class DipoleFittingSeA():
"""
Fit the atomic dipole with descriptor se_a
Parameters
----------
descrpt : tf.Tensor
The descrptor
neuron : List[int]
Number of neurons in each hidden layer of the fitting net
resnet_dt : bool
Time-step `dt` in the resnet construction:
y = x + dt * \phi (Wx + b)
sel_type : List[int]
The atom types selected to have an atomic dipole prediction. If is None, all atoms are selected.
seed : int
Random seed for initializing the network parameters.
activation_function : str
The activation function in the embedding net. Supported options are {0}
precision : str
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
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()),
list_to_doc(PRECISION_DICT.keys()))
def __init__(self,
descrpt: tf.Tensor,
neuron: List[int] = [120, 120, 120],
resnet_dt: bool = True,
sel_type: List[int] = None,
seed: int = None,
activation_function: str = 'tanh',
precision: str = 'default',
uniform_seed: bool = False) -> None:
"""
Constructor
"""
if not isinstance(descrpt, DescrptSeA):
raise RuntimeError('DipoleFittingSeA only supports DescrptSeA')
self.ntypes = descrpt.get_ntypes()
self.dim_descrpt = descrpt.get_dim_out()
# args = ClassArg()\
# .add('neuron', list, default = [120,120,120], alias = 'n_neuron')\
# .add('resnet_dt', bool, default = True)\
# .add('sel_type', [list,int], default = [ii for ii in range(self.ntypes)], alias = 'dipole_type')\
# .add('seed', int)\
# .add("activation_function", str, default = "tanh")\
# .add('precision', str, default = "default")
# class_data = args.parse(jdata)
self.n_neuron = neuron
self.resnet_dt = resnet_dt
self.sel_type = sel_type
if self.sel_type is None:
self.sel_type = [ii for ii in range(self.ntypes)]
self.sel_type = sel_type
self.seed = seed
self.uniform_seed = uniform_seed
self.seed_shift = one_layer_rand_seed_shift()
self.fitting_activation_fn = get_activation_func(activation_function)
self.fitting_precision = get_precision(precision)
self.dim_rot_mat_1 = descrpt.get_dim_rot_mat_1()
self.dim_rot_mat = self.dim_rot_mat_1 * 3
self.useBN = False
def get_sel_type(self) -> int:
"""
Get selected type
"""
return self.sel_type
def get_out_size(self) -> int:
"""
Get the output size. Should be 3
"""
return 3
def build(self,
input_d: tf.Tensor,
rot_mat: tf.Tensor,
natoms: tf.Tensor,
reuse: bool = None,
suffix: str = '') -> tf.Tensor:
"""
Build the computational graph for fitting net
Parameters
----------
input_d
The input descriptor
rot_mat
The rotation matrix from the descriptor.
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
reuse
The weights in the networks should be reused when get the variable.
suffix
Name suffix to identify this descriptor
Returns
-------
dipole
The atomic dipole.
"""
start_index = 0
inputs = tf.cast(
tf.reshape(input_d, [-1, self.dim_descrpt * natoms[0]]),
self.fitting_precision)
rot_mat = tf.reshape(rot_mat, [-1, self.dim_rot_mat * natoms[0]])
count = 0
for type_i in range(self.ntypes):
# cut-out inputs
inputs_i = tf.slice(inputs, [0, start_index * self.dim_descrpt],
[-1, natoms[2 + type_i] * self.dim_descrpt])
inputs_i = tf.reshape(inputs_i, [-1, self.dim_descrpt])
rot_mat_i = tf.slice(rot_mat, [0, start_index * self.dim_rot_mat],
[-1, natoms[2 + type_i] * self.dim_rot_mat])
rot_mat_i = tf.reshape(rot_mat_i, [-1, self.dim_rot_mat_1, 3])
start_index += natoms[2 + type_i]
if not type_i in self.sel_type:
continue
layer = inputs_i
for ii in range(0, len(self.n_neuron)):
if ii >= 1 and self.n_neuron[ii] == self.n_neuron[ii - 1]:
layer += one_layer(
layer,
self.n_neuron[ii],
name='layer_' + str(ii) + '_type_' + str(type_i) +
suffix,
reuse=reuse,
seed=self.seed,
use_timestep=self.resnet_dt,
activation_fn=self.fitting_activation_fn,
precision=self.fitting_precision,
uniform_seed=self.uniform_seed)
else:
layer = one_layer(layer,
self.n_neuron[ii],
name='layer_' + str(ii) + '_type_' +
str(type_i) + suffix,
reuse=reuse,
seed=self.seed,
activation_fn=self.fitting_activation_fn,
precision=self.fitting_precision,
uniform_seed=self.uniform_seed)
if (not self.uniform_seed) and (self.seed is not None):
self.seed += self.seed_shift
# (nframes x natoms) x naxis
final_layer = one_layer(layer,
self.dim_rot_mat_1,
activation_fn=None,
name='final_layer_type_' + str(type_i) +
suffix,
reuse=reuse,
seed=self.seed,
precision=self.fitting_precision,
uniform_seed=self.uniform_seed)
if (not self.uniform_seed) and (self.seed is not None):
self.seed += self.seed_shift
# (nframes x natoms) x 1 * naxis
final_layer = tf.reshape(final_layer, [
tf.shape(inputs)[0] * natoms[2 + type_i], 1, self.dim_rot_mat_1
])
# (nframes x natoms) x 1 x 3(coord)
final_layer = tf.matmul(final_layer, rot_mat_i)
# nframes x natoms x 3
final_layer = tf.reshape(
final_layer, [tf.shape(inputs)[0], natoms[2 + type_i], 3])
# concat the results
if count == 0:
outs = final_layer
else:
outs = tf.concat([outs, final_layer], axis=1)
count += 1
tf.summary.histogram('fitting_net_output', outs)
return tf.cast(tf.reshape(outs, [-1]), GLOBAL_TF_FLOAT_PRECISION)
class DescrptSeT(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
sel : list[str]
sel[i] specifies the maxmum number of type i atoms in the cut-off radius
neuron : list[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
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()),
list_to_doc(PRECISION_DICT.keys()))
def __init__(self,
rcut: float,
rcut_smth: float,
sel: List[str],
neuron: List[int] = [24, 48, 96],
resnet_dt: bool = False,
trainable: bool = True,
seed: int = None,
set_davg_zero: bool = False,
activation_function: str = 'tanh',
precision: str = 'default',
uniform_seed: bool = False) -> None:
"""
Constructor
"""
self.sel_a = sel
self.rcut_r = rcut
self.rcut_r_smth = rcut_smth
self.filter_neuron = neuron
self.filter_resnet_dt = resnet_dt
self.seed = seed
self.uniform_seed = uniform_seed
self.seed_shift = embedding_net_rand_seed_shift(self.filter_neuron)
self.trainable = trainable
self.filter_activation_fn = get_activation_func(activation_function)
self.filter_precision = get_precision(precision)
# self.exclude_types = set()
# for tt in exclude_types:
# assert(len(tt) == 2)
# self.exclude_types.add((tt[0], tt[1]))
# self.exclude_types.add((tt[1], tt[0]))
self.set_davg_zero = set_davg_zero
# descrpt config
self.sel_r = [0 for ii in range(len(self.sel_a))]
self.ntypes = len(self.sel_a)
assert (self.ntypes == len(self.sel_r))
self.rcut_a = -1
# numb of neighbors and numb of descrptors
self.nnei_a = np.cumsum(self.sel_a)[-1]
self.nnei_r = np.cumsum(self.sel_r)[-1]
self.nnei = self.nnei_a + self.nnei_r
self.ndescrpt_a = self.nnei_a * 4
self.ndescrpt_r = self.nnei_r * 1
self.ndescrpt = self.ndescrpt_a + self.ndescrpt_r
self.useBN = False
self.dstd = None
self.davg = None
self.embedding_net_variables = None
self.place_holders = {}
avg_zero = np.zeros([self.ntypes,
self.ndescrpt]).astype(GLOBAL_NP_FLOAT_PRECISION)
std_ones = np.ones([self.ntypes,
self.ndescrpt]).astype(GLOBAL_NP_FLOAT_PRECISION)
sub_graph = tf.Graph()
with sub_graph.as_default():
name_pfx = 'd_sea_'
for ii in ['coord', 'box']:
self.place_holders[ii] = tf.placeholder(
GLOBAL_NP_FLOAT_PRECISION, [None, None],
name=name_pfx + 't_' + ii)
self.place_holders['type'] = tf.placeholder(tf.int32, [None, None],
name=name_pfx +
't_type')
self.place_holders['natoms_vec'] = tf.placeholder(
tf.int32, [self.ntypes + 2], name=name_pfx + 't_natoms')
self.place_holders['default_mesh'] = tf.placeholder(
tf.int32, [None], name=name_pfx + 't_mesh')
self.stat_descrpt, descrpt_deriv, rij, nlist \
= op_module.prod_env_mat_a(self.place_holders['coord'],
self.place_holders['type'],
self.place_holders['natoms_vec'],
self.place_holders['box'],
self.place_holders['default_mesh'],
tf.constant(avg_zero),
tf.constant(std_ones),
rcut_a = self.rcut_a,
rcut_r = self.rcut_r,
rcut_r_smth = self.rcut_r_smth,
sel_a = self.sel_a,
sel_r = self.sel_r)
self.sub_sess = tf.Session(graph=sub_graph,
config=default_tf_session_config)
def get_rcut(self) -> float:
"""
Returns the cut-off radisu
"""
return self.rcut_r
def get_ntypes(self) -> int:
"""
Returns the number of atom types
"""
return self.ntypes
def get_dim_out(self) -> int:
"""
Returns the output dimension of this descriptor
"""
return self.filter_neuron[-1]
def get_nlist(self) -> Tuple[tf.Tensor, tf.Tensor, List[int], List[int]]:
"""
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
"""
return self.nlist, self.rij, self.sel_a, self.sel_r
def compute_input_stats(self, data_coord: list, data_box: list,
data_atype: list, natoms_vec: list, mesh: list,
input_dict: dict) -> None:
"""
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
"""
all_davg = []
all_dstd = []
if True:
sumr = []
suma = []
sumn = []
sumr2 = []
suma2 = []
for cc, bb, tt, nn, mm in zip(data_coord, data_box, data_atype,
natoms_vec, mesh):
sysr,sysr2,sysa,sysa2,sysn \
= self._compute_dstats_sys_smth(cc,bb,tt,nn,mm)
sumr.append(sysr)
suma.append(sysa)
sumn.append(sysn)
sumr2.append(sysr2)
suma2.append(sysa2)
sumr = np.sum(sumr, axis=0)
suma = np.sum(suma, axis=0)
sumn = np.sum(sumn, axis=0)
sumr2 = np.sum(sumr2, axis=0)
suma2 = np.sum(suma2, axis=0)
for type_i in range(self.ntypes):
davgunit = [sumr[type_i] / sumn[type_i], 0, 0, 0]
dstdunit = [
self._compute_std(sumr2[type_i], sumr[type_i],
sumn[type_i]),
self._compute_std(suma2[type_i], suma[type_i],
sumn[type_i]),
self._compute_std(suma2[type_i], suma[type_i],
sumn[type_i]),
self._compute_std(suma2[type_i], suma[type_i],
sumn[type_i])
]
davg = np.tile(davgunit, self.ndescrpt // 4)
dstd = np.tile(dstdunit, self.ndescrpt // 4)
all_davg.append(davg)
all_dstd.append(dstd)
if not self.set_davg_zero:
self.davg = np.array(all_davg)
self.dstd = np.array(all_dstd)
def build(self,
coord_: tf.Tensor,
atype_: tf.Tensor,
natoms: tf.Tensor,
box_: tf.Tensor,
mesh: tf.Tensor,
input_dict: dict,
reuse: bool = None,
suffix: str = '') -> tf.Tensor:
"""
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
"""
davg = self.davg
dstd = self.dstd
with tf.variable_scope('descrpt_attr' + suffix, reuse=reuse):
if davg is None:
davg = np.zeros([self.ntypes, self.ndescrpt])
if dstd is None:
dstd = np.ones([self.ntypes, self.ndescrpt])
t_rcut = tf.constant(np.max([self.rcut_r, self.rcut_a]),
name='rcut',
dtype=GLOBAL_TF_FLOAT_PRECISION)
t_ntypes = tf.constant(self.ntypes, name='ntypes', dtype=tf.int32)
t_ndescrpt = tf.constant(self.ndescrpt,
name='ndescrpt',
dtype=tf.int32)
t_sel = tf.constant(self.sel_a, name='sel', dtype=tf.int32)
self.t_avg = tf.get_variable(
't_avg',
davg.shape,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(davg))
self.t_std = tf.get_variable(
't_std',
dstd.shape,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(dstd))
coord = tf.reshape(coord_, [-1, natoms[1] * 3])
box = tf.reshape(box_, [-1, 9])
atype = tf.reshape(atype_, [-1, natoms[1]])
self.descrpt, self.descrpt_deriv, self.rij, self.nlist \
= op_module.prod_env_mat_a (coord,
atype,
natoms,
box,
mesh,
self.t_avg,
self.t_std,
rcut_a = self.rcut_a,
rcut_r = self.rcut_r,
rcut_r_smth = self.rcut_r_smth,
sel_a = self.sel_a,
sel_r = self.sel_r)
self.descrpt_reshape = tf.reshape(self.descrpt, [-1, self.ndescrpt])
self._identity_tensors(suffix=suffix)
self.dout, self.qmat = self._pass_filter(self.descrpt_reshape,
atype,
natoms,
input_dict,
suffix=suffix,
reuse=reuse,
trainable=self.trainable)
return self.dout
def prod_force_virial(
self, atom_ener: tf.Tensor,
natoms: tf.Tensor) -> Tuple[tf.Tensor, tf.Tensor, tf.Tensor]:
"""
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
"""
[net_deriv] = tf.gradients(atom_ener, self.descrpt_reshape)
net_deriv_reshape = tf.reshape(net_deriv,
[-1, natoms[0] * self.ndescrpt])
force \
= op_module.prod_force_se_a (net_deriv_reshape,
self.descrpt_deriv,
self.nlist,
natoms,
n_a_sel = self.nnei_a,
n_r_sel = self.nnei_r)
virial, atom_virial \
= op_module.prod_virial_se_a (net_deriv_reshape,
self.descrpt_deriv,
self.rij,
self.nlist,
natoms,
n_a_sel = self.nnei_a,
n_r_sel = self.nnei_r)
return force, virial, atom_virial
def _pass_filter(self,
inputs,
atype,
natoms,
input_dict,
reuse=None,
suffix='',
trainable=True):
start_index = 0
inputs = tf.reshape(inputs, [-1, self.ndescrpt * natoms[0]])
output = []
output_qmat = []
inputs_i = inputs
inputs_i = tf.reshape(inputs_i, [-1, self.ndescrpt])
type_i = -1
layer, qmat = self._filter(tf.cast(inputs_i, self.filter_precision),
type_i,
name='filter_type_all' + suffix,
natoms=natoms,
reuse=reuse,
trainable=trainable,
activation_fn=self.filter_activation_fn)
layer = tf.reshape(
layer, [tf.shape(inputs)[0], natoms[0] * self.get_dim_out()])
# qmat = tf.reshape(qmat, [tf.shape(inputs)[0], natoms[0] * self.get_dim_rot_mat_1() * 3])
output.append(layer)
# output_qmat.append(qmat)
output = tf.concat(output, axis=1)
# output_qmat = tf.concat(output_qmat, axis = 1)
return output, None
def _compute_dstats_sys_smth(self, data_coord, data_box, data_atype,
natoms_vec, mesh):
dd_all \
= run_sess(self.sub_sess, self.stat_descrpt,
feed_dict = {
self.place_holders['coord']: data_coord,
self.place_holders['type']: data_atype,
self.place_holders['natoms_vec']: natoms_vec,
self.place_holders['box']: data_box,
self.place_holders['default_mesh']: mesh,
})
natoms = natoms_vec
dd_all = np.reshape(dd_all, [-1, self.ndescrpt * natoms[0]])
start_index = 0
sysr = []
sysa = []
sysn = []
sysr2 = []
sysa2 = []
for type_i in range(self.ntypes):
end_index = start_index + self.ndescrpt * natoms[2 + type_i]
dd = dd_all[:, start_index:end_index]
dd = np.reshape(dd, [-1, self.ndescrpt])
start_index = end_index
# compute
dd = np.reshape(dd, [-1, 4])
ddr = dd[:, :1]
dda = dd[:, 1:]
sumr = np.sum(ddr)
suma = np.sum(dda) / 3.
