17.1.1.3. pysisyphus.cos package

17.1.1.3.1. Submodules

17.1.1.3.2. pysisyphus.cos.AdaptiveNEB module

17.1.1.3.3. pysisyphus.cos.ChainOfStates module

17.1.1.3.4. pysisyphus.cos.FreeEndNEB module

17.1.1.3.5. pysisyphus.cos.FreezingString module

class pysisyphus.cos.FreezingString.FreezingString(images, calc_getter, max_nodes=10, opt_steps=3)[source]

Bases: object

property allcoords
as_xyz()[source]
property coords
property energy
property forces
property fully_grown
get_new_image(coords, index)[source]
get_tangent()[source]
property left_frontier
reparametrize(energy, forces)[source]
property right_frontier
set_new_frontier_nodes()[source]

17.1.1.3.6. pysisyphus.cos.GrowingChainOfStates module

17.1.1.3.7. pysisyphus.cos.GrowingNT module

class pysisyphus.cos.GrowingNT.GrowingNT(geom, step_len=0.5, rms_thresh=0.0017, r=None, final_geom=None, between=None, bonds=None, r_update=True, r_update_thresh=1.0, stop_after_ts=False, require_imag_freq=0.0, hessian_at_ts=False, out_dir='.', dump=True)[source]

Bases: object

property P

Projector that keeps perpendicular component.

as_xyz()[source]
property atoms
calc_hessian_for(other_geom)[source]
property cart_coords
property cart_forces
check_convergence(*args, **kwargs)[source]
clear_passed()[source]
property coords
property energy
property forces
property freeze_atoms
get_additional_print(energy)[source]
get_energy_and_forces_at(coords)[source]
get_energy_at(coords)[source]
get_path(fn)[source]
static get_r(geom, final_geom, bonds, r)[source]
grow_image()[source]
initialize()[source]
log(message)[source]
logger = <Logger cos (DEBUG)>
property moving_atoms
property r

Parallel/search direction.

reparametrize(image_energies, _forces)[source]

Check if GNT can be grown.

17.1.1.3.8. pysisyphus.cos.GrowingString module

17.1.1.3.9. pysisyphus.cos.NEB module

17.1.1.3.10. pysisyphus.cos.SimpleZTS module

17.1.1.3.11. Module contents