deepmd.descriptor package

Submodules

deepmd.descriptor.descriptor module

class deepmd.descriptor.descriptor.Descriptor(*args, **kwargs)[source]

Bases: deepmd.utils.plugin.PluginVariant

The abstract class for descriptors. All specific descriptors should be based on this class.

The descriptor \(\mathcal{D}\) describes the environment of an atom, which should be a function of coordinates and types of its neighbour atoms.

Notes

Only methods and attributes defined in this class are generally public, that can be called by other classes.

Examples

>>> descript = Descriptor(type="se_e2_a", rcut=6., rcut_smth=0.5, sel=[50])
>>> type(descript)
<class 'deepmd.descriptor.se_a.DescrptSeA'>

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor.

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor.

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns neighbor information.

get_ntypes()

Returns the number of atom types.

get_rcut()

Returns the cut-off radius.

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given dict

pass_tensors_from_frz_model(*tensors)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial.

register(key)

Regiester a descriptor plugin.

abstract build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: Dict[str, Any], reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor.

Parameters
coord_tf.Tensor

The coordinate of atoms

atype_tf.Tensor

The type of atoms

natomstf.Tensor

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

boxtf.Tensor

The box of frames

meshtf.Tensor

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dictdict[str, Any]

Dictionary for additional inputs

reusebool, optional

The weights in the networks should be reused when get the variable.

suffixstr, optional

Name suffix to identify this descriptor

Returns
descriptor: tf.Tensor

The output descriptor

Notes

This method must be implemented, as it’s called by other classes.

abstract compute_input_stats(data_coord: List[numpy.ndarray], data_box: List[numpy.ndarray], data_atype: List[numpy.ndarray], natoms_vec: List[numpy.ndarray], mesh: List[numpy.ndarray], input_dict: Dict[str, List[numpy.ndarray]]) None[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coordlist[np.ndarray]

The coordinates. Can be generated by deepmd.model.model_stat.make_stat_input()

data_boxlist[np.ndarray]

The box. Can be generated by deepmd.model.model_stat.make_stat_input()

data_atypelist[np.ndarray]

The atom types. Can be generated by deepmd.model.model_stat.make_stat_input()

natoms_veclist[np.ndarray]

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.model_stat.make_stat_input()

meshlist[np.ndarray]

The mesh for neighbor searching. Can be generated by deepmd.model.model_stat.make_stat_input()

input_dictdict[str, list[np.ndarray]]

Dictionary for additional input

Notes

This method must be implemented, as it’s called by other classes.

enable_compression(min_nbor_dist: float, model_file: str = 'frozon_model.pb', table_extrapolate: float = 5.0, table_stride_1: float = 0.01, table_stride_2: float = 0.1, check_frequency: int = - 1, suffix: str = '') None[source]

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

Parameters
min_nbor_distfloat

The nearest distance between atoms

model_filestr, default: ‘frozon_model.pb’

The original frozen model, which will be compressed by the program

table_extrapolatefloat, default: 5.

The scale of model extrapolation

table_stride_1float, default: 0.01

The uniform stride of the first table

table_stride_2float, default: 0.1

The uniform stride of the second table

check_frequencyint, default: -1

The overflow check frequency

suffixstr, optional

The suffix of the scope

Notes

This method is called by others when the descriptor supported compression.

enable_mixed_precision(mixed_prec: Optional[dict] = None) None[source]

Reveive the mixed precision setting.

Parameters
mixed_prec

The mixed precision setting used in the embedding net

Notes

This method is called by others when the descriptor supported compression.

abstract get_dim_out() int[source]

Returns the output dimension of this descriptor.

Returns
int

the output dimension of this descriptor

Notes

This method must be implemented, as it’s called by other classes.

get_dim_rot_mat_1() int[source]

Returns the first dimension of the rotation matrix. The rotation is of shape dim_1 x 3

Returns
int

the first dimension of the rotation matrix

get_feed_dict(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor) Dict[str, tensorflow.python.framework.ops.Tensor][source]

Generate the feed_dict for current descriptor

Parameters
coord_tf.Tensor

The coordinate of atoms

atype_tf.Tensor

The type of atoms

natomstf.Tensor

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

boxtf.Tensor

The box. Can be generated by deepmd.model.make_stat_input

meshtf.Tensor

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

Returns
feed_dictdict[str, tf.Tensor]

The output feed_dict of current descriptor

get_nlist() Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, List[int], List[int]][source]

Returns neighbor information.