sumn = dd.shape[0]
sumr2 = np.sum(np.multiply(ddr, ddr))
suma2 = np.sum(np.multiply(dda, dda)) / 3.
sysr.append(sumr)
sysa.append(suma)
sysn.append(sumn)
sysr2.append(sumr2)
sysa2.append(suma2)
return sysr, sysr2, sysa, sysa2, sysn
def _compute_std(self, sumv2, sumv, sumn):
val = np.sqrt(sumv2 / sumn - np.multiply(sumv / sumn, sumv / sumn))
if np.abs(val) < 1e-2:
val = 1e-2
return val
def _filter(self,
inputs,
type_input,
natoms,
activation_fn=tf.nn.tanh,
stddev=1.0,
bavg=0.0,
name='linear',
reuse=None,
trainable=True):
# natom x (nei x 4)
shape = inputs.get_shape().as_list()
outputs_size = [1] + self.filter_neuron
with tf.variable_scope(name, reuse=reuse):
start_index_i = 0
result = None
for type_i in range(self.ntypes):
# cut-out inputs
# with natom x (nei_type_i x 4)
inputs_i = tf.slice(inputs, [0, start_index_i * 4],
[-1, self.sel_a[type_i] * 4])
start_index_j = start_index_i
start_index_i += self.sel_a[type_i]
nei_type_i = self.sel_a[type_i]
shape_i = inputs_i.get_shape().as_list()
assert (shape_i[1] == nei_type_i * 4)
# with natom x nei_type_i x 4
env_i = tf.reshape(inputs_i, [-1, nei_type_i, 4])
# with natom x nei_type_i x 3
env_i = tf.slice(env_i, [0, 0, 1], [-1, -1, -1])
for type_j in range(type_i, self.ntypes):
# with natom x (nei_type_j x 4)
inputs_j = tf.slice(inputs, [0, start_index_j * 4],
[-1, self.sel_a[type_j] * 4])
start_index_j += self.sel_a[type_j]
nei_type_j = self.sel_a[type_j]
shape_j = inputs_j.get_shape().as_list()
assert (shape_j[1] == nei_type_j * 4)
# with natom x nei_type_j x 4
env_j = tf.reshape(inputs_j, [-1, nei_type_j, 4])
# with natom x nei_type_i x 3
env_j = tf.slice(env_j, [0, 0, 1], [-1, -1, -1])
# with natom x nei_type_i x nei_type_j
env_ij = tf.einsum('ijm,ikm->ijk', env_i, env_j)
# with (natom x nei_type_i x nei_type_j)
ebd_env_ij = tf.reshape(env_ij, [-1, 1])
# with (natom x nei_type_i x nei_type_j) x out_size
ebd_env_ij = embedding_net(
ebd_env_ij,
self.filter_neuron,
self.filter_precision,
activation_fn=activation_fn,
resnet_dt=self.filter_resnet_dt,
name_suffix=f"_{type_i}_{type_j}",
stddev=stddev,
bavg=bavg,
seed=self.seed,
trainable=trainable,
uniform_seed=self.uniform_seed,
initial_variables=self.embedding_net_variables,
)
if (not self.uniform_seed) and (self.seed is not None):
self.seed += self.seed_shift
# with natom x nei_type_i x nei_type_j x out_size
ebd_env_ij = tf.reshape(
ebd_env_ij,
[-1, nei_type_i, nei_type_j, outputs_size[-1]])
# with natom x out_size
res_ij = tf.einsum('ijk,ijkm->im', env_ij, ebd_env_ij)
res_ij = res_ij * (1.0 / float(nei_type_i) /
float(nei_type_j))
if result is None:
result = res_ij
else:
result += res_ij
return result, None
class PolarFittingSeA (Fitting) :
"""
Fit the atomic polarizability with descriptor se_a
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()), list_to_doc(PRECISION_DICT.keys()))
def __init__ (self,
descrpt : tf.Tensor,
neuron : List[int] = [120,120,120],
resnet_dt : bool = True,
sel_type : List[int] = None,
fit_diag : bool = True,
scale : List[float] = None,
shift_diag : bool = True, # YWolfeee: will support the user to decide whether to use this function
#diag_shift : List[float] = None, YWolfeee: will not support the user to assign a shift
seed : int = None,
activation_function : str = 'tanh',
precision : str = 'default',
uniform_seed: bool = False
) -> None:
"""
Constructor
Parameters
----------
descrpt : tf.Tensor
The descrptor
neuron : List[int]
Number of neurons in each hidden layer of the fitting net
resnet_dt : bool
Time-step `dt` in the resnet construction:
y = x + dt * \phi (Wx + b)
sel_type : List[int]
The atom types selected to have an atomic polarizability prediction. If is None, all atoms are selected.
fit_diag : bool
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 : List[float]
The output of the fitting net (polarizability matrix) for type i atom will be scaled by scale[i]
diag_shift : List[float]
The diagonal part of the polarizability matrix of type i will be shifted by diag_shift[i]. The shift operation is carried out after scale.
seed : int
Random seed for initializing the network parameters.
activation_function : str
The activation function in the embedding net. Supported options are {0}
precision : str
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
"""
if not isinstance(descrpt, DescrptSeA) :
raise RuntimeError('PolarFittingSeA only supports DescrptSeA')
self.ntypes = descrpt.get_ntypes()
self.dim_descrpt = descrpt.get_dim_out()
# args = ClassArg()\
# .add('neuron', list, default = [120,120,120], alias = 'n_neuron')\
# .add('resnet_dt', bool, default = True)\
# .add('fit_diag', bool, default = True)\
# .add('diag_shift', [list,float], default = [0.0 for ii in range(self.ntypes)])\
# .add('scale', [list,float], default = [1.0 for ii in range(self.ntypes)])\
# .add('sel_type', [list,int], default = [ii for ii in range(self.ntypes)], alias = 'pol_type')\
# .add('seed', int)\
# .add("activation_function", str , default = "tanh")\
# .add('precision', str, default = "default")
# class_data = args.parse(jdata)
self.n_neuron = neuron
self.resnet_dt = resnet_dt
self.sel_type = sel_type
self.fit_diag = fit_diag
self.seed = seed
self.uniform_seed = uniform_seed
self.seed_shift = one_layer_rand_seed_shift()
#self.diag_shift = diag_shift
self.shift_diag = shift_diag
self.scale = scale
self.fitting_activation_fn = get_activation_func(activation_function)
self.fitting_precision = get_precision(precision)
if self.sel_type is None:
self.sel_type = [ii for ii in range(self.ntypes)]
if self.scale is None:
self.scale = [1.0 for ii in range(self.ntypes)]
#if self.diag_shift is None:
# self.diag_shift = [0.0 for ii in range(self.ntypes)]
if type(self.sel_type) is not list:
self.sel_type = [self.sel_type]
self.constant_matrix = np.zeros(len(self.sel_type)) # len(sel_type) x 1, store the average diagonal value
#if type(self.diag_shift) is not list:
# self.diag_shift = [self.diag_shift]
if type(self.scale) is not list:
self.scale = [self.scale]
self.dim_rot_mat_1 = descrpt.get_dim_rot_mat_1()
self.dim_rot_mat = self.dim_rot_mat_1 * 3
self.useBN = False
self.fitting_net_variables = None
self.mixed_prec = None
def get_sel_type(self) -> List[int]:
"""
Get selected atom types
"""
return self.sel_type
def get_out_size(self) -> int:
"""
Get the output size. Should be 9
"""
return 9
def compute_input_stats(self,
all_stat,
protection = 1e-2):
"""
Compute the input statistics
Parameters
----------
all_stat
Dictionary of inputs.
can be prepared by model.make_stat_input
protection
Divided-by-zero protection
"""
if not ('polarizability' in all_stat.keys()):
self.avgeig = np.zeros([9])
warnings.warn('no polarizability data, cannot do data stat. use zeros as guess')
return
data = all_stat['polarizability']
all_tmp = []
for ss in range(len(data)):
tmp = np.concatenate(data[ss], axis = 0)
tmp = np.reshape(tmp, [-1, 3, 3])
tmp,_ = np.linalg.eig(tmp)
tmp = np.absolute(tmp)
tmp = np.sort(tmp, axis = 1)
all_tmp.append(tmp)
all_tmp = np.concatenate(all_tmp, axis = 1)
self.avgeig = np.average(all_tmp, axis = 0)
# YWolfeee: support polar normalization, initialize to a more appropriate point
if self.shift_diag:
mean_polar = np.zeros([len(self.sel_type), 9])
sys_matrix, polar_bias = [], []
for ss in range(len(all_stat['type'])):
atom_has_polar = [w for w in all_stat['type'][ss][0] if (w in self.sel_type)] # select atom with polar
if all_stat['find_atomic_polarizability'][ss] > 0.0:
for itype in range(len(self.sel_type)): # Atomic polar mode, should specify the atoms
index_lis = [index for index, w in enumerate(atom_has_polar) \
if atom_has_polar[index] == self.sel_type[itype]] # select index in this type
sys_matrix.append(np.zeros((1,len(self.sel_type))))
sys_matrix[-1][0,itype] = len(index_lis)
polar_bias.append(np.sum(
all_stat['atomic_polarizability'][ss].reshape((-1,9))[index_lis],axis=0).reshape((1,9)))
else: # No atomic polar in this system, so it should have global polar
if not all_stat['find_polarizability'][ss] > 0.0: # This system is jsut a joke?
continue
# Till here, we have global polar
sys_matrix.append(np.zeros((1,len(self.sel_type)))) # add a line in the equations
for itype in range(len(self.sel_type)): # Atomic polar mode, should specify the atoms
index_lis = [index for index, w in enumerate(atom_has_polar) \
if atom_has_polar[index] == self.sel_type[itype]] # select index in this type
sys_matrix[-1][0,itype] = len(index_lis)
# add polar_bias
polar_bias.append(all_stat['polarizability'][ss].reshape((1,9)))
matrix, bias = np.concatenate(sys_matrix,axis=0), np.concatenate(polar_bias,axis=0)
atom_polar,_,_,_ \
= np.linalg.lstsq(matrix, bias, rcond = 1e-3)
for itype in range(len(self.sel_type)):
self.constant_matrix[itype] = np.mean(np.diagonal(atom_polar[itype].reshape((3,3))))
@cast_precision
def build (self,
input_d : tf.Tensor,
rot_mat : tf.Tensor,
natoms : tf.Tensor,
reuse : bool = None,
suffix : str = '') :
"""
Build the computational graph for fitting net
Parameters
----------
input_d
The input descriptor
rot_mat
The rotation matrix from the descriptor.
