17.1.1.12. pysisyphus.modefollow package

17.1.1.12.1. Submodules

17.1.1.12.2. pysisyphus.modefollow.NormalMode module

class pysisyphus.modefollow.NormalMode.NormalMode(l, masses)[source]

Bases: object

See http://gaussian.com/vib/

__init__(l, masses)[source]

NormalMode class.

Cartesian displacements are normalized to 1.

Parameters:

l (np.array) -- Cartesian, non-mass-weighted displacements.
masses (np.array) -- Atomic masses.

property l_mw

mw_norm_for_norm(norm=0.01)[source]

property red_mass

17.1.1.12.3. pysisyphus.modefollow.davidson module

class pysisyphus.modefollow.davidson.DavidsonResult(cur_cycle, converged, final_modes, qs, nus, mode_inds, res_rms)

Bases: tuple

converged: Alias for field number 1

cur_cycle: Alias for field number 0

final_modes: Alias for field number 2

mode_inds: Alias for field number 5

nus: Alias for field number 4

qs: Alias for field number 3

res_rms: Alias for field number 6

pysisyphus.modefollow.davidson.block_davidson(cart_coords, masses, forces_getter, guess_modes, lowest=None, trial_step_size=0.01, hessian_precon=None, max_cycles=25, res_rms_thresh=0.0001, start_precon=5, remove_trans_rot=True, print_level=1)[source]

pysisyphus.modefollow.davidson.forces_fin_diff(forces_getter, coords, b, step_size)[source]

pysisyphus.modefollow.davidson.geom_davidson(geom, *args, **kwargs)[source]

17.1.1.12.4. pysisyphus.modefollow.lanczos module

pysisyphus.modefollow.lanczos.geom_lanczos(geom, *args, **kwargs)[source]: Wraps Lanczos algorithm for use with Geometry objects.

pysisyphus.modefollow.lanczos.lanczos(coords, grad_getter, dx=0.005, dl=0.01, guess=None, max_cycles=25, reortho=True, logger=None)[source]

Lanczos method to determine smallest eigenvalue & -vector.

See [1] for description of algorithm.

17.1.1.12.5. Module contents

class pysisyphus.modefollow.NormalMode(l, masses)[source]