Source code for rgpycrumbs.basetypes

import datetime
from collections import namedtuple
from dataclasses import dataclass

import numpy as np

# namedtuple for storing NEB iteration data

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nebiter = namedtuple("nebiter", ["iteration", "nebpath"])



"""
A namedtuple representing an iteration of a Nudged Elastic Band (NEB) calculation.

Parameters
----------
iteration : int
    The iteration number of the NEB calculation.
nebpath : nebpath namedtuple
    The data for the NEB path at this iteration.

See Also
--------
nebpath : Stores the normalized arclength, actual arclength, and energy data for
    the NEB path.
"""

# namedtuple for storing the NEB path data

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nebpath = namedtuple("nebpath", ["norm_dist", "arc_dist", "energy"])




"""
A namedtuple representing the NEB path data.

Parameters
----------
norm_dist : float
    Normalized Arclength (0 to 1), representing the progression along the reaction path.
    Calculated as xcoord2 = arcS[img] / arcS[nim-1].
arc_dist : float
    Actual Arclength at each point along the reaction path. Calculated as
    xcoord = arcS[img] + dx(ii).
energy : float
    Interpolated Energy at each point, calculated using cubic polynomial
    interpolation. The energy is calculated using the formula:
    p = a*pow(dx(ii), 3.0) + b*pow(dx(ii), 2.0) + c*dx(ii) + d,
    where a, b, c, and d are coefficients of the cubic polynomial.

Notes
-----
The `nebpath` namedtuple is used within the `nebiter` namedtuple to store
detailed path information for each NEB iteration.
"""


@dataclass

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class DimerOpt:

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    saddle: str = "dimer"


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    rot: str = "lbfgs"


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    trans: str = "lbfgs"




@dataclass

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class SpinID:

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    mol_id: int


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    spin: str




@dataclass

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class MolGeom:

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    pos: np.array


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    energy: float


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    forces: np.array




@dataclass

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class SaddleMeasure:

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    pes_calls: int = 0


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    iter_steps: int = 0


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    tot_time: datetime.timedelta = datetime.timedelta(0).total_seconds()


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    saddle_energy: float = np.nan


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    saddle_fmax: float = np.nan


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    success: bool = False


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    method: str = "not run"


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    dimer_rot: str = "n/a"


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    dimer_trans: str = "n/a"


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    init_energy: float = np.nan


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    barrier: float = np.nan


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    mol_id: int = np.nan


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    spin: str = "unknown"


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    scf: float = np.nan


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    termination_status: str = "not set"