principia_materia.io_interface.compute_job_series module

class principia_materia.io_interface.compute_job_series.ComputeJobSeries(structure, root_directory, compute_engine, config_path=None, jobinput=None, joboutput=None)

Bases: object

Manage a series of jobs

Since many part of this package (for example, phonon irreducible derivatives computaiton), usually needs to create and read a series of calculations.

The series of jobs are assumed to have a hierarchical directory structure, that every job is in its own directory with the job name as the directory name.

Parameters:

  • structure (Crystal or CrystalFTG object) – The primitive crystal structure. Input input is a CrystalFTG object, the primitive cell will be used.

  • root_directory (str) – The root directory that hosts all the jobs of the series.

  • compute_engine (str, or a subclass of principia_materia.io_interface.compute_job.ComputeJob) – The compute engine, for example “vasp” or VASPJob is referring to VASP DFT engine.

  • config_path (str, optional, default to None) – The path of the configuration file, it is used to create the series of jobs as a template.

property config_path
create_directory(dirname, exists=False)

Create directory inside root directory of the job series.

Parameters:

dirname (str) – Directory name to create.

create_job(jobname, supa, prefix=None, displacement=None, strain=None, velocities=None, append=False, dry_run=False)

Create a job at the given jobname (jobname will be the directory name).

Parameters:

  • jobname (str) – The name of the job, as well as the directory name to create the job in.

  • supa (array of int, shape(dim, dim)) – The supercell matrix.

  • prefix (str, optional, default to None) – The prefixing directory of the job relative to the root directory of the job series.

  • displacement (array of float, optional, default to None) – The displacement to the crystal.

  • strain (array of float, shape(dim, dim), optional, default to None) – The strain matrix of the structure.

  • velocities (array of float, optional, default to None) – The initial velocities of the atoms of the crystal.

  • append (bool, optional, default to False) – If True, skip existing jobs. Otherwise, throw an error.

  • dry_run (bool, optional, default to False) – If True, don’t actually create the job.

create_jobs(jobnames, supa, prefix=None, displacements=None, strain=None, velocities=None, append=False, job_index_name=None, dry_run=False)

Create a series of jobs.

Parameters:

  • jobnames (list of str) – The names of the jobs, as well as the directory name to create the jobs in.

  • supa (array of int, shape(dim, dim)) – The supercell matrix.

  • prefix (str, optional, default to None) – The prefixing directory of the jobs relative to the root directory of the job series.

  • displacements (array of float, optional, default to None) – The displacements to the crystal for the jobs.

  • strain (array of float, shape(dim, dim), optional, default to None) – The strain matrix of the structure.

  • velocities (array of float, optional, default to None) – The initial velocities of the atoms of the crystal for the jobs.

  • append (bool, optional, default to False) – If True, skip existing jobs. Otherwise, throw an error.

  • dry_run (bool, optional, default to False) – If True, don’t actually create the job.

get_born_effective_charges_from_job(jobname, prefix=None)

Parse Born effective charges from the job.

Parameters:

jobname (str) – The name of the job, as well as the directory name to create the job in.

get_compute_job(jobname, prefix=None)

Get the job from the given jobname (jobname would be the directory name).

Parameters:

jobname (str) – The name of the job, as well as the directory name to create the job in.

get_dielectric_tensor_from_job(jobname, prefix=None)

Parse the dielectric tensor from the job.

Parameters:

jobname (str) – The name of the job, as well as the directory name to create the job in.

get_energy_from_job(jobname, prefix=None)

Parse the energy from the job.

Parameters:

jobname (str) – The name of the job, as well as the directory name to create the job in.

get_forces_from_job(jobname, prefix=None)

Parse forces from the job.

Parameters:

jobname (str) – The name of the job, as well as the directory name to create the job in.

get_metadata_path(filename)

Get the path to save the metadata file in.

Parameters:

filename (str) – The base name of metadata file.

get_results_from_jobs(jobnames, data_type, prefix=None)

Get results from a series of jobs.

Parameters:

  • jobnames (list of str) – The names of the jobs, as well as the directory name to create the jobs in.

  • data_type (str) – The type of results to retrieve, can be “forces”, “energy”, “stress”, “born_effective_charges” or “dielectric_tensor”.

  • prefix (str, optional, default to None) – The prefixing directory of the jobs relative to the root directory of the job series.

Returns:

data – The retrieved results from jobs.

Return type:

array of float

get_stress_from_job(jobname, prefix=None)

Parse the stress from the job.

Parameters:

jobname (str) – The name of the job, as well as the directory name to create the job in.

save_metadata(filename, metadata, dry_run=False)

Save metadata into a file in the root directory of job series.

Parameters:

  • filename (str) – The base name of metadata file.

  • metadata (str) – The metadata to save in plain text.

  • dry_run (bool, optional, default to False) – If True, don’t actually create the metadata file.

property series_exists

Whether if the root directory exists.

set_static_files(filenames, abspath=False)

Set a list of static files to copy into the job directory.

Parameters:

  • filenames (str of list of str) – The path names of the files to copy.

  • abspath (bool, optional, default to False) – Whether the input filenames are absolute path.

property structure