5.3. Training Parameters

Note

One can load, modify, and export the input file by using our effective web-based tool DP-GUI online or hosted using the command line interface dp gui. All training parameters below can be set in DP-GUI. By clicking “SAVE JSON”, one can download the input file for further training.

Note

One can benefit from IntelliSense and validation when writing JSON files using Visual Studio Code. See here to learn how to configure.

model:

type: dict

argument path: model

type_map:

type: typing.List[str], optional

argument path: model/type_map

A list of strings. Give the name to each type of atoms. It is noted that the number of atom type of training system must be less than 128 in a GPU environment. If not given, type.raw in each system should use the same type indexes, and type_map.raw will take no effect.

data_stat_nbatch:

type: int, optional, default: 10

argument path: model/data_stat_nbatch

The model determines the normalization from the statistics of the data. This key specifies the number of frames in each system used for statistics.

data_stat_protect:

type: float, optional, default: 0.01

argument path: model/data_stat_protect

Protect parameter for atomic energy regression.

data_bias_nsample:

type: int, optional, default: 10

argument path: model/data_bias_nsample

The number of training samples in a system to compute and change the energy bias.

use_srtab:

type: str, optional

argument path: model/use_srtab

The table for the short-range pairwise interaction added on top of DP. The table is a text data file with (N_t + 1) * N_t / 2 + 1 columes. The first colume is the distance between atoms. The second to the last columes are energies for pairs of certain types. For example we have two atom types, 0 and 1. The columes from 2nd to 4th are for 0-0, 0-1 and 1-1 correspondingly.

smin_alpha:

type: float, optional

argument path: model/smin_alpha

The short-range tabulated interaction will be swithed according to the distance of the nearest neighbor. This distance is calculated by softmin. This parameter is the decaying parameter in the softmin. It is only required when use_srtab is provided.

sw_rmin:

type: float, optional

argument path: model/sw_rmin

The lower boundary of the interpolation between short-range tabulated interaction and DP. It is only required when use_srtab is provided.

sw_rmax:

type: float, optional

argument path: model/sw_rmax

The upper boundary of the interpolation between short-range tabulated interaction and DP. It is only required when use_srtab is provided.

pair_exclude_types:

type: list, optional, default: []

argument path: model/pair_exclude_types

(Supported Backend: PyTorch) The atom pairs of the listed types are not treated to be neighbors, i.e. they do not see each other.

atom_exclude_types:

type: list, optional, default: []

argument path: model/atom_exclude_types

(Supported Backend: PyTorch) Exclude the atomic contribution of the listed atom types

srtab_add_bias:

type: bool, optional, default: True

argument path: model/srtab_add_bias

(Supported Backend: TensorFlow) Whether add energy bias from the statistics of the data to short-range tabulated atomic energy. It only takes effect when use_srtab is provided.

type_embedding:

type: dict, optional

argument path: model/type_embedding

(Supported Backend: TensorFlow) The type embedding.

neuron:

type: typing.List[int], optional, default: [8]

argument path: model/type_embedding/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model/type_embedding/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model/type_embedding/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:

type: str, optional, default: default

argument path: model/type_embedding/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model/type_embedding/trainable

If the parameters in the embedding net are trainable

seed:

type: NoneType | int, optional, default: None

argument path: model/type_embedding/seed

Random seed for parameter initialization

use_econf_tebd:

type: bool, optional, default: False

argument path: model/type_embedding/use_econf_tebd

Whether to use electronic configuration type embedding.

use_tebd_bias:

type: bool, optional, default: False

argument path: model/type_embedding/use_tebd_bias

Whether to use bias in the type embedding layer.

modifier:

type: dict, optional

argument path: model/modifier

(Supported Backend: TensorFlow) The modifier of model output.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: model/modifier/type

possible choices: dipole_charge

The type of modifier. See explanation below.

-dipole_charge: Use WFCC to model the electronic structure of the system. Correct the long-range interaction

When type is set to dipole_charge:

model_name:

type: str

argument path: model/modifier[dipole_charge]/model_name

The name of the frozen dipole model file.

model_charge_map:

type: typing.List[float]

argument path: model/modifier[dipole_charge]/model_charge_map

The charge of the WFCC. The list length should be the same as the `sel_type <model/fitting_net[dipole]/sel_type_>`_.

sys_charge_map:

type: typing.List[float]

argument path: model/modifier[dipole_charge]/sys_charge_map

The charge of real atoms. The list length should be the same as the type_map

ewald_beta:

type: float, optional, default: 0.4

argument path: model/modifier[dipole_charge]/ewald_beta

The splitting parameter of Ewald sum. Unit is A^-1

ewald_h:

type: float, optional, default: 1.0

argument path: model/modifier[dipole_charge]/ewald_h

The grid spacing of the FFT grid. Unit is A

compress:

type: dict, optional

argument path: model/compress

(Supported Backend: TensorFlow) Model compression configurations

spin:

type: dict, optional

argument path: model/spin

The settings for systems with spin.

use_spin:

type: typing.List[int] | typing.List[bool]

argument path: model/spin/use_spin

Whether to use atomic spin model for each atom type. List of boolean values with the shape of [ntypes] to specify which types use spin, or a list of integer values (Supported Backend: PyTorch) to indicate the index of the type that uses spin.

spin_norm:

type: typing.List[float], optional

argument path: model/spin/spin_norm

(Supported Backend: TensorFlow) The magnitude of atomic spin for each atom type with spin

virtual_len:

type: typing.List[float], optional

argument path: model/spin/virtual_len

(Supported Backend: TensorFlow) The distance between virtual atom representing spin and its corresponding real atom for each atom type with spin

virtual_scale:

type: float | typing.List[float], optional

argument path: model/spin/virtual_scale

(Supported Backend: PyTorch) The scaling factor to determine the virtual distance between a virtual atom representing spin and its corresponding real atom for each atom type with spin. This factor is defined as the virtual distance divided by the magnitude of atomic spin for each atom type with spin. The virtual coordinate is defined as the real coordinate plus spin * virtual_scale. List of float values with shape of [ntypes] or [ntypes_spin] or one single float value for all types, only used when use_spin is True for each atom type.

finetune_head:

type: str, optional

argument path: model/finetune_head

(Supported Backend: PyTorch) The chosen fitting net to fine-tune on, when doing multi-task fine-tuning. If not set or set to ‘RANDOM’, the fitting net will be randomly initialized.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key), default: standard

argument path: model/type

possible choices: standard, frozen, pairtab, pairwise_dprc, linear_ener

When type is set to standard:

Stardard model, which contains a descriptor and a fitting.

descriptor:

type: dict

argument path: model[standard]/descriptor

The descriptor of atomic environment.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: model[standard]/descriptor/type

possible choices: loc_frame, se_e2_a, se_e3, se_a_tpe, se_e2_r, hybrid, se_atten, se_atten_v2, dpa2, se_a_ebd_v2, se_a_mask

The type of the descritpor. See explanation below.

• loc_frame: Defines a local frame at each atom, and the compute the descriptor as local coordinates under this frame.

• se_e2_a: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor.

• se_e2_r: Used by the smooth edition of Deep Potential. Only the distance between atoms is used to construct the descriptor.

• se_e3: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor. Three-body embedding will be used by this descriptor.

• se_a_tpe: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor. Type embedding will be used by this descriptor.

• se_atten: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor. Attention mechanism will be used by this descriptor.

• se_atten_v2: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor. Attention mechanism with new modifications will be used by this descriptor.

• se_a_mask: Used by the smooth edition of Deep Potential. It can accept a variable number of atoms in a frame (Non-PBC system). aparam are required as an indicator matrix for the real/virtual sign of input atoms.

• hybrid: Concatenate of a list of descriptors as a new descriptor.