Returns
nlisttf.Tensor

Neighbor list

rijtf.Tensor

The relative distance between the neighbor and the center atom.

sel_alist[int]

The number of neighbors with full information

sel_rlist[int]

The number of neighbors with only radial information

abstract get_ntypes() int[source]

Returns the number of atom types.

Returns
int

the number of atom types

Notes

This method must be implemented, as it’s called by other classes.

abstract get_rcut() float[source]

Returns the cut-off radius.

Returns
float

the cut-off radius

Notes

This method must be implemented, as it’s called by other classes.

get_tensor_names(suffix: str = '') Tuple[str][source]

Get names of tensors.

Parameters
suffixstr

The suffix of the scope

Returns
Tuple[str]

Names of tensors

init_variables(model_file: str, suffix: str = '') None[source]

Init the embedding net variables with the given dict

Parameters
model_filestr

The input model file

suffixstr, optional

The suffix of the scope

Notes

This method is called by others when the descriptor supported initialization from the given variables.

pass_tensors_from_frz_model(*tensors: tensorflow.python.framework.ops.Tensor) None[source]

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

Parameters
*tensorstf.Tensor

passed tensors

Notes

The number of parameters in the method must be equal to the numbers of returns in get_tensor_names().

abstract prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial.

Parameters
atom_enertf.Tensor

The atomic energy

natomstf.Tensor

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
forcetf.Tensor

The force on atoms

virialtf.Tensor

The total virial

atom_virialtf.Tensor

The atomic virial

static register(key: str) deepmd.descriptor.descriptor.Descriptor[source]

Regiester a descriptor plugin.

Parameters
keystr

the key of a descriptor

Returns
Descriptor

the regiestered descriptor

Examples

>>> @Descriptor.register("some_descrpt")
    class SomeDescript(Descriptor):
        pass

deepmd.descriptor.hybrid module

class deepmd.descriptor.hybrid.DescrptHybrid(*args, **kwargs)[source]

Bases: deepmd.descriptor.descriptor.Descriptor

Concate a list of descriptors to form a new descriptor.

Parameters
listlist

Build a descriptor from the concatenation of the list of descriptors.

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns neighbor information.

get_nlist_i(ii)

Get the neighbor information of the ii-th descriptor

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radius

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given dict

pass_tensors_from_frz_model(*tensors)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord: list, data_box: list, data_atype: list, natoms_vec: list, mesh: list, input_dict: dict) None[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

enable_compression(min_nbor_dist: float, model_file: str = 'frozon_model.pb', table_extrapolate: float = 5.0, table_stride_1: float = 0.01, table_stride_2: float = 0.1, check_frequency: int = - 1, suffix: str = '') None[source]

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

Parameters
min_nbor_distfloat

The nearest distance between atoms

model_filestr, default: ‘frozon_model.pb’

The original frozen model, which will be compressed by the program

table_extrapolatefloat, default: 5.

The scale of model extrapolation

table_stride_1float, default: 0.01

The uniform stride of the first table

table_stride_2float, default: 0.1

The uniform stride of the second table

check_frequencyint, default: -1

The overflow check frequency

suffixstr, optional

The suffix of the scope

enable_mixed_precision(mixed_prec: Optional[dict] = None) None[source]

Reveive the mixed precision setting.

Parameters
mixed_prec

The mixed precision setting used in the embedding net

get_dim_out() int[source]

Returns the output dimension of this descriptor

get_nlist_i(ii: int) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, List[int], List[int]][source]

Get the neighbor information of the ii-th descriptor

Parameters
iiint

The index of the descriptor

Returns
nlist

Neighbor list

rij

The relative distance between the neighbor and the center atom.

sel_a

The number of neighbors with full information

sel_r

The number of neighbors with only radial information

get_ntypes() int[source]

Returns the number of atom types

get_rcut() float[source]

Returns the cut-off radius

get_tensor_names(suffix: str = '') Tuple[str][source]

Get names of tensors.

