pyiron.atomistics.structure.periodic_table module

class pyiron.atomistics.structure.periodic_table.ChemicalElement(sub)

Bases: object

An Object which contains the element specific parameters

add_tags(tag_dic)

Add tags to an existing element inside its specific panda series without overwriting the old tags

Parameters

tag_dic (dict) – dictionary containing e.g. key = “spin” value = “up”, more than one tag can be added at once

from_hdf(hdf)

loads an element with his parameters from the hdf5 job file and store it into its specific pandas series :param hdf: Hdfio object which will be used to read a hdf5 file :type hdf: Hdfio

property tags

to_hdf(hdf)

saves the element with his parameters into his hdf5 job file :param hdf: Hdfio object which will be used :type hdf: Hdfio

class pyiron.atomistics.structure.periodic_table.ElementColorDictionary

Bases: object

elementColors = {'Ac': [89, 112, 171, 250, 255], 'Ag': [47, 192, 192, 192, 255], 'Al': [13, 191, 166, 166, 255], 'Am': [95, 84, 92, 242, 255], 'Ar': [18, 128, 209, 227, 255], 'As': [33, 189, 128, 227, 255], 'At': [85, 117, 79, 69, 255], 'Au': [79, 255, 209, 35, 255], 'B': [5, 255, 181, 181, 255], 'Ba': [56, 0, 201, 0, 255], 'Be': [4, 194, 255, 0, 255], 'Bh': [107, 224, 0, 56, 255], 'Bi': [83, 158, 79, 181, 255], 'Bk': [97, 138, 79, 227, 255], 'Br': [35, 166, 41, 41, 255], 'C': [6, 144, 144, 144, 255], 'Ca': [20, 61, 255, 0, 255], 'Cd': [48, 255, 217, 143, 255], 'Ce': [58, 255, 255, 199, 255], 'Cf': [98, 161, 54, 212, 255], 'Cl': [17, 31, 240, 31, 255], 'Cm': [96, 120, 92, 227, 255], 'Co': [27, 240, 144, 160, 255], 'Cr': [24, 138, 153, 199, 255], 'Cs': [55, 87, 23, 143, 255], 'Cu': [29, 200, 128, 51, 255], 'Db': [105, 209, 0, 79, 255], 'Dy': [66, 31, 255, 199, 255], 'Er': [68, 0, 230, 117, 255], 'Es': [99, 179, 31, 212, 255], 'Eu': [63, 97, 255, 199, 255], 'F': [9, 144, 224, 80, 255], 'Fe': [26, 224, 102, 51, 255], 'Fm': [100, 179, 31, 186, 255], 'Fr': [87, 66, 0, 102, 255], 'Ga': [31, 194, 143, 143, 255], 'Gd': [64, 69, 255, 199, 255], 'Ge': [32, 102, 143, 143, 255], 'H': [1, 255, 255, 255, 255], 'He': [2, 217, 255, 255, 255], 'Hf': [72, 77, 194, 255, 255], 'Hg': [80, 184, 184, 208, 255], 'Ho': [67, 0, 255, 156, 255], 'Hs': [108, 230, 0, 46, 255], 'I': [53, 148, 0, 148, 255], 'In': [49, 166, 117, 115, 255], 'Ir': [77, 23, 84, 135, 255], 'K': [19, 143, 64, 212, 255], 'Kr': [36, 92, 184, 209, 255], 'La': [57, 112, 212, 255, 255], 'Li': [3, 204, 128, 255, 255], 'Lr': [103, 199, 0, 102, 255], 'Lu': [71, 0, 171, 36, 255], 'Md': [101, 179, 13, 166, 255], 'Mg': [12, 138, 255, 0, 255], 'Mn': [25, 156, 122, 199, 255], 'Mo': [42, 84, 181, 181, 255], 'Mt': [109, 235, 0, 38, 255], 'N': [7, 48, 80, 248, 255], 'Na': [11, 171, 92, 242, 255], 'Nb': [41, 115, 194, 201, 255], 'Nd': [60, 199, 255, 199, 255], 'Ne': [10, 179, 227, 245, 255], 'Ni': [28, 80, 208, 80, 255], 'No': [102, 189, 13, 135, 255], 'Np': [93, 0, 128, 255, 255], 'O': [8, 255, 13, 13, 255], 'Os': [76, 38, 102, 150, 255], 'P': [15, 255, 128, 0, 255], 'Pa': [91, 0, 161, 255, 255], 'Pb': [82, 87, 89, 97, 255], 'Pd': [46, 0, 105, 133, 255], 'Pm': [61, 163, 255, 199, 255], 'Po': [84, 171, 92, 0, 255], 'Pr': [59, 217, 255, 199, 255], 'Pt': [78, 208, 208, 224, 255], 'Pu': [94, 0, 107, 255, 255], 'Ra': [88, 0, 125, 0, 255], 'Rb': [37, 112, 46, 176, 255], 'Re': [75, 38, 125, 171, 255], 'Rf': [104, 204, 0, 89, 255], 'Rh': [45, 10, 125, 140, 255], 'Rn': [86, 66, 130, 150, 255], 'Ru': [44, 36, 143, 143, 255], 'S': [16, 255, 255, 48, 255], 'Sb': [51, 158, 99, 181, 255], 'Sc': [21, 230, 230, 230, 255], 'Se': [34, 255, 161, 0, 255], 'Sg': [106, 217, 0, 69, 255], 'Si': [14, 240, 200, 160, 255], 'Sm': [62, 143, 255, 199, 255], 'Sn': [50, 102, 128, 128, 255], 'Sr': [38, 0, 255, 0, 255], 'Ta': [73, 77, 166, 255, 255], 'Tb': [65, 48, 255, 199, 255], 'Tc': [43, 59, 158, 158, 255], 'Te': [52, 212, 122, 0, 255], 'Th': [90, 0, 186, 255, 255], 'Ti': [22, 191, 194, 199, 255], 'Tl': [81, 166, 84, 77, 255], 'Tm': [69, 0, 212, 82, 255], 'U': [92, 0, 143, 255, 255], 'V': [23, 166, 166, 171, 255], 'W': [74, 33, 148, 214, 255], 'Xe': [54, 66, 158, 176, 255], 'Y': [39, 148, 255, 255, 255], 'Yb': [70, 0, 191, 56, 255], 'Zn': [30, 125, 128, 176, 255], 'Zr': [40, 148, 224, 224, 255]}

