principia_materia.io_interface.jobs_db module

class principia_materia.io_interface.jobs_db.JobsDB(root_directory, db_path, db_type, structure, table=None)

Bases: object

Interface jobs with database.

Parameters:

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

  • db_path (str) – Path to database.

  • db_type (str) – Type of the database, for example “sqlite”.

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

add_filter(key, value)

Add a filtering condition for database action (query/update/insert).

Parameters:

  • key (str) – The name of the column.

  • value (str/int/float/array) – The filtering value of that column.

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

Create a job with the given jobname in the database.

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, additional_filters={}, dry_run=False)

Create a series of jobs in database.

Parameters:

  • jobnames (list of str) – The names of the jobs.

  • 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=None, step_index=None)

Get 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.

  • step_index (int) – The step index of the job in an finite difference calculation.

get_dielectric_tensor_from_job(jobname=None, step_index=None)

Get 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.

  • step_index (int) – The step index of the job in an finite difference calculation.

get_energy_from_job(jobname=None, step_index=None)

Get the energy from the job.

Parameters:

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

  • step_index (int) – The step index of the job in an finite difference calculation.

get_forces_from_job(jobname=None, step_index=None)

Get forces from the job.

Parameters:

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

  • step_index (int) – The step index of the job in an finite difference calculation.

get_metadata_path(filename)
get_results_from_jobs(jobnames, data_type, job_index_name=None)

Get results of a series of jobs from database.

Parameters:

  • jobnames (list of str) – The names of the jobs.

  • 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 prefix 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=None, step_index=None)

Get the stress from the job.

Parameters:

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

  • step_index (int) – The step index of the job in an finite difference calculation.

remove_filter(key)

Remive a filtering condition from database action.

Parameters:

key (str) – The name of the column.

reset_filters()

Reset the database filters.

save_metadata(filename, metadata, dry_run=False)
save_table_info(info_table, data)

Save some generic information of the table that the jobs are created in to an information table.

Parameters:

  • info_table (str) – The name of the information table.

  • data (dict) – The generic information to save in the information table.

set_table(table)

Set name of the table to access.

Parameters:

table (str) – Table name.

property structure