When type is set to loc_frame:

(Supported Backend: TensorFlow)

sel_a:

type: typing.List[int]

argument path: model[standard]/descriptor[loc_frame]/sel_a

A list of integers. The length of the list should be the same as the number of atom types in the system. sel_a[i] gives the selected number of type-i neighbors. The full relative coordinates of the neighbors are used by the descriptor.

sel_r:

type: typing.List[int]

argument path: model[standard]/descriptor[loc_frame]/sel_r

A list of integers. The length of the list should be the same as the number of atom types in the system. sel_r[i] gives the selected number of type-i neighbors. Only relative distance of the neighbors are used by the descriptor. sel_a[i] + sel_r[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[loc_frame]/rcut

The cut-off radius. The default value is 6.0

axis_rule:

type: typing.List[int]

argument path: model[standard]/descriptor[loc_frame]/axis_rule

A list of integers. The length should be 6 times of the number of types.

• axis_rule[i*6+0]: class of the atom defining the first axis of type-i atom. 0 for neighbors with full coordinates and 1 for neighbors only with relative distance.

• axis_rule[i*6+1]: type of the atom defining the first axis of type-i atom.

• axis_rule[i*6+2]: index of the axis atom defining the first axis. Note that the neighbors with the same class and type are sorted according to their relative distance.

• axis_rule[i*6+3]: class of the atom defining the second axis of type-i atom. 0 for neighbors with full coordinates and 1 for neighbors only with relative distance.

• axis_rule[i*6+4]: type of the atom defining the second axis of type-i atom.

• axis_rule[i*6+5]: index of the axis atom defining the second axis. Note that the neighbors with the same class and type are sorted according to their relative distance.

When type is set to se_e2_a (or its alias se_a):

sel:

type: typing.List[int] | str, optional, default: auto

argument path: model[standard]/descriptor[se_e2_a]/sel

This parameter set the number of selected neighbors for each type of atom. It can be:

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius. It is noted that the total sel value must be less than 4096 in a GPU environment.

• str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_e2_a]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_e2_a]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_e2_a]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 4, alias: n_axis_neuron

argument path: model[standard]/descriptor[se_e2_a]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_e2_a]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e2_a]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e2_a]/type_one_side

If true, the embedding network parameters vary by types of neighbor atoms only, so there will be $N_text{types}$ sets of embedding network parameters. Otherwise, the embedding network parameters vary by types of centric atoms and types of neighbor atoms, so there will be $N_text{types}^2$ sets of embedding network parameters.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_e2_a]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_e2_a]/trainable

If the parameters in the embedding net is trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_e2_a]/seed

Random seed for parameter initialization

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_e2_a]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_e2_a]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

set_davg_zero:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e2_a]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

When type is set to se_e3 (or its aliases se_at, se_a_3be, se_t):

sel:

type: typing.List[int] | str, optional, default: auto

argument path: model[standard]/descriptor[se_e3]/sel

This parameter set the number of selected neighbors for each type of atom. It can be:

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius. It is noted that the total sel value must be less than 4096 in a GPU environment.

• str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_e3]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_e3]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_e3]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_e3]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e3]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_e3]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_e3]/trainable

If the parameters in the embedding net are trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_e3]/seed

Random seed for parameter initialization

set_davg_zero:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e3]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_e3]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_e3]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

When type is set to se_a_tpe (or its alias se_a_ebd):

(Supported Backend: TensorFlow)

sel:

type: typing.List[int] | str, optional, default: auto

argument path: model[standard]/descriptor[se_a_tpe]/sel

This parameter set the number of selected neighbors for each type of atom. It can be:

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius. It is noted that the total sel value must be less than 4096 in a GPU environment.

• str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_a_tpe]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_a_tpe]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_a_tpe]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 4, alias: n_axis_neuron

argument path: model[standard]/descriptor[se_a_tpe]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_a_tpe]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_tpe]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_tpe]/type_one_side

If true, the embedding network parameters vary by types of neighbor atoms only, so there will be $N_text{types}$ sets of embedding network parameters. Otherwise, the embedding network parameters vary by types of centric atoms and types of neighbor atoms, so there will be $N_text{types}^2$ sets of embedding network parameters.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_a_tpe]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_a_tpe]/trainable

If the parameters in the embedding net is trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_a_tpe]/seed

Random seed for parameter initialization

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_a_tpe]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_a_tpe]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

set_davg_zero:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_tpe]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

type_nchanl:

type: int, optional, default: 4

argument path: model[standard]/descriptor[se_a_tpe]/type_nchanl

number of channels for type embedding

type_nlayer:

type: int, optional, default: 2

argument path: model[standard]/descriptor[se_a_tpe]/type_nlayer

number of hidden layers of type embedding net

numb_aparam:

type: int, optional, default: 0

argument path: model[standard]/descriptor[se_a_tpe]/numb_aparam

dimension of atomic parameter. if set to a value > 0, the atomic parameters are embedded.

When type is set to se_e2_r (or its alias se_r):

sel:

type: typing.List[int] | str, optional, default: auto

argument path: model[standard]/descriptor[se_e2_r]/sel

This parameter set the number of selected neighbors for each type of atom. It can be:

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius. It is noted that the total sel value must be less than 4096 in a GPU environment.

• str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_e2_r]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_e2_r]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_e2_r]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_e2_r]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e2_r]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e2_r]/type_one_side

If true, the embedding network parameters vary by types of neighbor atoms only, so there will be $N_text{types}$ sets of embedding network parameters. Otherwise, the embedding network parameters vary by types of centric atoms and types of neighbor atoms, so there will be $N_text{types}^2$ sets of embedding network parameters.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_e2_r]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_e2_r]/trainable

If the parameters in the embedding net are trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_e2_r]/seed

Random seed for parameter initialization

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_e2_r]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

set_davg_zero:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_e2_r]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_e2_r]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

When type is set to hybrid:

list:

type: list

argument path: model[standard]/descriptor[hybrid]/list

A list of descriptor definitions

When type is set to se_atten (or its alias dpa1):

sel:

type: typing.List[int] | str | int, optional, default: auto

argument path: model[standard]/descriptor[se_atten]/sel

This parameter set the number of selected neighbors. Note that this parameter is a little different from that in other descriptors. Instead of separating each type of atoms, only the summation matters. And this number is highly related with the efficiency, thus one should not make it too large. Usually 200 or less is enough, far away from the GPU limitation 4096. It can be:

• int. The maximum number of neighbor atoms to be considered. We recommend it to be less than 200.

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. Only the summation of sel[i] matters, and it is recommended to be less than 200. - str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_atten]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_atten]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_atten]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 4, alias: n_axis_neuron

argument path: model[standard]/descriptor[se_atten]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_atten]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten]/type_one_side

If ‘False’, type embeddings of both neighbor and central atoms are considered. If ‘True’, only type embeddings of neighbor atoms are considered. Default is ‘False’.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_atten]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten]/trainable

If the parameters in the embedding net is trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_atten]/seed

Random seed for parameter initialization

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_atten]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_atten]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

attn:

type: int, optional, default: 128

argument path: model[standard]/descriptor[se_atten]/attn

The length of hidden vectors in attention layers

attn_layer:

type: int, optional, default: 2

argument path: model[standard]/descriptor[se_atten]/attn_layer

The number of attention layers. Note that model compression of se_atten is only enabled when attn_layer==0 and tebd_input_mode==’strip’

attn_dotr:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten]/attn_dotr

Whether to do dot product with the normalized relative coordinates

attn_mask:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten]/attn_mask

Whether to do mask on the diagonal in the attention matrix

stripped_type_embedding:

type: bool | NoneType, optional, default: None

argument path: model[standard]/descriptor[se_atten]/stripped_type_embedding

(Deprecated, kept only for compatibility.) Whether to strip the type embedding into a separate embedding network. Setting this parameter to True is equivalent to setting tebd_input_mode to ‘strip’. Setting it to False is equivalent to setting tebd_input_mode to ‘concat’.The default value is None, which means the tebd_input_mode setting will be used instead.

smooth_type_embedding:

type: bool, optional, default: False, alias: smooth_type_embdding

argument path: model[standard]/descriptor[se_atten]/smooth_type_embedding

Whether to use smooth process in attention weights calculation. (Supported Backend: TensorFlow) When using stripped type embedding, whether to dot smooth factor on the network output of type embedding to keep the network smooth, instead of setting set_davg_zero to be True.

set_davg_zero:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten]/set_davg_zero

Set the normalization average to zero. This option should be set when se_atten descriptor or atom_ener in the energy fitting is used

trainable_ln:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten]/trainable_ln