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
reuse
The weights in the networks should be reused when get the variable.
suffix
Name suffix to identify this descriptor
Returns
-------
atomic_polar
The atomic polarizability
"""
start_index = 0
inputs = tf.reshape(input_d, [-1, self.dim_descrpt * natoms[0]])
rot_mat = tf.reshape(rot_mat, [-1, self.dim_rot_mat * natoms[0]])
count = 0
outs_list = []
for type_i in range(self.ntypes):
# cut-out inputs
inputs_i = tf.slice (inputs,
[ 0, start_index* self.dim_descrpt],
[-1, natoms[2+type_i]* self.dim_descrpt] )
inputs_i = tf.reshape(inputs_i, [-1, self.dim_descrpt])
rot_mat_i = tf.slice (rot_mat,
[ 0, start_index* self.dim_rot_mat],
[-1, natoms[2+type_i]* self.dim_rot_mat] )
rot_mat_i = tf.reshape(rot_mat_i, [-1, self.dim_rot_mat_1, 3])
start_index += natoms[2+type_i]
if not type_i in self.sel_type :
continue
layer = inputs_i
for ii in range(0,len(self.n_neuron)) :
if ii >= 1 and self.n_neuron[ii] == self.n_neuron[ii-1] :
layer+= one_layer(layer, self.n_neuron[ii], name='layer_'+str(ii)+'_type_'+str(type_i)+suffix, reuse=reuse, seed = self.seed, use_timestep = self.resnet_dt, activation_fn = self.fitting_activation_fn, precision = self.fitting_precision, uniform_seed = self.uniform_seed, initial_variables = self.fitting_net_variables, mixed_prec = self.mixed_prec)
else :
layer = one_layer(layer, self.n_neuron[ii], name='layer_'+str(ii)+'_type_'+str(type_i)+suffix, reuse=reuse, seed = self.seed, activation_fn = self.fitting_activation_fn, precision = self.fitting_precision, uniform_seed = self.uniform_seed, initial_variables = self.fitting_net_variables, mixed_prec = self.mixed_prec)
if (not self.uniform_seed) and (self.seed is not None): self.seed += self.seed_shift
if self.fit_diag :
bavg = np.zeros(self.dim_rot_mat_1)
# bavg[0] = self.avgeig[0]
# bavg[1] = self.avgeig[1]
# bavg[2] = self.avgeig[2]
# (nframes x natoms) x naxis
final_layer = one_layer(layer, self.dim_rot_mat_1, activation_fn = None, name='final_layer_type_'+str(type_i)+suffix, reuse=reuse, seed = self.seed, bavg = bavg, precision = self.fitting_precision, uniform_seed = self.uniform_seed, initial_variables = self.fitting_net_variables, mixed_prec = self.mixed_prec, final_layer = True)
if (not self.uniform_seed) and (self.seed is not None): self.seed += self.seed_shift
# (nframes x natoms) x naxis
final_layer = tf.reshape(final_layer, [tf.shape(inputs)[0] * natoms[2+type_i], self.dim_rot_mat_1])
# (nframes x natoms) x naxis x naxis
final_layer = tf.matrix_diag(final_layer)
else :
bavg = np.zeros(self.dim_rot_mat_1*self.dim_rot_mat_1)
# bavg[0*self.dim_rot_mat_1+0] = self.avgeig[0]
# bavg[1*self.dim_rot_mat_1+1] = self.avgeig[1]
# bavg[2*self.dim_rot_mat_1+2] = self.avgeig[2]
# (nframes x natoms) x (naxis x naxis)
final_layer = one_layer(layer, self.dim_rot_mat_1*self.dim_rot_mat_1, activation_fn = None, name='final_layer_type_'+str(type_i)+suffix, reuse=reuse, seed = self.seed, bavg = bavg, precision = self.fitting_precision, uniform_seed = self.uniform_seed, initial_variables = self.fitting_net_variables, mixed_prec = self.mixed_prec, final_layer = True)
if (not self.uniform_seed) and (self.seed is not None): self.seed += self.seed_shift
# (nframes x natoms) x naxis x naxis
final_layer = tf.reshape(final_layer, [tf.shape(inputs)[0] * natoms[2+type_i], self.dim_rot_mat_1, self.dim_rot_mat_1])
# (nframes x natoms) x naxis x naxis
final_layer = final_layer + tf.transpose(final_layer, perm = [0,2,1])
# (nframes x natoms) x naxis x 3(coord)
final_layer = tf.matmul(final_layer, rot_mat_i)
# (nframes x natoms) x 3(coord) x 3(coord)
final_layer = tf.matmul(rot_mat_i, final_layer, transpose_a = True)
# nframes x natoms x 3 x 3
final_layer = tf.reshape(final_layer, [tf.shape(inputs)[0], natoms[2+type_i], 3, 3])
# shift and scale
sel_type_idx = self.sel_type.index(type_i)
final_layer = final_layer * self.scale[sel_type_idx]
final_layer = final_layer + self.constant_matrix[sel_type_idx] * tf.eye(3, batch_shape=[tf.shape(inputs)[0], natoms[2+type_i]], dtype = GLOBAL_TF_FLOAT_PRECISION)
# concat the results
outs_list.append(final_layer)
count += 1
outs = tf.concat(outs_list, axis = 1)
tf.summary.histogram('fitting_net_output', outs)
return tf.reshape(outs, [-1])
def init_variables(self,
graph: tf.Graph,
graph_def: tf.GraphDef,
suffix : str = "",
) -> None:
"""
Init the fitting net variables with the given dict
Parameters
----------
graph : tf.Graph
The input frozen model graph
graph_def : tf.GraphDef
The input frozen model graph_def
suffix : str
suffix to name scope
"""
self.fitting_net_variables = get_fitting_net_variables_from_graph_def(graph_def)
def enable_mixed_precision(self, mixed_prec : dict = None) -> None:
"""
Reveive the mixed precision setting.
Parameters
----------
mixed_prec
The mixed precision setting used in the embedding net
"""
self.mixed_prec = mixed_prec
self.fitting_precision = get_precision(mixed_prec['output_prec'])
class GlobalPolarFittingSeA () :
"""
Fit the system polarizability with descriptor se_a
Parameters
----------
descrpt : tf.Tensor
The descrptor
neuron : List[int]
Number of neurons in each hidden layer of the fitting net
resnet_dt : bool
Time-step `dt` in the resnet construction:
y = x + dt * \phi (Wx + b)
sel_type : List[int]
The atom types selected to have an atomic polarizability prediction
fit_diag : bool
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 : List[float]
The output of the fitting net (polarizability matrix) for type i atom will be scaled by scale[i]
diag_shift : List[float]
The diagonal part of the polarizability matrix of type i will be shifted by diag_shift[i]. The shift operation is carried out after scale.
seed : int
Random seed for initializing the network parameters.
activation_function : str
The activation function in the embedding net. Supported options are {0}
precision : str
The precision of the embedding net parameters. Supported options are {1}
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()), list_to_doc(PRECISION_DICT.keys()))
def __init__ (self,
descrpt : tf.Tensor,
neuron : List[int] = [120,120,120],
resnet_dt : bool = True,
sel_type : List[int] = None,
fit_diag : bool = True,
scale : List[float] = None,
diag_shift : List[float] = None,
seed : int = None,
activation_function : str = 'tanh',
precision : str = 'default'
) -> None:
"""
Constructor
"""
if not isinstance(descrpt, DescrptSeA) :
raise RuntimeError('GlobalPolarFittingSeA only supports DescrptSeA')
self.ntypes = descrpt.get_ntypes()
self.dim_descrpt = descrpt.get_dim_out()
self.polar_fitting = PolarFittingSeA(descrpt,
neuron,
resnet_dt,
sel_type,
fit_diag,
scale,
diag_shift,
seed,
activation_function,
precision)
def get_sel_type(self) -> int:
"""
Get selected atom types
"""
return self.polar_fitting.get_sel_type()
def get_out_size(self) -> int:
"""
Get the output size. Should be 9
"""
return self.polar_fitting.get_out_size()
def build (self,
input_d,
rot_mat,
natoms,
reuse = None,
suffix = '') -> tf.Tensor:
"""
Build the computational graph for fitting net
Parameters
----------
input_d
The input descriptor
rot_mat
The rotation matrix from the descriptor.
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
reuse
The weights in the networks should be reused when get the variable.
suffix
Name suffix to identify this descriptor
Returns
-------
polar
The system polarizability
"""
inputs = tf.reshape(input_d, [-1, self.dim_descrpt * natoms[0]])
outs = self.polar_fitting.build(input_d, rot_mat, natoms, reuse, suffix)
# nframes x natoms x 9
outs = tf.reshape(outs, [tf.shape(inputs)[0], -1, 9])
outs = tf.reduce_sum(outs, axis = 1)
tf.summary.histogram('fitting_net_output', outs)
return tf.reshape(outs, [-1])
def init_variables(self,
graph: tf.Graph,
graph_def: tf.GraphDef,
suffix : str = "",
) -> None:
"""
Init the fitting net variables with the given dict
Parameters
----------
graph : tf.Graph
The input frozen model graph
graph_def : tf.GraphDef
The input frozen model graph_def
suffix : str
suffix to name scope
"""
self.polar_fitting.init_variables(graph=graph, graph_def=graph_def, suffix=suffix)
def enable_mixed_precision(self, mixed_prec : dict = None) -> None:
"""
Reveive the mixed precision setting.
Parameters
----------
mixed_prec
The mixed precision setting used in the embedding net
"""
self.polar_fitting.enable_mixed_precision(mixed_prec)
class DescrptSeA(DescrptSe):
r"""DeepPot-SE constructed from all information (both angular and radial) of
atomic configurations. The embedding takes the distance between atoms as input.
The descriptor :math:`\mathcal{D}^i \in \mathcal{R}^{M_1 \times M_2}` is given by [1]_
.. math::
\mathcal{D}^i = (\mathcal{G}^i)^T \mathcal{R}^i (\mathcal{R}^i)^T \mathcal{G}^i_<
where :math:`\mathcal{R}^i \in \mathbb{R}^{N \times 4}` is the coordinate
matrix, and each row of :math:`\mathcal{R}^i` can be constructed as follows
.. math::
(\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 :math:`\mathbf{R}_{ji}=\mathbf{R}_j-\mathbf{R}_i = (x_{ji}, y_{ji}, z_{ji})` is
the relative coordinate and :math:`r_{ji}=\lVert \mathbf{R}_{ji} \lVert` is its norm.
The switching function :math:`s(r)` is defined as:
.. math::
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}
Each row of the embedding matrix :math:`\mathcal{G}^i \in \mathbb{R}^{N \times M_1}` consists of outputs
of a embedding network :math:`\mathcal{N}` of :math:`s(r_{ji})`:
.. math::
(\mathcal{G}^i)_j = \mathcal{N}(s(r_{ji}))
:math:`\mathcal{G}^i_< \in \mathbb{R}^{N \times M_2}` takes first :math:`M_2`$` columns of
:math:`\mathcal{G}^i`$`. The equation of embedding network :math:`\mathcal{N}` can be found at
:meth:`deepmd.utils.network.embedding_net`.
Parameters
----------
rcut
The cut-off radius :math:`r_c`
rcut_smth
From where the environment matrix should be smoothed :math:`r_s`
sel : list[str]
sel[i] specifies the maxmum number of type i atoms in the cut-off radius
neuron : list[int]
Number of neurons in each hidden layers of the embedding net :math:`\mathcal{N}`
axis_neuron
Number of the axis neuron :math:`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_types : List[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.
