rgpycrumbs.basetypes¶

Classes¶

`nebiter`	A typed record representing an iteration of a Nudged Elastic Band (NEB) calculation.
`nebpath`	A typed record representing the NEB path data.
`DimerOpt`	Configuration for a dimer-based saddle point search.
`SpinID`	Identifier combining molecule ID and spin state.
`MolGeom`	Container for molecular geometry with energy and forces.
`SaddleMeasure`	Aggregated measurements from a saddle point search.

Module Contents¶

class rgpycrumbs.basetypes.nebiter[source]¶

A typed record representing an iteration of a Nudged Elastic Band (NEB) calculation.

Added in version 1.0.0.

Parameters¶

iterationint: The iteration number of the NEB calculation.
nebpathnebpath: The data for the NEB path at this iteration.

See Also¶

nebpathStores the normalized arclength, actual arclength, and energy data for: the NEB path.

iteration: int[source]¶

nebpath: nebiter.nebpath[source]¶

class rgpycrumbs.basetypes.nebpath[source]¶

A typed record representing the NEB path data.

Added in version 1.0.0.

Parameters¶

norm_distfloat: Normalized Arclength (0 to 1), representing the progression along the reaction path. Calculated as xcoord2 = arcS[img] / arcS[nim-1].
arc_distfloat: Actual Arclength at each point along the reaction path. Calculated as xcoord = arcS[img] + dx(ii).
energyfloat: 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 record is used within the nebiter record to store detailed path information for each NEB iteration.

norm_dist: float[source]¶

arc_dist: float[source]¶

energy: float[source]¶

class rgpycrumbs.basetypes.DimerOpt[source]¶

Configuration for a dimer-based saddle point search.

Added in version 1.0.0.

saddle: str = 'dimer'[source]¶

rot: str = 'lbfgs'[source]¶

trans: str = 'lbfgs'[source]¶

class rgpycrumbs.basetypes.SpinID[source]¶

Identifier combining molecule ID and spin state.

Added in version 1.0.0.

mol_id: int[source]¶

spin: str[source]¶

class rgpycrumbs.basetypes.MolGeom[source]¶

Container for molecular geometry with energy and forces.

Added in version 1.0.0.

pos: numpy.array[source]¶

energy: float[source]¶

forces: numpy.array[source]¶

class rgpycrumbs.basetypes.SaddleMeasure[source]¶

Aggregated measurements from a saddle point search.

Added in version 1.0.0.

pes_calls: int = 0[source]¶

iter_steps: int = 0[source]¶

tot_time: float[source]¶

saddle_energy: float[source]¶

saddle_fmax: float[source]¶

success: bool = False[source]¶

method: str = 'not run'[source]¶

dimer_rot: str = 'n/a'[source]¶

dimer_trans: str = 'n/a'[source]¶

init_energy: float[source]¶

barrier: float[source]¶

mol_id: int[source]¶

spin: str = 'unknown'[source]¶

scf: float[source]¶

termination_status: str = 'not set'[source]¶