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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.TransformCV

class sponge.colvar.TransformCV(colvar: Colvar, function: Callable, periodic: bool = False, shape: Tuple[int] = None, unit: str = None, name: str = 'transform')

Transformation of the values of the a collective variable $s(R)$ using a specific functions $f(x)$.

$$s^{\prime }=f[s(R)]$$

Parameters

• colvar (Colvar) – Collective variables (CVs) $s(R)$.

• function (Callable) – Transformation function $f(x)$.

• periodic (bool) – Whether the transformed collective variables is periodic. Default: False.

• shape (Tuple[int]) – Shape of the transformed collective variables. If None is given, then it will be assigned to the shape of the original colvar. 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: 'transform'.

Supported Platforms:

Ascend GPU

set_pbc(use_pbc: bool)

set whether to use periodic boundary condition