Whether to use trainable shift and scale weights in layer normalization.

ln_eps:

type: float | NoneType, optional, default: None

argument path: model[standard]/descriptor[se_atten]/ln_eps

The epsilon value for layer normalization. The default value for TensorFlow is set to 1e-3 to keep consistent with keras while set to 1e-5 in PyTorch and DP implementation.

tebd_dim:

type: int, optional, default: 8

argument path: model[standard]/descriptor[se_atten]/tebd_dim

(Supported Backend: PyTorch) The dimension of atom type embedding.

use_econf_tebd:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten]/use_econf_tebd

(Supported Backend: PyTorch) Whether to use electronic configuration type embedding. For TensorFlow backend, please set use_econf_tebd in type_embedding block instead.

use_tebd_bias:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten]/use_tebd_bias

Whether to use bias in the type embedding layer.

tebd_input_mode:

type: str, optional, default: concat

argument path: model[standard]/descriptor[se_atten]/tebd_input_mode

The input mode of the type embedding. Supported modes are [‘concat’, ‘strip’].- ‘concat’: Concatenate the type embedding with the smoothed radial information as the union input for the embedding network. When type_one_side is False, the input is input_ij = concat([r_ij, tebd_j, tebd_i]). When type_one_side is True, the input is input_ij = concat([r_ij, tebd_j]). The output is out_ij = embeding(input_ij) for the pair-wise representation of atom i with neighbor j.- ‘strip’: Use a separated embedding network for the type embedding and combine the output with the radial embedding network output. When type_one_side is False, the input is input_t = concat([tebd_j, tebd_i]). (Supported Backend: PyTorch) When type_one_side is True, the input is input_t = tebd_j. The output is out_ij = embeding_t(input_t) * embeding_s(r_ij) + embeding_s(r_ij) for the pair-wise representation of atom i with neighbor j.

scaling_factor:

type: float, optional, default: 1.0

argument path: model[standard]/descriptor[se_atten]/scaling_factor

(Supported Backend: PyTorch) The scaling factor of normalization in calculations of attention weights, which is used to scale the matmul(Q, K). If temperature is None, the scaling of attention weights is (N_hidden_dim * scaling_factor)**0.5. Else, the scaling of attention weights is setting to temperature.

normalize:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten]/normalize

(Supported Backend: PyTorch) Whether to normalize the hidden vectors during attention calculation.

temperature:

type: float, optional

argument path: model[standard]/descriptor[se_atten]/temperature

(Supported Backend: PyTorch) The scaling factor of normalization in calculations of attention weights, which is used to scale the matmul(Q, K).

concat_output_tebd:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten]/concat_output_tebd

(Supported Backend: PyTorch) Whether to concat type embedding at the output of the descriptor.

When type is set to se_atten_v2:

sel:

type: typing.List[int] | str | int, optional, default: auto

argument path: model[standard]/descriptor[se_atten_v2]/sel

This parameter set the number of selected neighbors. Note that this parameter is a little different from that in other descriptors. Instead of separating each type of atoms, only the summation matters. And this number is highly related with the efficiency, thus one should not make it too large. Usually 200 or less is enough, far away from the GPU limitation 4096. It can be:

• int. The maximum number of neighbor atoms to be considered. We recommend it to be less than 200.

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. Only the summation of sel[i] matters, and it is recommended to be less than 200. - str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_atten_v2]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_atten_v2]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_atten_v2]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 4, alias: n_axis_neuron

argument path: model[standard]/descriptor[se_atten_v2]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_atten_v2]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten_v2]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten_v2]/type_one_side

If ‘False’, type embeddings of both neighbor and central atoms are considered. If ‘True’, only type embeddings of neighbor atoms are considered. Default is ‘False’.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_atten_v2]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten_v2]/trainable

If the parameters in the embedding net is trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_atten_v2]/seed

Random seed for parameter initialization

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_atten_v2]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_atten_v2]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

attn:

type: int, optional, default: 128

argument path: model[standard]/descriptor[se_atten_v2]/attn

The length of hidden vectors in attention layers

attn_layer:

type: int, optional, default: 2

argument path: model[standard]/descriptor[se_atten_v2]/attn_layer

The number of attention layers. Note that model compression of se_atten is only enabled when attn_layer==0 and tebd_input_mode==’strip’

attn_dotr:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten_v2]/attn_dotr

Whether to do dot product with the normalized relative coordinates

attn_mask:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten_v2]/attn_mask

Whether to do mask on the diagonal in the attention matrix

set_davg_zero:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten_v2]/set_davg_zero

Set the normalization average to zero. This option should be set when se_atten descriptor or atom_ener in the energy fitting is used

trainable_ln:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten_v2]/trainable_ln

Whether to use trainable shift and scale weights in layer normalization.

ln_eps:

type: float | NoneType, optional, default: None

argument path: model[standard]/descriptor[se_atten_v2]/ln_eps

The epsilon value for layer normalization. The default value for TensorFlow is set to 1e-3 to keep consistent with keras while set to 1e-5 in PyTorch and DP implementation.

tebd_dim:

type: int, optional, default: 8

argument path: model[standard]/descriptor[se_atten_v2]/tebd_dim

(Supported Backend: PyTorch) The dimension of atom type embedding.

use_econf_tebd:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten_v2]/use_econf_tebd

(Supported Backend: PyTorch) Whether to use electronic configuration type embedding. For TensorFlow backend, please set use_econf_tebd in type_embedding block instead.

use_tebd_bias:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_atten_v2]/use_tebd_bias

Whether to use bias in the type embedding layer.

scaling_factor:

type: float, optional, default: 1.0

argument path: model[standard]/descriptor[se_atten_v2]/scaling_factor

(Supported Backend: PyTorch) The scaling factor of normalization in calculations of attention weights, which is used to scale the matmul(Q, K). If temperature is None, the scaling of attention weights is (N_hidden_dim * scaling_factor)**0.5. Else, the scaling of attention weights is setting to temperature.

normalize:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten_v2]/normalize

(Supported Backend: PyTorch) Whether to normalize the hidden vectors during attention calculation.

temperature:

type: float, optional

argument path: model[standard]/descriptor[se_atten_v2]/temperature

(Supported Backend: PyTorch) The scaling factor of normalization in calculations of attention weights, which is used to scale the matmul(Q, K).

concat_output_tebd:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_atten_v2]/concat_output_tebd

(Supported Backend: PyTorch) Whether to concat type embedding at the output of the descriptor.

When type is set to dpa2:

(Supported Backend: PyTorch)

repinit:

type: dict

argument path: model[standard]/descriptor[dpa2]/repinit

The arguments used to initialize the repinit block.

rcut:

type: float

argument path: model[standard]/descriptor[dpa2]/repinit/rcut

The cut-off radius.

rcut_smth:

type: float

argument path: model[standard]/descriptor[dpa2]/repinit/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth.

nsel:

type: int

argument path: model[standard]/descriptor[dpa2]/repinit/nsel

Maximally possible number of selected neighbors.

neuron:

type: list, optional, default: [25, 50, 100]

argument path: model[standard]/descriptor[dpa2]/repinit/neuron

Number of neurons in each hidden layers of the embedding net.When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 16

argument path: model[standard]/descriptor[dpa2]/repinit/axis_neuron

Size of the submatrix of G (embedding matrix).

tebd_dim:

type: int, optional, default: 8

argument path: model[standard]/descriptor[dpa2]/repinit/tebd_dim

The dimension of atom type embedding.

tebd_input_mode:

type: str, optional, default: concat

argument path: model[standard]/descriptor[dpa2]/repinit/tebd_input_mode

The input mode of the type embedding. Supported modes are [‘concat’, ‘strip’].- ‘concat’: Concatenate the type embedding with the smoothed radial information as the union input for the embedding network. When type_one_side is False, the input is input_ij = concat([r_ij, tebd_j, tebd_i]). When type_one_side is True, the input is input_ij = concat([r_ij, tebd_j]). The output is out_ij = embeding(input_ij) for the pair-wise representation of atom i with neighbor j.- ‘strip’: Use a separated embedding network for the type embedding and combine the output with the radial embedding network output. When type_one_side is False, the input is input_t = concat([tebd_j, tebd_i]). (Supported Backend: PyTorch) When type_one_side is True, the input is input_t = tebd_j. The output is out_ij = embeding_t(input_t) * embeding_s(r_ij) + embeding_s(r_ij) for the pair-wise representation of atom i with neighbor j.

set_davg_zero:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repinit/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[dpa2]/repinit/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”..