Parameters
suffixstr

The suffix of the scope

Returns
Tuple[str]

Names of tensors

init_variables(model_file: str, suffix: str = '') None[source]

Init the embedding net variables with the given dict

Parameters
model_filestr

The input frozen model file

suffixstr, optional

The suffix of the scope

pass_tensors_from_frz_model(*tensors: tensorflow.python.framework.ops.Tensor) None[source]

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

Parameters
*tensorstf.Tensor

passed tensors

prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial

Parameters
atom_ener

The atomic energy

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
force

The force on atoms

virial

The total virial

atom_virial

The atomic virial

deepmd.descriptor.loc_frame module

class deepmd.descriptor.loc_frame.DescrptLocFrame(*args, **kwargs)[source]

Bases: deepmd.descriptor.descriptor.Descriptor

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

Parameters
rcut

The cut-off radius

sel_alist[str]

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_rlist[str]

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.

axis_rule: list[int]

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.

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radisu

get_rot_mat()

Get rotational matrix

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given dict

pass_tensors_from_frz_model(*tensors)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord: list, data_box: list, data_atype: list, natoms_vec: list, mesh: list, input_dict: dict) None[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

get_dim_out() int[source]

Returns the output dimension of this descriptor

get_nlist() Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, List[int], List[int]][source]
Returns
nlist

Neighbor list

rij

The relative distance between the neighbor and the center atom.

sel_a

The number of neighbors with full information

sel_r

The number of neighbors with only radial information

get_ntypes() int[source]

Returns the number of atom types

get_rcut() float[source]

Returns the cut-off radisu

get_rot_mat() tensorflow.python.framework.ops.Tensor[source]

Get rotational matrix

prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial

Parameters
atom_ener

The atomic energy

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
force

The force on atoms

virial

The total virial

atom_virial

The atomic virial

deepmd.descriptor.se module

class deepmd.descriptor.se.DescrptSe(*args, **kwargs)[source]

Bases: deepmd.descriptor.descriptor.Descriptor

A base class for smooth version of descriptors.

Notes

All of these descriptors have an environmental matrix and an embedding network (deepmd.utils.network.embedding_net()), so they can share some similiar methods without defining them twice.

Attributes
embedding_net_variablesdict

initial embedding network variables

descrpt_reshapetf.Tensor

the reshaped descriptor

descrpt_derivtf.Tensor

the descriptor derivative

rijtf.Tensor

distances between two atoms

nlisttf.Tensor

the neighbor list

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor.

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor.

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns neighbor information.

get_ntypes()

Returns the number of atom types.

get_rcut()

Returns the cut-off radius.

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given frozen model

pass_tensors_from_frz_model(descrpt_reshape, ...)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial.

register(key)

Regiester a descriptor plugin.

get_tensor_names(suffix: str = '') Tuple[str][source]

Get names of tensors.

Parameters
suffixstr

The suffix of the scope

Returns
Tuple[str]

Names of tensors

init_variables(model_file: str, suffix: str = '') None[source]

Init the embedding net variables with the given frozen model

Parameters
model_filestr

The input frozen model file

suffixstr, optional

The suffix of the scope

pass_tensors_from_frz_model(descrpt_reshape: tensorflow.python.framework.ops.Tensor, descrpt_deriv: tensorflow.python.framework.ops.Tensor, rij: tensorflow.python.framework.ops.Tensor, nlist: tensorflow.python.framework.ops.Tensor)[source]

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

Parameters
descrpt_reshape

The passed descrpt_reshape tensor

descrpt_deriv

The passed descrpt_deriv tensor

rij

The passed rij tensor

nlist

The passed nlist tensor

deepmd.descriptor.se_a module

class deepmd.descriptor.se_a.DescrptSeA(*args, **kwargs)[source]

Bases: deepmd.descriptor.se.DescrptSe

DeepPot-SE constructed from all information (both angular and radial) of atomic configurations. The embedding takes the distance between atoms as input.

