dpgen.database package

class dpgen.database.DPPotcar(symbols=None, functional='PBE', pp_file=None, pp_lists=None)[source]

Bases: MSONable

Methods

`as_dict`()	A JSON serializable dict representation of an object.
`from_dict`(d)	param d: Dict representation.
`to_json`()	Returns a json string representation of the MSONable object.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

from_file
write_file

as_dict()[source]: A JSON serializable dict representation of an object.

classmethod from_dict(d)[source]

Parameters:: d – Dict representation.
Returns:: MSONable class.

classmethod from_file(filename)[source]

write_file(filename)[source]

class dpgen.database.Entry(composition, calculator, inputs, data, entry_id=None, attribute=None, tag=None)[source]

Bases: MSONable

An lightweight Entry object containing key computed data for storing purpose.

Parameters:

compositionComposition: Composition of the entry. For flexibility, this can take the form of all the typical input taken by a Composition, including a {symbol: amt} dict, a string formula, and others.
inputsdict: An dict of parameters associated with the entry. Defaults to None.
datadict: An dict of any additional data associated with the entry. Defaults to None.
entry_idobj: An optional id to uniquely identify the entry.
attribute: Optional attribute of the entry. This can be used to specify that the entry is a newly found compound, or to specify a particular label for the entry, or else … Used for further analysis and plotting purposes. An attribute can be anything but must be MSONable.

Attributes:

number_element

Methods

`as_dict`()	A JSON serializable dict representation of an object.
`from_dict`(d)	param d: Dict representation.
`to_json`()	Returns a json string representation of the MSONable object.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

as_dict()[source]: A JSON serializable dict representation of an object.

classmethod from_dict(d)[source]

Parameters:: d – Dict representation.
Returns:: MSONable class.

property number_element

class dpgen.database.VaspInput(incar, poscar, potcar, kpoints=None, optional_files=None, **kwargs)[source]

Bases: dict, MSONable

Class to contain a set of vasp input objects corresponding to a run.

Args:

incar: Incar object. kpoints: Kpoints object. poscar: Poscar object. potcar: Potcar object. optional_files: Other input files supplied as a dict of {

filename: object}. The object should follow standard pymatgen conventions in implementing a as_dict() and from_dict method.

Methods

`as_dict`()	A JSON serializable dict representation of an object.
`clear`()
`copy`()
`from_dict`(d)	param d: Dict representation.
`from_directory`(input_dir[, optional_files])	Read in a set of VASP input from a directory.
`fromkeys`(iterable[, value])	Create a new dictionary with keys from iterable and values set to value.
`get`(key[, default])	Return the value for key if key is in the dictionary, else default.
`items`()
`keys`()
`pop`(key[, default])	If the key is not found, return the default if given; otherwise, raise a KeyError.
`popitem`(/)	Remove and return a (key, value) pair as a 2-tuple.
`setdefault`(key[, default])	Insert key with a value of default if key is not in the dictionary.
`to_json`()	Returns a json string representation of the MSONable object.
`unsafe_hash`()	Returns an hash of the current object.
`update`([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x
`values`()
`write_input`([output_dir, ...])	Write VASP input to a directory.

as_dict()[source]: A JSON serializable dict representation of an object.

classmethod from_dict(d)[source]

Parameters:: d – Dict representation.
Returns:: MSONable class.

static from_directory(input_dir, optional_files=None)[source]

Read in a set of VASP input from a directory. Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified.

Parameters:

input_dirstr: Directory to read VASP input from.
optional_filesdict: Optional files to read in as well as a dict of {filename: Object type}. Object type must have a static method from_file.

write_input(output_dir='.', make_dir_if_not_present=True)[source]

Write VASP input to a directory.

Parameters:

output_dirstr: Directory to write to. Defaults to current directory (“.”).
make_dir_if_not_presentbool: Create the directory if not present. Defaults to True.

Submodules

dpgen.database.entry module

class dpgen.database.entry.Entry(composition, calculator, inputs, data, entry_id=None, attribute=None, tag=None)[source]

Bases: MSONable

An lightweight Entry object containing key computed data for storing purpose.

