Path Variables
This module implements the path variable as introduced by Branduardi et al.1
- class ndsimulator.colvars.path.Path(file_name: Optional[str] = None, sigma: float = 1.0, ref: Optional[numpy.ndarray] = None, ref_ind: Optional[numpy.ndarray] = None)
1 dimensional Path variable. The input file needs to contain a (n_ref, x) array that conform np.loadtxt syntax.
n_ref is the number of reference points for the path variable x is the dimension of the space plus 1
the first column contains the indices and the remaining columns contain the reference points
- Parameters
file_name (str, optional) – the txt file storing the path parameters. Defaults to None.
sigma (float, optional) – width of the path variable. Defaults to 1.0.
ref (np.ndarray, optional) – the reference position for the path. Defaults to None.
ref_ind (np.ndarray, optional) – the reference index for the path. Defaults to None.
- class ndsimulator.colvars.path.Path5dto2d(file_name: Optional[str] = None, sigma: float = 1.0, ref: Optional[numpy.ndarray] = None, ref_ind: Optional[numpy.ndarray] = None)
2 dimensional Path variable for a 5 dimensional space. The input file needs to contain a (n_ref, 3) array that conform np.loadtxt syntax.
n_ref is the number of reference points for the path variable.
- Parameters
file_name (str, optional) – the txt file storing the path parameters. Defaults to None.
sigma (float, optional) – width of the path variable. Defaults to 1.0.
ref (np.ndarray, optional) – the reference position for the path. Defaults to None.
ref_ind (np.ndarray, optional) – the reference index for the path. Defaults to None.
- 1
Davide Branduardi, Francesco Luigi Gervasio, and Michele Parrinello. From a to b in free energy space. The Journal of Chemical Physics, 126(5):054103, Feb 2007. 00287. doi:10.1063/1.2432340.