Parameters
Surrogate Hessian accelerated parallel line-search: parameters
- class stalk.params.GeometryResult(pos, axes=None, elem=None)
Bases:
object- axes = None
- elem = None
- get_axes()
- get_elem()
- get_pos()
- get_result()
- pos = None
- class stalk.params.LineSearchPoint(offset, value=None, error=0.0)
Bases:
object- property enabled
- property error
- property is_eqm
- property offset
- plot(ax: Axes, color='tab:blue', marker='o', linestyle='none', **kwargs)
- reset_value()
- tol = 1e-09
- property valid
The value is valid, when it is enabled and has a value
- property value
- class stalk.params.Parameter(value, error=0.0, label='p', unit='')
Bases:
object- property error
- label: str = ''
- shift(shift)
- unit: str = ''
- property value
- class stalk.params.ParameterHessian(hessian=None, structure=None, hessian_real=None, **kwargs)
Bases:
object- D = None
- Lambda = None
- P = None
- U = None
- compute_fdiff(pes: PesFunction, structure=None, dp=0.01, dpos_mode=False, **kwargs)
- property directions
- get_hessian(**kwargs)
- hessian = None
- property hessian_set
- init_hessian_array(hessian, **kwargs)
- init_hessian_real(hessian_real, structure=None)
- init_hessian_structure(structure)
Initialize the Hessian from a structure
- property lambdas
- set_structure(structure)
Set the Hessian location as a ParameterSet or derived object
- structure = None
- update_hessian(hessian)
- class stalk.params.ParameterSet(params=None, params_err=None, units=None, value=None, error=0.0, label=None, labels=None)
Bases:
LineSearchPoint- check_consistency()
- copy(params=None, params_err=None, label=None, offset=None)
- init_params(params, errors=None, units=None, labels=None)
- label = ''
- property params
- property params_err
- property params_list
- set_params(params, errors=None)
- shift_params(shifts)
- class stalk.params.ParameterStructure(forward=None, backward=None, pos=None, axes=None, elem=None, params=None, params_err=None, forward_args={}, backward_args={}, value=None, error=0.0, label='', units='B', dim=3, translate=True, tol=1e-07, **kwargs)
Bases:
ParameterSet- axes = None
- backward_args = None
- backward_func = None
- check_consistency(params=None, pos=None, axes=None, tol=None, verbose=False)
Check consistency of present forward-backward mapping. If params or pos/axes are supplied, check at the corresponding points. If not, check at the present point.
- property consistent
- copy(params=None, params_err=None, label=None, pos=None, axes=None, offset=None, **kwargs)
- dim = None
- elem = None
- forward_args = None
- forward_func = None
- get_params_distribution(N=100)
- jacobian(dp=0.001)
- load(path='relax', xyz_file=None, xsf_file=None, load_func=None, load_args={}, c_pos=1.0, c_axes=1.0, make_consistent=True, verbose=True, **kwargs)
- map_backward(params=None)
- map_forward(pos=None, axes=None)
- property periodic
- pos = None
- pos_difference(pos_ref)
- remap_forward(forward, N=None, fraction=0.159, **kwargs)
- set_axes(axes, check=True)
- set_backward_func(backward_func, backward_args={})
- set_elem(elem)
- set_forward_func(forward_func, forward_args={})
- set_params(params, params_err=None, dpos_mode=False)
- set_position(pos, axes=None, translate=True)
- shift_params(dparams, dpos_mode=False)
- shift_pos(dpos, translate=True)
- tol = None
- units = None
- class stalk.params.PesFunction(func, args={})
Bases:
FunctionCaller- evaluate(structure: ParameterSet, sigma=0.0, add_sigma=False, interactive=False, **kwargs)
- evaluate_all(structures: list[ParameterSet], sigmas=None, add_sigma=False, interactive=False, **kwargs)
- relax(structure: ParameterSet, **kwargs)
- stalk.params.bond_angle(r0, rc, r1, units='ang')
Return dihedral angle between 3 bodies
- stalk.params.distance(r0, r1)
Return Euclidean distance between two positions
- stalk.params.mean_distances(pairs)
Return average distance over (presumably) identical position pairs
- stalk.params.mean_param(params, tol=1e-06)