diff --git a/include/addition1.md b/include/addition1.md
index 5ba8b32..af384fd 100644
--- a/include/addition1.md
+++ b/include/addition1.md
@@ -1,7 +1,5 @@
This paragraph came from another file.
We can put a full blown Markdown files in this file.
-Under the hood, this included file will be translated into \LaTeX by pubsEngine.
-Then the \LaTeX code produced will be inserted into the main output file.
-\LaTeX macro that defined in the main source, would not implemented in this file.
-For example, this beautifully formatted symbol of \LaTeX was produced by the real macro `\LaTeX` instead of the more convenience version of `\latex` from the main source.
+Under the hood, this included file will be translated into \latex by pubsEngine.
+Then the \latex code produced will be inserted into the main output file.
This means, every figures that refered in this file should be refered as if relative to the main source, instead of that to this file.
diff --git a/manuscript.md b/manuscript.md
index 2f15a54..d6f7e00 100644
--- a/manuscript.md
+++ b/manuscript.md
@@ -37,10 +37,11 @@ acknowledgements:
Part of this work was supported by the German
*Deutsche Forschungsgemeinschaft, DFG* project
number Ts 17/2--1.
-include-headers: |
+header-includes: |
+ \usepackage{chemfig}
\newcommand\mC[1]{\multicolumn{1}{c}{#1}}
\newcommand\latex{\LaTeX\xspace }
- \newcommand\v[1]{\verb-#1-}
+#\newcommand\v[1]{\verb-#1-}
---
@@ -83,7 +84,7 @@ This section would shows several common syntax of Markdown.
More detailed syntax can be accessed in the Markdown cheatsheet.
## Headings
-We use \v{#} on various levels. Headings should be shown as a line that prefixed by \v{#}. (Ex. \v{# The First Level Heading}). Please include space after \v{#}.
+We use `#` on various levels. Headings should be shown as a line that prefixed by `#`. (Ex. `# The First Level Heading`). Please include space after `#`.
## Paragraph
blank line stands as a paragraph separator. No indentation for the first line (it only required in multilined lists to show that the next line is part of the item if it is non-blank and indented).
@@ -322,12 +323,66 @@ Above paragraph was included from `include/addition1.md`.
We can include a diagram script, following an Embedded domain-specific Language from Haskell [`diagrams`](https://hackage.haskell.org/package/diagrams). We can see the implementation of following CodeBlock as Figure \ref{fig:dia1}.
```
-~~~{#fig:dia1 .diagram}
+~~~{#fig:dia1 .diagram width=100 caption="dia"}
let x = circle 10
in x
~~~
```
+
+~~~{.diagram width=300 caption="complex diagram" width=100}
+type D2 = Diagram PGF
+
+main = onlineMain example
+
+mytext :: OnlineTex D2
+mytext = scale 2 . box 8 orange <$> hboxOnline (sizedVBox 18 txt)
+ where
+ txt = "The sum of the squares of the lengths of the legs equals the square "
+ ++ "of the length of the hypotenuse:"
+ ++ "$$ a^2 + b^2 = c^2 .$$"
+
+rightTriangle
+ = fromVertices [origin, mkP2 4 0, mkP2 4 3]
+ # closeTrail
+ # strokeTrail
+ # centerXY
+ # scale 12
+ # fc dodgerblue
+ # label (hboxPoint "\\chemfig{R-C-[::-60]O-[::-60]C-[::-60]R}") (V2 4 6)
+ # label (hboxPoint "\\chemfig{*5(-=--=)}") (V2 1 1)
+
+labeledTriangle :: OnlineTex D2
+labeledTriangle = scale 5 <$> do
+ a <- hboxOnline "$a$"
+ b <- hboxOnline "$b$"
+ c <- hboxOnline "$c$"
+
+ pure $ rightTriangle
+ # label a unit_X
+ # label b unit_Y
+ # label c (V2 4 3)
+
+example = frame 10 <$> liftA2 (|-|) labeledTriangle mytext
+
+a |-| b = a ||| strutX 25 ||| b
+
+box padding colour content
+ = centerXY content
+ <> roundedRect w h 2
+ # fc colour
+ where
+ V2 w h = (+padding) <$> size content
+
+sizedVBox w x = "\\hsize=" ++ show w ++ "em\\vbox{\\noindent " ++ x ++ "}"
+
+label l v a = besideWithGap 3 (perp v) a (centerXY l)
+
+besideWithGap g v a b = beside v a b'
+ where
+ b' = beside v (strut (g *^ signorm v)) b
+~~~
+
~~~{#fig:dia1 .diagram}
let x = circle 10
in x
@@ -364,8 +419,80 @@ As an example, the creation of table \ref{tbl:delegate}, can be delegated to `mu
~~~
```
+## Feynman diagram
+
+Feynman diagram can be generated using the following syntax.
+```
+~~~{.feynmp caption="test feynman diagram"}
+ \begin{equation}
+ \begin{gathered}
+ \begin{fmfgraph*}(65,50) %size 65,50
+ \fmfleft{i1,i2}
+ \fmfright{o1,o2}
+ \fmf{fermion}{i1,v1,o1}
+ \fmf{fermion}{i2,v2,o2}
+ \fmf{photon}{v1,v2}
+ \end{fmfgraph*}
+ \end{gathered}=-i\lambda
+ \end{equation}
+~~~
+```
+
+~~~{.feynmp caption="test feynman diagram"}
+ \begin{equation}
+ \begin{gathered}
+ \begin{fmfgraph*}(65,50) %size 65,50
+ \fmfleft{i1,i2}
+ \fmfright{o1,o2}
+ \fmf{fermion}{i1,v1,o1}
+ \fmf{fermion}{i2,v2,o2}
+ \fmf{photon}{v1,v2}
+ \end{fmfgraph*}
+ \end{gathered}=-i\lambda
+ \end{equation}
+~~~
+
+## Mermaid diagrams
+
+Inclusion of [Mermaid](https://github.com/Alxandr/pandoc-mermaid) diagrams can be done by the following syntax:
+
+```
+~~~{.mermaid caption="inilah new mermaid"}
+sequenceDiagram
+ participant Alice
+ participant Bob
+ Alice->John: Hello John, how are you?
+ loop Healthcheck
+ John->John: Fight against hypochondria
+ end
+ Note right of John: Rational thoughts
prevail...
+ John-->Alice: Great!
+ John->Bob: How about you?
+ Bob-->John: Jolly good!
+~~~
+```
+
+~~~{.mermaid caption="inilah new mermaid"}
+sequenceDiagram
+ participant Alice
+ participant Bob
+ Alice->John: Hello John, how are you?
+ loop Healthcheck
+ John->John: Fight against hypochondria
+ end
+ Note right of John: Rational thoughts
prevail...
+ John-->Alice: Great!
+ John->Bob: How about you?
+ Bob-->John: Jolly good!
+~~~
+## Presentation and Poster (Beamer)
+
+There are two CodeBlocks that can be used for beamer.
+For a TextBlock, we can use `~~~{.textblock w=150pt pos=(140pt,160pt)}`.
+We can include notes for beamer by `~~~{note}` CodeBlocks.
+
# Baker's standard one-zone model