Doxyfile cannot be installed from pip, therefore I precompiled with d…

…oxyfile to generated xml/ from C++. And then api_cc.rst can be generated by breathe from xml/.

doc/README

@@ -0,0 +1 @@
+To run the HTML documention build, doxygen have to be installed.

doc/conf.py

@@ -72,9 +72,13 @@ def mkindex(dirname):
 extensions = [
     "sphinx_rtd_theme",
     'myst_parser',
-    'sphinx.ext.autosummary'
+    'sphinx.ext.autosummary',
+    'breathe'
 ]
 
+breathe_projects = {"myproject": "xml/"}
+breathe_default_project = "myproject"
+
 myst_heading_anchors = 4
 
 # Add any paths that contain templates here, relative to this directory.

doc/development/api_cc.rst

@@ -0,0 +1,14 @@
+API of C++
+==========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. doxygenclass:: deepmd::DeepPot
+   :members:
+   :undoc-members:
+
+.. doxygenclass:: deepmd::DeepPotModelDevi
+   :members:
+   :undoc-members:

doc/development/index.md

@@ -1,4 +1,5 @@
 # Developer Guide
 
 - [API](api.rst)
+- [API of C++](api_cc.rst)
 - [Coding Conventions](coding-conventions.rst)

doc/xml/AtomMap_8h.xml

@@ -0,0 +1,87 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.9.2" xml:lang="en-US">
+  <compounddef id="AtomMap_8h" kind="file" language="C++">
+    <compoundname>AtomMap.h</compoundname>
+    <includes local="no">vector</includes>
+    <includedby refid="common_8h" local="yes">/home/abby/deepmd-kit/source/api_cc/include/common.h</includedby>
+    <incdepgraph>
+      <node id="1">
+        <label>/home/abby/deepmd-kit/source/api_cc/include/AtomMap.h</label>
+        <link refid="AtomMap_8h"/>
+        <childnode refid="2" relation="include">
+        </childnode>
+      </node>
+      <node id="2">
+        <label>vector</label>
+      </node>
+    </incdepgraph>
+    <invincdepgraph>
+      <node id="1">
+        <label>/home/abby/deepmd-kit/source/api_cc/include/AtomMap.h</label>
+        <link refid="AtomMap_8h"/>
+        <childnode refid="2" relation="include">
+        </childnode>
+      </node>
+      <node id="4">
+        <label>/home/abby/deepmd-kit/source/api_cc/include/DataModifier.h</label>
+        <link refid="DataModifier_8h_source"/>
+      </node>
+      <node id="3">
+        <label>/home/abby/deepmd-kit/source/api_cc/include/DeepPot.h</label>
+        <link refid="DeepPot_8h_source"/>
+        <childnode refid="4" relation="include">
+        </childnode>
+      </node>
+      <node id="5">
+        <label>/home/abby/deepmd-kit/source/api_cc/include/DeepTensor.h</label>
+        <link refid="DeepTensor_8h_source"/>
+      </node>
+      <node id="2">
+        <label>/home/abby/deepmd-kit/source/api_cc/include/common.h</label>
+        <link refid="common_8h_source"/>
+        <childnode refid="3" relation="include">
+        </childnode>
+        <childnode refid="5" relation="include">
+        </childnode>
+      </node>
+    </invincdepgraph>
+    <innerclass refid="classdeepmd_1_1AtomMap" prot="public">deepmd::AtomMap</innerclass>
+    <innernamespace refid="namespacedeepmd">deepmd</innernamespace>
+    <briefdescription>
+    </briefdescription>
+    <detaileddescription>
+    </detaileddescription>
+    <programlisting>
+<codeline lineno="1"><highlight class="preprocessor">#pragma<sp/>once</highlight><highlight class="normal"></highlight></codeline>
+<codeline lineno="2"><highlight class="normal"></highlight></codeline>
+<codeline lineno="3"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;vector&gt;</highlight><highlight class="normal"></highlight></codeline>
+<codeline lineno="4"><highlight class="normal"></highlight></codeline>
+<codeline lineno="5"><highlight class="normal"></highlight><highlight class="comment">//<sp/>using<sp/>namespace<sp/>std;</highlight><highlight class="normal"></highlight></codeline>
+<codeline lineno="6"><highlight class="normal"></highlight></codeline>
+<codeline lineno="7"><highlight class="normal"></highlight><highlight class="keyword">namespace<sp/></highlight><highlight class="normal">deepmd{</highlight></codeline>
+<codeline lineno="8"><highlight class="normal"></highlight><highlight class="keyword">template</highlight><highlight class="normal"><sp/>&lt;</highlight><highlight class="keyword">typename</highlight><highlight class="normal"><sp/>VALUETYPE&gt;</highlight></codeline>
