pyiron.atomistics.structure.periodic_table module¶
-
class
pyiron.atomistics.structure.periodic_table.
ChemicalElement
(sub)[source]¶ Bases:
object
An Object which contains the element specific parameters
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)[source]¶ 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
-
class
pyiron.atomistics.structure.periodic_table.
PeriodicTable
(file_name=None)[source]¶ 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)[source]¶ 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)
-
element
(arg, **qwargs)[source]¶ 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)[source]¶ 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:
-