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/repinit/type_one_side

If true, the embedding network parameters vary by types of neighbor atoms only, so there will be $N_text{types}$ sets of embedding network parameters. Otherwise, the embedding network parameters vary by types of centric atoms and types of neighbor atoms, so there will be $N_text{types}^2$ sets of embedding network parameters.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/repinit/resnet_dt

Whether to use a “Timestep” in the skip connection.

repformer:

type: dict

argument path: model[standard]/descriptor[dpa2]/repformer

The arguments used to initialize the repformer block.

rcut:

type: float

argument path: model[standard]/descriptor[dpa2]/repformer/rcut

The cut-off radius.

rcut_smth:

type: float

argument path: model[standard]/descriptor[dpa2]/repformer/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth.

nsel:

type: int

argument path: model[standard]/descriptor[dpa2]/repformer/nsel

Maximally possible number of selected neighbors.

nlayers:

type: int, optional, default: 3

argument path: model[standard]/descriptor[dpa2]/repformer/nlayers

The number of repformer layers.

g1_dim:

type: int, optional, default: 128

argument path: model[standard]/descriptor[dpa2]/repformer/g1_dim

The dimension of invariant single-atom representation.

g2_dim:

type: int, optional, default: 16

argument path: model[standard]/descriptor[dpa2]/repformer/g2_dim

The dimension of invariant pair-atom representation.

axis_neuron:

type: int, optional, default: 4

argument path: model[standard]/descriptor[dpa2]/repformer/axis_neuron

The number of dimension of submatrix in the symmetrization ops.

direct_dist:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/repformer/direct_dist

Whether or not use direct distance as input for the embedding net to get g2 instead of smoothed 1/r.

update_g1_has_conv:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/update_g1_has_conv

Update the g1 rep with convolution term.

update_g1_has_drrd:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/update_g1_has_drrd

Update the g1 rep with the drrd term.

update_g1_has_grrg:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/update_g1_has_grrg

Update the g1 rep with the grrg term.

update_g1_has_attn:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/update_g1_has_attn

Update the g1 rep with the localized self-attention.

update_g2_has_g1g1:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/update_g2_has_g1g1

Update the g2 rep with the g1xg1 term.

update_g2_has_attn:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/update_g2_has_attn

Update the g2 rep with the gated self-attention.

update_h2:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/repformer/update_h2

Update the h2 rep.

attn1_hidden:

type: int, optional, default: 64

argument path: model[standard]/descriptor[dpa2]/repformer/attn1_hidden

The hidden dimension of localized self-attention to update the g1 rep.

attn1_nhead:

type: int, optional, default: 4

argument path: model[standard]/descriptor[dpa2]/repformer/attn1_nhead

The number of heads in localized self-attention to update the g1 rep.

attn2_hidden:

type: int, optional, default: 16

argument path: model[standard]/descriptor[dpa2]/repformer/attn2_hidden

The hidden dimension of gated self-attention to update the g2 rep.

attn2_nhead:

type: int, optional, default: 4

argument path: model[standard]/descriptor[dpa2]/repformer/attn2_nhead

The number of heads in gated self-attention to update the g2 rep.

attn2_has_gate:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/repformer/attn2_has_gate

Whether to use gate in the gated self-attention to update the g2 rep.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[dpa2]/repformer/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”..

update_style:

type: str, optional, default: res_avg

argument path: model[standard]/descriptor[dpa2]/repformer/update_style

Style to update a representation. Supported options are: -‘res_avg’: Updates a rep u with: u = 1/sqrt{n+1} (u + u_1 + u_2 + … + u_n) -‘res_incr’: Updates a rep u with: u = u + 1/sqrt{n} (u_1 + u_2 + … + u_n)-‘res_residual’: Updates a rep u with: u = u + (r1*u_1 + r2*u_2 + … + r3*u_n) where r1, r2 … r3 are residual weights defined by update_residual and update_residual_init.

update_residual:

type: float, optional, default: 0.001

argument path: model[standard]/descriptor[dpa2]/repformer/update_residual

When update using residual mode, the initial std of residual vector weights.

update_residual_init:

type: str, optional, default: norm

argument path: model[standard]/descriptor[dpa2]/repformer/update_residual_init

When update using residual mode, the initialization mode of residual vector weights.Supported modes are: [‘norm’, ‘const’].

set_davg_zero:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used.

trainable_ln:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/repformer/trainable_ln

Whether to use trainable shift and scale weights in layer normalization.

ln_eps:

type: float | NoneType, optional, default: None

argument path: model[standard]/descriptor[dpa2]/repformer/ln_eps

The epsilon value for layer normalization. The default value for TensorFlow is set to 1e-3 to keep consistent with keras while set to 1e-5 in PyTorch and DP implementation.

concat_output_tebd:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/concat_output_tebd

Whether to concat type embedding at the output of the descriptor.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[dpa2]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

smooth:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/smooth

Whether to use smoothness in processes such as attention weights calculation.

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[dpa2]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[dpa2]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[dpa2]/trainable

If the parameters in the embedding net is trainable.

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[dpa2]/seed

Random seed for parameter initialization.

add_tebd_to_repinit_out:

type: bool, optional, default: False, alias: repformer_add_type_ebd_to_seq

argument path: model[standard]/descriptor[dpa2]/add_tebd_to_repinit_out

Add type embedding to the output representation from repinit before inputting it into repformer.

use_econf_tebd:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/use_econf_tebd

(Supported Backend: PyTorch) Whether to use electronic configuration type embedding.

use_tebd_bias:

type: bool, optional, default: False

argument path: model[standard]/descriptor[dpa2]/use_tebd_bias

Whether to use bias in the type embedding layer.

When type is set to se_a_ebd_v2 (or its alias se_a_tpe_v2):

(Supported Backend: TensorFlow)

sel:

type: typing.List[int] | str, optional, default: auto

argument path: model[standard]/descriptor[se_a_ebd_v2]/sel

This parameter set the number of selected neighbors for each type of atom. It can be:

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius. It is noted that the total sel value must be less than 4096 in a GPU environment.

• str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

rcut:

type: float, optional, default: 6.0

argument path: model[standard]/descriptor[se_a_ebd_v2]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model[standard]/descriptor[se_a_ebd_v2]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_a_ebd_v2]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 4, alias: n_axis_neuron

argument path: model[standard]/descriptor[se_a_ebd_v2]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_a_ebd_v2]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_ebd_v2]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_ebd_v2]/type_one_side

If true, the embedding network parameters vary by types of neighbor atoms only, so there will be $N_text{types}$ sets of embedding network parameters. Otherwise, the embedding network parameters vary by types of centric atoms and types of neighbor atoms, so there will be $N_text{types}^2$ sets of embedding network parameters.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_a_ebd_v2]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_a_ebd_v2]/trainable

If the parameters in the embedding net is trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_a_ebd_v2]/seed

Random seed for parameter initialization

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_a_ebd_v2]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

env_protection:

type: float, optional, default: 0.0

argument path: model[standard]/descriptor[se_a_ebd_v2]/env_protection

(Supported Backend: PyTorch) Protection parameter to prevent division by zero errors during environment matrix calculations. For example, when using paddings, there may be zero distances of neighbors, which may make division by zero error during environment matrix calculations without protection.

set_davg_zero:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_ebd_v2]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

When type is set to se_a_mask:

(Supported Backend: TensorFlow)

sel:

type: typing.List[int] | str, optional, default: auto

argument path: model[standard]/descriptor[se_a_mask]/sel

This parameter sets the number of selected neighbors for each type of atom. It can be:

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius. It is noted that the total sel value must be less than 4096 in a GPU environment.

