diff --git a/deepmd/descriptor/se_a.py b/deepmd/descriptor/se_a.py index d49c329353..2bff523608 100644 --- a/deepmd/descriptor/se_a.py +++ b/deepmd/descriptor/se_a.py @@ -96,8 +96,8 @@ class DescrptSeA(DescrptSe): .. 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 + :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 diff --git a/deepmd/descriptor/se_a_mask.py b/deepmd/descriptor/se_a_mask.py index 00b23232f1..93256e3910 100644 --- a/deepmd/descriptor/se_a_mask.py +++ b/deepmd/descriptor/se_a_mask.py @@ -70,8 +70,8 @@ class DescrptSeAMask(DescrptSeA): .. 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 + :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`. Specially for descriptor se_a_mask is a concise implementation of se_a. The difference is that se_a_mask only considered a non-pbc system. diff --git a/deepmd/fit/ener.py b/deepmd/fit/ener.py index 53c3b1d468..c9f70117f7 100644 --- a/deepmd/fit/ener.py +++ b/deepmd/fit/ener.py @@ -59,9 +59,9 @@ class EnerFitting(Fitting): \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}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}` + where :math:`\mathbf{x} \in \mathbb{R}^{N_1}` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}` is the output vector. :math:`\mathbf{w} \in \mathbb{R}^{N_1 \times N_2}` and - :math:`\mathbf{b} \in \mathbb{R}^{N_2}`$` are weights and biases, respectively, + :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. @@ -71,9 +71,9 @@ class EnerFitting(Fitting): \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}}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}` + where :math:`\mathbf{x} \in \mathbb{R}^{N_{n-1}}` is the input vector and :math:`\mathbf{y} \in \mathbb{R}` is the output scalar. :math:`\mathbf{w} \in \mathbb{R}^{N_{n-1}}` and - :math:`\mathbf{b} \in \mathbb{R}`$` are weights and bias, respectively, + :math:`\mathbf{b} \in \mathbb{R}` are weights and bias, respectively, both of which are trainable if `trainable[n]` is `True`. Parameters diff --git a/deepmd/utils/network.py b/deepmd/utils/network.py index e5ce249f45..a718da0b26 100644 --- a/deepmd/utils/network.py +++ b/deepmd/utils/network.py @@ -144,9 +144,9 @@ def embedding_net( \boldsymbol{\phi}(\mathbf{x}^T\mathbf{w}+\mathbf{b}), & \text{otherwise} \\ \end{cases} - where :math:`\mathbf{x} \in \mathbb{R}^{N_1}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}` + where :math:`\mathbf{x} \in \mathbb{R}^{N_1}` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}` is the output vector. :math:`\mathbf{w} \in \mathbb{R}^{N_1 \times N_2}` and - :math:`\mathbf{b} \in \mathbb{R}^{N_2}`$` are weights and biases, respectively, + :math:`\mathbf{b} \in \mathbb{R}^{N_2}` are weights and biases, respectively, both of which are trainable if `trainable` is `True`. :math:`\boldsymbol{\phi}` is the activation function. diff --git a/doc/conf.py b/doc/conf.py index e338274f0e..2fd0dcdc33 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -305,6 +305,10 @@ def setup(app): "fontpkg": r""" \usepackage{fontspec} \setmainfont{Symbola} +""", + "preamble": r""" +\usepackage{enumitem} +\setlistdepth{99} """, }