pyiron_contrib.atomistics.atomicrex.function_factory module

class pyiron_contrib.atomistics.atomicrex.function_factory.AbstractMetaFunction(*args, **kwargs)

Bases: DataContainer, MetaFunctionMixin

class pyiron_contrib.atomistics.atomicrex.function_factory.BaseFunctionMixin

Bases: object

copy_final_to_initial_params(filter_func=None)

count_parameters(enabled_only=True)

lock_parameters(filter_func=None)

set_max_values(constant=None, factor=None, filter_func=None)

Convenience function so set max values for all parameters at once. Can either use a constant value or a factor. If both are given factor is used.

Parameters

• constant ([type], optional) – param.max_val = constant. Defaults to None.

• factor ([type], optional) – param.max_val = abs(start_val)*factor. Defaults to None.

• filter_func ([type], optional) – Optional function to filter params. Should take param as argument and return True or False. Defaults to None.

Raises

ValueError – Raises when constant and factor are None.

set_min_values(constant=None, factor=None, filter_func=None)

Convenience function so set min values for all parameters at once. Can either use a constant value or a factor. If both are given factor is used.

Parameters

• constant ([type], optional) – param.min_val = constant. Defaults to None.

• factor ([type], optional) – param.min_val = -abs(start_val)*factor. Defaults to None.

• filter_func ([type], optional) – Optional function to filter params. Should take param as argument and return True or False. Defaults to None.

Raises

ValueError – Raises when constant and factor are None.

class pyiron_contrib.atomistics.atomicrex.function_factory.Constant(*args, **kwargs)

Bases: SpecialFunction

class pyiron_contrib.atomistics.atomicrex.function_factory.ExpA(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.ExpB(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.ExpGaussian(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.ExtendedMishinCuF(*args, **kwargs)

Bases: SpecialFunction

class pyiron_contrib.atomistics.atomicrex.function_factory.FunctionFactory

Bases: PyironFactory

Class to conveniently create different function objects. for detailed information about the function visit the atomicrex documentation.

static MishinCuF(identifier, F0, F2, q1, q2, q3, q4, Q1, Q2, species=['*'])

static MishinCuRho(identifier, a, r1, r2, beta1, beta2, species=['*', '*'])

static MishinCuV(identifier, E1, E2, alpha1, alpha2, r01, r02, delta, cutoff, h, S1, rs1, S2, rs2, S3, rs3, species=['*', '*'])

static RsMinusRPowN(identifier, S, rs, N, species=['*', '*'], cutoff=None)

static constant(identifier, constant, species=['*', '*'])

static equidistant_spline(identifier, n_nodes, cutoff, initial_value_func, min_distance=0.0, derivative_left=0.0, d_left_enabled=True, derivative_right=0.0, d_right_enabled=False, endpoint_val=0.0, species=['*', '*'])

Convenience function to create a spline function with equidistant node points.

Parameters

• identifier (str) – function identifier. Should be unique within the job

• n_nodes (int) – number of node points

• cutoff (float) – values after are 0

• initial_value_func (function(x)) – function to calculate start values for nodes.

• min_distance (float, optional) – x coordinate of first node point. Defaults to 0.

• derivative_left (int, optional) – . Defaults to 0.

• d_left_enabled (bool, optional) – Whether to fit. Defaults to True.

• derivative_right (int, optional) – [description]. Defaults to 0.

• d_right_enabled (bool, optional) – Whether to fit. Should be False for most functions, beside Embedding terms. Defaults to False.

• endpoint_val (float, None, bool, optional) – Start val for endpoint, enabled=False if float, if False endpoint is not included. If None endpoint is included, enabled and start_val is calculated like other points. Defaults to 0.0, which should be used in most cases.

• species (list of str, optional) – Only needs to be changed for multi element fits. Defaults to [“*”, “*”].

