17.1.1.3. pysisyphus.cos package
17.1.1.3.1. Submodules
17.1.1.3.2. pysisyphus.cos.AdaptiveNEB module
- class pysisyphus.cos.AdaptiveNEB.AdaptiveNEB(images, adapt=True, adapt_fact=0.25, adapt_between=1, scale_fact=False, keep_hei=True, free_ends=True, **kwargs)[source]
Bases:
NEB
- __init__(images, adapt=True, adapt_fact=0.25, adapt_between=1, scale_fact=False, keep_hei=True, free_ends=True, **kwargs)[source]
(Free-End) Adaptive Nudged Elastic Band.
- Parameters:
images (list of Geometry objects) -- Images of the band.
adapt (bool, default True) -- Whether to adapt the image number or not. This switch is included to support the FreeEndNEB class, that is just a thin wrapper around this class.
adapt_fact (positive float) -- Factor that is used to decide wether to adapt. The inital threshold is calculated by multiplying the RMS force of the band with this factor. When the RMS of the force falls below this threshold adaption takes place.
adapat_between (positive integer) -- Number of images to interpolate between the highest energy image and its neighbours. The number of starting images must be higher or equal then 2*adapt_between+3, as we reuse/transfer the calculators from the starting images onto the new ones.
scale_fact (bool, default False) -- Whether to increase adapt_fact in deeper levels. This may lead to earlier adapation.
keep_hei (bool, optional) -- Whether to keep the highest energy image (usually a very good idea) or to interpolate only between the neighbouring images.
free_ends (bool, default True) -- Whether to use modified forces on the end images.
- adapt_this_cycle(forces)[source]
Decide wether to adapt.
- Parameters:
forces (np.array) -- Forces of the previous optimization cycle.
- Returns:
adapt -- Flag that indicates if adaption should take place in this cycle.
- Return type:
bool
- property forces
See Eq. (7) in [2].
17.1.1.3.3. pysisyphus.cos.ChainOfStates module
- class pysisyphus.cos.ChainOfStates.ChainOfStates(images, fix_first=True, fix_last=True, align_fixed=True, climb=False, climb_rms=0.005, climb_lanczos=False, climb_lanczos_rms=0.005, climb_fixed=True, energy_min_mix=False, scheduler=None, progress=False)[source]
Bases:
object
- property atoms
- property calculator
- property cart_coords
Return a flat 1d array containing the cartesian coordinates of all images.
- property coords
Return a flat 1d array containing the coordinates of all images.
- property coords3d
- property energy
- property forces
- get_tangent(i, kind='upwinding', lanczos_guess=None, disable_lanczos=False)[source]
[1] Equations (8) - (11)
- property gradient
- property image_coords
- property image_inds
- property last_index
- logger = <Logger cos (DEBUG)>
- property masses_rep
- property max_image_num
- property moving_images
- property moving_indices
Returns the indices of the images that aren't fixed and can be optimized.
- property perpendicular_forces
- prepare_opt_cycle(last_coords, last_energies, last_forces)[source]
Implements additional logic in preparation of the next optimization cycle.
Should be called by the optimizer at the beginning of a new optimization cycle. Can be used to implement additional logic as needed for AdaptiveNEB etc.
- property results
- rms(arr)[source]
Root mean square
Returns the root mean square of the given array.
- Parameters:
arr (iterable of numbers) --
- Returns:
rms -- Root mean square of the given array.
- Return type:
float
- set_coords_at(i, coords)[source]
Called from helpers.procrustes with cartesian coordinates. Then tries to set cartesian coordinate as self.images[i].coords which will raise an error when coord_type != "cart".
- set_zero_forces_for_fixed_images()[source]
This is always done in cartesian coordinates, independent of the actual coord_type of the images as setting forces only work with cartesian forces.
- valid_coord_types = ('cart', 'cartesian', 'dlc')
17.1.1.3.4. pysisyphus.cos.FreeEndNEB module
- class pysisyphus.cos.FreeEndNEB.FreeEndNEB(*args, fix_first=False, fix_last=False, **kwargs)[source]
Bases:
AdaptiveNEB
- __init__(*args, fix_first=False, fix_last=False, **kwargs)[source]
Simple Free-End-NEB method.
Derived from AdaptiveNEB with disabled adaptation. Only implements Eq. (7) from [2]. For other implementations please see the commit 01bc8812ca6f1cd3645d43e0337d9e3c5fb0ba55. There the other variants are present but I think Eq. (7) in [2] is the simplest & best bet.
17.1.1.3.5. pysisyphus.cos.FreezingString module
17.1.1.3.6. pysisyphus.cos.GrowingChainOfStates module
- class pysisyphus.cos.GrowingChainOfStates.GrowingChainOfStates(images, calc_getter, max_nodes=10, **kwargs)[source]
Bases:
ChainOfStates
- property arc_dims
- property max_image_num
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.
- property atoms
- property cart_coords
- property cart_forces
- property coords
- property energy
- property forces
- logger = <Logger cos (DEBUG)>
- property r
Parallel/search direction.
17.1.1.3.8. pysisyphus.cos.GrowingString module
- class pysisyphus.cos.GrowingString.GrowingString(images, calc_getter, perp_thresh=0.05, param='equi', reparam_every=2, reparam_every_full=3, reparam_tol=None, reparam_check='rms', max_micro_cycles=5, reset_dlc=True, climb=False, **kwargs)[source]
Bases:
GrowingChainOfStates
- property forces
- property full_string_image_inds
- property fully_grown
Returns wether the string is fully grown. Don't count the first and last node.
- get_new_image(ref_index)[source]
Get new image by taking a step from self.images[ref_index] towards the center of the string.
- property image_inds
- property left_size
- property lf_ind
Index of the left frontier node in self.images.
- property nodes_missing
Returns the number of nodes to be grown.
- property rf_ind
Index of the right frontier node in self.images.
- property right_size
- property string_size
17.1.1.3.9. pysisyphus.cos.NEB module
- class pysisyphus.cos.NEB.NEB(images, variable_springs=False, k_max=0.3, k_min=0.1, perp_spring_forces=None, bandwidth=None, **kwargs)[source]
Bases:
ChainOfStates
- property forces
- property parallel_forces
17.1.1.3.10. pysisyphus.cos.SimpleZTS module
- class pysisyphus.cos.SimpleZTS.SimpleZTS(images, param='equal', **kwargs)[source]
Bases:
ChainOfStates