pymatgen.io.abinit.utils module

Tools and helper functions for abinit calculations

class Condition(cmap=None)

Bases: object

This object receives a dictionary that defines a boolean condition whose syntax is similar to the one used in mongodb (albeit not all the operators available in mongodb are supported here).

Example:

$gt: {field: {$gt: value} }

$gt selects those documents where the value of the field is greater than (i.e. >) the specified value.

$and performs a logical AND operation on an array of two or more expressions (e.g. <expression1>, <expression2>, etc.) and selects the documents that satisfy all the expressions in the array.

{ $and: [ { <expression1> }, { <expression2> } , … , { <expressionN> } ] }

Consider the following example:

db.inventory.find( { qty: { $gt: 20 } } ) This query will select all documents in the inventory collection where the qty field value is greater than 20. Consider the following example:

db.inventory.find( { qty: { $gt: 20 } } ) db.inventory.find({ $and: [ { price: 1.99 }, { qty: { $lt: 20 } }, { sale: true } ] } )

classmethod as_condition(obj)

Convert obj into Condition

class Directory(path)

Bases: object

Very simple class that provides helper functions wrapping the most commonly used functions defined in os.path.

property basename

Directory basename.

clean()

Remove all files in the directory tree while preserving the directory

copy_abiext(inext, outext)

Copy the Abinit file with extension inext to a new file withw extension outext

copy_r(dst)

Implements a recursive copy function similar to Unix’s “cp -r” command.

property exists

True if file exists.

find_1den_files()

Abinit adds the idir-ipert index at the end of the 1DEN file and this breaks the extension e.g. out_DEN1. This method scans the files in the directories and returns a list of namedtuple Each named tuple gives the path of the 1DEN file and the pertcase index.

find_1wf_files()

Abinit adds the idir-ipert index at the end of the 1WF file and this breaks the extension e.g. out_1WF4. This method scans the files in the directories and returns a list of namedtuple Each named tuple gives the path of the 1FK file and the pertcase index.

find_last_timden_file()

ABINIT produces lots of out_TIM1_DEN files for each step and we need to find the lat one in order to prepare the restart or to connect other tasks to the structural relaxation.

This function finds all the TIM?_DEN files in self and return a namedtuple (path, step) where path is the path of the last TIM?_DEN file and step is the iteration number. Returns None if the directory does not contain TIM?_DEN files.

has_abiext(ext, single_file=True)

Returns the absolute path of the ABINIT file with extension ext. Support both Fortran files and netcdf files. In the later case, we check whether a file with extension ext + “.nc” is present in the directory. Returns empty string is file is not present.

Raises

• ValueError –

• This implies that this method is not compatible with multiple datasets. –

list_filepaths(wildcard=None)

Return the list of absolute filepaths in the directory.

Parameters

wildcard –

String of tokens separated by “|”. Each token represents a pattern. If wildcard is not None, we return only those files that match the given shell pattern (uses fnmatch). .. rubric:: Example

wildcard=”.nc|.pdf” selects only those files that end with .nc or .pdf

makedirs()

Super-mkdir; create a leaf directory and all intermediate ones. Works like mkdir, except that any intermediate path segment (not just the rightmost) will be created if it does not exist.

property path

Absolute path of the directory.

path_in(file_basename)

Return the absolute path of filename in the directory.

path_join(*p)

Join two or more pathname components, inserting ‘/’ as needed. If any component is an absolute path, all previous path components will be discarded.

property relpath

Relative path.

remove_exts(exts)

Remove the files with the given extensions. Unlike rmtree, this function preserves the directory path. Return list with the absolute paths of the files that have been removed.

rename_abiext(inext, outext)

Rename the Abinit file with extension inext with the new extension outext

rmtree()

Recursively delete the directory tree

symlink_abiext(inext, outext)

Create a simbolic link (outext –> inext). The file names are implicitly given by the ABINIT file extension.

Example

outdir.symlink_abiext(‘1WF’, ‘DDK’)

creates the link out_DDK that points to out_1WF

Return: 0 if success.

Raise: RuntimeError

class Dirviz(top)

Bases: object

get_cluster_graph(engine='fdp', graph_attr=None, node_attr=None, edge_attr=None)

Generate directory graph in the DOT language. Directories are shown as clusters

Warning

This function scans the entire directory tree starting from top so the resulting graph can be really big.

