def coord_num_array_specific(
self,
distance_dict: Dict[str, float],
run_start: int,
run_end: int,
center_atom: str = "cation",
counter_atom: str = "anion",
) -> Dict[str, np.ndarray]:
"""Calculates the coordination number array of multiple species of specific
coordination types (SSIP, CIP, AGG).
Args:
distance_dict: A dict of coordination cutoff distance of the neighbor species.
run_start: Start frame of analysis.
run_end: End frame of analysis.
center_atom: The solvation shell center atom. Default to "cation".
counter_atom: The neighbor counter ion species. Default to "anion".
Return:
A diction containing the coordination number sequence of each specified neighbor species
and the total coordination number sequence in the specified frame range.
"""
nvt_run = self.wrapped_run
center_atoms = nvt_run.select_atoms(self.select_dict.get(center_atom))
num_array_dict = concat_coord_array(
nvt_run,
num_of_neighbor_specific,
center_atoms,
distance_dict,
self.select_dict,
run_start,
run_end,
counter_atom=counter_atom,
)
return num_array_dict
def coord_type_array(
self,
distance: float,
run_start: int,
run_end: int,
center_atom: str = "cation",
counter_atom: str = "anion",
) -> np.ndarray:
"""Calculates the solvation structure type (1 for SSIP, 2 for CIP,
3 for AGG) array of the solvation structure ``center_atom`` (typically the cation).
Args:
distance: The coordination cutoff distance.
run_start: Start frame of analysis.
run_end: End frame of analysis.
center_atom: The solvation shell center atom. Default to "cation".
counter_atom: The neighbor counter ion species. Default to "anion".
Return:
An array of the solvation structure type in the specified frame range.
"""
nvt_run = self.wrapped_run
distance_dict = {counter_atom: distance}
center_atoms = nvt_run.select_atoms(self.select_dict.get(center_atom))
num_array = concat_coord_array(
nvt_run,
num_of_neighbor_simple,
center_atoms,
distance_dict,
self.select_dict,
run_start,
run_end,
)["total"]
return num_array
def coord_num_array_single_species(
self,
species: str,
distance: float,
run_start: int,
run_end: int,
center_atom: str = "cation",
) -> np.ndarray:
"""Calculates the coordination number array of one ``species`` around the interested ``center_atom``.
Args:
species: The neighbor species.
distance: The coordination cutoff distance.
run_start: Start frame of analysis.
run_end: End frame of analysis.
center_atom: The solvation shell center atom. Default to "cation".
Return:
An array of coordination number in the frame range.
"""
nvt_run = self.wrapped_run
distance_dict = {species: distance}
center_atoms = nvt_run.select_atoms(self.select_dict.get(center_atom))
num_array = concat_coord_array(
nvt_run,
num_of_neighbor,
center_atoms,
distance_dict,
self.select_dict,
run_start,
run_end,
)["total"]
return num_array
def angle_array(
self,
distance_dict: Dict[str, float],
run_start: int,
run_end: int,
center_atom: str = "cation",
cip=True,
):
"""
Calculates the angle of a-c-b in the specified frame range.
Args:
distance_dict: A dict of coordination cutoff distance of the neighbor species.
The dictionary key must be in the order of a, b, where a is the neighbor species
used for determining coordination type, b is the other neighbor species, and the
corresponding values are cutoff distance of a->c and b->c, where c is the center species.
run_start: Start frame of analysis.
run_end: End frame of analysis.
center_atom: The center atom species.
cip: Only includes contact ion pair structures with only one `a` and one `c` atoms.
Default to True.
Returns:
An array of angles of a-c-b in the specified frames.
"""
nvt_run = self.wrapped_run
center_atoms = nvt_run.select_atoms(self.select_dict.get(center_atom))
assert len(distance_dict) == 2, "Only distance a->c, b->c shoud be specified in the distance_dict."
distance_dict[center_atom] = list(distance_dict.values())[0]
ang_array = concat_coord_array(
nvt_run,
angular_dist_of_neighbor,
center_atoms,
distance_dict,
self.select_dict,
run_start,
run_end,
cip=cip,
)["total"]
return ang_array