Merge pull request #313 from amcadmus/devel

Implement type embedding
deepmodeling · Dec 22, 2020 · 66bdc69 · 66bdc69
2 parents 698cf3a + b1e254b
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diff --git a/doc/train-input-auto.rst b/doc/train-input-auto.rst
@@ -230,6 +230,156 @@ model:
             Set the normalization average to zero. This option should be set when `atom_ener` in the energy fitting is used
 
 
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]"></a>
+        When *type* is set to ``se_a_ebd``: 
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/sel"></a>
+        sel: 
+            | type: ``list``
+            | argument path: ``model/descriptor[se_a_ebd]/sel``
+
+            A list of integers. The length of the list should be the same as the number of atom types in the system. `sel[i]` gives the selected number of type-i neighbors. `sel[i]` is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/rcut"></a>
+        rcut: 
+            | type: ``float``, optional, default: ``6.0``
+            | argument path: ``model/descriptor[se_a_ebd]/rcut``
+
+            The cut-off radius.
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/rcut_smth"></a>
+        rcut_smth: 
+            | type: ``float``, optional, default: ``0.5``
+            | argument path: ``model/descriptor[se_a_ebd]/rcut_smth``
+
+            Where to start smoothing. For example the 1/r term is smoothed from `rcut` to `rcut_smth`
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/neuron"></a>
+        neuron: 
+            | type: ``list``, optional, default: ``[10, 20, 40]``
+            | argument path: ``model/descriptor[se_a_ebd]/neuron``
+
+            Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/axis_neuron"></a>
+        axis_neuron: 
+            | type: ``int``, optional, default: ``4``
+            | argument path: ``model/descriptor[se_a_ebd]/axis_neuron``
+
+            Size of the submatrix of G (embedding matrix).
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/activation_function"></a>
+        activation_function: 
+            | type: ``str``, optional, default: ``tanh``
+            | argument path: ``model/descriptor[se_a_ebd]/activation_function``
+
+            The activation function in the embedding net. Supported activation functions are "relu", "relu6", "softplus", "sigmoid", "tanh", "gelu".
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/resnet_dt"></a>
+        resnet_dt: 
+            | type: ``bool``, optional, default: ``False``
+            | argument path: ``model/descriptor[se_a_ebd]/resnet_dt``
+
+            Whether to use a "Timestep" in the skip connection
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/type_one_side"></a>
+        type_one_side: 
+            | type: ``bool``, optional, default: ``False``
+            | argument path: ``model/descriptor[se_a_ebd]/type_one_side``
+
+            Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/precision"></a>
+        precision: 
+            | type: ``str``, optional, default: ``float64``
+            | argument path: ``model/descriptor[se_a_ebd]/precision``
+
+            The precision of the embedding net parameters, supported options are "float64", "float32", "float16".
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/trainable"></a>
+        trainable: 
+            | type: ``bool``, optional, default: ``True``
+            | argument path: ``model/descriptor[se_a_ebd]/trainable``
+
+            If the parameters in the embedding net is trainable
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/seed"></a>
+        seed: 
+            | type: ``int`` | ``NoneType``, optional
+            | argument path: ``model/descriptor[se_a_ebd]/seed``
+
+            Random seed for parameter initialization
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/exclude_types"></a>
+        exclude_types: 
+            | type: ``list``, optional, default: ``[]``
+            | argument path: ``model/descriptor[se_a_ebd]/exclude_types``
+
+            The Excluded types
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/set_davg_zero"></a>
+        set_davg_zero: 
+            | type: ``bool``, optional, default: ``False``
+            | argument path: ``model/descriptor[se_a_ebd]/set_davg_zero``
+
+            Set the normalization average to zero. This option should be set when `atom_ener` in the energy fitting is used
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/type_nchanl"></a>
+        type_nchanl: 
+            | type: ``int``, optional, default: ``4``
+            | argument path: ``model/descriptor[se_a_ebd]/type_nchanl``
+
+            number of channels for type embedding
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/type_nlayer"></a>
+        type_nlayer: 
+            | type: ``int``, optional, default: ``2``
+            | argument path: ``model/descriptor[se_a_ebd]/type_nlayer``
+
+            number of hidden layers of type embedding net
+
+        .. raw:: html
+
+           <a id="model/descriptor[se_a_ebd]/numb_aparam"></a>
+        numb_aparam: 
+            | type: ``int``, optional, default: ``0``
+            | argument path: ``model/descriptor[se_a_ebd]/numb_aparam``
+
+            dimension of atomic parameter. if set to a value > 0, the atomic parameters are embedded.
+
+
         .. raw:: html
 
            <a id="model/descriptor[se_r]"></a>
@@ -962,7 +1112,7 @@ training:
 
        <a id="training/numb_test"></a>
     numb_test: 
-        | type: ``int``, optional, default: ``1``
+        | type: ``int`` | ``list`` | ``str``, optional, default: ``1``
         | argument path: ``training/numb_test``
 
         Number of frames used for the test during training.