Parameters:

compositionComposition: Composition of the entry. For flexibility, this can take the form of all the typical input taken by a Composition, including a {symbol: amt} dict, a string formula, and others.
inputsdict: An dict of parameters associated with the entry. Defaults to None.
datadict: An dict of any additional data associated with the entry. Defaults to None.
entry_idobj: An optional id to uniquely identify the entry.
attribute: Optional attribute of the entry. This can be used to specify that the entry is a newly found compound, or to specify a particular label for the entry, or else … Used for further analysis and plotting purposes. An attribute can be anything but must be MSONable.

Attributes:

number_element

Methods

`as_dict`()	A JSON serializable dict representation of an object.
`from_dict`(d)	param d: Dict representation.
`to_json`()	Returns a json string representation of the MSONable object.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

as_dict()[source]: A JSON serializable dict representation of an object.

classmethod from_dict(d)[source]

Parameters:: d – Dict representation.
Returns:: MSONable class.

property number_element

dpgen.database.run module

dpgen.database.run.db_run(args)[source]

dpgen.database.run.parsing_gaussian(path, output='dpgen_db.json')[source]

dpgen.database.run.parsing_pwscf(path, output='dpgen_db.json')[source]

dpgen.database.run.parsing_vasp(path, config_info_dict, skip_init, output='dpgen_db.json', id_prefix=None)[source]

dpgen.database.vasp module

class dpgen.database.vasp.DPPotcar(symbols=None, functional='PBE', pp_file=None, pp_lists=None)[source]

Bases: MSONable

Methods

`as_dict`()	A JSON serializable dict representation of an object.
`from_dict`(d)	param d: Dict representation.
`to_json`()	Returns a json string representation of the MSONable object.
`unsafe_hash`()	Returns an hash of the current object.
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x

from_file
write_file

as_dict()[source]: A JSON serializable dict representation of an object.

classmethod from_dict(d)[source]

Parameters:: d – Dict representation.
Returns:: MSONable class.

classmethod from_file(filename)[source]

write_file(filename)[source]

class dpgen.database.vasp.VaspInput(incar, poscar, potcar, kpoints=None, optional_files=None, **kwargs)[source]

Bases: dict, MSONable

Class to contain a set of vasp input objects corresponding to a run.

Args:

incar: Incar object. kpoints: Kpoints object. poscar: Poscar object. potcar: Potcar object. optional_files: Other input files supplied as a dict of {

filename: object}. The object should follow standard pymatgen conventions in implementing a as_dict() and from_dict method.

Methods

`as_dict`()	A JSON serializable dict representation of an object.
`clear`()
`copy`()
`from_dict`(d)	param d: Dict representation.
`from_directory`(input_dir[, optional_files])	Read in a set of VASP input from a directory.
`fromkeys`(iterable[, value])	Create a new dictionary with keys from iterable and values set to value.
`get`(key[, default])	Return the value for key if key is in the dictionary, else default.
`items`()
`keys`()
`pop`(key[, default])	If the key is not found, return the default if given; otherwise, raise a KeyError.
`popitem`(/)	Remove and return a (key, value) pair as a 2-tuple.
`setdefault`(key[, default])	Insert key with a value of default if key is not in the dictionary.
`to_json`()	Returns a json string representation of the MSONable object.
`unsafe_hash`()	Returns an hash of the current object.
`update`([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
`validate_monty_v1`(_MSONable__input_value)	Pydantic validator with correct signature for pydantic v1.x
`validate_monty_v2`(_MSONable__input_value, _)	Pydantic validator with correct signature for pydantic v2.x
`values`()
`write_input`([output_dir, ...])	Write VASP input to a directory.

as_dict()[source]: A JSON serializable dict representation of an object.

classmethod from_dict(d)[source]

Parameters:: d – Dict representation.
Returns:: MSONable class.

static from_directory(input_dir, optional_files=None)[source]

Read in a set of VASP input from a directory. Note that only the standard INCAR, POSCAR, POTCAR and KPOINTS files are read unless optional_filenames is specified.

Parameters:

input_dirstr: Directory to read VASP input from.
optional_filesdict: Optional files to read in as well as a dict of {filename: Object type}. Object type must have a static method from_file.

write_input(output_dir='.', make_dir_if_not_present=True)[source]

Write VASP input to a directory.

Parameters:

output_dirstr: Directory to write to. Defaults to current directory (“.”).
make_dir_if_not_presentbool: Create the directory if not present. Defaults to True.