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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

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- 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

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- Incorrect code.

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- Wrong screenshots.

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

Risk Warnings

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Content Compliance

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sponge.colvar

API Name	Description	Supported Platforms
`sponge.colvar.AllAtoms`	All atoms of the simulation system.	`Ascend` `GPU`
`sponge.colvar.AtomsBase`	Base class for specific atoms group, used as the "atoms group module" in MindSPONGE.	`Ascend` `GPU`
`sponge.colvar.Atoms`	Specific atoms group initialized using an array of atomic indices.	`Ascend` `GPU`
`sponge.colvar.BatchedAtoms`	A batched version of Atoms Cell.	`Ascend` `GPU`
`sponge.colvar.Center`	Center of specific atoms	`Ascend` `GPU`
`sponge.colvar.Group`	Group of atoms.	`Ascend` `GPU`
`sponge.colvar.Position`	Virtual atom(s) in fixed position(s).	`Ascend` `GPU`
`sponge.colvar.BatchedPosition`	Virtual atom(s) in fixed position(s) with batched coordinate	`Ascend` `GPU`
`sponge.colvar.Vector`	Vector between specific atoms or virtual atoms.	`Ascend` `GPU`
`sponge.colvar.Angle`	Colvar for angle.	`Ascend` `GPU`
`sponge.colvar.ConstantValue`	Constant value.	`Ascend` `GPU` `CPU`
`sponge.colvar.Distance`	Colvar for distance.	`Ascend` `GPU`
`sponge.colvar.Torsion`	Colvar for torsional (dihedral) angle.	`Ascend` `GPU`
`sponge.colvar.Volume`	Volume of simulation system.	`Ascend` `GPU`
`sponge.colvar.CombineCV`	Polynomial combination of a set of Colvar $s_{i}$ with shape (S_1, S_2, ..., S_n).	`Ascend` `GPU`
`sponge.colvar.ColvarCombine`	See CombineCV.	`Ascend` `GPU`
`sponge.colvar.CosCV`	Cosine of collective variables (CVs) $s (R)$ .	`Ascend` `GPU`
`sponge.colvar.FunctionCV`	A composite Colvar that combines a set of collective variables (CVs) $s_{i} (R)$ using a custom function $f (s_{1} (R), s_{2} (R), . . ., s_{i} (R))$ .	`Ascend` `GPU`
`sponge.colvar.SinCV`	Sine of collective variables (CVs) $s (R)$ .	`Ascend` `GPU`
`sponge.colvar.TransformCV`	Transformation of the values of the a collective variable $s (R)$ using a specific functions $f (x)$ .	`Ascend` `GPU`
`sponge.colvar.Colvar`	Base class for generalized collective variables (CVs) $s (R)$ .	`Ascend` `GPU`
`sponge.colvar.ColvarGroup`	Concatenate a group of Colvar classes into one Colvar class	`Ascend` `GPU`
`sponge.colvar.get_colvar`	get group of collective variables.	To Be Developed
`sponge.colvar.get_atoms`	get atom(s) or group.	To Be Developed