Parameters

• engine – Layout command used. [‘dot’, ‘neato’, ‘twopi’, ‘circo’, ‘fdp’, ‘sfdp’, ‘patchwork’, ‘osage’]

• graph_attr – Mapping of (attribute, value) pairs for the graph.

• node_attr – Mapping of (attribute, value) pairs set for all nodes.

• edge_attr – Mapping of (attribute, value) pairs set for all edges.

Returns: graphviz.Digraph <https://graphviz.readthedocs.io/en/stable/api.html#digraph>

class Editor(editor=None)

Bases: object

Wrapper class that calls the editor specified by the user or the one specified in the $EDITOR env variable.

If editor is None, $EDITOR is used.

edit_file(fname)

edit_files(fnames, ask_for_exit=True)

static user_wants_to_exit()

Show an interactive prompt asking if exit is wanted.

class File(path)

Bases: object

Very simple class used to store file basenames, absolute paths and directory names. Provides wrappers for the most commonly used functions defined in os.path.

property basename

File basename.

chmod(mode)

Change the access permissions of a file.

property dirname

Absolute path of the directory where the file is located.

property exists

True if file exists.

get_stat()

Results from os.stat

getsize()

Return the size, in bytes, of path. Return 0 if the file is empty or it does not exist.

property isncfile

True if self is a NetCDF file

make_dir()

Make the directory where the file is located.

move(dst)

Recursively move a file or directory to another location. This is similar to the Unix “mv” command.

property path

Absolute path of the file.

read()

Read data from file.

readlines()

Read lines from files.

property relpath

Relative path.

remove()

Remove the file.

write(string)

Write string to file.

writelines(lines)

Write a list of strings to file.

class FilepathFixer

Bases: object

This object modifies the names of particular output files produced by ABINIT so that the file extension is preserved. Having a one-to-one mapping between file extension and data format is indeed fundamental for the correct behaviour of abinit since:

• We locate the output file by just inspecting the extension

• We select the variables that must be added to the input file on the basis of the extension specified by the user during the initialization of the AbinitFlow.

Unfortunately, ABINIT developers like to append extra stuff to the initial extension and therefore we have to call FilepathFixer to fix the output files produced by the run.

Example:

>>> fixer = FilepathFixer()
>>> assert fixer.fix_paths('/foo/out_1WF17') == {'/foo/out_1WF17': '/foo/out_1WF'}
>>> assert fixer.fix_paths('/foo/out_1WF5.nc') == {'/foo/out_1WF5.nc': '/foo/out_1WF.nc'}

fix_paths(paths)

Fix the filenames in the iterable paths

Returns

Mapping old_path –> new_path

Return type

old2new

class SparseHistogram(items, key=None, num=None, step=None)

Bases: object

plot(ax=None, **kwargs)

Plot the histogram with matplotlib, returns matplotlib figure.

Keyword arguments controlling the display of the figure:

kwargs	Meaning
title	Title of the plot (Default: None).
show	True to show the figure (default: True).
savefig	“abc.png” or “abc.eps” to save the figure to a file.
size_kwargs	Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout	True to call fig.tight_layout (default: False)
ax_grid	True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate	Add labels to subplots e.g. (a), (b). Default: False

abi_extensions()

List with all the ABINIT extensions that are registered.

abi_splitext(filename)

Split the ABINIT extension from a filename. “Extension” are found by searching in an internal database.

Returns “(root, ext)” where ext is the registered ABINIT extension The final “.nc” is included (if any)

>>> assert abi_splitext("foo_WFK") == ('foo_', 'WFK')
>>> assert abi_splitext("/home/guido/foo_bar_WFK.nc") == ('foo_bar_', 'WFK.nc')

as_bool(s)

Convert a string into a boolean.

>>> assert as_bool(True) is True and as_bool("Yes") is True and as_bool("false") is False

evaluate_rpn(rpn)

Evaluates the RPN form produced my map2rpn.

Returns

bool

irdvars_for_ext(ext)

Returns a dictionary with the ABINIT variables that must be used to read the file with extension ext.

map2rpn(map, obj)

Convert a Mongodb-like dictionary to a RPN list of operands and operators.

Reverse Polish notation (RPN) is a mathematical notation in which every operator follows all of its operands, e.g.

3 - 4 + 5 –> 3 4 - 5 +

>>> d = {2.0: {'$eq': 1.0}}
>>> assert map2rpn(d, None) == [2.0, 1.0, '$eq']