The descriptor \(\mathcal{D}^i \in \mathcal{R}^{M_1 \times M_2}\) is given by [1]

\[\mathcal{D}^i = (\mathcal{G}^i)^T \mathcal{R}^i (\mathcal{R}^i)^T \mathcal{G}^i_<\]

where \(\mathcal{R}^i \in \mathbb{R}^{N \times 4}\) is the coordinate matrix, and each row of \(\mathcal{R}^i\) can be constructed as follows

\[(\mathcal{R}^i)_j = [ \begin{array}{c} s(r_{ji}) & \frac{s(r_{ji})x_{ji}}{r_{ji}} & \frac{s(r_{ji})y_{ji}}{r_{ji}} & \frac{s(r_{ji})z_{ji}}{r_{ji}} \end{array} ]\]

where \(\mathbf{R}_{ji}=\mathbf{R}_j-\mathbf{R}_i = (x_{ji}, y_{ji}, z_{ji})\) is the relative coordinate and \(r_{ji}=\lVert \mathbf{R}_{ji} \lVert\) is its norm. The switching function \(s(r)\) is defined as:

\[\begin{split}s(r)= \begin{cases} \frac{1}{r}, & r<r_s \\ \frac{1}{r} \{ {(\frac{r - r_s}{ r_c - r_s})}^3 (-6 {(\frac{r - r_s}{ r_c - r_s})}^2 +15 \frac{r - r_s}{ r_c - r_s} -10) +1 \}, & r_s \leq r<r_c \\ 0, & r \geq r_c \end{cases}\end{split}\]

Each row of the embedding matrix \(\mathcal{G}^i \in \mathbb{R}^{N \times M_1}\) consists of outputs of a embedding network \(\mathcal{N}\) of \(s(r_{ji})\):

\[(\mathcal{G}^i)_j = \mathcal{N}(s(r_{ji}))\]

\(\mathcal{G}^i_< \in \mathbb{R}^{N \times M_2}\) takes first \(M_2\) columns of \(\mathcal{G}^i\). The equation of embedding network \(\mathcal{N}\) can be found at deepmd.utils.network.embedding_net().

Parameters
rcut

The cut-off radius \(r_c\)

rcut_smth

From where the environment matrix should be smoothed \(r_s\)

sellist[str]

sel[i] specifies the maxmum number of type i atoms in the cut-off radius

neuronlist[int]

Number of neurons in each hidden layers of the embedding net \(\mathcal{N}\)

axis_neuron

Number of the axis neuron \(M_2\) (number of columns of the sub-matrix of the embedding matrix)

resnet_dt

Time-step dt in the resnet construction: y = x + dt * phi (Wx + b)

trainable

If the weights of embedding net are trainable.

seed

Random seed for initializing the network parameters.

type_one_side

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

exclude_typesList[List[int]]

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

Set the shift of embedding net input to zero.

activation_function

The activation function in the embedding net. Supported options are {0}

precision

The precision of the embedding net parameters. Supported options are {1}

uniform_seed

Only for the purpose of backward compatibility, retrieves the old behavior of using the random seed

References

1

Linfeng Zhang, Jiequn Han, Han Wang, Wissam A. Saidi, Roberto Car, and E. Weinan. 2018. End-to-end symmetry preserving inter-atomic potential energy model for finite and extended systems. In Proceedings of the 32nd International Conference on Neural Information Processing Systems (NIPS’18). Curran Associates Inc., Red Hook, NY, USA, 4441–4451.

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radius

get_rot_mat()

Get rotational matrix

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given frozen model

pass_tensors_from_frz_model(descrpt_reshape, ...)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord: list, data_box: list, data_atype: list, natoms_vec: list, mesh: list, input_dict: dict) None[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

enable_compression(min_nbor_dist: float, model_file: str = 'frozon_model.pb', table_extrapolate: float = 5, table_stride_1: float = 0.01, table_stride_2: float = 0.1, check_frequency: int = - 1, suffix: str = '') None[source]

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

Parameters
min_nbor_dist

The nearest distance between atoms

model_file

The original frozen model, which will be compressed by the program

table_extrapolate

The scale of model extrapolation

table_stride_1

The uniform stride of the first table

table_stride_2

The uniform stride of the second table

check_frequency

The overflow check frequency

suffixstr, optional

The suffix of the scope

enable_mixed_precision(mixed_prec: Optional[dict] = None) None[source]

Reveive the mixed precision setting.

