(key, type, parameter=None, citation=None, **kwargs)

Create algorithm sub-object

Parameters:

Name Type Description Default
key str

algorithm key must come from CRIPT controlled vocabulary

 required
type str

algorithm type must come from CRIPT controlled vocabulary

 required
parameter List[Parameter], optional

parameter sub-object, by default None

 None
citation List[Citation], optional

citation sub-object, by default None

 None

Examples:

>>> import cript
>>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")

Returns:

Type Description
None

instantiate an algorithm node
Source code in cript/nodes/subobjects/algorithm.py 
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
def __init__(self, key: str, type: str, parameter: Optional[List[Parameter]] = None, citation: Optional[List[Citation]] = None, **kwargs):  # ignored
    """
    Create algorithm sub-object

    Parameters
    ----------
    key : str
        algorithm key must come from
        [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/algorithm_key)
    type : str
        algorithm type must come from
        [CRIPT controlled vocabulary](https://app.criptapp.org/vocab/algorithm_type)
    parameter : List[Parameter], optional
        parameter sub-object, by default None
    citation : List[Citation], optional
        citation sub-object, by default None

    Examples
    --------
    >>> import cript
    >>> my_algorithm = cript.Algorithm(key="mc_barostat", type="barostat")

    Returns
    -------
    None
        instantiate an algorithm node
    """
    if parameter is None:
        parameter = []
    if citation is None:
        citation = []
    super().__init__(**kwargs)
    self._json_attrs = replace(self._json_attrs, key=key, type=type, parameter=parameter)
    self.validate()