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()),
list_to_doc(PRECISION_DICT.keys()))
def __init__(self,
rcut: float,
rcut_smth: float,
sel: List[str],
neuron: List[int] = [24, 48, 96],
axis_neuron: int = 8,
resnet_dt: bool = False,
trainable: bool = True,
seed: int = None,
type_one_side: bool = True,
exclude_types: List[List[int]] = [],
set_davg_zero: bool = False,
activation_function: str = 'tanh',
precision: str = 'default',
uniform_seed: bool = False) -> None:
"""
Constructor
"""
self.sel_a = sel
self.rcut_r = rcut
self.rcut_r_smth = rcut_smth
self.filter_neuron = neuron
self.n_axis_neuron = axis_neuron
self.filter_resnet_dt = resnet_dt
self.seed = seed
self.uniform_seed = uniform_seed
self.seed_shift = embedding_net_rand_seed_shift(self.filter_neuron)
self.trainable = trainable
self.compress_activation_fn = get_activation_func(activation_function)
self.filter_activation_fn = get_activation_func(activation_function)
self.filter_precision = get_precision(precision)
self.exclude_types = set()
for tt in exclude_types:
assert (len(tt) == 2)
self.exclude_types.add((tt[0], tt[1]))
self.exclude_types.add((tt[1], tt[0]))
self.set_davg_zero = set_davg_zero
self.type_one_side = type_one_side
if self.type_one_side and len(exclude_types) != 0:
raise RuntimeError(
'"type_one_side" is not compatible with "exclude_types"')
# descrpt config
self.sel_r = [0 for ii in range(len(self.sel_a))]
self.ntypes = len(self.sel_a)
assert (self.ntypes == len(self.sel_r))
self.rcut_a = -1
# numb of neighbors and numb of descrptors
self.nnei_a = np.cumsum(self.sel_a)[-1]
self.nnei_r = np.cumsum(self.sel_r)[-1]
self.nnei = self.nnei_a + self.nnei_r
self.ndescrpt_a = self.nnei_a * 4
self.ndescrpt_r = self.nnei_r * 1
self.ndescrpt = self.ndescrpt_a + self.ndescrpt_r
self.useBN = False
self.dstd = None
self.davg = None
self.compress = False
self.embedding_net_variables = None
self.place_holders = {}
nei_type = np.array([])
for ii in range(self.ntypes):
nei_type = np.append(nei_type,
ii * np.ones(self.sel_a[ii])) # like a mask
self.nei_type = tf.constant(nei_type, dtype=tf.int32)
avg_zero = np.zeros([self.ntypes,
self.ndescrpt]).astype(GLOBAL_NP_FLOAT_PRECISION)
std_ones = np.ones([self.ntypes,
self.ndescrpt]).astype(GLOBAL_NP_FLOAT_PRECISION)
sub_graph = tf.Graph()
with sub_graph.as_default():
name_pfx = 'd_sea_'
for ii in ['coord', 'box']:
self.place_holders[ii] = tf.placeholder(
GLOBAL_NP_FLOAT_PRECISION, [None, None],
name=name_pfx + 't_' + ii)
self.place_holders['type'] = tf.placeholder(tf.int32, [None, None],
name=name_pfx +
't_type')
self.place_holders['natoms_vec'] = tf.placeholder(
tf.int32, [self.ntypes + 2], name=name_pfx + 't_natoms')
self.place_holders['default_mesh'] = tf.placeholder(
tf.int32, [None], name=name_pfx + 't_mesh')
self.stat_descrpt, descrpt_deriv, rij, nlist \
= op_module.prod_env_mat_a(self.place_holders['coord'],
self.place_holders['type'],
self.place_holders['natoms_vec'],
self.place_holders['box'],
self.place_holders['default_mesh'],
tf.constant(avg_zero),
tf.constant(std_ones),
rcut_a = self.rcut_a,
rcut_r = self.rcut_r,
rcut_r_smth = self.rcut_r_smth,
sel_a = self.sel_a,
sel_r = self.sel_r)
self.sub_sess = tf.Session(graph=sub_graph,
config=default_tf_session_config)
def get_rcut(self) -> float:
"""
Returns the cut-off radius
"""
return self.rcut_r
def get_ntypes(self) -> int:
"""
Returns the number of atom types
"""
return self.ntypes
def get_dim_out(self) -> int:
"""
Returns the output dimension of this descriptor
"""
return self.filter_neuron[-1] * self.n_axis_neuron
def get_dim_rot_mat_1(self) -> int:
"""
Returns the first dimension of the rotation matrix. The rotation is of shape dim_1 x 3
"""
return self.filter_neuron[-1]
def get_nlist(self) -> Tuple[tf.Tensor, tf.Tensor, List[int], List[int]]:
"""
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
"""
return self.nlist, self.rij, self.sel_a, self.sel_r
def compute_input_stats(self, data_coord: list, data_box: list,
data_atype: list, natoms_vec: list, mesh: list,
input_dict: dict) -> None:
"""
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
"""
all_davg = []
all_dstd = []
if True:
sumr = []
suma = []
sumn = []
sumr2 = []
suma2 = []
for cc, bb, tt, nn, mm in zip(data_coord, data_box, data_atype,
natoms_vec, mesh):
sysr,sysr2,sysa,sysa2,sysn \
= self._compute_dstats_sys_smth(cc,bb,tt,nn,mm)
sumr.append(sysr)
suma.append(sysa)
sumn.append(sysn)
sumr2.append(sysr2)
suma2.append(sysa2)
sumr = np.sum(sumr, axis=0)
suma = np.sum(suma, axis=0)
sumn = np.sum(sumn, axis=0)
sumr2 = np.sum(sumr2, axis=0)
suma2 = np.sum(suma2, axis=0)
for type_i in range(self.ntypes):
davgunit = [sumr[type_i] / (sumn[type_i] + 1e-15), 0, 0, 0]
dstdunit = [
self._compute_std(sumr2[type_i], sumr[type_i],
sumn[type_i]),
self._compute_std(suma2[type_i], suma[type_i],
sumn[type_i]),
self._compute_std(suma2[type_i], suma[type_i],
sumn[type_i]),
self._compute_std(suma2[type_i], suma[type_i],
sumn[type_i])
]
davg = np.tile(davgunit, self.ndescrpt // 4)
dstd = np.tile(dstdunit, self.ndescrpt // 4)
all_davg.append(davg)
all_dstd.append(dstd)
if not self.set_davg_zero:
self.davg = np.array(all_davg)
self.dstd = np.array(all_dstd)
def enable_compression(
self,
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:
"""
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
suffix : str, optional
The suffix of the scope
"""
assert (
not self.filter_resnet_dt
), "Model compression error: descriptor resnet_dt must be false!"
self.compress = True
self.table = DPTabulate(model_file,
self.type_one_side,
self.exclude_types,
self.compress_activation_fn,
suffix=suffix)
self.table_config = [
table_extrapolate, table_stride_1, table_stride_2, check_frequency
]
self.lower, self.upper \
= self.table.build(min_nbor_dist,
table_extrapolate,
table_stride_1,
table_stride_2)
graph, _ = load_graph_def(model_file)
self.davg = get_tensor_by_name_from_graph(
graph, 'descrpt_attr%s/t_avg' % suffix)
self.dstd = get_tensor_by_name_from_graph(
graph, 'descrpt_attr%s/t_std' % suffix)
def build(self,
coord_: tf.Tensor,
atype_: tf.Tensor,
natoms: tf.Tensor,
box_: tf.Tensor,
mesh: tf.Tensor,
input_dict: dict,
reuse: bool = None,
suffix: str = '') -> tf.Tensor:
"""
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
"""
davg = self.davg
dstd = self.dstd
with tf.variable_scope('descrpt_attr' + suffix, reuse=reuse):
if davg is None:
davg = np.zeros([self.ntypes, self.ndescrpt])
if dstd is None:
dstd = np.ones([self.ntypes, self.ndescrpt])
t_rcut = tf.constant(np.max([self.rcut_r, self.rcut_a]),
name='rcut',
dtype=GLOBAL_TF_FLOAT_PRECISION)
t_ntypes = tf.constant(self.ntypes, name='ntypes', dtype=tf.int32)
t_ndescrpt = tf.constant(self.ndescrpt,
name='ndescrpt',
dtype=tf.int32)
t_sel = tf.constant(self.sel_a, name='sel', dtype=tf.int32)
self.t_avg = tf.get_variable(
't_avg',
davg.shape,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(davg))
self.t_std = tf.get_variable(
't_std',
dstd.shape,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(dstd))
coord = tf.reshape(coord_, [-1, natoms[1] * 3])
box = tf.reshape(box_, [-1, 9])
atype = tf.reshape(atype_, [-1, natoms[1]])
self.descrpt, self.descrpt_deriv, self.rij, self.nlist \
= op_module.prod_env_mat_a (coord,
atype,
natoms,
box,
mesh,
self.t_avg,
self.t_std,
rcut_a = self.rcut_a,
rcut_r = self.rcut_r,
rcut_r_smth = self.rcut_r_smth,
sel_a = self.sel_a,
sel_r = self.sel_r)
# only used when tensorboard was set as true
tf.summary.histogram('descrpt', self.descrpt)
tf.summary.histogram('rij', self.rij)
tf.summary.histogram('nlist', self.nlist)
self.descrpt_reshape = tf.reshape(self.descrpt, [-1, self.ndescrpt])
self._identity_tensors(suffix=suffix)
self.dout, self.qmat = self._pass_filter(self.descrpt_reshape,
atype,
natoms,
input_dict,
suffix=suffix,
reuse=reuse,
trainable=self.trainable)
# only used when tensorboard was set as true
tf.summary.histogram('embedding_net_output', self.dout)
return self.dout
def get_rot_mat(self) -> tf.Tensor:
"""
Get rotational matrix
"""
return self.qmat
def prod_force_virial(
self, atom_ener: tf.Tensor,
natoms: tf.Tensor) -> Tuple[tf.Tensor, tf.Tensor, tf.Tensor]:
"""
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
"""
[net_deriv] = tf.gradients(atom_ener, self.descrpt_reshape)
tf.summary.histogram('net_derivative', net_deriv)
net_deriv_reshape = tf.reshape(net_deriv,
[-1, natoms[0] * self.ndescrpt])
force \
= op_module.prod_force_se_a (net_deriv_reshape,
self.descrpt_deriv,
self.nlist,
natoms,
n_a_sel = self.nnei_a,
n_r_sel = self.nnei_r)
virial, atom_virial \
= op_module.prod_virial_se_a (net_deriv_reshape,
self.descrpt_deriv,
self.rij,
self.nlist,
natoms,
n_a_sel = self.nnei_a,
n_r_sel = self.nnei_r)
tf.summary.histogram('force', force)
tf.summary.histogram('virial', virial)
tf.summary.histogram('atom_virial', atom_virial)
return force, virial, atom_virial
def _pass_filter(self,
inputs,
atype,
natoms,
input_dict,
reuse=None,
suffix='',
trainable=True):
if input_dict is not None:
type_embedding = input_dict.get('type_embedding', None)
else:
type_embedding = None
start_index = 0
inputs = tf.reshape(inputs, [-1, self.ndescrpt * natoms[0]])
output = []
output_qmat = []
if not self.type_one_side and type_embedding is None:
for type_i in range(self.ntypes):
inputs_i = tf.slice(inputs, [0, start_index * self.ndescrpt],
[-1, natoms[2 + type_i] * self.ndescrpt])
inputs_i = tf.reshape(inputs_i, [-1, self.ndescrpt])
layer, qmat = self._filter(
tf.cast(inputs_i, self.filter_precision),
type_i,
name='filter_type_' + str(type_i) + suffix,
natoms=natoms,
reuse=reuse,
trainable=trainable,
activation_fn=self.filter_activation_fn)
layer = tf.reshape(layer, [
tf.shape(inputs)[0],
natoms[2 + type_i] * self.get_dim_out()
])
qmat = tf.reshape(qmat, [
tf.shape(inputs)[0],
natoms[2 + type_i] * self.get_dim_rot_mat_1() * 3
])
output.append(layer)
output_qmat.append(qmat)
start_index += natoms[2 + type_i]
else:
inputs_i = inputs
inputs_i = tf.reshape(inputs_i, [-1, self.ndescrpt])
type_i = -1
layer, qmat = self._filter(tf.cast(inputs_i,
self.filter_precision),
type_i,
name='filter_type_all' + suffix,
natoms=natoms,
reuse=reuse,
trainable=trainable,
activation_fn=self.filter_activation_fn,
type_embedding=type_embedding)
layer = tf.reshape(
layer, [tf.shape(inputs)[0], natoms[0] * self.get_dim_out()])
qmat = tf.reshape(qmat, [
tf.shape(inputs)[0], natoms[0] * self.get_dim_rot_mat_1() * 3
])
output.append(layer)
output_qmat.append(qmat)
output = tf.concat(output, axis=1)
output_qmat = tf.concat(output_qmat, axis=1)
return output, output_qmat
def _compute_dstats_sys_smth(self, data_coord, data_box, data_atype,
natoms_vec, mesh):
dd_all \
= run_sess(self.sub_sess, self.stat_descrpt,
feed_dict = {
self.place_holders['coord']: data_coord,
self.place_holders['type']: data_atype,
self.place_holders['natoms_vec']: natoms_vec,
self.place_holders['box']: data_box,
self.place_holders['default_mesh']: mesh,
})
natoms = natoms_vec
dd_all = np.reshape(dd_all, [-1, self.ndescrpt * natoms[0]])
start_index = 0
sysr = []
sysa = []
sysn = []
sysr2 = []
sysa2 = []
for type_i in range(self.ntypes):
end_index = start_index + self.ndescrpt * natoms[2 + type_i]
dd = dd_all[:, start_index:end_index]
dd = np.reshape(dd, [-1, self.ndescrpt])
start_index = end_index
# compute
dd = np.reshape(dd, [-1, 4])
ddr = dd[:, :1]
dda = dd[:, 1:]
sumr = np.sum(ddr)
suma = np.sum(dda) / 3.
