for a more clean document

* archive docs into different classes
* add more detail gitignore
* some small fix
* as a part of #ECF-139

.gitignore

@@ -1,8 +1,221 @@
+# Update scripts
+update.sh
+
+# macOS items
+# General
 .DS_Store
-_site
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# Jekyll items
+_site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+# Ignore folders generated by Bundler
+.bundle/
+vendor/
+
+# Ruby items
+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/spec/examples.txt
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+# Used by dotenv library to load environment variables.
+# .env
+
+# Ignore Byebug command history file.
+.byebug_history
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+*.bridgesupport
+build-iPhoneOS/
+build-iPhoneSimulator/
+
+## Specific to RubyMotion (use of CocoaPods):
+#
+# We recommend against adding the Pods directory to your .gitignore. However
+# you should judge for yourself, the pros and cons are mentioned at:
+# https://guides.cocoapods.org/using/using-cocoapods.html#should-i-check-the-pods-directory-into-source-control
+#
+# vendor/Pods/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalization:
+/.bundle/
+/vendor/bundle
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
 Gemfile.lock
-vendor
-.bundle
-.idea
-update.sh
-.history
+.ruby-version
+.ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+
+# Used by RuboCop. Remote config files pulled in from inherit_from directive.
+# .rubocop-https?--*
+
+# JetBrains items
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+# VSCode items
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+*.code-workspace
+
+# Local History for Visual Studio Code
+.history/
+
+# Vim items
+# Swap
+[._]*.s[a-v][a-z]
+!*.svg  # comment out if you don't need vector files
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+Sessionx.vim
+
+# Temporary
+.netrwhist
+*~
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+
+# Linux items
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*

_config.yml

@@ -26,7 +26,7 @@ description: > # this means to ignore newlines until "baseurl:"
 baseurl: / # the subpath of your site, e.g. /blog
 
 # This is mostly for testing
-url: "chenggroup.github.io" # the base hostname & protocol for your site
+url: "https://wiki.cheng-group.net" # the base hostname & protocol for your site
 
 # Social (First three Required)
 repo: "https://github.com/chenggroup/chenggroup.github.io" # the repo of web source code 

_includes/navigation.html

@@ -27,8 +27,10 @@
         <nav class="md-header-nav md-grid">
             <div class=md-flex>
                 <div class="md-flex__cell md-flex__cell--shrink">
-                  <a class="md-header-nav__button md-logo" href="{{ site.baseurl }}" title="{{ site.title }}">
-                    {% if site.logo %}<img height="{{ site.logo_pixels }}" src="{{ site.baseurl }}/{{ site.logo }}" width="{{ site.logo_pixels }}">{% else %}<i class="md-icon" style="margin-top:0px"></i>{% endif %}</a>
+                    <a class="md-header-nav__button md-logo" href="{{ site.url }}" title="{{ site.title }}">
+                        {% if site.logo %}<img height="{{ site.logo_pixels }}" src="{{ site.baseurl }}/{{ site.logo }}" width="{{ site.logo_pixels }}">
+                        {% else %}<i class="md-icon" style="margin-top:0px"></i>{% endif %}
+                    </a>
                 </div>
                 <div class="md-flex__cell md-flex__cell--shrink">
                     <label class="md-icon md-icon--menu md-header-nav__button" for=__drawer></label>

_wiki/miscellaneous.md

@@ -1,5 +1,9 @@
 ---
-Authors: Yongbin Zhuang
+Authors:
+  - Yongbin Zhuang
+  - Yunpei Liu
+  - Jingfang Xiong
+title: 杂项（Miscellaneous）
 priority: 100.1
 
 ---

_wiki/软件使用/DP-GEN.md

@@ -39,7 +39,7 @@ DP-GEN的工作流是由以下三步组成的循环：
 {% include alert.html type='warning' content='<code>machine.json</code>只指定计算执行的地址，计算生成的数据存储在<code>param.json</code>和<code>machine.json</code>所在文件夹下,计算所需的训练集和结构文件在<code>param.json</code>中指定路径（位于<code>dpgen run</code>命令所在服务服务器上）。Metal上的计算执行地址和提交任务建议写在<code>\bigdata</code>文件夹下，Zeus建议在<code>\data</code>下。' %}
 
 {% capture machine_note %}
-在 Metal 和 Zeus 集群上配置 <code>machine.json</code>，请参阅<a href="{{ site.baseurl }}{% link _wiki/集群使用/gpu_usage.md %}">GPU使用说明</a>中的
+在 Metal 和 Zeus 集群上配置 <code>machine.json</code>，请参阅<a href="{{ site.baseurl }}{% link _wiki/集群使用/gpu_usage.md %}#dpgen-提交-GPU-任务参数设置">GPU使用说明</a>
 {% endcapture %}
 
 {% include alert.html type='tip' content=machine_note %}

_wiki/softwares.md → _wiki/软件安装/softwares.md

@@ -1,6 +1,7 @@
 ---
 title: Guidances for installation of codes
 authors: Yongbin Zhuang
+priority: 2.0
 ---
 
 # Installation Guide for Codes and Libraries

pages/index.md

@@ -6,11 +6,11 @@ permalink: /
 
 # 欢迎来到程组Wiki
 
-这是程俊课题组的组内wiki。我们欢迎其他访问者一起浏览和提升！如果有其他建议请在github issue提出。
+这里是厦门大学程俊课题组的组内wiki。我们欢迎其他访问者一起浏览和提升！如果有其他建议请在github issue提出。
 
 # Welcome to ChengGroup Wiki
 
-This is group wiki for chenggroup which is personal academic group. Visitors are welcomed to have look in our wiki. It's better if you would like to post any suggestions for us. This Wiki are mainly written in **Simplified Chinese**.
+This is group wiki for chenggroup of XMU which is personal academic group. Visitors are welcomed to have look in our wiki. It's better if you would like to post any suggestions for us. This Wiki are mainly written in **Simplified Chinese**.
 
 
 
@@ -21,8 +21,8 @@ This is group wiki for chenggroup which is personal academic group. Visitors are
 1. [新生用: 组内安排和入门教程顺序]({{ site.baseurl }}/wiki/新生培训/toc)
 2. [组员用: 集群使用基础]({{ site.baseurl }}/wiki/集群使用/cluster_usage)
 3. [组员用: 集群GPU使用]({{ site.baseurl }}/wiki/集群使用/gpu_usage)
-4. [组员用: 如何修改与贡献Wiki]({{ site.baseurl }}/wiki/开始/howtodo)
-5. [集群管理人员用: 常用的软件安装]({{ site.baseurl }}/wiki/softwares)
+4. [组员用: 如何修改与贡献Wiki]({{ site.baseurl }}/wiki/开始编辑/howtodo)
+5. [集群管理人员用: 常用的软件安装]({{ site.baseurl }}/wiki/软件安装/softwares)
 
 ## 其他部分