pyiron_contrib.atomistics.atomicrex.general_input module

class pyiron_contrib.atomistics.atomicrex.general_input.AlgorithmFactory

Bases: PyironFactory

Factory class to conveniently acces the different fitting algorithms available in atomicrex.

static ar_lbfgs(conv_threshold=1e-10, max_iter=50, gradient_epsilon=None)

static ar_spa(spa_iterations=20, seed=42)

static g_mlsl(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static g_mlsl_lds(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gd_stogo(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gd_stogo_rand(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gn_crs2_lm(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gn_direct(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gn_direct_l(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gn_esch(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static gn_isres(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ld_ccsaq(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ld_lbfgs(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ld_mma(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ld_slsqp(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ld_var1(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ld_var2(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_bobyqa(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_cobyla(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_neldermead(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_newuoa(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_newuoa_bound(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_praxis(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static ln_sbplx(stopval=1e-10, max_iter=50, maxtime=None, ftol_rel=None, ftol_abs=None, xtol_rel=None, seed=None)

static scipy_algorithm()

class pyiron_contrib.atomistics.atomicrex.general_input.AtomTypes(*args, **kwargs)

Bases: DataContainer

DataContainer used to specify elements in the fit job. Elements can be added using dictionary or attribute syntax. Their value should None or a (mass, index) tuple as value. If value is None the mass and index are taken from the ase package. Examples: job.input.atom_types.Cu = None job.input.atom_types[“Cu”] = None job.input.atom_types.Cu = (63.546, 29)

class pyiron_contrib.atomistics.atomicrex.general_input.AtomicrexAlgorithm(*args, **kwargs)

Bases: DataContainer

Class to inherit from. If more algorithms will be implemented in atomicrex at some point they can be implemented similar to the AR_LBFGS class.

class pyiron_contrib.atomistics.atomicrex.general_input.GeneralARInput(*args, **kwargs)

Bases: DataContainer

Class to store general input of an atomicrex job, f.e. the fit algorithm.

class pyiron_contrib.atomistics.atomicrex.general_input.NloptAlgorithm(*args, **kwargs)

Bases: DataContainer

Nlopt algorithms should inherit from this class.

class pyiron_contrib.atomistics.atomicrex.general_input.NloptGlobalLocal(*args, **kwargs)

Bases: NloptAlgorithm

Nlopt global optimizers that additionally need a local minimizer similar to the spa algorithm implemented in atomicrex

class pyiron_contrib.atomistics.atomicrex.general_input.ScipyAlgorithm

Bases: object

from_hdf(hdf, group_name)

to_hdf(hdf, group_name)

class pyiron_contrib.atomistics.atomicrex.general_input.SpaMinimizer(*args, **kwargs)

Bases: DataContainer

Global optimizer implemented in atomicrex. Should be used in combination with a local minimizer. See the atomicrex documentation for details.

property name