to_lut()

Returns:

class pyiron.atomistics.structure.periodic_table.PeriodicTable(file_name=None)

Bases: object

An Object which stores an elementary table which can be modified for the current session

add_element(parent_element, new_element, use_parent_potential=False, **qwargs)

Add “additional” chemical elements to the Periodic Table. These can be used to distinguish between the various potentials which may exist for a given species or to introduce artificial elements such as pseudohydrogen. For this case set use_parent_potential = False and add in the directory containing the potential files a new file which is derived from the name new element.

This function may be also used to provide additional information for the identical chemical element, e.g., to define a Fe_up and Fe_down to perform the correct symmetry search as well as initialization.

Parameters

• parent_element (str) – name of parent element

• new_element (str) – name of new element

• use_parent_potential – True: use the potential from the parent species

• **qwargs – define tags and their values, e.g. spin = “up”, relax = [True, True, True]

Returns: new element (ChemicalElement)

atomic_number_to_abbreviation(atom_no)

Parameters

atom_no –

Returns:

element(arg, **qwargs)

The method searches through the periodic table. If the table contains the element, it will return an Object of the type ChemicalElement containing all parameters from the periodic table. The option **qwargs allows a direct modification of the tag-values during the creation process :param arg: sort of element :type arg: str, ChemicalElement :param **qwargs: e.g. a dictionary of tags

Returns element (ChemicalElement): a element with all its properties (Abbreviation, AtomicMass, Weight, …)

from_hdf(hdf)

loads an element with his parameters from the hdf5 job file by creating an Object of the ChemicalElement type. The new element will be stored in the current periodic table. Changes in the tags will also be modified inside the periodic table.

Parameters

hdf (Hdfio) – Hdfio object which will be used to read the data from a hdf5 file

Returns:

is_element(symbol)

Compares the Symbol with the Abbreviations of elements inside the periodic table :param symbol: name of element, str :type symbol: str

Returns boolean: true for the same element, false otherwise