• str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

neuron:

type: typing.List[int], optional, default: [10, 20, 40]

argument path: model[standard]/descriptor[se_a_mask]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:

type: int, optional, default: 4, alias: n_axis_neuron

argument path: model[standard]/descriptor[se_a_mask]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/descriptor[se_a_mask]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_mask]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:

type: bool, optional, default: False

argument path: model[standard]/descriptor[se_a_mask]/type_one_side

If true, the embedding network parameters vary by types of neighbor atoms only, so there will be $N_text{types}$ sets of embedding network parameters. Otherwise, the embedding network parameters vary by types of centric atoms and types of neighbor atoms, so there will be $N_text{types}^2$ sets of embedding network parameters.

exclude_types:

type: typing.List[typing.List[int]], optional, default: []

argument path: model[standard]/descriptor[se_a_mask]/exclude_types

The excluded pairs of types which have no interaction with each other. For example, [[0, 1]] means no interaction between type 0 and type 1.

precision:

type: str, optional, default: default

argument path: model[standard]/descriptor[se_a_mask]/precision

The precision of the embedding net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

trainable:

type: bool, optional, default: True

argument path: model[standard]/descriptor[se_a_mask]/trainable

If the parameters in the embedding net is trainable

seed:

type: NoneType | int, optional

argument path: model[standard]/descriptor[se_a_mask]/seed

Random seed for parameter initialization

fitting_net:

type: dict

argument path: model[standard]/fitting_net

The fitting of physical properties.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key), default: ener

argument path: model[standard]/fitting_net/type

possible choices: ener, dos, polar, dipole

The type of the fitting. See explanation below.

• ener: Fit an energy model (potential energy surface).

• dos : Fit a density of states model. The total density of states / site-projected density of states labels should be provided by dos.npy or atom_dos.npy in each data system. The file has number of frames lines and number of energy grid columns (times number of atoms in atom_dos.npy). See loss parameter.

• dipole: Fit an atomic dipole model. Global dipole labels or atomic dipole labels for all the selected atoms (see sel_type) should be provided by dipole.npy in each data system. The file either has number of frames lines and 3 times of number of selected atoms columns, or has number of frames lines and 3 columns. See loss parameter.

• polar: Fit an atomic polarizability model. Global polarizazbility labels or atomic polarizability labels for all the selected atoms (see sel_type) should be provided by polarizability.npy in each data system. The file eith has number of frames lines and 9 times of number of selected atoms columns, or has number of frames lines and 9 columns. See loss parameter.

When type is set to ener:

numb_fparam:

type: int, optional, default: 0

argument path: model[standard]/fitting_net[ener]/numb_fparam

The dimension of the frame parameter. If set to >0, file fparam.npy should be included to provided the input fparams.

numb_aparam:

type: int, optional, default: 0

argument path: model[standard]/fitting_net[ener]/numb_aparam

The dimension of the atomic parameter. If set to >0, file aparam.npy should be included to provided the input aparams.

neuron:

type: typing.List[int], optional, default: [120, 120, 120], alias: n_neuron

argument path: model[standard]/fitting_net[ener]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/fitting_net[ener]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

precision:

type: str, optional, default: default

argument path: model[standard]/fitting_net[ener]/precision

The precision of the fitting net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

resnet_dt:

type: bool, optional, default: True

argument path: model[standard]/fitting_net[ener]/resnet_dt

Whether to use a “Timestep” in the skip connection

trainable:

type: bool | typing.List[bool], optional, default: True

argument path: model[standard]/fitting_net[ener]/trainable

Whether the parameters in the fitting net are trainable. This option can be

• bool: True if all parameters of the fitting net are trainable, False otherwise.

• list of bool(Supported Backend: TensorFlow) : Specifies if each layer is trainable. Since the fitting net is composed by hidden layers followed by a output layer, the length of this list should be equal to len(neuron)+1.

rcond:

type: float | NoneType, optional, default: None

argument path: model[standard]/fitting_net[ener]/rcond

The condition number used to determine the inital energy shift for each type of atoms. See rcond in numpy.linalg.lstsq() for more details.

seed:

type: NoneType | int, optional

argument path: model[standard]/fitting_net[ener]/seed

Random seed for parameter initialization of the fitting net

atom_ener:

type: typing.List[typing.Optional[float]], optional, default: []

argument path: model[standard]/fitting_net[ener]/atom_ener

Specify the atomic energy in vacuum for each type

layer_name:

type: typing.List[str], optional

argument path: model[standard]/fitting_net[ener]/layer_name

The name of the each layer. The length of this list should be equal to n_neuron + 1. If two layers, either in the same fitting or different fittings, have the same name, they will share the same neural network parameters. The shape of these layers should be the same. If null is given for a layer, parameters will not be shared.

use_aparam_as_mask:

type: bool, optional, default: False

argument path: model[standard]/fitting_net[ener]/use_aparam_as_mask

Whether to use the aparam as a mask in input.If True, the aparam will not be used in fitting net for embedding.When descrpt is se_a_mask, the aparam will be used as a mask to indicate the input atom is real/virtual. And use_aparam_as_mask should be set to True.

When type is set to dos:

numb_fparam:

type: int, optional, default: 0

argument path: model[standard]/fitting_net[dos]/numb_fparam

The dimension of the frame parameter. If set to >0, file fparam.npy should be included to provided the input fparams.

numb_aparam:

type: int, optional, default: 0

argument path: model[standard]/fitting_net[dos]/numb_aparam

The dimension of the atomic parameter. If set to >0, file aparam.npy should be included to provided the input aparams.

neuron:

type: typing.List[int], optional, default: [120, 120, 120]

argument path: model[standard]/fitting_net[dos]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/fitting_net[dos]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

precision:

type: str, optional, default: float64

argument path: model[standard]/fitting_net[dos]/precision

The precision of the fitting net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

resnet_dt:

type: bool, optional, default: True

argument path: model[standard]/fitting_net[dos]/resnet_dt

Whether to use a “Timestep” in the skip connection

trainable:

type: bool | typing.List[bool], optional, default: True

argument path: model[standard]/fitting_net[dos]/trainable

Whether the parameters in the fitting net are trainable. This option can be

• bool: True if all parameters of the fitting net are trainable, False otherwise.

• list of bool: Specifies if each layer is trainable. Since the fitting net is composed by hidden layers followed by a output layer, the length of tihs list should be equal to len(neuron)+1.

rcond:

type: float | NoneType, optional, default: None

argument path: model[standard]/fitting_net[dos]/rcond

The condition number used to determine the inital energy shift for each type of atoms. See rcond in numpy.linalg.lstsq() for more details.

seed:

type: NoneType | int, optional

argument path: model[standard]/fitting_net[dos]/seed

Random seed for parameter initialization of the fitting net

numb_dos:

type: int, optional, default: 300

argument path: model[standard]/fitting_net[dos]/numb_dos

The number of gridpoints on which the DOS is evaluated (NEDOS in VASP)

When type is set to polar:

neuron:

type: typing.List[int], optional, default: [120, 120, 120], alias: n_neuron

argument path: model[standard]/fitting_net[polar]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/fitting_net[polar]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: True

argument path: model[standard]/fitting_net[polar]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:

type: str, optional, default: default

argument path: model[standard]/fitting_net[polar]/precision

The precision of the fitting net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

fit_diag:

type: bool, optional, default: True

argument path: model[standard]/fitting_net[polar]/fit_diag

Fit the diagonal part of the rotational invariant polarizability matrix, which will be converted to normal polarizability matrix by contracting with the rotation matrix.

scale:

type: float | typing.List[float], optional, default: 1.0

argument path: model[standard]/fitting_net[polar]/scale

The output of the fitting net (polarizability matrix) will be scaled by scale

shift_diag:

type: bool, optional, default: True

argument path: model[standard]/fitting_net[polar]/shift_diag

Whether to shift the diagonal of polar, which is beneficial to training. Default is true.

