pymatgen.io.abinit.pseudos module¶
This module provides objects describing the basic parameters of the pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
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class
Pseudo
[source]¶ Bases:
monty.json.MSONable
Abstract base class defining the methods that must be implemented by the concrete pseudopotential sub-classes.
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abstract property
Z
¶ The atomic number of the atom.
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abstract property
Z_val
¶ Valence charge.
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classmethod
as_pseudo
(obj)[source]¶ Convert obj into a pseudo. Accepts:
Pseudo object.
string defining a valid path.
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as_tmpfile
(tmpdir=None)[source]¶ Copy the pseudopotential to a temporary a file and returns a new pseudopotential object. Useful for unit tests in which we have to change the content of the file.
- Parameters
tmpdir – If None, a new temporary directory is created and files are copied here else tmpdir is used.
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property
basename
¶ File basename.
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property
djrepo_path
¶ The path of the djrepo file. None if file does not exist.
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property
element
¶ Pymatgen
Element
.
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property
filepath
¶ Absolute path to pseudopotential file.
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static
from_file
(filename)[source]¶ Build an instance of a concrete Pseudo subclass from filename. Note: the parser knows the concrete class that should be instantiated Client code should rely on the abstract interface provided by Pseudo.
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property
has_dojo_report
¶ True if the pseudo has an associated DOJO_REPORT section.
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property
has_hints
¶ True if self provides hints on the cutoff energy.
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hint_for_accuracy
(accuracy='normal')[source]¶ Returns a
Hint
object with the suggested value of ecut [Ha] and pawecutdg [Ha] for the given accuracy. ecut and pawecutdg are set to zero if no hint is available.- Parameters
accuracy – [“low”, “normal”, “high”]
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property
isnc
¶ True if norm-conserving pseudopotential.
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property
ispaw
¶ True if PAW pseudopotential.
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abstract property
l_local
¶ Angular momentum used for the local part.
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abstract property
l_max
¶ Maximum angular momentum.
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open_pspsfile
(ecut=20, pawecutdg=None)[source]¶ Calls Abinit to compute the internal tables for the application of the pseudopotential part. Returns
PspsFile
object providing methods to plot and analyze the data or None if file is not found or it’s not readable.- Parameters
ecut – Cutoff energy in Hartree.
pawecutdg – Cutoff energy for the PAW double grid.
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abstract property
summary
¶ String summarizing the most important properties.
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abstract property
supports_soc
¶ True if the pseudo can be used in a calculation with spin-orbit coupling. Base classes should provide a concrete implementation that computes this value.
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property
symbol
¶ Element symbol.
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property
type
¶ Type of pseudo.
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abstract property
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class
PseudoTable
(pseudos)[source]¶ Bases:
collections.abc.Sequence
,monty.json.MSONable
Define the pseudopotentials from the element table. Individidual elements are accessed by name, symbol or atomic number.
For example, the following all retrieve iron:
print elements[26] Fe print elements.Fe Fe print elements.symbol(‘Fe’) Fe print elements.name(‘iron’) Fe print elements.isotope(‘Fe’) Fe
- Parameters
pseudos – List of pseudopotentials or filepaths
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all_combinations_for_elements
(element_symbols)[source]¶ Return a list with all the the possible combination of pseudos for the given list of element_symbols. Each item is a list of pseudopotential objects.
Example:
table.all_combinations_for_elements(["Li", "F"])
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property
allnc
¶ True if all pseudos are norm-conserving.
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property
allpaw
¶ True if all pseudos are PAW.
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classmethod
as_table
(items)[source]¶ Return an instance of
PseudoTable
from the iterable items.
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classmethod
from_dir
(top, exts=None, exclude_dirs='_*')[source]¶ Find all pseudos in the directory tree starting from top.
- Parameters
top – Top of the directory tree
exts – List of files extensions. if exts == “all_files” we try to open all files in top
exclude_dirs – Wildcard used to exclude directories.
return:
PseudoTable
sorted by atomic number Z.
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get_pseudos_for_structure
(structure)[source]¶ Return the list of
Pseudo
objects to be used for thisStructure
.- Parameters
structure – pymatgen
Structure
.- Raises
ValueError –
multiple occurences are present in the table. –
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is_complete
(zmax=118)[source]¶ True if table is complete i.e. all elements with Z < zmax have at least on pseudopotential
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print_table
(stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, filter_function=None)[source]¶ A pretty ASCII printer for the periodic table, based on some filter_function.
- Parameters
stream – file-like object
filter_function – A filtering function that take a Pseudo as input and returns a boolean. For example, setting filter_function = lambda p: p.Z_val > 2 will print a periodic table containing only pseudos with Z_val > 2.
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pseudo_with_symbol
(symbol, allow_multi=False)[source]¶ Return the pseudo with the given chemical symbol.
- Parameters
symbols – String with the chemical symbol of the element
allow_multi – By default, the method raises ValueError if multiple occurrences are found. Use allow_multi to prevent this.
- Raises
ValueError if symbol is not found or multiple occurences are present and not allow_multi –
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pseudos_with_symbols
(symbols)[source]¶ Return the pseudos with the given chemical symbols.
- Raises
ValueError if one of the symbols is not found or multiple occurences are present. –
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select
(condition)[source]¶ Select only those pseudopotentials for which condition is True. Return new class:PseudoTable object.
- Parameters
condition – Function that accepts a
Pseudo
object and returns True or False.
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select_family
(family)[source]¶ Return PseudoTable with element beloging to the specified family, e.g. familiy=”alkaline”
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select_rows
(rows)[source]¶ Return new class:PseudoTable object with pseudos in the given rows of the periodic table. rows can be either a int or a list of integers.
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select_symbols
(symbols, ret_list=False)[source]¶ Return a
PseudoTable
with the pseudopotentials with the given list of chemical symbols.- Parameters
symbols – str or list of symbols Prepend the symbol string with “-“, to exclude pseudos.
ret_list – if True a list of pseudos is returned instead of a
PseudoTable
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sort_by_z
()[source]¶ Return a new
PseudoTable
with pseudos sorted by Z
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sorted
(attrname, reverse=False)[source]¶ Sort the table according to the value of attribute attrname.
- Returns
PseudoTable object
- Return type
New class
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with_dojo_report
()[source]¶ Select pseudos containing the DOJO_REPORT section. Return new class:PseudoTable object.
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property
zlist
¶ Ordered list with the atomic numbers available in the table.