sumn = dd.shape[0]
sumr2 = np.sum(np.multiply(ddr, ddr))
suma2 = np.sum(np.multiply(dda, dda)) / 3.
sysr.append(sumr)
sysa.append(suma)
sysn.append(sumn)
sysr2.append(sumr2)
sysa2.append(suma2)
return sysr, sysr2, sysa, sysa2, sysn
def _compute_std(self, sumv2, sumv, sumn):
if sumn == 0:
return 1e-2
val = np.sqrt(sumv2 / sumn - np.multiply(sumv / sumn, sumv / sumn))
if np.abs(val) < 1e-2:
val = 1e-2
return val
def _concat_type_embedding(
self,
xyz_scatter,
nframes,
natoms,
type_embedding,
):
'''Concatenate `type_embedding` of neighbors and `xyz_scatter`.
If not self.type_one_side, concatenate `type_embedding` of center atoms as well.
Parameters
----------
xyz_scatter:
shape is [nframes*natoms[0]*self.nnei, 1]
nframes:
shape is []
natoms:
shape is [1+1+self.ntypes]
type_embedding:
shape is [self.ntypes, Y] where Y=jdata['type_embedding']['neuron'][-1]
Returns
-------
embedding:
environment of each atom represented by embedding.
'''
te_out_dim = type_embedding.get_shape().as_list()[-1]
nei_embed = tf.nn.embedding_lookup(
type_embedding,
tf.cast(self.nei_type,
dtype=tf.int32)) # shape is [self.nnei, 1+te_out_dim]
nei_embed = tf.tile(
nei_embed,
(nframes * natoms[0],
1)) # shape is [nframes*natoms[0]*self.nnei, te_out_dim]
nei_embed = tf.reshape(nei_embed, [-1, te_out_dim])
embedding_input = tf.concat(
[xyz_scatter, nei_embed],
1) # shape is [nframes*natoms[0]*self.nnei, 1+te_out_dim]
if not self.type_one_side:
atm_embed = embed_atom_type(
self.ntypes, natoms,
type_embedding) # shape is [natoms[0], te_out_dim]
atm_embed = tf.tile(
atm_embed,
(nframes, self.nnei
)) # shape is [nframes*natoms[0], self.nnei*te_out_dim]
atm_embed = tf.reshape(
atm_embed,
[-1, te_out_dim
]) # shape is [nframes*natoms[0]*self.nnei, te_out_dim]
embedding_input = tf.concat(
[embedding_input, atm_embed], 1
) # shape is [nframes*natoms[0]*self.nnei, 1+te_out_dim+te_out_dim]
return embedding_input
def _filter_lower(
self,
type_i,
type_input,
start_index,
incrs_index,
inputs,
nframes,
natoms,
type_embedding=None,
is_exclude=False,
activation_fn=None,
bavg=0.0,
stddev=1.0,
trainable=True,
suffix='',
):
"""
input env matrix, returns R.G
"""
outputs_size = [1] + self.filter_neuron
# cut-out inputs
# with natom x (nei_type_i x 4)
inputs_i = tf.slice(inputs, [0, start_index * 4],
[-1, incrs_index * 4])
shape_i = inputs_i.get_shape().as_list()
natom = tf.shape(inputs_i)[0]
# with (natom x nei_type_i) x 4
inputs_reshape = tf.reshape(inputs_i, [-1, 4])
# with (natom x nei_type_i) x 1
xyz_scatter = tf.reshape(tf.slice(inputs_reshape, [0, 0], [-1, 1]),
[-1, 1])
if type_embedding is not None:
type_embedding = tf.cast(type_embedding, self.filter_precision)
xyz_scatter = self._concat_type_embedding(xyz_scatter, nframes,
natoms, type_embedding)
if self.compress:
raise RuntimeError(
'compression of type embedded descriptor is not supported at the moment'
)
# with (natom x nei_type_i) x out_size
if self.compress and (not is_exclude):
info = [
self.lower, self.upper, self.upper * self.table_config[0],
self.table_config[1], self.table_config[2],
self.table_config[3]
]
if self.type_one_side:
net = 'filter_-1_net_' + str(type_i)
else:
net = 'filter_' + str(type_input) + '_net_' + str(type_i)
return op_module.tabulate_fusion(
tf.cast(self.table.data[net], self.filter_precision),
info,
xyz_scatter,
tf.reshape(inputs_i, [natom, shape_i[1] // 4, 4]),
last_layer_size=outputs_size[-1])
else:
if (not is_exclude):
xyz_scatter = embedding_net(
xyz_scatter,
self.filter_neuron,
self.filter_precision,
activation_fn=activation_fn,
resnet_dt=self.filter_resnet_dt,
name_suffix=suffix,
stddev=stddev,
bavg=bavg,
seed=self.seed,
trainable=trainable,
uniform_seed=self.uniform_seed,
initial_variables=self.embedding_net_variables)
if (not self.uniform_seed) and (self.seed is not None):
self.seed += self.seed_shift
else:
# we can safely return the final xyz_scatter filled with zero directly
return tf.cast(tf.fill((natom, 4, outputs_size[-1]), 0.),
GLOBAL_TF_FLOAT_PRECISION)
# natom x nei_type_i x out_size
xyz_scatter = tf.reshape(xyz_scatter,
(-1, shape_i[1] // 4, outputs_size[-1]))
# When using tf.reshape(inputs_i, [-1, shape_i[1]//4, 4]) below
# [588 24] -> [588 6 4] correct
# but if sel is zero
# [588 0] -> [147 0 4] incorrect; the correct one is [588 0 4]
# So we need to explicitly assign the shape to tf.shape(inputs_i)[0] instead of -1
return tf.matmul(tf.reshape(inputs_i, [natom, shape_i[1] // 4, 4]),
xyz_scatter,
transpose_a=True)
def _filter(self,
inputs,
type_input,
natoms,
type_embedding=None,
activation_fn=tf.nn.tanh,
stddev=1.0,
bavg=0.0,
name='linear',
reuse=None,
trainable=True):
nframes = tf.shape(tf.reshape(inputs,
[-1, natoms[0], self.ndescrpt]))[0]
# natom x (nei x 4)
shape = inputs.get_shape().as_list()
outputs_size = [1] + self.filter_neuron
outputs_size_2 = self.n_axis_neuron
all_excluded = all([(type_input, type_i) in self.exclude_types
for type_i in range(self.ntypes)])
if all_excluded:
# all types are excluded so result and qmat should be zeros
# we can safaly return a zero matrix...
# See also https://stackoverflow.com/a/34725458/9567349
# result: natom x outputs_size x outputs_size_2
# qmat: natom x outputs_size x 3
natom = tf.shape(inputs)[0]
result = tf.cast(
tf.fill((natom, outputs_size_2, outputs_size[-1]), 0.),
GLOBAL_TF_FLOAT_PRECISION)
qmat = tf.cast(tf.fill((natom, outputs_size[-1], 3), 0.),
GLOBAL_TF_FLOAT_PRECISION)
return result, qmat
with tf.variable_scope(name, reuse=reuse):
start_index = 0
type_i = 0
# natom x 4 x outputs_size
if type_embedding is None:
for type_i in range(self.ntypes):
ret = self._filter_lower(type_i,
type_input,
start_index,
self.sel_a[type_i],
inputs,
nframes,
natoms,
type_embedding=type_embedding,
is_exclude=(type_input, type_i)
in self.exclude_types,
activation_fn=activation_fn,
stddev=stddev,
bavg=bavg,
trainable=trainable,
suffix="_" + str(type_i))
if type_i == 0:
xyz_scatter_1 = ret
elif (type_input, type_i) not in self.exclude_types:
# add zero is meaningless; skip
xyz_scatter_1 += ret
start_index += self.sel_a[type_i]
else:
xyz_scatter_1 = self._filter_lower(
type_i,
type_input,
start_index,
np.cumsum(self.sel_a)[-1],
inputs,
nframes,
natoms,
type_embedding=type_embedding,
is_exclude=False,
activation_fn=activation_fn,
stddev=stddev,
bavg=bavg,
trainable=trainable)
# natom x nei x outputs_size
# xyz_scatter = tf.concat(xyz_scatter_total, axis=1)
# natom x nei x 4
# inputs_reshape = tf.reshape(inputs, [-1, shape[1]//4, 4])
# natom x 4 x outputs_size
# xyz_scatter_1 = tf.matmul(inputs_reshape, xyz_scatter, transpose_a = True)
xyz_scatter_1 = xyz_scatter_1 * (4.0 / shape[1])
# natom x 4 x outputs_size_2
xyz_scatter_2 = tf.slice(xyz_scatter_1, [0, 0, 0],
[-1, -1, outputs_size_2])
# # natom x 3 x outputs_size_2
# qmat = tf.slice(xyz_scatter_2, [0,1,0], [-1, 3, -1])
# natom x 3 x outputs_size_1
qmat = tf.slice(xyz_scatter_1, [0, 1, 0], [-1, 3, -1])
# natom x outputs_size_1 x 3
qmat = tf.transpose(qmat, perm=[0, 2, 1])
# natom x outputs_size x outputs_size_2
result = tf.matmul(xyz_scatter_1, xyz_scatter_2, transpose_a=True)
# natom x (outputs_size x outputs_size_2)
result = tf.reshape(result,
[-1, outputs_size_2 * outputs_size[-1]])
return result, qmat
class DescrptSeR (Descriptor):
"""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
sel : list[str]
sel[i] specifies the maxmum number of type i atoms in the cut-off radius
neuron : list[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_types : List[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
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()), list_to_doc(PRECISION_DICT.keys()))
def __init__ (self,
rcut: float,
rcut_smth: float,
sel: List[str],
neuron: List[int] = [24,48,96],
resnet_dt: bool = False,
trainable: bool = True,
seed: int = None,
type_one_side: bool = True,
exclude_types: List[List[int]] = [],
set_davg_zero: bool = False,
activation_function: str = 'tanh',
precision: str = 'default',
uniform_seed: bool = False
) -> None:
"""
Constructor
"""
# args = ClassArg()\
# .add('sel', list, must = True) \
# .add('rcut', float, default = 6.0) \
# .add('rcut_smth',float, default = 0.5) \
# .add('neuron', list, default = [10, 20, 40]) \
# .add('resnet_dt',bool, default = False) \
# .add('trainable',bool, default = True) \
# .add('seed', int) \
# .add('type_one_side', bool, default = False) \
# .add('exclude_types', list, default = []) \
# .add('set_davg_zero', bool, default = False) \
# .add("activation_function", str, default = "tanh") \
# .add("precision", str, default = "default")
# class_data = args.parse(jdata)
self.sel_r = sel
self.rcut = rcut
self.rcut_smth = rcut_smth
self.filter_neuron = neuron
self.filter_resnet_dt = resnet_dt
self.seed = seed
self.uniform_seed = uniform_seed
self.seed_shift = embedding_net_rand_seed_shift(self.filter_neuron)
self.trainable = trainable
self.filter_activation_fn = get_activation_func(activation_function)
self.filter_precision = get_precision(precision)
exclude_types = exclude_types
self.exclude_types = set()
for tt in exclude_types:
assert(len(tt) == 2)
self.exclude_types.add((tt[0], tt[1]))
self.exclude_types.add((tt[1], tt[0]))
self.set_davg_zero = set_davg_zero
self.type_one_side = type_one_side
# descrpt config
self.sel_a = [ 0 for ii in range(len(self.sel_r)) ]
self.ntypes = len(self.sel_r)
# numb of neighbors and numb of descrptors
self.nnei_a = np.cumsum(self.sel_a)[-1]
self.nnei_r = np.cumsum(self.sel_r)[-1]
self.nnei = self.nnei_a + self.nnei_r
self.ndescrpt_a = self.nnei_a * 4
self.ndescrpt_r = self.nnei_r * 1
self.ndescrpt = self.nnei_r
self.useBN = False
self.davg = None
self.dstd = None
self.place_holders = {}
avg_zero = np.zeros([self.ntypes,self.ndescrpt]).astype(GLOBAL_NP_FLOAT_PRECISION)
