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Doxyfile cannot be installed from pip, therefore I precompiled with doxyfile to generated xml/ from C++. And then api_cc.rst can be generated by breathe from xml/
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27 files changed

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‎doc/Doxyfile‎

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@@ -58,7 +58,7 @@ PROJECT_LOGO =
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# entered, it will be relative to the location where doxygen was started. If
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# left blank the current directory will be used.
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OUTPUT_DIRECTORY = _build/
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OUTPUT_DIRECTORY =
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# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
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# directories (in 2 levels) under the output directory of each output format and

‎doc/conf.py‎

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@@ -76,7 +76,7 @@ def mkindex(dirname):
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'breathe'
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]
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breathe_projects = {"myproject": "_build/xml/"}
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breathe_projects = {"myproject": "xml/"}
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breathe_default_project = "myproject"
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myst_heading_anchors = 4

‎doc/xml/AtomMap_8h.xml‎

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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
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<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.9.2" xml:lang="en-US">
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<compounddef id="AtomMap_8h" kind="file" language="C++">
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<compoundname>AtomMap.h</compoundname>
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<includes local="no">vector</includes>
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<includedby refid="common_8h" local="yes">/home/abby/deepmd-kit/source/api_cc/include/common.h</includedby>
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<incdepgraph>
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<node id="1">
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<label>/home/abby/deepmd-kit/source/api_cc/include/AtomMap.h</label>
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<link refid="AtomMap_8h"/>
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<childnode refid="2" relation="include">
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</childnode>
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</node>
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<node id="2">
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<label>vector</label>
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</node>
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</incdepgraph>
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<invincdepgraph>
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<node id="1">
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<label>/home/abby/deepmd-kit/source/api_cc/include/AtomMap.h</label>
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<link refid="AtomMap_8h"/>
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<childnode refid="2" relation="include">
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</childnode>
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</node>
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<node id="4">
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<label>/home/abby/deepmd-kit/source/api_cc/include/DataModifier.h</label>
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<link refid="DataModifier_8h_source"/>
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</node>
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<node id="3">
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<label>/home/abby/deepmd-kit/source/api_cc/include/DeepPot.h</label>
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<link refid="DeepPot_8h_source"/>
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<childnode refid="4" relation="include">
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</childnode>
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</node>
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<node id="5">
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<label>/home/abby/deepmd-kit/source/api_cc/include/DeepTensor.h</label>
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<link refid="DeepTensor_8h_source"/>
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</node>
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<node id="2">
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<label>/home/abby/deepmd-kit/source/api_cc/include/common.h</label>
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<link refid="common_8h_source"/>
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<childnode refid="3" relation="include">
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</childnode>
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<childnode refid="5" relation="include">
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</childnode>
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</node>
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</invincdepgraph>
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<innerclass refid="classdeepmd_1_1AtomMap" prot="public">deepmd::AtomMap</innerclass>
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<innernamespace refid="namespacedeepmd">deepmd</innernamespace>
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<briefdescription>
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</briefdescription>
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<detaileddescription>
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</detaileddescription>
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<programlisting>
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<codeline lineno="1"><highlight class="preprocessor">#pragma<sp/>once</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="2"><highlight class="normal"></highlight></codeline>
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<codeline lineno="3"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;vector&gt;</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="4"><highlight class="normal"></highlight></codeline>
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<codeline lineno="5"><highlight class="normal"></highlight><highlight class="comment">//<sp/>using<sp/>namespace<sp/>std;</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="6"><highlight class="normal"></highlight></codeline>
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<codeline lineno="7"><highlight class="normal"></highlight><highlight class="keyword">namespace<sp/></highlight><highlight class="normal">deepmd{</highlight></codeline>
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<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>
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<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>
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<codeline lineno="10"><highlight class="normal">{</highlight></codeline>
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<codeline lineno="11"><highlight class="normal"></highlight><highlight class="keyword">public</highlight><highlight class="normal">:</highlight></codeline>
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<codeline lineno="12"><highlight class="normal"><sp/><sp/><ref refid="classdeepmd_1_1AtomMap" kindref="compound">AtomMap</ref>();</highlight></codeline>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<codeline lineno="24"><highlight class="normal"></highlight><highlight class="keyword">private</highlight><highlight class="normal">:</highlight></codeline>
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<codeline lineno="25"><highlight class="normal"><sp/><sp/>std::vector&lt;int&gt;<sp/>idx_map;</highlight></codeline>
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<codeline lineno="26"><highlight class="normal"><sp/><sp/>std::vector&lt;int&gt;<sp/>fwd_idx_map;</highlight></codeline>
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<codeline lineno="27"><highlight class="normal"><sp/><sp/>std::vector&lt;int&gt;<sp/>atype;</highlight></codeline>
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<codeline lineno="28"><highlight class="normal">};</highlight></codeline>
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<codeline lineno="29"><highlight class="normal">}</highlight></codeline>
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</programlisting>
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<location file="/home/abby/deepmd-kit/source/api_cc/include/AtomMap.h"/>
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</compounddef>
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</doxygen>

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