deepmd_utils package

Untilization methods for DeePMD-kit.

The __init__ module should not import any modules for performance.

Subpackages

• deepmd_utils.entrypoints package
  • Submodules
  • deepmd_utils.entrypoints.doc module
    • doc_train_input()
  • deepmd_utils.entrypoints.gui module
    • start_dpgui()
• deepmd_utils.loggers package
  • set_log_handles()
  • Submodules
  • deepmd_utils.loggers.loggers module
    • set_log_handles()
• deepmd_utils.model_format package
  • DescrptSeA
    • DescrptSeA.cal_g()
    • DescrptSeA.call()
    • DescrptSeA.deserialize()
    • DescrptSeA.serialize()
  • EmbeddingNet
  • EnvMat
    • EnvMat.call()
    • EnvMat.deserialize()
    • EnvMat.serialize()
  • FittingNet
  • FittingOutputDef
    • FittingOutputDef.get_data()
    • FittingOutputDef.keys()
  • ModelOutputDef
    • ModelOutputDef.get_data()
    • ModelOutputDef.keys()
    • ModelOutputDef.keys_derv_c()
    • ModelOutputDef.keys_derv_r()
    • ModelOutputDef.keys_outp()
    • ModelOutputDef.keys_redu()
  • NativeLayer
    • NativeLayer.call()
    • NativeLayer.check_shape_consistency()
    • NativeLayer.check_type_consistency()
    • NativeLayer.deserialize()
    • NativeLayer.dim_in()
    • NativeLayer.dim_out()
    • NativeLayer.serialize()
  • NativeNet
  • NativeOP
    • NativeOP.call()
  • NetworkCollection
    • NetworkCollection.NETWORK_TYPE_MAP
    • NetworkCollection.check_completeness()
    • NetworkCollection.deserialize()
    • NetworkCollection.serialize()
  • OutputVariableDef
  • fitting_check_output()
  • get_deriv_name()
  • get_reduce_name()
  • load_dp_model()
  • make_embedding_network()
  • make_fitting_network()
  • make_multilayer_network()
  • model_check_output()
  • save_dp_model()
  • traverse_model_dict()
  • Submodules
  • deepmd_utils.model_format.common module
    • NativeOP
      • NativeOP.call()
  • deepmd_utils.model_format.env_mat module
    • EnvMat
      • EnvMat.call()
      • EnvMat.deserialize()
      • EnvMat.serialize()
    • compute_smooth_weight()
  • deepmd_utils.model_format.network module
    • Counter
    • EmbeddingNet
    • FittingNet
    • NativeLayer
      • NativeLayer.call()
      • NativeLayer.check_shape_consistency()
      • NativeLayer.check_type_consistency()
      • NativeLayer.deserialize()
      • NativeLayer.dim_in()
      • NativeLayer.dim_out()
      • NativeLayer.serialize()
    • NativeNet
    • NetworkCollection
      • NetworkCollection.NETWORK_TYPE_MAP
      • NetworkCollection.check_completeness()
      • NetworkCollection.deserialize()
      • NetworkCollection.serialize()
    • load_dp_model()
    • make_embedding_network()
    • make_fitting_network()
    • make_multilayer_network()
    • save_dp_model()
    • traverse_model_dict()
  • deepmd_utils.model_format.output_def module
    • FittingOutputDef
      • FittingOutputDef.get_data()
      • FittingOutputDef.keys()
    • ModelOutputDef
      • ModelOutputDef.get_data()
      • ModelOutputDef.keys()
      • ModelOutputDef.keys_derv_c()
      • ModelOutputDef.keys_derv_r()
      • ModelOutputDef.keys_outp()
      • ModelOutputDef.keys_redu()
    • OutputVariableDef
    • check_shape()
    • check_var()
    • do_derivative()
    • do_reduce()
    • fitting_check_output()
    • get_deriv_name()
    • get_reduce_name()
    • model_check_output()
  • deepmd_utils.model_format.se_e2_a module
    • DescrptSeA
      • DescrptSeA.cal_g()
      • DescrptSeA.call()
      • DescrptSeA.deserialize()
      • DescrptSeA.serialize()
• deepmd_utils.utils package
  • Submodules
  • deepmd_utils.utils.argcheck module
    • ArgsPlugin
      • ArgsPlugin.get_all_argument()
      • ArgsPlugin.register()
    • descrpt_hybrid_args()
    • descrpt_local_frame_args()
    • descrpt_se_a_args()
    • descrpt_se_a_ebd_v2_args()
    • descrpt_se_a_mask_args()
    • descrpt_se_a_tpe_args()
    • descrpt_se_atten_args()
    • descrpt_se_atten_common_args()
    • descrpt_se_atten_v2_args()
    • descrpt_se_r_args()
    • descrpt_se_t_args()
    • descrpt_variant_type_args()
    • fitting_dipole()
    • fitting_dos()
    • fitting_ener()
    • fitting_polar()
    • fitting_variant_type_args()
    • frozen_model_args()
    • gen_args()
    • gen_doc()
    • gen_json()
    • learning_rate_args()
    • learning_rate_dict_args()
    • learning_rate_exp()