sel_type:

type: NoneType | typing.List[int] | int, optional, alias: pol_type

argument path: model[standard]/fitting_net[polar]/sel_type

The atom types for which the atomic polarizability will be provided. If not set, all types will be selected.(Supported Backend: TensorFlow)

seed:

type: NoneType | int, optional

argument path: model[standard]/fitting_net[polar]/seed

Random seed for parameter initialization of the fitting net

When type is set to dipole:

neuron:

type: typing.List[int], optional, default: [120, 120, 120], alias: n_neuron

argument path: model[standard]/fitting_net[dipole]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:

type: str, optional, default: tanh

argument path: model[standard]/fitting_net[dipole]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “tanh”, “softplus”, “linear”, “relu6”, “none”, “gelu”, “gelu_tf”, “sigmoid”. Note that “gelu” denotes the custom operator version, and “gelu_tf” denotes the TF standard version. If you set “None” or “none” here, no activation function will be used.

resnet_dt:

type: bool, optional, default: True

argument path: model[standard]/fitting_net[dipole]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:

type: str, optional, default: default

argument path: model[standard]/fitting_net[dipole]/precision

The precision of the fitting net parameters, supported options are “float32”, “default”, “float16”, “float64”. Default follows the interface precision.

sel_type:

type: NoneType | typing.List[int] | int, optional, alias: dipole_type

argument path: model[standard]/fitting_net[dipole]/sel_type

The atom types for which the atomic dipole will be provided. If not set, all types will be selected.(Supported Backend: TensorFlow)

seed:

type: NoneType | int, optional

argument path: model[standard]/fitting_net[dipole]/seed

Random seed for parameter initialization of the fitting net

When type is set to frozen:

model_file:

type: str

argument path: model[frozen]/model_file

Path to the frozen model file.

When type is set to pairtab:

(Supported Backend: TensorFlow) Pairwise tabulation energy model.

tab_file:

type: str

argument path: model[pairtab]/tab_file

Path to the tabulation file.

rcut:

type: float

argument path: model[pairtab]/rcut

The cut-off radius.

sel:

type: typing.List[int] | str | int

argument path: model[pairtab]/sel

This parameter set the number of selected neighbors. Note that this parameter is a little different from that in other descriptors. Instead of separating each type of atoms, only the summation matters. And this number is highly related with the efficiency, thus one should not make it too large. Usually 200 or less is enough, far away from the GPU limitation 4096. It can be:

• int. The maximum number of neighbor atoms to be considered. We recommend it to be less than 200.

• List[int]. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. Only the summation of sel[i] matters, and it is recommended to be less than 200. - str. Can be “auto:factor” or “auto”. “factor” is a float number larger than 1. This option will automatically determine the sel. In detail it counts the maximal number of neighbors with in the cutoff radius for each type of neighbor, then multiply the maximum by the “factor”. Finally the number is wraped up to 4 divisible. The option “auto” is equivalent to “auto:1.1”.

When type is set to pairwise_dprc:

(Supported Backend: TensorFlow)

qm_model:

type: dict

argument path: model[pairwise_dprc]/qm_model

qmmm_model:

type: dict

argument path: model[pairwise_dprc]/qmmm_model

When type is set to linear_ener:

(Supported Backend: TensorFlow)

models:

type: dict | list

argument path: model[linear_ener]/models

The sub-models.

weights:

type: list | str

argument path: model[linear_ener]/weights

If the type is list of float, a list of weights for each model. If “mean”, the weights are set to be 1 / len(models). If “sum”, the weights are set to be 1.

learning_rate:

type: dict, optional

argument path: learning_rate

The definitio of learning rate

scale_by_worker:

type: str, optional, default: linear

argument path: learning_rate/scale_by_worker

When parallel training or batch size scaled, how to alter learning rate. Valid values are linear`(default), `sqrt or none.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key), default: exp

argument path: learning_rate/type

possible choices: exp

The type of the learning rate.

When type is set to exp:

start_lr:

type: float, optional, default: 0.001

argument path: learning_rate[exp]/start_lr

The learning rate at the start of the training.

stop_lr:

type: float, optional, default: 1e-08

argument path: learning_rate[exp]/stop_lr

The desired learning rate at the end of the training. When decay_rate (Supported Backend: PyTorch) is explicitly set, this value will serve as the minimum learning rate during training. In other words, if the learning rate decays below stop_lr, stop_lr will be applied instead.

decay_steps:

type: int, optional, default: 5000

argument path: learning_rate[exp]/decay_steps

The learning rate is decaying every this number of training steps.

decay_rate:

type: float | NoneType, optional, default: None

argument path: learning_rate[exp]/decay_rate

(Supported Backend: PyTorch) The decay rate for the learning rate. If this is provided, it will be used directly as the decay rate for learning rate instead of calculating it through interpolation between start_lr and stop_lr.

loss:

type: dict, optional

argument path: loss

The definition of loss function. The loss type should be set to tensor, ener or left unset.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key), default: ener

argument path: loss/type

possible choices: ener, ener_spin, dos, tensor

The type of the loss. When the fitting type is ener, the loss type should be set to ener or left unset. When the fitting type is dipole or polar, the loss type should be set to tensor.

When type is set to ener:

start_pref_e:

type: float | int, optional, default: 0.02

argument path: loss[ener]/start_pref_e

The prefactor of energy loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the energy label should be provided by file energy.npy in each data system. If both start_pref_e and limit_pref_e are set to 0, then the energy will be ignored.

limit_pref_e:

type: float | int, optional, default: 1.0

argument path: loss[ener]/limit_pref_e

The prefactor of energy loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_f:

type: float | int, optional, default: 1000

argument path: loss[ener]/start_pref_f

The prefactor of force loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the force label should be provided by file force.npy in each data system. If both start_pref_f and limit_pref_f are set to 0, then the force will be ignored.

limit_pref_f:

type: float | int, optional, default: 1.0

argument path: loss[ener]/limit_pref_f

The prefactor of force loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_v:

type: float | int, optional, default: 0.0

argument path: loss[ener]/start_pref_v

The prefactor of virial loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the virial label should be provided by file virial.npy in each data system. If both start_pref_v and limit_pref_v are set to 0, then the virial will be ignored.

limit_pref_v:

type: float | int, optional, default: 0.0

argument path: loss[ener]/limit_pref_v

The prefactor of virial loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_ae:

type: float | int, optional, default: 0.0

argument path: loss[ener]/start_pref_ae

The prefactor of atomic energy loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the atom_ener label should be provided by file atom_ener.npy in each data system. If both start_pref_ae and limit_pref_ae are set to 0, then the atomic energy will be ignored.

limit_pref_ae:

type: float | int, optional, default: 0.0

argument path: loss[ener]/limit_pref_ae

The prefactor of atomic energy loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_pf:

type: float | int, optional, default: 0.0

argument path: loss[ener]/start_pref_pf

The prefactor of atomic prefactor force loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the atom_pref label should be provided by file atom_pref.npy in each data system. If both start_pref_pf and limit_pref_pf are set to 0, then the atomic prefactor force will be ignored.

limit_pref_pf:

type: float | int, optional, default: 0.0

argument path: loss[ener]/limit_pref_pf

The prefactor of atomic prefactor force loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

relative_f:

type: float | NoneType, optional

argument path: loss[ener]/relative_f

If provided, relative force error will be used in the loss. The difference of force will be normalized by the magnitude of the force in the label with a shift given by relative_f, i.e. DF_i / ( || F || + relative_f ) with DF denoting the difference between prediction and label and || F || denoting the L2 norm of the label.

enable_atom_ener_coeff:

type: bool, optional, default: False

argument path: loss[ener]/enable_atom_ener_coeff

If true, the energy will be computed as sum_i c_i E_i. c_i should be provided by file atom_ener_coeff.npy in each data system, otherwise it’s 1.

start_pref_gf:

type: float, optional, default: 0.0

argument path: loss[ener]/start_pref_gf

The prefactor of generalized force loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the drdq label should be provided by file drdq.npy in each data system. If both start_pref_gf and limit_pref_gf are set to 0, then the generalized force will be ignored.

limit_pref_gf:

type: float, optional, default: 0.0

argument path: loss[ener]/limit_pref_gf

The prefactor of generalized force loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

numb_generalized_coord:

type: int, optional, default: 0

argument path: loss[ener]/numb_generalized_coord

The dimension of generalized coordinates. Required when generalized force loss is used.

