train-input-auto.rst

model:

type: dict

argument path: model

type_map:

type: list, 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.

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.

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.

type_embedding:

type: dict, optional

argument path: model/type_embedding

The type embedding.

neuron:

type: list, optional, default: [2, 4, 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", "relu6", "softplus", "sigmoid", "tanh", "gelu".

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: float64

argument path: model/type_embedding/precision

The precision of the embedding net parameters, supported options are "default", "float16", "float32", "float64".

trainable:

type: bool, optional, default: True

argument path: model/type_embedding/trainable

If the parameters in the embedding net are trainable

seed:

type: int | NoneType, optional

argument path: model/type_embedding/seed

Random seed for parameter initialization

descriptor:

type: dict

argument path: model/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/descriptor/type

possible choices: loc_frame, se_e2_a, se_e2_r, se_e3, se_a_tpe, hybrid

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

When type is set to loc_frame:

sel_a:

type: list

argument path: model/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: list

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

The cut-off radius. The default value is 6.0

axis_rule:

type: list

argument path: model/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 first 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]: 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.

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

sel:

type: list | str, optional, default: auto

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

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model/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: list, optional, default: [10, 20, 40]

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

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model/descriptor[se_e2_a]/activation_function

The activation function in the embedding net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

resnet_dt:

type: bool, optional, default: False

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

Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets

precision:

type: str, optional, default: float64

argument path: model/descriptor[se_e2_a]/precision

The precision of the embedding net parameters, supported options are "default", "float16", "float32", "float64".

trainable:

type: bool, optional, default: True

argument path: model/descriptor[se_e2_a]/trainable

If the parameters in the embedding net is trainable

seed:

type: int | NoneType, optional

argument path: model/descriptor[se_e2_a]/seed

Random seed for parameter initialization

exclude_types:

type: list, optional, default: []

argument path: model/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.

set_davg_zero:

type: bool, optional, default: False

argument path: model/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_e2_r (or its alias se_r):

sel:

type: list | str, optional, default: auto

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

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model/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: list, optional, default: [10, 20, 40]

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

The activation function in the embedding net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

resnet_dt:

type: bool, optional, default: False

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

Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets

precision:

type: str, optional, default: float64

argument path: model/descriptor[se_e2_r]/precision

The precision of the embedding net parameters, supported options are "default", "float16", "float32", "float64".

trainable:

type: bool, optional, default: True

argument path: model/descriptor[se_e2_r]/trainable

If the parameters in the embedding net are trainable

seed:

type: int | NoneType, optional

argument path: model/descriptor[se_e2_r]/seed

Random seed for parameter initialization

exclude_types:

type: list, optional, default: []

argument path: model/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/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

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

sel:

type: list | str, optional, default: auto

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

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model/descriptor[se_e3]/rcut_smth

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

neuron:

type: list, optional, default: [10, 20, 40]

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

The activation function in the embedding net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

resnet_dt:

type: bool, optional, default: False

argument path: model/descriptor[se_e3]/resnet_dt

Whether to use a "Timestep" in the skip connection

precision:

type: str, optional, default: float64

argument path: model/descriptor[se_e3]/precision

The precision of the embedding net parameters, supported options are "default", "float16", "float32", "float64".

trainable:

type: bool, optional, default: True

argument path: model/descriptor[se_e3]/trainable

If the parameters in the embedding net are trainable

seed:

type: int | NoneType, optional

argument path: model/descriptor[se_e3]/seed

Random seed for parameter initialization

set_davg_zero:

type: bool, optional, default: False

argument path: model/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

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

sel:

type: list | str, optional, default: auto

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

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model/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: list, optional, default: [10, 20, 40]

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

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model/descriptor[se_a_tpe]/activation_function

The activation function in the embedding net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

resnet_dt:

type: bool, optional, default: False

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

Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets

precision:

type: str, optional, default: float64

argument path: model/descriptor[se_a_tpe]/precision

The precision of the embedding net parameters, supported options are "default", "float16", "float32", "float64".

trainable:

type: bool, optional, default: True

argument path: model/descriptor[se_a_tpe]/trainable

If the parameters in the embedding net is trainable

seed:

type: int | NoneType, optional

argument path: model/descriptor[se_a_tpe]/seed

Random seed for parameter initialization

exclude_types:

type: list, optional, default: []

argument path: model/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.

set_davg_zero:

type: bool, optional, default: False

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

number of channels for type embedding

type_nlayer:

type: int, optional, default: 2

argument path: model/descriptor[se_a_tpe]/type_nlayer

number of hidden layers of type embedding net

numb_aparam:

type: int, optional, default: 0

argument path: model/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 hybrid:

list:

type: list

argument path: model/descriptor[hybrid]/list

A list of descriptor definitions

fitting_net:

type: dict

argument path: model/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/fitting_net/type

possible choices: ener, dipole, polar

The type of the fitting. See explanation below.