std_ones = np.ones ([self.ntypes,self.ndescrpt]).astype(GLOBAL_NP_FLOAT_PRECISION)
sub_graph = tf.Graph()
with sub_graph.as_default():
name_pfx = 'd_ser_'
for ii in ['coord', 'box']:
self.place_holders[ii] = tf.placeholder(GLOBAL_NP_FLOAT_PRECISION, [None, None], name = name_pfx+'t_'+ii)
self.place_holders['type'] = tf.placeholder(tf.int32, [None, None], name=name_pfx+'t_type')
self.place_holders['natoms_vec'] = tf.placeholder(tf.int32, [self.ntypes+2], name=name_pfx+'t_natoms')
self.place_holders['default_mesh'] = tf.placeholder(tf.int32, [None], name=name_pfx+'t_mesh')
self.stat_descrpt, descrpt_deriv, rij, nlist \
= op_module.prod_env_mat_r(self.place_holders['coord'],
self.place_holders['type'],
self.place_holders['natoms_vec'],
self.place_holders['box'],
self.place_holders['default_mesh'],
tf.constant(avg_zero),
tf.constant(std_ones),
rcut = self.rcut,
rcut_smth = self.rcut_smth,
sel = self.sel_r)
self.sub_sess = tf.Session(graph = sub_graph, config=default_tf_session_config)
def get_rcut (self) :
"""
Returns the cut-off radisu
"""
return self.rcut
def get_ntypes (self) :
"""
Returns the number of atom types
"""
return self.ntypes
def get_dim_out (self) :
"""
Returns the output dimension of this descriptor
"""
return self.filter_neuron[-1]
def get_nlist (self) :
"""
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
"""
return self.nlist, self.rij, self.sel_a, self.sel_r
def compute_input_stats (self,
data_coord,
data_box,
data_atype,
natoms_vec,
mesh,
input_dict) :
"""
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
"""
all_davg = []
all_dstd = []
sumr = []
sumn = []
sumr2 = []
for cc,bb,tt,nn,mm in zip(data_coord,data_box,data_atype,natoms_vec,mesh) :
sysr,sysr2,sysn \
= self._compute_dstats_sys_se_r(cc,bb,tt,nn,mm)
sumr.append(sysr)
sumn.append(sysn)
sumr2.append(sysr2)
sumr = np.sum(sumr, axis = 0)
sumn = np.sum(sumn, axis = 0)
sumr2 = np.sum(sumr2, axis = 0)
for type_i in range(self.ntypes) :
davgunit = [sumr[type_i]/sumn[type_i]]
dstdunit = [self._compute_std(sumr2[type_i], sumr[type_i], sumn[type_i])]
davg = np.tile(davgunit, self.ndescrpt // 1)
dstd = np.tile(dstdunit, self.ndescrpt // 1)
all_davg.append(davg)
all_dstd.append(dstd)
if not self.set_davg_zero:
self.davg = np.array(all_davg)
self.dstd = np.array(all_dstd)
def build (self,
coord_ : tf.Tensor,
atype_ : tf.Tensor,
natoms : tf.Tensor,
box_ : tf.Tensor,
mesh : tf.Tensor,
input_dict : dict,
reuse : bool = None,
suffix : str = ''
) -> tf.Tensor:
"""
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
"""
davg = self.davg
dstd = self.dstd
with tf.variable_scope('descrpt_attr' + suffix, reuse = reuse) :
if davg is None:
davg = np.zeros([self.ntypes, self.ndescrpt])
if dstd is None:
dstd = np.ones ([self.ntypes, self.ndescrpt])
t_rcut = tf.constant(self.rcut,
name = 'rcut',
dtype = GLOBAL_TF_FLOAT_PRECISION)
t_ntypes = tf.constant(self.ntypes,
name = 'ntypes',
dtype = tf.int32)
t_ndescrpt = tf.constant(self.ndescrpt,
name = 'ndescrpt',
dtype = tf.int32)
t_sel = tf.constant(self.sel_a,
name = 'sel',
dtype = tf.int32)
self.t_avg = tf.get_variable('t_avg',
davg.shape,
dtype = GLOBAL_TF_FLOAT_PRECISION,
trainable = False,
initializer = tf.constant_initializer(davg))
self.t_std = tf.get_variable('t_std',
dstd.shape,
dtype = GLOBAL_TF_FLOAT_PRECISION,
trainable = False,
initializer = tf.constant_initializer(dstd))
coord = tf.reshape (coord_, [-1, natoms[1] * 3])
box = tf.reshape (box_, [-1, 9])
atype = tf.reshape (atype_, [-1, natoms[1]])
self.descrpt, self.descrpt_deriv, self.rij, self.nlist \
= op_module.prod_env_mat_r(coord,
atype,
natoms,
box,
mesh,
self.t_avg,
self.t_std,
rcut = self.rcut,
rcut_smth = self.rcut_smth,
sel = self.sel_r)
self.descrpt_reshape = tf.reshape(self.descrpt, [-1, self.ndescrpt])
self.descrpt_reshape = tf.identity(self.descrpt_reshape, name = 'o_rmat')
self.descrpt_deriv = tf.identity(self.descrpt_deriv, name = 'o_rmat_deriv')
self.rij = tf.identity(self.rij, name = 'o_rij')
self.nlist = tf.identity(self.nlist, name = 'o_nlist')
# only used when tensorboard was set as true
tf.summary.histogram('descrpt', self.descrpt)
tf.summary.histogram('rij', self.rij)
tf.summary.histogram('nlist', self.nlist)
self.dout = self._pass_filter(self.descrpt_reshape, natoms, suffix = suffix, reuse = reuse, trainable = self.trainable)
tf.summary.histogram('embedding_net_output', self.dout)
return self.dout
def prod_force_virial(self,
atom_ener : tf.Tensor,
natoms : tf.Tensor
) -> Tuple[tf.Tensor, tf.Tensor, tf.Tensor]:
"""
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
"""
[net_deriv] = tf.gradients (atom_ener, self.descrpt_reshape)
tf.summary.histogram('net_derivative', net_deriv)
net_deriv_reshape = tf.reshape (net_deriv, [-1, natoms[0] * self.ndescrpt])
force \
= op_module.prod_force_se_r (net_deriv_reshape,
self.descrpt_deriv,
self.nlist,
natoms)
virial, atom_virial \
= op_module.prod_virial_se_r (net_deriv_reshape,
self.descrpt_deriv,
self.rij,
self.nlist,
natoms)
tf.summary.histogram('force', force)
tf.summary.histogram('virial', virial)
tf.summary.histogram('atom_virial', atom_virial)
return force, virial, atom_virial
def _pass_filter(self,
inputs,
natoms,
reuse = None,
suffix = '',
trainable = True) :
start_index = 0
inputs = tf.reshape(inputs, [-1, self.ndescrpt * natoms[0]])
output = []
if not self.type_one_side:
for type_i in range(self.ntypes):
inputs_i = tf.slice (inputs,
[ 0, start_index* self.ndescrpt],
[-1, natoms[2+type_i]* self.ndescrpt] )
inputs_i = tf.reshape(inputs_i, [-1, self.ndescrpt])
layer = self._filter_r(tf.cast(inputs_i, self.filter_precision), type_i, name='filter_type_'+str(type_i)+suffix, natoms=natoms, reuse=reuse, trainable = trainable, activation_fn = self.filter_activation_fn)
layer = tf.reshape(layer, [tf.shape(inputs)[0], natoms[2+type_i] * self.get_dim_out()])
output.append(layer)
start_index += natoms[2+type_i]
else :
inputs_i = inputs
inputs_i = tf.reshape(inputs_i, [-1, self.ndescrpt])
type_i = -1
layer = self._filter_r(tf.cast(inputs_i, self.filter_precision), type_i, name='filter_type_all'+suffix, natoms=natoms, reuse=reuse, trainable = trainable, activation_fn = self.filter_activation_fn)
layer = tf.reshape(layer, [tf.shape(inputs)[0], natoms[0] * self.get_dim_out()])
output.append(layer)
output = tf.concat(output, axis = 1)
return output
def _compute_dstats_sys_se_r (self,
data_coord,
data_box,
data_atype,
natoms_vec,
mesh) :
dd_all \
= run_sess(self.sub_sess, self.stat_descrpt,
feed_dict = {
self.place_holders['coord']: data_coord,
self.place_holders['type']: data_atype,
self.place_holders['natoms_vec']: natoms_vec,
self.place_holders['box']: data_box,
self.place_holders['default_mesh']: mesh,
})
natoms = natoms_vec
dd_all = np.reshape(dd_all, [-1, self.ndescrpt * natoms[0]])
start_index = 0
sysr = []
sysn = []
sysr2 = []
for type_i in range(self.ntypes):
end_index = start_index + self.ndescrpt * natoms[2+type_i]
dd = dd_all[:, start_index:end_index]
dd = np.reshape(dd, [-1, self.ndescrpt])
start_index = end_index
# compute
dd = np.reshape (dd, [-1, 1])
ddr = dd[:,:1]
sumr = np.sum(ddr)
sumn = dd.shape[0]
sumr2 = np.sum(np.multiply(ddr, ddr))
sysr.append(sumr)
sysn.append(sumn)
sysr2.append(sumr2)
return sysr, sysr2, sysn
def _compute_std (self,sumv2, sumv, sumn) :
val = np.sqrt(sumv2/sumn - np.multiply(sumv/sumn, sumv/sumn))
if np.abs(val) < 1e-2:
val = 1e-2
return val
def _filter_r(self,
inputs,
type_input,
natoms,
activation_fn=tf.nn.tanh,
stddev=1.0,
bavg=0.0,
name='linear',
reuse=None,
trainable = True):
# natom x nei
outputs_size = [1] + self.filter_neuron
with tf.variable_scope(name, reuse=reuse):
start_index = 0
xyz_scatter_total = []
for type_i in range(self.ntypes):
# cut-out inputs
# with natom x nei_type_i
inputs_i = tf.slice (inputs,
[ 0, start_index ],
[-1, self.sel_r[type_i]] )
start_index += self.sel_r[type_i]
shape_i = inputs_i.get_shape().as_list()
# with (natom x nei_type_i) x 1
xyz_scatter = tf.reshape(inputs_i, [-1, 1])
if (type_input, type_i) not in self.exclude_types:
xyz_scatter = embedding_net(xyz_scatter,
self.filter_neuron,
self.filter_precision,
activation_fn = activation_fn,
resnet_dt = self.filter_resnet_dt,
name_suffix = "_"+str(type_i),
stddev = stddev,
bavg = bavg,
seed = self.seed,
trainable = trainable,
uniform_seed = self.uniform_seed)
if (not self.uniform_seed) and (self.seed is not None): self.seed += self.seed_shift
# natom x nei_type_i x out_size
xyz_scatter = tf.reshape(xyz_scatter, (-1, shape_i[1], outputs_size[-1]))
else:
natom = tf.shape(inputs)[0]
xyz_scatter = tf.cast(tf.fill((natom, shape_i[1], outputs_size[-1]), 0.), GLOBAL_TF_FLOAT_PRECISION)
xyz_scatter_total.append(xyz_scatter)
# natom x nei x outputs_size
xyz_scatter = tf.concat(xyz_scatter_total, axis=1)
# natom x outputs_size
#
res_rescale = 1./5.
result = tf.reduce_mean(xyz_scatter, axis = 1) * res_rescale
return result
class EnerFitting(Fitting):
r"""Fitting the energy of the system. The force and the virial can also be trained.
The potential energy :math:`E` is a fitting network function of the descriptor :math:`\mathcal{D}`:
.. math::
E(\mathcal{D}) = \mathcal{L}^{(n)} \circ \mathcal{L}^{(n-1)}
\circ \cdots \circ \mathcal{L}^{(1)} \circ \mathcal{L}^{(0)}
The first :math:`n` hidden layers :math:`\mathcal{L}^{(0)}, \cdots, \mathcal{L}^{(n-1)}` are given by
.. math::
\mathbf{y}=\mathcal{L}(\mathbf{x};\mathbf{w},\mathbf{b})=
\boldsymbol{\phi}(\mathbf{x}^T\mathbf{w}+\mathbf{b})
where :math:`\mathbf{x} \in \mathbb{R}^{N_1}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}`
is the output vector. :math:`\mathbf{w} \in \mathbb{R}^{N_1 \times N_2}` and
:math:`\mathbf{b} \in \mathbb{R}^{N_2}`$` are weights and biases, respectively,
both of which are trainable if `trainable[i]` is `True`. :math:`\boldsymbol{\phi}`
is the activation function.