Parameters
mixed_prec

The mixed precision setting used in the embedding net

get_dim_out() int[source]

Returns the output dimension of this descriptor

get_dim_rot_mat_1() int[source]

Returns the first dimension of the rotation matrix. The rotation is of shape dim_1 x 3

get_nlist() Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, List[int], List[int]][source]
Returns
nlist

Neighbor list

rij

The relative distance between the neighbor and the center atom.

sel_a

The number of neighbors with full information

sel_r

The number of neighbors with only radial information

get_ntypes() int[source]

Returns the number of atom types

get_rcut() float[source]

Returns the cut-off radius

get_rot_mat() tensorflow.python.framework.ops.Tensor[source]

Get rotational matrix

prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial

Parameters
atom_ener

The atomic energy

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
force

The force on atoms

virial

The total virial

atom_virial

The atomic virial

deepmd.descriptor.se_a_ebd module

class deepmd.descriptor.se_a_ebd.DescrptSeAEbd(*args, **kwargs)[source]

Bases: deepmd.descriptor.se_a.DescrptSeA

DeepPot-SE descriptor with type embedding approach.

Parameters
rcut

The cut-off radius

rcut_smth

From where the environment matrix should be smoothed

sellist[str]

sel[i] specifies the maxmum number of type i atoms in the cut-off radius

neuronlist[int]

Number of neurons in each hidden layers of the embedding net

axis_neuron

Number of the axis neuron (number of columns of the sub-matrix of the embedding matrix)

resnet_dt

Time-step dt in the resnet construction: y = x + dt * phi (Wx + b)

trainable

If the weights of embedding net are trainable.

seed

Random seed for initializing the network parameters.

type_one_side

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

type_nchanl

Number of channels for type representation

type_nlayer

Number of hidden layers for the type embedding net (skip connected).

numb_aparam

Number of atomic parameters. If >0 it will be embedded with atom types.

set_davg_zero

Set the shift of embedding net input to zero.

activation_function

The activation function in the embedding net. Supported options are {0}

precision

The precision of the embedding net parameters. Supported options are {1}

exclude_typesList[List[int]]

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.

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radius

get_rot_mat()

Get rotational matrix

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given frozen model

pass_tensors_from_frz_model(descrpt_reshape, ...)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

deepmd.descriptor.se_a_ef module

class deepmd.descriptor.se_a_ef.DescrptSeAEf(*args, **kwargs)[source]

Bases: deepmd.descriptor.descriptor.Descriptor

Parameters
rcut

The cut-off radius

rcut_smth

From where the environment matrix should be smoothed

sellist[str]

sel[i] specifies the maxmum number of type i atoms in the cut-off radius

neuronlist[int]

Number of neurons in each hidden layers of the embedding net

axis_neuron

Number of the axis neuron (number of columns of the sub-matrix of the embedding matrix)

resnet_dt

Time-step dt in the resnet construction: y = x + dt * phi (Wx + b)

trainable

If the weights of embedding net are trainable.

seed

Random seed for initializing the network parameters.

type_one_side

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

exclude_typesList[List[int]]

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

Set the shift of embedding net input to zero.

activation_function

The activation function in the embedding net. Supported options are {0}

precision

The precision of the embedding net parameters. Supported options are {1}

uniform_seed

Only for the purpose of backward compatibility, retrieves the old behavior of using the random seed

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radisu

get_rot_mat()

Get rotational matrix

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given dict

pass_tensors_from_frz_model(*tensors)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs. Should have ‘efield’.

