principia_materia.io_interface package

Submodules

• principia_materia.io_interface.array_io module
• principia_materia.io_interface.base_data_wrapper module
  • BaseDataWrapper
    • BaseDataWrapper.add_item()
    • BaseDataWrapper.copy()
    • BaseDataWrapper.delete_item()
    • BaseDataWrapper.dump()
    • BaseDataWrapper.dumps()
    • BaseDataWrapper.get_alias_map()
    • BaseDataWrapper.get_all_names_aliases()
    • BaseDataWrapper.load()
    • BaseDataWrapper.loads()
    • BaseDataWrapper.register_dtype()
    • BaseDataWrapper.self_check()
    • BaseDataWrapper.verify_data()
• principia_materia.io_interface.compute_job module
  • ComputeJob
    • ComputeJob.copy_files()
    • ComputeJob.create_job()
    • ComputeJob.get_born_effective_charges()
    • ComputeJob.get_cutoff()
    • ComputeJob.get_dielectric_tensor()
    • ComputeJob.get_energy()
    • ComputeJob.get_forces()
    • ComputeJob.get_kmesh()
    • ComputeJob.get_magnetic_moments()
    • ComputeJob.get_natoms()
    • ComputeJob.get_relaxation_displacement()
    • ComputeJob.get_stress()
    • ComputeJob.initialize_configuration()
    • ComputeJob.is_job_finished
    • ComputeJob.path
    • ComputeJob.rescale_kmesh()
    • ComputeJob.set_kmesh()
    • ComputeJob.set_output()
    • ComputeJob.structure
• principia_materia.io_interface.compute_job_series module
  • ComputeJobSeries
    • ComputeJobSeries.config_path
    • ComputeJobSeries.create_directory()
    • ComputeJobSeries.create_job()
    • ComputeJobSeries.create_jobs()
    • ComputeJobSeries.get_born_effective_charges_from_job()
    • ComputeJobSeries.get_compute_job()
    • ComputeJobSeries.get_dielectric_tensor_from_job()
    • ComputeJobSeries.get_energy_from_job()
    • ComputeJobSeries.get_forces_from_job()
    • ComputeJobSeries.get_metadata_path()
    • ComputeJobSeries.get_results_from_jobs()
    • ComputeJobSeries.get_stress_from_job()
    • ComputeJobSeries.save_metadata()
    • ComputeJobSeries.series_exists
    • ComputeJobSeries.set_static_files()
    • ComputeJobSeries.structure
• principia_materia.io_interface.data_wrapper module
  • DataWrapper
    • DataWrapper.dump()
    • DataWrapper.dumps()
    • DataWrapper.load()
    • DataWrapper.load_dict()
    • DataWrapper.load_generic()
    • DataWrapper.loads()
• principia_materia.io_interface.hdf5_wrapper module
  • HDF5Wrapper
    • HDF5Wrapper.add_item()
    • HDF5Wrapper.dump()
    • HDF5Wrapper.dump_h5file()
    • HDF5Wrapper.dumps()
    • HDF5Wrapper.load()
    • HDF5Wrapper.load_h5file()
    • HDF5Wrapper.loads()
• principia_materia.io_interface.jobs_db module
  • JobsDB
    • JobsDB.add_filter()
    • JobsDB.create_job()
    • JobsDB.create_jobs()
    • JobsDB.get_born_effective_charges_from_job()
    • JobsDB.get_dielectric_tensor_from_job()
    • JobsDB.get_energy_from_job()
    • JobsDB.get_forces_from_job()
    • JobsDB.get_metadata_path()
    • JobsDB.get_results_from_jobs()
    • JobsDB.get_stress_from_job()
    • JobsDB.remove_filter()
    • JobsDB.reset_filters()
    • JobsDB.save_metadata()
    • JobsDB.save_table_info()
    • JobsDB.set_table()
    • JobsDB.structure
• principia_materia.io_interface.qpoints_io module
  • array_to_list()
  • array_to_tuple()
• principia_materia.io_interface.vasp module
  • parse_poscar()
  • write_poscar()
• principia_materia.io_interface.yaml_dump module
  • yaml_dumps()

Module contents

principia_materia.io_interface.format_tensor(tensor, prec=8, cell_length=None, flat=False, yaml_style=False, indices=True, index_width=5)

Format a tensor into string

Format float arrays from 1 or more dimensions into string, with several settings to control the format.

Parameters:

• tensor (array of floats) – The tensor to format.

• prec (int, optional, default to 8) – The decimal points to round the floating point numbers to.

• cell_length (int, optional, default to None) – The width to align numbers in.

• flat (bool, optional, default to False) – If True, print out every single tensor entry along side its index. If True, flat yaml_style, and indices are ignored. If False, if input tensor is a vector or matrix, print them out directly, if input tensor has rank greater than 2, loop over all the axes except the last 2, and print the last 2 axes out as a matrix.

• yaml_style (bool, optional, default to False) – If True, print out tensor in YAML nested list format.

• indices (bool, optional, default to True) – If True, print out the indices of the matrix when rank of tensor is greater than 2.

• index_width (int, optional, default to 5) – The width to align indices numbers in.

principia_materia.io_interface.get_compute_engine_map()

Load First-Principle Interfaces.

Returns:

compute_engine_map – A dictionary containing the available first-principle interfaces in the form of subclasses of ComputeJob.

Return type:

dict

principia_materia.io_interface.indent(text, prefix='  ', initial_indent=None)

Indent text

Create indentation for text, the function can also treat first line with special indentation.

Parameters:

• text (str) – Text to indent

• prefix (str or int, optional, default to " ") – The indentation, if type is str, prepend the prefix to each line, if type is int, prepend the amount of spaces to each line.

• initial_indent (str, optional, default to None) – If not None, prepend the input string to the first line of text.

principia_materia.io_interface.jobs_series_to_jobs_db(jobs_db, jobs_series, search_conditions=[], update=True)

Read Jobs in from ComputeJobSeries and store them into database with JobsDB.

Parameters:

• jobs_db (JobsDB) – The interface of the database for storing the jobs.

• jobs_series (ComputeJobSeries) – The interface to the job series for reading the jobs.

• search_conditions (list, optional) – Additional search conditions for filtering the jobs.

• update (bool, optional) – If True, only read and store the jobs that haven’t been read in before. If False, overwrite the data already in the database.

principia_materia.io_interface.tuple_to_str(tup, prec=8, strip=True)

Format tuple into string.

Recursively format tuples into string.

Parameters:

• tup (tuple) – Input tuple.

• prec (int, optional, default to 8) – The decimal points to round the floating point numbers to.

• strip (bool, optional, default to True) – Whether to strip whitespaces from formatted numbers.