    • learning_rate_variant_type_args()
    • limit_pref()
    • linear_ener_model_args()
    • list_to_doc()
    • loss_args()
    • loss_dict_args()
    • loss_dos()
    • loss_ener()
    • loss_ener_spin()
    • loss_tensor()
    • loss_variant_type_args()
    • make_index()
    • make_link()
    • mixed_precision_args()
    • model_args()
    • model_compression()
    • model_compression_type_args()
    • modifier_dipole_charge()
    • modifier_variant_type_args()
    • multi_model_args()
    • normalize()
    • normalize_data_dict()
    • normalize_fitting_net_dict()
    • normalize_fitting_weight()
    • normalize_learning_rate_dict()
    • normalize_learning_rate_dict_with_single_learning_rate()
    • normalize_loss_dict()
    • normalize_multi_task()
    • pairtab_model_args()
    • pairwise_dprc()
    • spin_args()
    • standard_model_args()
    • start_pref()
    • training_args()
    • training_data_args()
    • type_embedding_args()
    • validation_data_args()
  • deepmd_utils.utils.argcheck_nvnmd module
    • nvnmd_args()
  • deepmd_utils.utils.batch_size module
    • AutoBatchSize
      • AutoBatchSize.execute()
      • AutoBatchSize.execute_all()
      • AutoBatchSize.is_gpu_available()
      • AutoBatchSize.is_oom_error()
  • deepmd_utils.utils.compat module
    • convert_input_v0_v1()
    • convert_input_v1_v2()
    • deprecate_numb_test()
    • remove_decay_rate()
    • update_deepmd_input()
  • deepmd_utils.utils.data module
    • DeepmdData
      • DeepmdData.add()
      • DeepmdData.avg()
      • DeepmdData.check_batch_size()
      • DeepmdData.check_test_size()
      • DeepmdData.get_atom_type()
      • DeepmdData.get_batch()
      • DeepmdData.get_data_dict()
      • DeepmdData.get_natoms()
      • DeepmdData.get_natoms_vec()
      • DeepmdData.get_ntypes()
      • DeepmdData.get_numb_batch()
      • DeepmdData.get_numb_set()
      • DeepmdData.get_sys_numb_batch()
      • DeepmdData.get_test()
      • DeepmdData.get_type_map()
      • DeepmdData.reduce()
      • DeepmdData.reset_get_batch()
  • deepmd_utils.utils.data_system module
    • DeepmdDataSystem
      • DeepmdDataSystem.add()
      • DeepmdDataSystem.add_dict()
      • DeepmdDataSystem.compute_energy_shift()
      • DeepmdDataSystem.default_mesh
      • DeepmdDataSystem.get_batch()
      • DeepmdDataSystem.get_batch_mixed()
      • DeepmdDataSystem.get_batch_size()
      • DeepmdDataSystem.get_batch_standard()
      • DeepmdDataSystem.get_data_dict()
      • DeepmdDataSystem.get_nbatches()
      • DeepmdDataSystem.get_nsystems()
      • DeepmdDataSystem.get_ntypes()
      • DeepmdDataSystem.get_sys()
      • DeepmdDataSystem.get_sys_ntest()
      • DeepmdDataSystem.get_test()
      • DeepmdDataSystem.get_type_map()
      • DeepmdDataSystem.print_summary()
      • DeepmdDataSystem.reduce()
      • DeepmdDataSystem.set_sys_probs()
    • prob_sys_size_ext()
    • process_sys_probs()
  • deepmd_utils.utils.errors module
    • OutOfMemoryError
  • deepmd_utils.utils.model_stat module
    • make_stat_input()
    • merge_sys_stat()
  • deepmd_utils.utils.pair_tab module
    • PairTab
      • PairTab.get()
      • PairTab.reinit()
  • deepmd_utils.utils.path module
    • DPH5Path
      • DPH5Path.glob()
      • DPH5Path.is_dir()
      • DPH5Path.is_file()
      • DPH5Path.load_numpy()
      • DPH5Path.load_txt()
      • DPH5Path.rglob()
    • DPOSPath
      • DPOSPath.glob()
      • DPOSPath.is_dir()
      • DPOSPath.is_file()
      • DPOSPath.load_numpy()
      • DPOSPath.load_txt()
      • DPOSPath.rglob()
    • DPPath
      • DPPath.glob()
      • DPPath.is_dir()
      • DPPath.is_file()
      • DPPath.load_numpy()
      • DPPath.load_txt()
      • DPPath.rglob()
  • deepmd_utils.utils.plugin module
    • Plugin
      • Plugin.get_plugin()
      • Plugin.register()
    • PluginVariant
    • VariantABCMeta
    • VariantMeta
  • deepmd_utils.utils.random module
    • choice()
    • random()
    • seed()
    • shuffle()
  • deepmd_utils.utils.weight_avg module
    • weighted_average()

Submodules

deepmd_utils.common module

deepmd_utils.common.add_data_requirement(key: str, ndof: int, atomic: bool = False, must: bool = False, high_prec: bool = False, type_sel: Optional[bool] = None, repeat: int = 1, default: float = 0.0, dtype: Optional[dtype] = None)

Specify data requirements for training.