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord: list, data_box: list, data_atype: list, natoms_vec: list, mesh: list, input_dict: dict) None[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

get_dim_out() int[source]

Returns the output dimension of this descriptor

get_dim_rot_mat_1() int[source]

Returns the first dimension of the rotation matrix. The rotation is of shape dim_1 x 3

get_nlist() Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, List[int], List[int]][source]
Returns
nlist

Neighbor list

rij

The relative distance between the neighbor and the center atom.

sel_a

The number of neighbors with full information

sel_r

The number of neighbors with only radial information

get_ntypes() int[source]

Returns the number of atom types

get_rcut() float[source]

Returns the cut-off radisu

get_rot_mat() tensorflow.python.framework.ops.Tensor[source]

Get rotational matrix

prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial

Parameters
atom_ener

The atomic energy

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
force

The force on atoms

virial

The total virial

atom_virial

The atomic virial

class deepmd.descriptor.se_a_ef.DescrptSeAEfLower(*args, **kwargs)[source]

Bases: deepmd.descriptor.se_a.DescrptSeA

Helper class for implementing DescrptSeAEf

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radius

get_rot_mat()

Get rotational matrix

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given frozen model

pass_tensors_from_frz_model(descrpt_reshape, ...)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_, atype_, natoms, box_, mesh, input_dict, suffix='', reuse=None)[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord, data_box, data_atype, natoms_vec, mesh, input_dict)[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

deepmd.descriptor.se_r module

class deepmd.descriptor.se_r.DescrptSeR(*args, **kwargs)[source]

Bases: deepmd.descriptor.se.DescrptSe

DeepPot-SE constructed from radial information of atomic configurations.

The embedding takes the distance between atoms as input.

Parameters
rcut

The cut-off radius

rcut_smth

From where the environment matrix should be smoothed

sellist[str]

sel[i] specifies the maxmum number of type i atoms in the cut-off radius

neuronlist[int]

Number of neurons in each hidden layers of the embedding net

resnet_dt

Time-step dt in the resnet construction: y = x + dt * phi (Wx + b)

trainable

If the weights of embedding net are trainable.

seed

Random seed for initializing the network parameters.

type_one_side

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

exclude_typesList[List[int]]

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.

activation_function

The activation function in the embedding net. Supported options are {0}

precision

The precision of the embedding net parameters. Supported options are {1}

uniform_seed

Only for the purpose of backward compatibility, retrieves the old behavior of using the random seed

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radisu

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given frozen model

pass_tensors_from_frz_model(descrpt_reshape, ...)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord, data_box, data_atype, natoms_vec, mesh, input_dict)[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

get_dim_out()[source]

Returns the output dimension of this descriptor

get_nlist()[source]
Returns
nlist

Neighbor list

rij

The relative distance between the neighbor and the center atom.

sel_a

The number of neighbors with full information

sel_r

The number of neighbors with only radial information

get_ntypes()[source]

Returns the number of atom types

get_rcut()[source]

Returns the cut-off radisu

prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial

Parameters
atom_ener

The atomic energy

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
force

The force on atoms

virial

The total virial

atom_virial

The atomic virial

deepmd.descriptor.se_t module

class deepmd.descriptor.se_t.DescrptSeT(*args, **kwargs)[source]

Bases: deepmd.descriptor.se.DescrptSe

DeepPot-SE constructed from all information (both angular and radial) of atomic configurations.

The embedding takes angles between two neighboring atoms as input.

Parameters
rcut

The cut-off radius

rcut_smth

From where the environment matrix should be smoothed

sellist[str]

sel[i] specifies the maxmum number of type i atoms in the cut-off radius

neuronlist[int]

Number of neurons in each hidden layers of the embedding net

resnet_dt

Time-step dt in the resnet construction: y = x + dt * phi (Wx + b)

trainable

If the weights of embedding net are trainable.

seed

Random seed for initializing the network parameters.

set_davg_zero

Set the shift of embedding net input to zero.

activation_function

The activation function in the embedding net. Supported options are {0}

precision

The precision of the embedding net parameters. Supported options are {1}

uniform_seed

Only for the purpose of backward compatibility, retrieves the old behavior of using the random seed

Methods

build(coord_, atype_, natoms, box_, mesh, ...)

Build the computational graph for the descriptor

compute_input_stats(data_coord, data_box, ...)

