abilab¶
abilab
Module¶
This module gathers the most important classes and helper functions used for scripting.
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abipy.abilab.
abiopen_ext2class_table
()[source]¶ Print the association table between file extensions and File classes.
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abipy.abilab.
extcls_supporting_panel
(as_table=True, **tabulate_kwargs)[source]¶ Return list of (ext, cls) tuples where ext is the file extension supporting the get_panel method i.e files that can be integrated with the panel dashboard and cls the python class associated to it.
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abipy.abilab.
abipanel
(**kwargs)[source]¶ Activate panel extensions used by AbiPy. Return panel module.
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abipy.abilab.
abifile_subclass_from_filename
(filename)[source]¶ Returns the appropriate class associated to the given filename.
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abipy.abilab.
dir2abifiles
(top, recurse=True)[source]¶ Analyze the filesystem starting from directory top and return an ordered dictionary mapping the directory name to the list of files supported by
abiopen
contained within that directory. If notrecurse
, children directories are not analyzed.
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abipy.abilab.
abiopen
(filepath)[source]¶ Factory function that opens any file supported by abipy. File type is detected from the extension
- Parameters
filepath – string with the filename.
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abipy.abilab.
abirobot
(filepaths)[source]¶ Factory function to create and return a Robot subclass from a list of filenames The Robot subclass is detected from the extension of the first file hence all files are assumed to have the same extension.
- Parameters
filepaths – List of strings with the filename.
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abipy.abilab.
display_structure
(obj, **kwargs)[source]¶ Use Jsmol to display a structure in the jupyter notebook. Requires nbjsmol notebook extension installed on the local machine. Install it with pip install nbjsmol. See also https://github.com/gmatteo/nbjsmol.
- Parameters
obj – Structure object or file with a structure or python object with a structure attribute.
kwargs – Keyword arguments passed to nbjsmol_display
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abipy.abilab.
mjson_load
(filepath, **kwargs)[source]¶ Read JSON file in MSONable format with MontyDecoder. Return dict with python objects.
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abipy.abilab.
mjson_loads
(string, **kwargs)[source]¶ Read JSON string in MSONable format with MontyDecoder. Return dict with python objects.
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abipy.abilab.
mjson_write
(d, filepath, **kwargs)[source]¶ Write dictionary d to filepath in JSON format using MontyDecoder
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abipy.abilab.
software_stack
(as_dataframe=False)[source]¶ Import all the hard dependencies and some optional packages. Returns ordered dict: package –> string with version info or pandas dataframe if as_dataframe.
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abipy.abilab.
abicheck
(verbose=0)[source]¶ This function tests if the most important ABINIT executables can be found in $PATH and whether the python modules needed at run-time can be imported. Return string with error messages, empty if success.
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abipy.abilab.
install_config_files
(workdir=None, force_reinstall=False)[source]¶ Install pre-defined configuration files for the TaskManager and the Scheduler in the workdir directory.
- Parameters
workdir – Directory when configuration files should be produced. Use ~/abinit/abipy/ if None
force_reinstall – Allow overwrite pre-existent configuration files. By default, the function raises RuntimeError if configuration files are already present.