The output layer :math:`\mathcal{L}^{(n)}` is given by
.. math::
\mathbf{y}=\mathcal{L}^{(n)}(\mathbf{x};\mathbf{w},\mathbf{b})=
\mathbf{x}^T\mathbf{w}+\mathbf{b}
where :math:`\mathbf{x} \in \mathbb{R}^{N_{n-1}}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}`
is the output scalar. :math:`\mathbf{w} \in \mathbb{R}^{N_{n-1}}` and
:math:`\mathbf{b} \in \mathbb{R}`$` are weights and bias, respectively,
both of which are trainable if `trainable[n]` is `True`.
Parameters
----------
descrpt
The descrptor :math:`\mathcal{D}`
neuron
Number of neurons :math:`N` in each hidden layer of the fitting net
resnet_dt
Time-step `dt` in the resnet construction:
:math:`y = x + dt * \phi (Wx + b)`
numb_fparam
Number of frame parameter
numb_aparam
Number of atomic parameter
rcond
The condition number for the regression of atomic energy.
tot_ener_zero
Force the total energy to zero. Useful for the charge fitting.
trainable
If the weights of fitting net are trainable.
Suppose that we have :math:`N_l` hidden layers in the fitting net,
this list is of length :math:`N_l + 1`, specifying if the hidden layers and the output layer are trainable.
seed
Random seed for initializing the network parameters.
atom_ener
Specifying atomic energy contribution in vacuum. The `set_davg_zero` key in the descrptor should be set.
activation_function
The activation function :math:`\boldsymbol{\phi}` 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
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()),
list_to_doc(PRECISION_DICT.keys()))
def __init__(self,
descrpt: tf.Tensor,
neuron: List[int] = [120, 120, 120],
resnet_dt: bool = True,
numb_fparam: int = 0,
numb_aparam: int = 0,
rcond: float = 1e-3,
tot_ener_zero: bool = False,
trainable: List[bool] = None,
seed: int = None,
atom_ener: List[float] = [],
activation_function: str = 'tanh',
precision: str = 'default',
uniform_seed: bool = False) -> None:
"""
Constructor
"""
# model param
self.ntypes = descrpt.get_ntypes()
self.dim_descrpt = descrpt.get_dim_out()
# args = ()\
# .add('numb_fparam', int, default = 0)\
# .add('numb_aparam', int, default = 0)\
# .add('neuron', list, default = [120,120,120], alias = 'n_neuron')\
# .add('resnet_dt', bool, default = True)\
# .add('rcond', float, default = 1e-3) \
# .add('tot_ener_zero', bool, default = False) \
# .add('seed', int) \
# .add('atom_ener', list, default = [])\
# .add("activation_function", str, default = "tanh")\
# .add("precision", str, default = "default")\
# .add("trainable", [list, bool], default = True)
self.numb_fparam = numb_fparam
self.numb_aparam = numb_aparam
self.n_neuron = neuron
self.resnet_dt = resnet_dt
self.rcond = rcond
self.seed = seed
self.uniform_seed = uniform_seed
self.seed_shift = one_layer_rand_seed_shift()
self.tot_ener_zero = tot_ener_zero
self.fitting_activation_fn = get_activation_func(activation_function)
self.fitting_precision = get_precision(precision)
self.trainable = trainable
if self.trainable is None:
self.trainable = [True for ii in range(len(self.n_neuron) + 1)]
if type(self.trainable) is bool:
self.trainable = [self.trainable] * (len(self.n_neuron) + 1)
assert (len(self.trainable) == len(self.n_neuron) +
1), 'length of trainable should be that of n_neuron + 1'
self.atom_ener = []
self.atom_ener_v = atom_ener
for at, ae in enumerate(atom_ener):
if ae is not None:
self.atom_ener.append(
tf.constant(ae,
self.fitting_precision,
name="atom_%d_ener" % at))
else:
self.atom_ener.append(None)
self.useBN = False
self.bias_atom_e = None
# data requirement
if self.numb_fparam > 0:
add_data_requirement('fparam',
self.numb_fparam,
atomic=False,
must=True,
high_prec=False)
self.fparam_avg = None
self.fparam_std = None
self.fparam_inv_std = None
if self.numb_aparam > 0:
add_data_requirement('aparam',
self.numb_aparam,
atomic=True,
must=True,
high_prec=False)
self.aparam_avg = None
self.aparam_std = None
self.aparam_inv_std = None
self.fitting_net_variables = None
self.mixed_prec = None
def get_numb_fparam(self) -> int:
"""
Get the number of frame parameters
"""
return self.numb_fparam
def get_numb_aparam(self) -> int:
"""
Get the number of atomic parameters
"""
return self.numb_fparam
def compute_output_stats(self, all_stat: dict) -> None:
"""
Compute the ouput statistics
Parameters
----------
all_stat
must have the following components:
all_stat['energy'] of shape n_sys x n_batch x n_frame
can be prepared by model.make_stat_input
"""
self.bias_atom_e = self._compute_output_stats(all_stat,
rcond=self.rcond)
def _compute_output_stats(self, all_stat, rcond=1e-3):
data = all_stat['energy']
# data[sys_idx][batch_idx][frame_idx]
sys_ener = np.array([])
for ss in range(len(data)):
sys_data = []
for ii in range(len(data[ss])):
for jj in range(len(data[ss][ii])):
sys_data.append(data[ss][ii][jj])
sys_data = np.concatenate(sys_data)
sys_ener = np.append(sys_ener, np.average(sys_data))
data = all_stat['natoms_vec']
sys_tynatom = np.array([])
nsys = len(data)
for ss in range(len(data)):
sys_tynatom = np.append(sys_tynatom,
data[ss][0].astype(np.float64))
sys_tynatom = np.reshape(sys_tynatom, [nsys, -1])
sys_tynatom = sys_tynatom[:, 2:]
if len(self.atom_ener) > 0:
# Atomic energies stats are incorrect if atomic energies are assigned.
# In this situation, we directly use these assigned energies instead of computing stats.
# This will make the loss decrease quickly
assigned_atom_ener = np.array(
list((ee for ee in self.atom_ener_v if ee is not None)))
assigned_ener_idx = list((ii
for ii, ee in enumerate(self.atom_ener_v)
if ee is not None))
# np.dot out size: nframe
sys_ener -= np.dot(sys_tynatom[:, assigned_ener_idx],
assigned_atom_ener)
sys_tynatom[:, assigned_ener_idx] = 0.
energy_shift,resd,rank,s_value \
= np.linalg.lstsq(sys_tynatom, sys_ener, rcond = rcond)
if len(self.atom_ener) > 0:
for ii in assigned_ener_idx:
energy_shift[ii] = self.atom_ener_v[ii]
return energy_shift
def compute_input_stats(self,
all_stat: dict,
protection: float = 1e-2) -> None:
"""
Compute the input statistics
Parameters
----------
all_stat
if numb_fparam > 0 must have all_stat['fparam']
if numb_aparam > 0 must have all_stat['aparam']
can be prepared by model.make_stat_input
protection
Divided-by-zero protection
"""
# stat fparam
if self.numb_fparam > 0:
cat_data = np.concatenate(all_stat['fparam'], axis=0)
cat_data = np.reshape(cat_data, [-1, self.numb_fparam])
self.fparam_avg = np.average(cat_data, axis=0)
self.fparam_std = np.std(cat_data, axis=0)
for ii in range(self.fparam_std.size):
if self.fparam_std[ii] < protection:
self.fparam_std[ii] = protection
self.fparam_inv_std = 1. / self.fparam_std
# stat aparam
if self.numb_aparam > 0:
sys_sumv = []
sys_sumv2 = []
sys_sumn = []
for ss_ in all_stat['aparam']:
ss = np.reshape(ss_, [-1, self.numb_aparam])
sys_sumv.append(np.sum(ss, axis=0))
sys_sumv2.append(np.sum(np.multiply(ss, ss), axis=0))
sys_sumn.append(ss.shape[0])
sumv = np.sum(sys_sumv, axis=0)
sumv2 = np.sum(sys_sumv2, axis=0)
sumn = np.sum(sys_sumn)
self.aparam_avg = (sumv) / sumn
self.aparam_std = self._compute_std(sumv2, sumv, sumn)
for ii in range(self.aparam_std.size):
if self.aparam_std[ii] < protection:
self.aparam_std[ii] = protection
self.aparam_inv_std = 1. / self.aparam_std
def _compute_std(self, sumv2, sumv, sumn):
return np.sqrt(sumv2 / sumn - np.multiply(sumv / sumn, sumv / sumn))
def _build_lower(self,
start_index,
natoms,
inputs,
fparam=None,
aparam=None,
bias_atom_e=0.0,
suffix='',
reuse=None):
# cut-out inputs
inputs_i = tf.slice(inputs, [0, start_index * self.dim_descrpt],
[-1, natoms * self.dim_descrpt])
inputs_i = tf.reshape(inputs_i, [-1, self.dim_descrpt])
layer = inputs_i
if fparam is not None:
ext_fparam = tf.tile(fparam, [1, natoms])
ext_fparam = tf.reshape(ext_fparam, [-1, self.numb_fparam])
ext_fparam = tf.cast(ext_fparam, self.fitting_precision)
layer = tf.concat([layer, ext_fparam], axis=1)
if aparam is not None:
ext_aparam = tf.slice(aparam, [0, start_index * self.numb_aparam],
[-1, natoms * self.numb_aparam])
ext_aparam = tf.reshape(ext_aparam, [-1, self.numb_aparam])
ext_aparam = tf.cast(ext_aparam, self.fitting_precision)
layer = tf.concat([layer, ext_aparam], axis=1)
for ii in range(0, len(self.n_neuron)):
if ii >= 1 and self.n_neuron[ii] == self.n_neuron[ii - 1]:
layer += one_layer(
layer,
self.n_neuron[ii],
name='layer_' + str(ii) + suffix,
reuse=reuse,
seed=self.seed,
use_timestep=self.resnet_dt,
activation_fn=self.fitting_activation_fn,
precision=self.fitting_precision,
trainable=self.trainable[ii],
uniform_seed=self.uniform_seed,
initial_variables=self.fitting_net_variables,
mixed_prec=self.mixed_prec)
else:
layer = one_layer(layer,
self.n_neuron[ii],
name='layer_' + str(ii) + suffix,
reuse=reuse,
seed=self.seed,
activation_fn=self.fitting_activation_fn,
precision=self.fitting_precision,
trainable=self.trainable[ii],
uniform_seed=self.uniform_seed,
initial_variables=self.fitting_net_variables,
mixed_prec=self.mixed_prec)
if (not self.uniform_seed) and (self.seed is not None):
self.seed += self.seed_shift
final_layer = one_layer(layer,
1,
activation_fn=None,
bavg=bias_atom_e,
name='final_layer' + suffix,
reuse=reuse,
seed=self.seed,
precision=self.fitting_precision,
trainable=self.trainable[-1],
uniform_seed=self.uniform_seed,
initial_variables=self.fitting_net_variables,
mixed_prec=self.mixed_prec,
final_layer=True)
if (not self.uniform_seed) and (self.seed is not None):
self.seed += self.seed_shift
return final_layer
@cast_precision
def build(
self,
inputs: tf.Tensor,
natoms: tf.Tensor,
input_dict: dict = None,
reuse: bool = None,
suffix: str = '',
) -> tf.Tensor:
"""
Build the computational graph for fitting net
Parameters
----------
inputs
The input descriptor
input_dict
Additional dict for inputs.
if numb_fparam > 0, should have input_dict['fparam']
if numb_aparam > 0, should have input_dict['aparam']
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
reuse
The weights in the networks should be reused when get the variable.