Returns

[description]

Return type

[type]

static exp_A_screening(identifier, cutoff, species=['*', '*'], is_screening_function=True)

static exp_B_screening(identifier, cutoff, rc, alpha, exponent, species=['*', '*'], is_screening_function=True)

static exp_gaussian_screening(identifier, cutoff, stddev, alpha, exponent, species=['*', '*'], is_screening_function=True)

static extendedMishinCuF(identifier, F0, F2, f3, f4, f5, f6, a3, a4, a5, a6, d3, d4, d5, species=['*'])

static gaussian(identifier, prefactor, eta, mu, species=['*', '*'], cutoff=None)

static gaussians_sum(n_gaussians, eta, identifier, node_points=None, cutoff=None, initial_prefactors=None, min_prefactors=None, max_prefactors=None, species=['*', '*'])

static morse_A(identifier, D0, r0, alpha, species=['*', '*'])

static morse_B(identifier, D0, r0, beta, S, delta, species=['*', '*'])

static morse_C(identifier, A, B, mu, lambda_val, delta, species=['*', '*'])

static poly(identifier, cutoff, species=['*', '*'])

TAKE CARE !!! The polynomial function implemented in atomicrex does not handle derivatives at the cutoff right now, i.e. when using this as a pair function or similar there will be massive jumps in forces.

static product(identifier, species=['*', '*'])

static spline(identifier, cutoff, derivative_left=0, derivative_right=0, species=['*', '*'])

static sum(identifier, species=['*', '*'])

static user_function(identifier, input_variable='r', species=['*', '*'], is_screening_function=False, cutoff=None)

static x_pow_n_cutoff(identifier, cutoff, h=1, N=4, species=['*', '*'], is_screening_function=True)

class pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameter(*args, **kwargs)

Bases: DataContainer

Function parameter. For detailed information about the attributes see the atomicrex documentation. Objects should only be created using the add_parameter method of the FunctionParameterList class.

copy_final_to_start_value(filter_func=None)

Copies the final value to start_val.

Raises

ValueError – Raises if fitting of the parameter is enabled, but the final value is None. This should only be the case if the job aborted or was not run yet.

lock(filter_func=None)

set_max_val(constant=None, factor=None, filter_func=None)

set_min_val(constant=None, factor=None, filter_func=None)

class pyiron_contrib.atomistics.atomicrex.function_factory.FunctionParameterList(*args, **kwargs)

Bases: DataContainer

add_parameter(param, start_val, enabled=True, reset=False, min_val=None, max_val=None, tag=None, fitable=True)

Add a function parameter named param to a function. This needs to be done manually for user functions and not for special functions.

Parameters

• param (str) – Name of the parameter. Must exactly match the name in the function expression.

• start_val (float) – Starting value of the parameter

• enabled (bool, optional) – Determines if the paremeter is varied during fitting. Defaults to True.

• reset (bool, optional) – Determine if the parameter should be reset every iteration

• False. (Can help with global optimization. Defaults to) –

• min_val (float, optional) – Highly recommended for global optimization. Defaults to None.

• max_val (float, optional) – Highly recommended for global optimization. Defaults to None.

• tag (str, optional) – [description]. Only necessary for ABOP potentials .Defaults to None.

• fitable (bool, optional) – [description]. Changing could cause bugs. Defaults to True.

fit_dofs_to_xml_element()

Internal function Returns fit dofs as atomicrex xml element.

class pyiron_contrib.atomistics.atomicrex.function_factory.GaussianFunc(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.MetaFunctionMixin

Bases: object

copy_final_to_initial_params(filter_func=None)

count_parameters(enabled_only=True)

lock_parameters(filter_func=None)

set_max_values(constant=None, factor=None, filter_func=None)

Convenience function so set max values for all parameters at once. Can either use a constant value or a factor. If both are given factor is used.

Parameters

• constant ([type], optional) – param.max_val = constant. Defaults to None.

• factor ([type], optional) – param.max_val = abs(start_val)*factor. Defaults to None.

• filter_func ([type], optional) – Optional function to filter params. Should take param as argument and return True or False. Defaults to None.