+<codeline lineno="9" refid="classdeepmd_1_1AtomMap" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">class<sp/></highlight><highlight class="normal"><ref refid="classdeepmd_1_1AtomMap" kindref="compound">AtomMap</ref><sp/></highlight></codeline>
+<codeline lineno="10"><highlight class="normal">{</highlight></codeline>
+<codeline lineno="11"><highlight class="normal"></highlight><highlight class="keyword">public</highlight><highlight class="normal">:</highlight></codeline>
+<codeline lineno="12"><highlight class="normal"><sp/><sp/><ref refid="classdeepmd_1_1AtomMap" kindref="compound">AtomMap</ref>();</highlight></codeline>
+<codeline lineno="13"><highlight class="normal"><sp/><sp/><ref refid="classdeepmd_1_1AtomMap" kindref="compound">AtomMap</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>std::vector&lt;int<sp/>&gt;::const_iterator<sp/>in_begin,<sp/></highlight></codeline>
+<codeline lineno="14"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>std::vector&lt;int<sp/>&gt;::const_iterator<sp/>in_end);</highlight></codeline>
+<codeline lineno="15"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>forward<sp/>(</highlight><highlight class="keyword">typename</highlight><highlight class="normal"><sp/>std::vector&lt;VALUETYPE<sp/>&gt;::iterator<sp/>out,</highlight></codeline>
+<codeline lineno="16"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">typename</highlight><highlight class="normal"><sp/>std::vector&lt;VALUETYPE<sp/>&gt;::const_iterator<sp/>in,<sp/></highlight></codeline>
+<codeline lineno="17"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>stride<sp/>=<sp/>1)<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>;</highlight></codeline>
+<codeline lineno="18"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>backward<sp/>(</highlight><highlight class="keyword">typename</highlight><highlight class="normal"><sp/>std::vector&lt;VALUETYPE<sp/>&gt;::iterator<sp/>out,</highlight></codeline>
+<codeline lineno="19"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">typename</highlight><highlight class="normal"><sp/>std::vector&lt;VALUETYPE<sp/>&gt;::const_iterator<sp/>in,<sp/></highlight></codeline>
+<codeline lineno="20"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>stride<sp/>=<sp/>1)<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>;</highlight></codeline>
+<codeline lineno="21"><highlight class="normal"><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>std::vector&lt;int<sp/>&gt;<sp/>&amp;<sp/>get_type<sp/>()</highlight><highlight class="keyword"><sp/>const<sp/></highlight><highlight class="normal">{</highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>atype;}</highlight></codeline>
+<codeline lineno="22"><highlight class="normal"><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>std::vector&lt;int<sp/>&gt;<sp/>&amp;<sp/>get_fwd_map<sp/>()</highlight><highlight class="keyword"><sp/>const<sp/></highlight><highlight class="normal">{</highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>fwd_idx_map;}</highlight></codeline>
+<codeline lineno="23"><highlight class="normal"><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/>std::vector&lt;int<sp/>&gt;<sp/>&amp;<sp/>get_bkw_map<sp/>()</highlight><highlight class="keyword"><sp/>const<sp/></highlight><highlight class="normal">{</highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>idx_map;}</highlight></codeline>
+<codeline lineno="24"><highlight class="normal"></highlight><highlight class="keyword">private</highlight><highlight class="normal">:</highlight></codeline>
+<codeline lineno="25"><highlight class="normal"><sp/><sp/>std::vector&lt;int&gt;<sp/>idx_map;</highlight></codeline>
+<codeline lineno="26"><highlight class="normal"><sp/><sp/>std::vector&lt;int&gt;<sp/>fwd_idx_map;</highlight></codeline>
+<codeline lineno="27"><highlight class="normal"><sp/><sp/>std::vector&lt;int&gt;<sp/>atype;</highlight></codeline>
+<codeline lineno="28"><highlight class="normal">};</highlight></codeline>
+<codeline lineno="29"><highlight class="normal">}</highlight></codeline>
+    </programlisting>
+    <location file="/home/abby/deepmd-kit/source/api_cc/include/AtomMap.h"/>
+  </compounddef>
+</doxygen>