16.1.1.17. pysisyphus.tsoptimizers package
16.1.1.17.1. Submodules
16.1.1.17.2. pysisyphus.tsoptimizers.RSIRFOptimizer module
- class pysisyphus.tsoptimizers.RSIRFOptimizer.RSIRFOptimizer(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
TSHessianOptimizer
16.1.1.17.3. pysisyphus.tsoptimizers.RSPRFOptimizer module
- class pysisyphus.tsoptimizers.RSPRFOptimizer.RSPRFOptimizer(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
TSHessianOptimizer
16.1.1.17.4. pysisyphus.tsoptimizers.TRIM module
- class pysisyphus.tsoptimizers.TRIM.TRIM(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
TSHessianOptimizer
16.1.1.17.5. pysisyphus.tsoptimizers.TSHessianOptimizer module
- class pysisyphus.tsoptimizers.TSHessianOptimizer.TSHessianOptimizer(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
HessianOptimizer
Optimizer to find first-order saddle points.
- __init__(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Baseclass for transition state optimizers utilizing Hessian information.
Several arguments expect a typed primitive or an iterable of typed primitives. A typed primitive is specified as (PrimType, int, int, ...), e.g., for a bond between atoms 0 and 1: (BOND, 0, 1) or for a bend between the atom triple 0, 1, 2 as (BEND, 0, 1, 2).
- Parameters
geometry (
Geometry
) -- Geometry to be optimized.root (
int
, default:0
) -- Index of imaginary mode to maximize along.hessian_ref (
Optional
[str
], default:None
) -- Filename pointing to a pysisyphus HDF5 Hessian.prim_coord (typed_prim) -- Select initial root/imaginary mode by overlap with this internal coordinate.
rx_coords (iterable of (typed_prim)) -- Construct imaginary mode comprising the given typed prims by modifying a model Hessian.
rx_mode (iterable of (typed_prim, phase_factor)) -- Select initial root by overlap with a mode constructed from the given typed primitives.
hessian_init (
Literal
['calc', 'unit', 'fischer', 'lindh', 'simple', 'swart', 'xtb', 'xtb1', 'xtbff'], default:'calc'
) -- Type of initial model Hessian.hessian_update (
Literal
['none', None, False, 'bfgs', 'damped_bfgs', 'flowchart', 'bofill', 'ts_bfgs', 'ts_bfgs_org', 'ts_bfgs_rev'], default:'bofill'
) -- Type of Hessian update. Defaults to BFGS for minimizations and Bofill for saddle point searches.hessian_recalc_reset (
bool
, default:True
) -- Whether to skip Hessian recalculation after reset. Undocumented.max_micro_cycles (
int
, default:50
) -- Maximum number of RS iterations.trust_radius (
float
, default:0.3
) -- Initial trust radius in whatever unit the optimization is carried out.trust_max (
float
, default:0.5
) -- Maximum trust radius.augment_bonds (
bool
, default:False
) -- Try to derive additional streching coordinates from the imaginary mode.min_line_search (
bool
, default:False
) -- Carry out line search along the imaginary mode.max_line_search (
bool
, default:False
) -- Carry out line search in the subspace that is minimized.assert_neg_eigval (
bool
, default:False
) -- Check for the existences for at least one significant negative eigenvalue. If enabled and no negative eigenvalue is present the optimization will be aborted.**kwargs -- Keyword arguments passed to the HessianOptimizer/Optimizer baseclass.
- valid_updates = ('bofill', 'ts_bfgs', 'ts_bfgs_org', 'ts_bfgs_rev')
16.1.1.17.6. Module contents
- class pysisyphus.tsoptimizers.RSIRFOptimizer(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
TSHessianOptimizer
- class pysisyphus.tsoptimizers.RSPRFOptimizer(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
TSHessianOptimizer
- class pysisyphus.tsoptimizers.TRIM(geometry, root=0, hessian_ref=None, prim_coord=None, rx_coords=None, rx_mode=None, hessian_init='calc', hessian_update='bofill', hessian_recalc_reset=True, max_micro_cycles=50, trust_radius=0.3, trust_max=0.5, augment_bonds=False, min_line_search=False, max_line_search=False, assert_neg_eigval=False, **kwargs)[source]
Bases:
TSHessianOptimizer