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Specifications and Common Mistakes

- Specifications and Common Mistakes:

- Misspellings or punctuation mistakes,incorrect formulas, abnormal display.

- Incorrect links, empty cells, or wrong formats.

- Chinese characters in English context.

- Minor inconsistencies between the UI and descriptions.

- Low writing fluency that does not affect understanding.

- Incorrect version numbers, including software package names and version numbers on the UI.

Usability

- Usability:

- Incorrect or missing key steps.

- Missing main function descriptions, keyword explanation, necessary prerequisites, or precautions.

- Ambiguous descriptions, unclear reference, or contradictory context.

- Unclear logic, such as missing classifications, items, and steps.

Correctness

- Correctness:

- Technical principles, function descriptions, supported platforms, parameter types, or exceptions inconsistent with that of software implementation.

- Incorrect schematic or architecture diagrams.

- Incorrect commands or command parameters.

- Incorrect code.

- Commands inconsistent with the functions.

- Wrong screenshots.

- Sample code running error, or running results inconsistent with the expectation.

Risk Warnings

- Risk Warnings:

- Lack of risk warnings for operations that may damage the system or important data.

Content Compliance

- Content Compliance:

- Contents that may violate applicable laws and regulations or geo-cultural context-sensitive words and expressions.

- Copyright infringement.

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sponge.colvar.FunctionCV

class sponge.colvar.FunctionCV(colvar: Union[Colvar, List[Colvar], Tuple[Colvar]], function: Callable, periodic: bool, shape: Tuple[int] = None, unit: str = None, use_pbc: bool = None, name: str = 'function')

A composite Colvar that combines a set of collective variables (CVs) $s_i(R)$ using a custom function $f(s_1(R),s_2(R),...,s_i(R))$.

$$S=f(s_1(R),s_2(R),...s_i(R))$$

Parameters

• colvar (Union[Colvar, List[Colvar], Tuple[Colvar]]) – Collective variables to be combined $s_i(R)$.

• function (callable) – Custom function $f(s_1(R),s_2(R),...s_i(R))$.

• periodic (bool) – Whether the custom collective variables is periodic.

• shape (tuple) – Shape of custom collective variables. If None is given and all CVs in the colvar have the same shape, then it will be assigned the shape. If the shape of each CV in colvar is not exactly the same, the shape must be set. Default: None.

• unit (str) – Unit of the collective variables. Default: None. NOTE: This is not the Units Cell that wraps length and energy.

• name (str) – Name of the collective variables. Default: 'combine'.

Supported Platforms:

Ascend GPU

set_pbc(use_pbc: bool)

set whether to use periodic boundary condition