Raises

ValueError – Raises when constant and factor are None.

set_min_values(constant=None, factor=None, filter_func=None)

Convenience function so set min values for all parameters at once. Can either use a constant value or a factor. If both are given factor is used.

Parameters

• constant ([type], optional) – param.min_val = constant. Defaults to None.

• factor ([type], optional) – param.min_val = -abs(start_val)*factor. Defaults to None.

• filter_func ([type], optional) – Optional function to filter params. Should take param as argument and return True or False. Defaults to None.

Raises

ValueError – Raises when constant and factor are None.

class pyiron_contrib.atomistics.atomicrex.function_factory.MishinCuF(*args, **kwargs)

Bases: SpecialFunction

class pyiron_contrib.atomistics.atomicrex.function_factory.MishinCuRho(*args, **kwargs)

Bases: SpecialFunction

class pyiron_contrib.atomistics.atomicrex.function_factory.MorseA(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.MorseB(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.MorseC(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.Node(*args, **kwargs)

Bases: FunctionParameter

Function parameter, but for spline interpolation.

class pyiron_contrib.atomistics.atomicrex.function_factory.NodeList(*args, **kwargs)

Bases: DataContainer

add_node(x, start_val, enabled=True, reset=False, min_val=None, max_val=None)

Add a node to the spline interpolation function.

Parameters

• x (float) – x coordinate of the node. Does not change during fitting.

• start_val (float) – Initial y coordinate of the node.

• enabled (bool, optional) – Determines if y is changed during fitting. Defaults to True.

• reset (bool, optional) – Determines if y should be reset every iteration. Defaults to False.

• min_val (float, optional) – Highly recommended for global optimization. Defaults to None.

• max_val (float, optional) – Highly recommended for global optimization. Defaults to None.

create_from_arrays(x, y, min_vals=None, max_vals=None)

Convenience function to create nodes from lists or arrays of values. Allows to easily start the fitting process with physically motivated values or values taken from previous potentials. Creates len(x) nodes at position x with starting values y. All given arrays must have the same length.

Parameters

• x (list or array) – x values of the nodes

• y (list or array) – corresponding y (starting) values

• min_vals ([type], optional) – Highly recommended for global optimization. Defaults to None.

• max_vals ([type], optional) – Highly recommended for global optimization. Defaults to None.

class pyiron_contrib.atomistics.atomicrex.function_factory.Poly(*args, **kwargs)

Bases: DataContainer, BaseFunctionMixin

Polynomial interpolation function.

class pyiron_contrib.atomistics.atomicrex.function_factory.PolyCoeff(*args, **kwargs)

Bases: FunctionParameter

Function parameter, but for polynomial interpolation.

class pyiron_contrib.atomistics.atomicrex.function_factory.PolyCoeffList(*args, **kwargs)

Bases: DataContainer

add_coeff(n, start_val, enabled=True, reset=False, min_val=None, max_val=None)

Add a term in the form of a*x^n.

Parameters

• n (int) – Order n of the coefficient

• start_val (float) – Starting value of a.

• enabled (bool, optional) – Determines if it should be fitted. Defaults to True.

• reset (bool, optional) – Determines if it should be reset after each iteration. Defaults to False.

• min_val (float, optional) – Highly recommended for global optimization. Defaults to None.

• max_val (float, optional) – Highly recommended for global optimization. Defaults to None.

class pyiron_contrib.atomistics.atomicrex.function_factory.Product(*args, **kwargs)

Bases: AbstractMetaFunction, MetaFunctionMixin

class pyiron_contrib.atomistics.atomicrex.function_factory.RsMinusRPowN(*args, **kwargs)

Bases: SpecialFunction

property func

class pyiron_contrib.atomistics.atomicrex.function_factory.SpecialFunction(*args, **kwargs)

Bases: DataContainer, BaseFunctionMixin

Analytic functions defined within atomicrex should inherit from this class https://atomicrex.org/potentials/functions.html#index-1 https://atomicrex.org/potentials/functions.html#specialized-functions

property func

plot()

class pyiron_contrib.atomistics.atomicrex.function_factory.Spline(*args, **kwargs)

Bases: DataContainer, BaseFunctionMixin

Spline interpolation function

copy_final_to_initial_params(filter_func=None)

count_parameters(enabled_only=True)

lock_parameters(filter_func=None)

set_max_values(constant=None, factor=None, filter_func=None)

Convenience function so set max values for all parameters at once. Can either use a constant value or a factor. If both are given factor is used.

