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.

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.

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.

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

The type of the descritpor. Valid types are loc_frame, se_a, se_r and se_ar.

• loc_frame: Defines a local frame at each atom, and the compute the descriptor as local coordinates under this frame.
• se_a: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor.
• se_r: Used by the smooth edition of Deep Potential. Only the distance between atoms is used to construct the descriptor.
• se_ar: A hybrid of se_a and se_r. Typically se_a has a smaller cut-off while the se_r has a larger cut-off.

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_a:

sel:

type: list

argument path: model/descriptor[se_a]/sel

A list of integers. 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.

rcut:

type: float, optional, default: 6.0

argument path: model/descriptor[se_a]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model/descriptor[se_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_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

argument path: model/descriptor[se_a]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:

type: str, optional, default: tanh

argument path: model/descriptor[se_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_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_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_a]/precision

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

trainable:

type: bool, optional, default: True

argument path: model/descriptor[se_a]/trainable

If the parameters in the embedding net is trainable

seed:

type: int | NoneType, optional

argument path: model/descriptor[se_a]/seed

Random seed for parameter initialization

exclude_types:

type: list, optional, default: []

argument path: model/descriptor[se_a]/exclude_types

The Excluded types

set_davg_zero:

type: bool, optional, default: False

argument path: model/descriptor[se_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_r:

sel:

type: list

argument path: model/descriptor[se_r]/sel

A list of integers. 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.

rcut:

type: float, optional, default: 6.0

argument path: model/descriptor[se_r]/rcut

The cut-off radius.

rcut_smth:

type: float, optional, default: 0.5

argument path: model/descriptor[se_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_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_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_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_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_r]/precision

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

trainable:

type: bool, optional, default: True

argument path: model/descriptor[se_r]/trainable

If the parameters in the embedding net is trainable

seed:

type: int | NoneType, optional

argument path: model/descriptor[se_r]/seed

Random seed for parameter initialization

exclude_types:

type: list, optional, default: []

argument path: model/descriptor[se_r]/exclude_types

The Excluded types

set_davg_zero:

type: bool, optional, default: False

argument path: model/descriptor[se_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_ar:

a:

type: dict

argument path: model/descriptor[se_ar]/a

The parameters of descriptor se_a

r:

type: dict

argument path: model/descriptor[se_ar]/r

The parameters of descriptor se_r

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

The type of the fitting. Valid types are ener, dipole, polar and global_polar.

• ener: Fit an energy model (potential energy surface).
• dipole: Fit an atomic dipole model. Atomic dipole labels for all the selected atoms (see sel_type) should be provided by dipole.npy in each data system. The file has number of frames lines and 3 times of number of selected atoms columns.
• polar: Fit an atomic polarizability model. Atomic polarizability labels for all the selected atoms (see sel_type) should be provided by polarizability.npy in each data system. The file has number of frames lines and 9 times of number of selected atoms columns.
• global_polar: Fit a polarizability model. Polarizability labels should be provided by polarizability.npy in each data system. The file has number of frames lines and 9 columns.

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]

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 "float64", "float32", "float16".

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: bool | list, 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]

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 "float64", "float32", "float16".

sel_type:

type: int | NoneType | list, optional

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]

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 "float64", "float32", "float16".

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

diag_shift:

type: float | list, optional, default: 0.0

argument path: model/fitting_net[polar]/diag_shift

The diagonal part of the polarizability matrix will be shifted by diag_shift. The shift operation is carried out after scale.

sel_type:

type: int | NoneType | list, optional

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

When type is set to global_polar:

neuron:

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

argument path: model/fitting_net[global_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[global_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[global_polar]/resnet_dt

Whether to use a "Timestep" in the skip connection

precision:

type: str, optional, default: float64

argument path: model/fitting_net[global_polar]/precision

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

fit_diag:

type: bool, optional, default: True

argument path: model/fitting_net[global_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[global_polar]/scale

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

diag_shift:

type: float | list, optional, default: 0.0

argument path: model/fitting_net[global_polar]/diag_shift

The diagonal part of the polarizability matrix will be shifted by diag_shift. The shift operation is carried out after scale.

sel_type:

type: int | NoneType | list, optional

argument path: model/fitting_net[global_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[global_polar]/seed

Random seed for parameter initialization of the fitting net

loss:

type: dict

argument path: loss

The definition of loss function. The type of the loss depends on the type of the fitting. For fitting type ener, the prefactors before energy, force, virial and atomic energy losses may be provided. For fitting type dipole, polar and global_polar, the loss may be an empty dict or unset.

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

type:

type: str (flag key), default: ener

argument path: loss/type

The type of the loss. For fitting type ener, the loss type should be set to ener or left unset. For tensorial fitting types dipole, polar and global_polar, the type should be left unset. .

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 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_ae:

type: float | int, optional, default: 0.0

argument path: loss[ener]/limit_pref_ae

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.

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.

learning_rate:

type: dict

argument path: learning_rate

The learning rate options

start_lr:

type: float, optional, default: 0.001

argument path: learning_rate/start_lr

The learning rate the start of the training.

stop_lr:

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

argument path: learning_rate/stop_lr

The desired learning rate at the end of the training.

decay_steps:

type: int, optional, default: 5000

argument path: learning_rate/decay_steps

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

training:

type: dict

argument path: training

The training options

systems:

type: list | str

argument path: training/systems

The data systems. This key can be provided with a listthat 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/set_prefix

The prefix of the sets in the systems.

stop_batch:

type: int

argument path: training/stop_batch

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

batch_size:

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

argument path: training/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 uses the same batch size.
• string "auto": automatically determines the batch size os 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 os that the batch_size times the number of atoms in the system is no less than N.

seed:

type: int | NoneType, optional

argument path: training/seed

The random seed for training.

disp_file:

type: str, optional, default: lcueve.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: int | list | 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.