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Specifications and Common Mistakes

- Specifications and Common Mistakes:

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

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sponge.colvar.CombineCV

class sponge.colvar.CombineCV(colvar: Union[List[Colvar], Tuple[Colvar]], weights: Union[float, List[float], Tuple[float], Tensor] = 1, offsets: Union[float, List[float], Tuple[float], Tensor] = 0, exponents: Union[float, List[float], Tuple[float], Tensor] = 1, normal: bool = False, periodic_min: Union[float, ndarray, Tensor] = None, periodic_max: Union[float, ndarray, Tensor] = None, periodic_mask: Union[Tensor, ndarray] = None, use_pbc: bool = None, name: str = 'combine')

Polynomial combination of a set of Colvar $s_i$ with shape (S_1, S_2, …, S_n). {S_i} means dimensions of collective variables.

$$S=\sum _i^n{w}_i(s_i-o_i{)}^{p_i}$$

Parameters

• colvar (Union[List[Colvar], Tuple[Colvar]]) – Array of Colvar to be combined $s_i$.

• weights (Union[List[float], Tuple[Float], float, Tensor]) – Weights $w_i$ for each Colvar. If a list or tuple is given, the number of the elements should be equal to the number of CVs. If a float or Tensor is given, the value will be used for all Colvar. Default: 1

• offsets (Union[List[float], Tuple[Float], float, Tensor]) – Offsets $o_i$ for each Colvar. If a list or tuple is given, the number of the elements should be equal to the number of CVs. If a float or Tensor is given, the value will be used for all Colvar. Default: 0

• exponents (Union[List[float], Tuple[Float], float, Tensor]) – Exponents $p_i$ for each Colvar. If a list or tuple is given, the number of the elements should be equal to the number of CVs. If a float or Tensor is given, the value will be used for all Colvar. Default: 1

• normal (bool) – Whether to normalize all weights to 1. Default: False.

• periodic_min (Union[float, ndarray, Tensor]) – The periodic minimum of the output of the combination of the CVs. If the output is not periodic, it should be None. Default: None.

• periodic_max (Union[float, ndarray, Tensor]) – The periodic maximum of the output of the combination of the CVs. If the output is not periodic, it should be None. Default: None.

• periodic_mask (Union[Tensor, ndarray]) – Mask for the periodicity of the outputs. The shape of the tensor should be as the same as the outputs, i.e. (S_1, S_2, …, S_n). Default: None.

• use_pbc (bool) – Whether to use periodic boundary condition. If None is given, it will determine whether to use periodic boundary conditions based on whether the pbc_box is provided. Default: None.

• 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