When type is set to ener_spin:

start_pref_e:

type: float | int, optional, default: 0.02

argument path: loss[ener_spin]/start_pref_e

The prefactor of energy loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the energy label should be provided by file energy.npy in each data system. If both start_pref_energy and limit_pref_energy are set to 0, then the energy will be ignored.

limit_pref_e:

type: float | int, optional, default: 1.0

argument path: loss[ener_spin]/limit_pref_e

The prefactor of energy loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_fr:

type: float | int, optional, default: 1000

argument path: loss[ener_spin]/start_pref_fr

The prefactor of force_real_atom loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the force_real_atom label should be provided by file force_real_atom.npy in each data system. If both start_pref_force_real_atom and limit_pref_force_real_atom are set to 0, then the force_real_atom will be ignored.

limit_pref_fr:

type: float | int, optional, default: 1.0

argument path: loss[ener_spin]/limit_pref_fr

The prefactor of force_real_atom loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_fm:

type: float | int, optional, default: 10000

argument path: loss[ener_spin]/start_pref_fm

The prefactor of force_magnetic loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the force_magnetic label should be provided by file force_magnetic.npy in each data system. If both start_pref_force_magnetic and limit_pref_force_magnetic are set to 0, then the force_magnetic will be ignored.

limit_pref_fm:

type: float | int, optional, default: 10.0

argument path: loss[ener_spin]/limit_pref_fm

The prefactor of force_magnetic loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_v:

type: float | int, optional, default: 0.0

argument path: loss[ener_spin]/start_pref_v

The prefactor of virial loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the virial label should be provided by file virial.npy in each data system. If both start_pref_virial and limit_pref_virial are set to 0, then the virial will be ignored.

limit_pref_v:

type: float | int, optional, default: 0.0

argument path: loss[ener_spin]/limit_pref_v

The prefactor of virial loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_ae:

type: float | int, optional, default: 0.0

argument path: loss[ener_spin]/start_pref_ae

The prefactor of atom_ener loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the atom_ener label should be provided by file atom_ener.npy in each data system. If both start_pref_atom_ener and limit_pref_atom_ener are set to 0, then the atom_ener will be ignored.

limit_pref_ae:

type: float | int, optional, default: 0.0

argument path: loss[ener_spin]/limit_pref_ae

The prefactor of atom_ener loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_pf:

type: float | int, optional, default: 0.0

argument path: loss[ener_spin]/start_pref_pf

The prefactor of atom_pref loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the atom_pref label should be provided by file atom_pref.npy in each data system. If both start_pref_atom_pref and limit_pref_atom_pref are set to 0, then the atom_pref will be ignored.

limit_pref_pf:

type: float | int, optional, default: 0.0

argument path: loss[ener_spin]/limit_pref_pf

The prefactor of atom_pref loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

relative_f:

type: float | NoneType, optional

argument path: loss[ener_spin]/relative_f

If provided, relative force error will be used in the loss. The difference of force will be normalized by the magnitude of the force in the label with a shift given by relative_f, i.e. DF_i / ( || F || + relative_f ) with DF denoting the difference between prediction and label and || F || denoting the L2 norm of the label.

enable_atom_ener_coeff:

type: bool, optional, default: False

argument path: loss[ener_spin]/enable_atom_ener_coeff

If true, the energy will be computed as sum_i c_i E_i. c_i should be provided by file atom_ener_coeff.npy in each data system, otherwise it’s 1.

When type is set to dos:

start_pref_dos:

type: float | int, optional, default: 0.0

argument path: loss[dos]/start_pref_dos

The prefactor of Density of State (DOS) loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the Density of State (DOS) label should be provided by file Density of State (DOS).npy in each data system. If both start_pref_Density of State (DOS) and limit_pref_Density of State (DOS) are set to 0, then the Density of State (DOS) will be ignored.

limit_pref_dos:

type: float | int, optional, default: 0.0

argument path: loss[dos]/limit_pref_dos

The prefactor of Density of State (DOS) loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_cdf:

type: float | int, optional, default: 0.0

argument path: loss[dos]/start_pref_cdf

The prefactor of Cumulative Distribution Function (cumulative intergral of DOS) loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the Cumulative Distribution Function (cumulative intergral of DOS) label should be provided by file Cumulative Distribution Function (cumulative intergral of DOS).npy in each data system. If both start_pref_Cumulative Distribution Function (cumulative intergral of DOS) and limit_pref_Cumulative Distribution Function (cumulative intergral of DOS) are set to 0, then the Cumulative Distribution Function (cumulative intergral of DOS) will be ignored.

limit_pref_cdf:

type: float | int, optional, default: 0.0

argument path: loss[dos]/limit_pref_cdf

The prefactor of Cumulative Distribution Function (cumulative intergral of DOS) loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_ados:

type: float | int, optional, default: 1.0

argument path: loss[dos]/start_pref_ados

The prefactor of atomic DOS (site-projected DOS) loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the atomic DOS (site-projected DOS) label should be provided by file atomic DOS (site-projected DOS).npy in each data system. If both start_pref_atomic DOS (site-projected DOS) and limit_pref_atomic DOS (site-projected DOS) are set to 0, then the atomic DOS (site-projected DOS) will be ignored.

limit_pref_ados:

type: float | int, optional, default: 1.0

argument path: loss[dos]/limit_pref_ados

The prefactor of atomic DOS (site-projected DOS) loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_acdf:

type: float | int, optional, default: 0.0

argument path: loss[dos]/start_pref_acdf

The prefactor of Cumulative integral of atomic DOS loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the Cumulative integral of atomic DOS label should be provided by file Cumulative integral of atomic DOS.npy in each data system. If both start_pref_Cumulative integral of atomic DOS and limit_pref_Cumulative integral of atomic DOS are set to 0, then the Cumulative integral of atomic DOS will be ignored.

limit_pref_acdf:

type: float | int, optional, default: 0.0

argument path: loss[dos]/limit_pref_acdf

The prefactor of Cumulative integral of atomic DOS loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

When type is set to tensor:

pref:

type: float | int

argument path: loss[tensor]/pref

The prefactor of the weight of global loss. It should be larger than or equal to 0. If controls the weight of loss corresponding to global label, i.e. ‘polarizability.npy` or dipole.npy, whose shape should be #frames x [9 or 3]. If it’s larger than 0.0, this npy should be included.

pref_atomic:

type: float | int

argument path: loss[tensor]/pref_atomic

The prefactor of the weight of atomic loss. It should be larger than or equal to 0. If controls the weight of loss corresponding to atomic label, i.e. atomic_polarizability.npy or atomic_dipole.npy, whose shape should be #frames x ([9 or 3] x #selected atoms). If it’s larger than 0.0, this npy should be included. Both pref and pref_atomic should be provided, and either can be set to 0.0.

training:

type: dict

argument path: training

The training options.

training_data:

type: dict, optional

argument path: training/training_data

Configurations of training data.

systems:

type: typing.List[str] | str

argument path: training/training_data/systems

The data systems for training. This key can be provided with a list that specifies the systems, or be provided with a string by which the prefix of all systems are given and the list of the systems is automatically generated.

batch_size:

type: typing.List[int] | str | int, optional, default: auto

argument path: training/training_data/batch_size

This key can be

• list: the length of which is the same as the systems. The batch size of each system is given by the elements of the list.

• int: all systems use the same batch size.

• string “auto”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than 32.

• string “auto:N”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than N.

• string “mixed:N”: the batch data will be sampled from all systems and merged into a mixed system with the batch size N. Only support the se_atten descriptor for Tensorflow backend.