Parameters

keystr

type of data stored in corresponding *.npy file e.g. forces or energy

ndofint

number of the degrees of freedom, this is tied to atomic parameter e.g. forces have atomic=True and ndof=3

atomicbool, optional

specifies whwther the ndof keyworrd applies to per atom quantity or not, by default False

mustbool, optional

specifi if the *.npy data file must exist, by default False

high_precbool, optional

if true load data to np.float64 else np.float32, by default False

type_selbool, optional

select only certain type of atoms, by default None

repeatint, optional

if specify repaeat data repeat times, by default 1

defaultfloat, optional, default=0.

default value of data

dtypenp.dtype, optional

the dtype of data, overwrites high_prec if provided

deepmd_utils.common.expand_sys_str(root_dir: Union[str, Path]) → List[str]

Recursively iterate over directories taking those that contain type.raw file.

Parameters

root_dirUnion[str, Path]

starting directory

Returns

List[str]

list of string pointing to system directories

deepmd_utils.common.get_np_precision(precision: _PRECISION) → dtype

Get numpy precision constant from string.

Parameters

precision_PRECISION

string name of numpy constant or default

Returns

np.dtype

numpy presicion constant

Raises

RuntimeError

if string is invalid

deepmd_utils.common.j_loader(filename: Union[str, Path]) → Dict[str, Any]

Load yaml or json settings file.

Parameters

filenameUnion[str, Path]

path to file

Returns

Dict[str, Any]

loaded dictionary

Raises

TypeError

if the supplied file is of unsupported type

deepmd_utils.common.j_must_have(jdata: Dict[str, _DICT_VAL], key: str, deprecated_key: List[str] = []) → _DICT_VAL

Assert that supplied dictionary conaines specified key.

Returns

_DICT_VAL

value that was store unde supplied key

Raises

RuntimeError

if the key is not present

deepmd_utils.common.make_default_mesh(pbc: bool, mixed_type: bool) → ndarray

Make mesh.

Only the size of mesh matters, not the values: * 6 for PBC, no mixed types * 0 for no PBC, no mixed types * 7 for PBC, mixed types * 1 for no PBC, mixed types

Parameters

pbcbool

if True, the mesh will be made for periodic boundary conditions

mixed_typebool

if True, the mesh will be made for mixed types

Returns

np.ndarray

mesh

deepmd_utils.common.select_idx_map(atom_types: ndarray, select_types: ndarray) → ndarray

Build map of indices for element supplied element types from all atoms list.

Parameters

atom_typesnp.ndarray

array specifing type for each atoms as integer

select_typesnp.ndarray

types of atoms you want to find indices for

Returns

np.ndarray

indices of types of atoms defined by select_types in atom_types array

Warning

select_types array will be sorted before finding indices in atom_types

deepmd_utils.env module

deepmd_utils.env.GLOBAL_ENER_FLOAT_PRECISION

alias of float64

deepmd_utils.env.GLOBAL_NP_FLOAT_PRECISION

alias of float64

deepmd_utils.main module

The entry points for DeePMD-kit.

If only printing the help message, this module does not call the main DeePMD-kit module to avoid the slow import of TensorFlow.

class deepmd_utils.main.RawTextArgumentDefaultsHelpFormatter(prog, indent_increment=2, max_help_position=24, width=None)

Bases: RawTextHelpFormatter, ArgumentDefaultsHelpFormatter

This formatter is used to print multile-line help message with default value.

Methods

format_help()
start_section(heading)

add_argument
add_arguments
add_text
add_usage
end_section

deepmd_utils.main.get_ll(log_level: str) → int

Convert string to python logging level.

Parameters

log_levelstr

allowed input values are: DEBUG, INFO, WARNING, ERROR, 3, 2, 1, 0

Returns

int

one of python logging module log levels - 10, 20, 30 or 40

deepmd_utils.main.main()

DeePMD-kit new entry point.

Raises

RuntimeError

if no command was input

deepmd_utils.main.main_parser() → ArgumentParser

DeePMD-Kit commandline options argument parser.

Returns

argparse.ArgumentParser

main parser of DeePMD-kit

deepmd_utils.main.parse_args(args: Optional[List[str]] = None) → Namespace

Parse arguments and convert argument strings to objects.

Parameters

argsList[str]

list of command line arguments, main purpose is testing default option None takes arguments from sys.argv

Returns

argparse.Namespace

the populated namespace