Compute the statisitcs (avg and std) of the training data.

enable_compression(min_nbor_dist[, ...])

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

enable_mixed_precision([mixed_prec])

Reveive the mixed precision setting.

get_dim_out()

Returns the output dimension of this descriptor

get_dim_rot_mat_1()

Returns the first dimension of the rotation matrix.

get_feed_dict(coord_, atype_, natoms, box, mesh)

Generate the feed_dict for current descriptor

get_nlist()

Returns

get_ntypes()

Returns the number of atom types

get_rcut()

Returns the cut-off radisu

get_tensor_names([suffix])

Get names of tensors.

init_variables(model_file[, suffix])

Init the embedding net variables with the given frozen model

pass_tensors_from_frz_model(descrpt_reshape, ...)

Pass the descrpt_reshape tensor as well as descrpt_deriv tensor from the frz graph_def

prod_force_virial(atom_ener, natoms)

Compute force and virial

register(key)

Regiester a descriptor plugin.

build(coord_: tensorflow.python.framework.ops.Tensor, atype_: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor, box_: tensorflow.python.framework.ops.Tensor, mesh: tensorflow.python.framework.ops.Tensor, input_dict: dict, reuse: Optional[bool] = None, suffix: str = '') tensorflow.python.framework.ops.Tensor[source]

Build the computational graph for the descriptor

Parameters
coord_

The coordinate of atoms

atype_

The type of atoms

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

mesh

For historical reasons, only the length of the Tensor matters. if size of mesh == 6, pbc is assumed. if size of mesh == 0, no-pbc is assumed.

input_dict

Dictionary for additional inputs

reuse

The weights in the networks should be reused when get the variable.

suffix

Name suffix to identify this descriptor

Returns
descriptor

The output descriptor

compute_input_stats(data_coord: list, data_box: list, data_atype: list, natoms_vec: list, mesh: list, input_dict: dict) None[source]

Compute the statisitcs (avg and std) of the training data. The input will be normalized by the statistics.

Parameters
data_coord

The coordinates. Can be generated by deepmd.model.make_stat_input

data_box

The box. Can be generated by deepmd.model.make_stat_input

data_atype

The atom types. Can be generated by deepmd.model.make_stat_input

natoms_vec

The vector for the number of atoms of the system and different types of atoms. Can be generated by deepmd.model.make_stat_input

mesh

The mesh for neighbor searching. Can be generated by deepmd.model.make_stat_input

input_dict

Dictionary for additional input

enable_compression(min_nbor_dist: float, model_file: str = 'frozon_model.pb', table_extrapolate: float = 5, table_stride_1: float = 0.01, table_stride_2: float = 0.1, check_frequency: int = - 1, suffix: str = '') None[source]

Reveive the statisitcs (distance, max_nbor_size and env_mat_range) of the training data.

Parameters
min_nbor_dist

The nearest distance between atoms

model_file

The original frozen model, which will be compressed by the program

table_extrapolate

The scale of model extrapolation

table_stride_1

The uniform stride of the first table

table_stride_2

The uniform stride of the second table

check_frequency

The overflow check frequency

suffixstr, optional

The suffix of the scope

get_dim_out() int[source]

Returns the output dimension of this descriptor

get_nlist() Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, List[int], List[int]][source]
Returns
nlist

Neighbor list

rij

The relative distance between the neighbor and the center atom.

sel_a

The number of neighbors with full information

sel_r

The number of neighbors with only radial information

get_ntypes() int[source]

Returns the number of atom types

get_rcut() float[source]

Returns the cut-off radisu

prod_force_virial(atom_ener: tensorflow.python.framework.ops.Tensor, natoms: tensorflow.python.framework.ops.Tensor) Tuple[tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor, tensorflow.python.framework.ops.Tensor][source]

Compute force and virial

Parameters
atom_ener

The atomic energy

natoms

The number of atoms. This tensor has the length of Ntypes + 2 natoms[0]: number of local atoms natoms[1]: total number of atoms held by this processor natoms[i]: 2 <= i < Ntypes+2, number of type i atoms

Returns
force

The force on atoms

virial

The total virial

atom_virial

The atomic virial