Parameters

• constant ([type], optional) – param.max_val = constant. Defaults to None.

• factor ([type], optional) – param.max_val = abs(start_val)*factor. Defaults to None.

• filter_func ([type], optional) – Optional function to filter params. Should take param as argument and return True or False. Defaults to None.

Raises

ValueError – Raises when constant and factor are None.

set_min_values(constant=None, factor=None, filter_func=None)

Convenience function so set min values for all parameters at once. Can either use a constant value or a factor. If both are given factor is used.

Parameters

• constant ([type], optional) – param.min_val = constant. Defaults to None.

• factor ([type], optional) – param.min_val = -abs(start_val)*factor. Defaults to None.

• filter_func ([type], optional) – Optional function to filter params. Should take param as argument and return True or False. Defaults to None.

Raises

ValueError – Raises when constant and factor are None.

class pyiron_contrib.atomistics.atomicrex.function_factory.Sum(*args, **kwargs)

Bases: AbstractMetaFunction, MetaFunctionMixin

class pyiron_contrib.atomistics.atomicrex.function_factory.UserFunction(*args, **kwargs)

Bases: DataContainer, BaseFunctionMixin

Analytic functions that are not implemented in atomicrex can be provided as user functions. All parameters defined in the function should be added using the UserFunction.parameters.add_parameter() method.

class pyiron_contrib.atomistics.atomicrex.function_factory.XpowNCutoff(*args, **kwargs)