If MPI is used, the value should be considered as the batch size per task.

auto_prob:

type: str, optional, default: prob_sys_size, alias: auto_prob_style

argument path: training/training_data/auto_prob

Determine the probability of systems automatically. The method is assigned by this key and can be

• “prob_uniform” : the probability all the systems are equal, namely 1.0/self.get_nsystems()

• “prob_sys_size” : the probability of a system is proportional to the number of batches in the system

• “prob_sys_size;stt_idx:end_idx:weight;stt_idx:end_idx:weight;…” : the list of systems is devided into blocks. A block is specified by stt_idx:end_idx:weight, where stt_idx is the starting index of the system, end_idx is then ending (not including) index of the system, the probabilities of the systems in this block sums up to weight, and the relatively probabilities within this block is proportional to the number of batches in the system.

sys_probs:

type: NoneType | typing.List[float], optional, default: None, alias: sys_weights

argument path: training/training_data/sys_probs

A list of float if specified. Should be of the same length as systems, specifying the probability of each system.

validation_data:

type: NoneType | dict, optional, default: None

argument path: training/validation_data

Configurations of validation data. Similar to that of training data, except that a numb_btch argument may be configured

systems:

type: typing.List[str] | str

argument path: training/validation_data/systems

The data systems for validation. This key can be provided with a list that specifies the systems, or be provided with a string by which the prefix of all systems are given and the list of the systems is automatically generated.

batch_size:

type: typing.List[int] | str | int, optional, default: auto

argument path: training/validation_data/batch_size

This key can be

• list: the length of which is the same as the systems. The batch size of each system is given by the elements of the list.

• int: all systems use the same batch size.

• string “auto”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than 32.

• string “auto:N”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than N.

auto_prob:

type: str, optional, default: prob_sys_size, alias: auto_prob_style

argument path: training/validation_data/auto_prob

Determine the probability of systems automatically. The method is assigned by this key and can be

• “prob_uniform” : the probability all the systems are equal, namely 1.0/self.get_nsystems()

• “prob_sys_size” : the probability of a system is proportional to the number of batches in the system

• “prob_sys_size;stt_idx:end_idx:weight;stt_idx:end_idx:weight;…” : the list of systems is devided into blocks. A block is specified by stt_idx:end_idx:weight, where stt_idx is the starting index of the system, end_idx is then ending (not including) index of the system, the probabilities of the systems in this block sums up to weight, and the relatively probabilities within this block is proportional to the number of batches in the system.

sys_probs:

type: NoneType | typing.List[float], optional, default: None, alias: sys_weights

argument path: training/validation_data/sys_probs

A list of float if specified. Should be of the same length as systems, specifying the probability of each system.

numb_btch:

type: int, optional, default: 1, alias: numb_batch

argument path: training/validation_data/numb_btch

An integer that specifies the number of batches to be sampled for each validation period.

stat_file:

type: str, optional

argument path: training/stat_file

(Supported Backend: PyTorch) The file path for saving the data statistics results. If set, the results will be saved and directly loaded during the next training session, avoiding the need to recalculate the statistics. If the file extension is .h5 or .hdf5, an HDF5 file is used to store the statistics; otherwise, a directory containing NumPy binary files are used.

mixed_precision:

type: dict, optional

argument path: training/mixed_precision

Configurations of mixed precision.

output_prec:

type: str, optional, default: float32

argument path: training/mixed_precision/output_prec

The precision for mixed precision params. “ “The trainable variables precision during the mixed precision training process, “ “supported options are float32 only currently.

compute_prec:

type: str

argument path: training/mixed_precision/compute_prec

The precision for mixed precision compute. “ “The compute precision during the mixed precision training process, “” “supported options are float16 and bfloat16 currently.

numb_steps:

type: int, alias: stop_batch

argument path: training/numb_steps

Number of training batch. Each training uses one batch of data.

seed:

type: NoneType | int, optional

argument path: training/seed

The random seed for getting frames from the training data set.

disp_file:

type: str, optional, default: lcurve.out

argument path: training/disp_file

The file for printing learning curve.

disp_freq:

type: int, optional, default: 1000

argument path: training/disp_freq

The frequency of printing learning curve.

save_freq:

type: int, optional, default: 1000

argument path: training/save_freq

The frequency of saving check point.

save_ckpt:

type: str, optional, default: model.ckpt

argument path: training/save_ckpt

The path prefix of saving check point files.

max_ckpt_keep:

type: int, optional, default: 5

argument path: training/max_ckpt_keep

The maximum number of checkpoints to keep. The oldest checkpoints will be deleted once the number of checkpoints exceeds max_ckpt_keep. Defaults to 5.

change_bias_after_training:

type: bool, optional, default: False

argument path: training/change_bias_after_training

Whether to change the output bias after the last training step, by performing predictions using trained model on training data and doing least square on the errors to add the target shift on the bias.

disp_training:

type: bool, optional, default: True

argument path: training/disp_training

Displaying verbose information during training.

time_training:

type: bool, optional, default: True

argument path: training/time_training

Timing durining training.

profiling:

type: bool, optional, default: False

argument path: training/profiling

Export the profiling results to the Chrome JSON file for performance analysis, driven by the legacy TensorFlow profiling API or PyTorch Profiler. The output file will be saved to profiling_file.

profiling_file:

type: str, optional, default: timeline.json

argument path: training/profiling_file

Output file for profiling.

enable_profiler:

type: bool, optional, default: False

argument path: training/enable_profiler

Export the profiling results to the TensorBoard log for performance analysis, driven by TensorFlow Profiler (available in TensorFlow 2.3) or PyTorch Profiler. The log will be saved to tensorboard_log_dir.

tensorboard:

type: bool, optional, default: False

argument path: training/tensorboard

Enable tensorboard

tensorboard_log_dir:

type: str, optional, default: log

argument path: training/tensorboard_log_dir

The log directory of tensorboard outputs

tensorboard_freq:

type: int, optional, default: 1

argument path: training/tensorboard_freq

The frequency of writing tensorboard events.

warmup_steps:

type: int, optional

argument path: training/warmup_steps

(Supported Backend: PyTorch) The number of steps for learning rate warmup. During warmup, the learning rate begins at zero and progressively increases linearly to start_lr, rather than starting directly from start_lr

gradient_max_norm:

type: float, optional

argument path: training/gradient_max_norm

(Supported Backend: PyTorch) Clips the gradient norm to a maximum value. If the gradient norm exceeds this value, it will be clipped to this limit. No gradient clipping will occur if set to 0.

Depending on the value of opt_type, different sub args are accepted.

opt_type:

type: str (flag key), default: Adam

argument path: training/opt_type

possible choices: Adam, LKF

(Supported Backend: PyTorch) The type of optimizer to use.

When opt_type is set to Adam:

When opt_type is set to LKF:

kf_blocksize:

type: int, optional

argument path: training[LKF]/kf_blocksize

(Supported Backend: PyTorch) The blocksize for the Kalman filter.

nvnmd:

type: dict, optional

argument path: nvnmd

The nvnmd options.

version:

type: int

argument path: nvnmd/version

configuration the nvnmd version (0 | 1), 0 for 4 types, 1 for 32 types

max_nnei:

type: int

argument path: nvnmd/max_nnei

configuration the max number of neighbors, 128|256 for version 0, 128 for version 1

net_size:

type: int

argument path: nvnmd/net_size

configuration the number of nodes of fitting_net, just can be set as 128

map_file:

type: str

argument path: nvnmd/map_file

A file containing the mapping tables to replace the calculation of embedding nets

config_file:

type: str

argument path: nvnmd/config_file

A file containing the parameters about how to implement the model in certain hardware

weight_file:

type: str

argument path: nvnmd/weight_file

a *.npy file containing the weights of the model

enable:

type: bool

argument path: nvnmd/enable

enable the nvnmd training

restore_descriptor:

type: bool

argument path: nvnmd/restore_descriptor

enable to restore the parameter of embedding_net from weight.npy

restore_fitting_net:

type: bool

argument path: nvnmd/restore_fitting_net

enable to restore the parameter of fitting_net from weight.npy

quantize_descriptor:

type: bool

argument path: nvnmd/quantize_descriptor

enable the quantizatioin of descriptor

quantize_fitting_net:

type: bool

argument path: nvnmd/quantize_fitting_net

enable the quantizatioin of fitting_net

5.3.1. Writing JSON files using Visual Studio Code

When writing JSON files using Visual Studio Code, one can benefit from IntelliSense and validation by adding a JSON schema. To do so, in a VS Code workspace, one can generate a JSON schema file for the input file by running the following command:

dp doc-train-input --out-type json_schema > deepmd.json

Then one can map the schema by updating the workspace settings in the .vscode/settings.json file as follows:

{
   "json.schemas": [
      {
            "fileMatch": [
               "/**/*.json"
            ],
            "url": "./deepmd.json"
      }
   ]
}