• ener: Fit an energy model (potential energy surface).
• 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/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/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: list, optional, default: [120, 120, 120], alias: n_neuron

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

The activation function in the fitting net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

precision:

type: str, optional, default: float64

argument path: model/fitting_net[ener]/precision

The precision of the fitting net parameters, supported options are "default", "float16", "float32", "float64".

resnet_dt:

type: bool, optional, default: True

argument path: model/fitting_net[ener]/resnet_dt

Whether to use a "Timestep" in the skip connection

trainable:

type: list | bool, optional, default: True

argument path: model/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: 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, optional, default: 0.001

argument path: model/fitting_net[ener]/rcond

The condition number used to determine the inital energy shift for each type of atoms.

seed:

type: int | NoneType, optional

argument path: model/fitting_net[ener]/seed

Random seed for parameter initialization of the fitting net

atom_ener:

type: list, optional, default: []

argument path: model/fitting_net[ener]/atom_ener

Specify the atomic energy in vacuum for each type

When type is set to dipole:

neuron:

type: list, optional, default: [120, 120, 120], alias: n_neuron

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

The activation function in the fitting net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

resnet_dt:

type: bool, optional, default: True

argument path: model/fitting_net[dipole]/resnet_dt

Whether to use a "Timestep" in the skip connection

precision:

type: str, optional, default: float64

argument path: model/fitting_net[dipole]/precision

The precision of the fitting net parameters, supported options are "default", "float16", "float32", "float64".

sel_type:

type: list | int | NoneType, optional, alias: dipole_type

argument path: model/fitting_net[dipole]/sel_type

The atom types for which the atomic dipole will be provided. If not set, all types will be selected.

seed:

type: int | NoneType, optional

argument path: model/fitting_net[dipole]/seed

Random seed for parameter initialization of the fitting net

When type is set to polar:

neuron:

type: list, optional, default: [120, 120, 120], alias: n_neuron

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

The activation function in the fitting net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".

resnet_dt:

type: bool, optional, default: True

argument path: model/fitting_net[polar]/resnet_dt

Whether to use a "Timestep" in the skip connection

precision:

type: str, optional, default: float64

argument path: model/fitting_net[polar]/precision

The precision of the fitting net parameters, supported options are "default", "float16", "float32", "float64".

fit_diag:

type: bool, optional, default: True

argument path: model/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 | list, optional, default: 1.0

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

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

sel_type:

type: list | int | NoneType, optional, alias: pol_type

argument path: model/fitting_net[polar]/sel_type

The atom types for which the atomic polarizability will be provided. If not set, all types will be selected.

seed:

type: int | NoneType, optional

argument path: model/fitting_net[polar]/seed

Random seed for parameter initialization of the fitting net

modifier:

type: dict, optional

argument path: model/modifier

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: list

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.

sys_charge_map:

type: list

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

Model compression configurations

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

type:

type: str (flag key), default: se_e2_a

argument path: model/compress/type

possible choices: se_e2_a

The type of model compression, which should be consistent with the descriptor type.

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

compress:

type: bool

argument path: model/compress[se_e2_a]/compress

The name of the frozen model file.

model_file:

type: str

argument path: model/compress[se_e2_a]/model_file

The input model file, which will be compressed by the DeePMD-kit.

table_config:

type: list

argument path: model/compress[se_e2_a]/table_config

The arguments of model compression, including extrapolate(scale of model extrapolation), stride(uniform stride of tabulation's first and second table), and frequency(frequency of tabulation overflow check).

min_nbor_dist:

type: float

argument path: model/compress[se_e2_a]/min_nbor_dist

The nearest distance between neighbor atoms saved in the frozen model.

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, 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_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]/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_force and limit_pref_force 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_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]/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 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]/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.

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.

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.

learning_rate:

type: dict

argument path: learning_rate

The definitio of learning rate

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 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.

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.

training:

type: dict

argument path: training

The training options.

training_data:

type: dict

argument path: training/training_data

Configurations of training data.

systems:

type: list | 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.

set_prefix:

type: str, optional, default: set

argument path: training/training_data/set_prefix

The prefix of the sets in the systems.

batch_size:

type: list | int | str, 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.

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: list | NoneType, 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: dict | NoneType, 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: list | 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.

set_prefix:

type: str, optional, default: set

argument path: training/validation_data/set_prefix

The prefix of the sets in the systems.

batch_size:

type: list | int | str, 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: list | NoneType, 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 systems to be sampled for each validation period.

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: int | NoneType, 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.

numb_test:

type: list | int | str, optional, default: 1

argument path: training/numb_test

Number of frames used for the test during training.

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 file name of saving check point.

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

Profiling during training.

profiling_file:

type: str, optional, default: timeline.json

argument path: training/profiling_file

Output file for profiling.

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.