Bases: SpecialFunction

property func

pyiron_contrib.atomistics.atomicrex.function_factory.plot(func, x=array([0.01, 0.02997143, 0.04994286, 0.06991429, 0.08988571, 0.10985714, 0.12982857, 0.1498, 0.16977143, 0.18974286, 0.20971429, 0.22968571, 0.24965714, 0.26962857, 0.2896, 0.30957143, 0.32954286, 0.34951429, 0.36948571, 0.38945714, 0.40942857, 0.4294, 0.44937143, 0.46934286, 0.48931429, 0.50928571, 0.52925714, 0.54922857, 0.5692, 0.58917143, 0.60914286, 0.62911429, 0.64908571, 0.66905714, 0.68902857, 0.709, 0.72897143, 0.74894286, 0.76891429, 0.78888571, 0.80885714, 0.82882857, 0.8488, 0.86877143, 0.88874286, 0.90871429, 0.92868571, 0.94865714, 0.96862857, 0.9886, 1.00857143, 1.02854286, 1.04851429, 1.06848571, 1.08845714, 1.10842857, 1.1284, 1.14837143, 1.16834286, 1.18831429, 1.20828571, 1.22825714, 1.24822857, 1.2682, 1.28817143, 1.30814286, 1.32811429, 1.34808571, 1.36805714, 1.38802857, 1.408, 1.42797143, 1.44794286, 1.46791429, 1.48788571, 1.50785714, 1.52782857, 1.5478, 1.56777143, 1.58774286, 1.60771429, 1.62768571, 1.64765714, 1.66762857, 1.6876, 1.70757143, 1.72754286, 1.74751429, 1.76748571, 1.78745714, 1.80742857, 1.8274, 1.84737143, 1.86734286, 1.88731429, 1.90728571, 1.92725714, 1.94722857, 1.9672, 1.98717143, 2.00714286, 2.02711429, 2.04708571, 2.06705714, 2.08702857, 2.107, 2.12697143, 2.14694286, 2.16691429, 2.18688571, 2.20685714, 2.22682857, 2.2468, 2.26677143, 2.28674286, 2.30671429, 2.32668571, 2.34665714, 2.36662857, 2.3866, 2.40657143, 2.42654286, 2.44651429, 2.46648571, 2.48645714, 2.50642857, 2.5264, 2.54637143, 2.56634286, 2.58631429, 2.60628571, 2.62625714, 2.64622857, 2.6662, 2.68617143, 2.70614286, 2.72611429, 2.74608571, 2.76605714, 2.78602857, 2.806, 2.82597143, 2.84594286, 2.86591429, 2.88588571, 2.90585714, 2.92582857, 2.9458, 2.96577143, 2.98574286, 3.00571429, 3.02568571, 3.04565714, 3.06562857, 3.0856, 3.10557143, 3.12554286, 3.14551429, 3.16548571, 3.18545714, 3.20542857, 3.2254, 3.24537143, 3.26534286, 3.28531429, 3.30528571, 3.32525714, 3.34522857, 3.3652, 3.38517143, 3.40514286, 3.42511429, 3.44508571, 3.46505714, 3.48502857, 3.505, 3.52497143, 3.54494286, 3.56491429, 3.58488571, 3.60485714, 3.62482857, 3.6448, 3.66477143, 3.68474286, 3.70471429, 3.72468571, 3.74465714, 3.76462857, 3.7846, 3.80457143, 3.82454286, 3.84451429, 3.86448571, 3.88445714, 3.90442857, 3.9244, 3.94437143, 3.96434286, 3.98431429, 4.00428571, 4.02425714, 4.04422857, 4.0642, 4.08417143, 4.10414286, 4.12411429, 4.14408571, 4.16405714, 4.18402857, 4.204, 4.22397143, 4.24394286, 4.26391429, 4.28388571, 4.30385714, 4.32382857, 4.3438, 4.36377143, 4.38374286, 4.40371429, 4.42368571, 4.44365714, 4.46362857, 4.4836, 4.50357143, 4.52354286, 4.54351429, 4.56348571, 4.58345714, 4.60342857, 4.6234, 4.64337143, 4.66334286, 4.68331429, 4.70328571, 4.72325714, 4.74322857, 4.7632, 4.78317143, 4.80314286, 4.82311429, 4.84308571, 4.86305714, 4.88302857, 4.903, 4.92297143, 4.94294286, 4.96291429, 4.98288571, 5.00285714, 5.02282857, 5.0428, 5.06277143, 5.08274286, 5.10271429, 5.12268571, 5.14265714, 5.16262857, 5.1826, 5.20257143, 5.22254286, 5.24251429, 5.26248571, 5.28245714, 5.30242857, 5.3224, 5.34237143, 5.36234286, 5.38231429, 5.40228571, 5.42225714, 5.44222857, 5.4622, 5.48217143, 5.50214286, 5.52211429, 5.54208571, 5.56205714, 5.58202857, 5.602, 5.62197143, 5.64194286, 5.66191429, 5.68188571, 5.70185714, 5.72182857, 5.7418, 5.76177143, 5.78174286, 5.80171429, 5.82168571, 5.84165714, 5.86162857, 5.8816, 5.90157143, 5.92154286, 5.94151429, 5.96148571, 5.98145714, 6.00142857, 6.0214, 6.04137143, 6.06134286, 6.08131429, 6.10128571, 6.12125714, 6.14122857, 6.1612, 6.18117143, 6.20114286, 6.22111429, 6.24108571, 6.26105714, 6.28102857, 6.301, 6.32097143, 6.34094286, 6.36091429, 6.38088571, 6.40085714, 6.42082857, 6.4408, 6.46077143, 6.48074286, 6.50071429, 6.52068571, 6.54065714, 6.56062857, 6.5806, 6.60057143, 6.62054286, 6.64051429, 6.66048571, 6.68045714, 6.70042857, 6.7204, 6.74037143, 6.76034286, 6.78031429, 6.80028571, 6.82025714, 6.84022857, 6.8602, 6.88017143, 6.90014286, 6.92011429, 6.94008571, 6.96005714, 6.98002857, 7.]))