suffix
Name suffix to identify this descriptor
Returns
-------
ener
The system energy
"""
if input_dict is None:
input_dict = {}
bias_atom_e = self.bias_atom_e
if self.numb_fparam > 0 and (self.fparam_avg is None
or self.fparam_inv_std is None):
raise RuntimeError(
'No data stat result. one should do data statisitic, before build'
)
if self.numb_aparam > 0 and (self.aparam_avg is None
or self.aparam_inv_std is None):
raise RuntimeError(
'No data stat result. one should do data statisitic, before build'
)
with tf.variable_scope('fitting_attr' + suffix, reuse=reuse):
t_dfparam = tf.constant(self.numb_fparam,
name='dfparam',
dtype=tf.int32)
t_daparam = tf.constant(self.numb_aparam,
name='daparam',
dtype=tf.int32)
if self.numb_fparam > 0:
t_fparam_avg = tf.get_variable(
't_fparam_avg',
self.numb_fparam,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(self.fparam_avg))
t_fparam_istd = tf.get_variable(
't_fparam_istd',
self.numb_fparam,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(self.fparam_inv_std))
if self.numb_aparam > 0:
t_aparam_avg = tf.get_variable(
't_aparam_avg',
self.numb_aparam,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(self.aparam_avg))
t_aparam_istd = tf.get_variable(
't_aparam_istd',
self.numb_aparam,
dtype=GLOBAL_TF_FLOAT_PRECISION,
trainable=False,
initializer=tf.constant_initializer(self.aparam_inv_std))
inputs = tf.reshape(inputs, [-1, self.dim_descrpt * natoms[0]])
if len(self.atom_ener):
# only for atom_ener
nframes = input_dict.get('nframes')
if nframes is not None:
# like inputs, but we don't want to add a dependency on inputs
inputs_zero = tf.zeros((nframes, self.dim_descrpt * natoms[0]),
dtype=self.fitting_precision)
else:
inputs_zero = tf.zeros_like(inputs,
dtype=self.fitting_precision)
if bias_atom_e is not None:
assert (len(bias_atom_e) == self.ntypes)
fparam = None
aparam = None
if self.numb_fparam > 0:
fparam = input_dict['fparam']
fparam = tf.reshape(fparam, [-1, self.numb_fparam])
fparam = (fparam - t_fparam_avg) * t_fparam_istd
if self.numb_aparam > 0:
aparam = input_dict['aparam']
aparam = tf.reshape(aparam, [-1, self.numb_aparam])
aparam = (aparam - t_aparam_avg) * t_aparam_istd
aparam = tf.reshape(aparam, [-1, self.numb_aparam * natoms[0]])
type_embedding = input_dict.get('type_embedding', None)
if type_embedding is not None:
atype_embed = embed_atom_type(self.ntypes, natoms, type_embedding)
atype_embed = tf.tile(atype_embed, [tf.shape(inputs)[0], 1])
else:
atype_embed = None
if atype_embed is None:
start_index = 0
outs_list = []
for type_i in range(self.ntypes):
if bias_atom_e is None:
type_bias_ae = 0.0
else:
type_bias_ae = bias_atom_e[type_i]
final_layer = self._build_lower(start_index,
natoms[2 + type_i],
inputs,
fparam,
aparam,
bias_atom_e=type_bias_ae,
suffix='_type_' + str(type_i) +
suffix,
reuse=reuse)
# concat the results
if type_i < len(
self.atom_ener) and self.atom_ener[type_i] is not None:
zero_layer = self._build_lower(start_index,
natoms[2 + type_i],
inputs_zero,
fparam,
aparam,
bias_atom_e=type_bias_ae,
suffix='_type_' +
str(type_i) + suffix,
reuse=True)
final_layer += self.atom_ener[type_i] - zero_layer
final_layer = tf.reshape(
final_layer, [tf.shape(inputs)[0], natoms[2 + type_i]])
outs_list.append(final_layer)
start_index += natoms[2 + type_i]
# concat the results
# concat once may be faster than multiple concat
outs = tf.concat(outs_list, axis=1)
# with type embedding
else:
if len(self.atom_ener) > 0:
raise RuntimeError(
"setting atom_ener is not supported by type embedding")
atype_embed = tf.cast(atype_embed, self.fitting_precision)
type_shape = atype_embed.get_shape().as_list()
inputs = tf.concat(
[tf.reshape(inputs, [-1, self.dim_descrpt]), atype_embed],
axis=1)
self.dim_descrpt = self.dim_descrpt + type_shape[1]
inputs = tf.reshape(inputs, [-1, self.dim_descrpt * natoms[0]])
final_layer = self._build_lower(0,
natoms[0],
inputs,
fparam,
aparam,
bias_atom_e=0.0,
suffix=suffix,
reuse=reuse)
outs = tf.reshape(final_layer, [tf.shape(inputs)[0], natoms[0]])
if self.tot_ener_zero:
force_tot_ener = 0.0
outs = tf.reshape(outs, [-1, natoms[0]])
outs_mean = tf.reshape(tf.reduce_mean(outs, axis=1), [-1, 1])
outs_mean = outs_mean - tf.ones_like(
outs_mean, dtype=GLOBAL_TF_FLOAT_PRECISION) * (
force_tot_ener / global_cvt_2_tf_float(natoms[0]))
outs = outs - outs_mean
outs = tf.reshape(outs, [-1])
tf.summary.histogram('fitting_net_output', outs)
return tf.reshape(outs, [-1])
def init_variables(self, model_file: str) -> None:
"""
Init the fitting net variables with the given frozen model
Parameters
----------
model_file : str
The input frozen model file
"""
self.fitting_net_variables = get_fitting_net_variables(model_file)
def enable_compression(self, model_file: str, suffix: str = "") -> None:
"""
Set the fitting net attributes from the frozen model_file when fparam or aparam is not zero
Parameters
----------
model_file : str
The input frozen model file
suffix : str, optional
The suffix of the scope
"""
if self.numb_fparam > 0 or self.numb_aparam > 0:
graph, _ = load_graph_def(model_file)
if self.numb_fparam > 0:
self.fparam_avg = get_tensor_by_name_from_graph(
graph, 'fitting_attr%s/t_fparam_avg' % suffix)
self.fparam_inv_std = get_tensor_by_name_from_graph(
graph, 'fitting_attr%s/t_fparam_istd' % suffix)
if self.numb_aparam > 0:
self.aparam_avg = get_tensor_by_name_from_graph(
graph, 'fitting_attr%s/t_aparam_avg' % suffix)
self.aparam_inv_std = get_tensor_by_name_from_graph(
graph, 'fitting_attr%s/t_aparam_istd' % suffix)
def enable_mixed_precision(self, mixed_prec: dict = None) -> None:
"""
Reveive the mixed precision setting.
Parameters
----------
mixed_prec
The mixed precision setting used in the embedding net
"""
self.mixed_prec = mixed_prec
self.fitting_precision = get_precision(mixed_prec['output_prec'])
class DescrptSeAEf(Descriptor):
"""
Parameters
----------
rcut
The cut-off radius
rcut_smth
From where the environment matrix should be smoothed
sel : list[str]
sel[i] specifies the maxmum number of type i atoms in the cut-off radius
neuron : list[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_types : List[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
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()),
list_to_doc(PRECISION_DICT.keys()))
def __init__(self,
rcut: float,
rcut_smth: float,
sel: List[str],
neuron: List[int] = [24, 48, 96],
axis_neuron: int = 8,
resnet_dt: bool = False,
trainable: bool = True,
seed: int = None,
type_one_side: bool = True,
exclude_types: List[List[int]] = [],
set_davg_zero: bool = False,
activation_function: str = 'tanh',
precision: str = 'default',
uniform_seed=False) -> None:
"""
Constructor
"""
self.descrpt_para = DescrptSeAEfLower(
op_module.descrpt_se_a_ef_para,
rcut,
rcut_smth,
sel,
neuron,
axis_neuron,
resnet_dt,
trainable,
seed,
type_one_side,
exclude_types,
set_davg_zero,
activation_function,
precision,
uniform_seed,
)
self.descrpt_vert = DescrptSeAEfLower(
op_module.descrpt_se_a_ef_vert,
rcut,
rcut_smth,
sel,
neuron,
axis_neuron,
resnet_dt,
trainable,
seed,
type_one_side,
exclude_types,
set_davg_zero,
activation_function,
precision,
uniform_seed,
)
def get_rcut(self) -> float:
"""
Returns the cut-off radisu
"""
return self.descrpt_vert.rcut_r
def get_ntypes(self) -> int:
"""
Returns the number of atom types
"""
return self.descrpt_vert.ntypes
def get_dim_out(self) -> int:
"""
Returns the output dimension of this descriptor
"""
return self.descrpt_vert.get_dim_out() + self.descrpt_para.get_dim_out(
)
def get_dim_rot_mat_1(self) -> int:
"""
Returns the first dimension of the rotation matrix. The rotation is of shape dim_1 x 3
"""
return self.descrpt_vert.filter_neuron[-1]
def get_rot_mat(self) -> tf.Tensor:
"""
Get rotational matrix
"""
return self.qmat
def get_nlist(self) -> Tuple[tf.Tensor, tf.Tensor, List[int], List[int]]:
"""
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
"""
return \
self.descrpt_vert.nlist, \
self.descrpt_vert.rij, \
self.descrpt_vert.sel_a, \
self.descrpt_vert.sel_r
def compute_input_stats(self, data_coord: list, data_box: list,
data_atype: list, natoms_vec: list, mesh: list,
input_dict: dict) -> None:
"""
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
"""
self.descrpt_vert.compute_input_stats(data_coord, data_box, data_atype,
natoms_vec, mesh, input_dict)
self.descrpt_para.compute_input_stats(data_coord, data_box, data_atype,
natoms_vec, mesh, input_dict)
def build(self,
coord_: tf.Tensor,
atype_: tf.Tensor,
natoms: tf.Tensor,
box_: tf.Tensor,
mesh: tf.Tensor,
input_dict: dict,
reuse: bool = None,
suffix: str = '') -> tf.Tensor:
"""
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
"""
self.dout_vert = self.descrpt_vert.build(coord_, atype_, natoms, box_,
mesh, input_dict)
self.dout_para = self.descrpt_para.build(coord_,
atype_,
natoms,
box_,
mesh,
input_dict,
reuse=True)
coord = tf.reshape(coord_, [-1, natoms[1] * 3])
nframes = tf.shape(coord)[0]
self.dout_vert = tf.reshape(
self.dout_vert,
[nframes * natoms[0],
self.descrpt_vert.get_dim_out()])
self.dout_para = tf.reshape(
self.dout_para,
[nframes * natoms[0],
self.descrpt_para.get_dim_out()])
self.dout = tf.concat([self.dout_vert, self.dout_para], axis=1)
self.dout = tf.reshape(self.dout,
[nframes, natoms[0] * self.get_dim_out()])
self.qmat = self.descrpt_vert.qmat + self.descrpt_para.qmat
tf.summary.histogram('embedding_net_output', self.dout)
return self.dout
def prod_force_virial(
self, atom_ener: tf.Tensor,
natoms: tf.Tensor) -> Tuple[tf.Tensor, tf.Tensor, tf.Tensor]:
"""
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
"""
f_vert, v_vert, av_vert \
= self.descrpt_vert.prod_force_virial(atom_ener, natoms)
f_para, v_para, av_para \
= self.descrpt_para.prod_force_virial(atom_ener, natoms)
force = f_vert + f_para
virial = v_vert + v_para
atom_vir = av_vert + av_para
return force, virial, atom_vir
class TypeEmbedNet():
"""
Parameters
----------
neuron : list[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)
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}
trainable
If the weights of embedding net are trainable.
seed
Random seed for initializing the network parameters.
uniform_seed
Only for the purpose of backward compatibility, retrieves the old behavior of using the random seed
"""
@docstring_parameter(list_to_doc(ACTIVATION_FN_DICT.keys()), list_to_doc(PRECISION_DICT.keys()))
def __init__(
self,
neuron: List[int]=[],
resnet_dt: bool = False,
activation_function: str = 'tanh',
precision: str = 'default',
trainable: bool = True,
seed: int = None,
uniform_seed: bool = False,
)->None:
"""
Constructor
"""
self.neuron = neuron
self.seed = seed
self.filter_resnet_dt = resnet_dt
self.filter_precision = get_precision(precision)
self.filter_activation_fn = get_activation_func(activation_function)
self.trainable = trainable
self.uniform_seed = uniform_seed
self.type_embedding_net_variables = None
def build(
self,
ntypes: int,
reuse = None,
suffix = '',
):
"""
Build the computational graph for the descriptor
Parameters
----------
ntypes
Number of atom types.
reuse
The weights in the networks should be reused when get the variable.
suffix
Name suffix to identify this descriptor
Returns
-------
embedded_types
The computational graph for embedded types
"""
types = tf.convert_to_tensor(
[ii for ii in range(ntypes)],
dtype = tf.int32
)
ebd_type = tf.cast(tf.one_hot(tf.cast(types,dtype=tf.int32),int(ntypes)), self.filter_precision)
ebd_type = tf.reshape(ebd_type, [-1, ntypes])
name = 'type_embed_net' + suffix
with tf.variable_scope(name, reuse=reuse):
ebd_type = embedding_net(
ebd_type,
self.neuron,
activation_fn = self.filter_activation_fn,
precision = self.filter_precision,
resnet_dt = self.filter_resnet_dt,
seed = self.seed,
trainable = self.trainable,
initial_variables = self.type_embedding_net_variables,
uniform_seed = self.uniform_seed)
ebd_type = tf.reshape(ebd_type, [-1, self.neuron[-1]]) # nnei * neuron[-1]
self.ebd_type = tf.identity(ebd_type, name ='t_typeebd')
return self.ebd_type
def init_variables(self,
graph: tf.Graph,
graph_def: tf.GraphDef,
suffix = '',
) -> None:
"""
Init the type embedding net variables with the given dict
Parameters
----------
graph : tf.Graph
The input frozen model graph
graph_def : tf.GraphDef
The input frozen model graph_def
suffix
Name suffix to identify this descriptor
"""
self.type_embedding_net_variables = get_type_embedding_net_variables_from_graph_def(graph_def, suffix = suffix)