You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
1819 lines
76 KiB
1819 lines
76 KiB
--- |
|
shorttitle: "pubsEngine" |
|
shortauthor: "Author One, et al." |
|
title: "pubsEngine: Manuscript Engine" |
|
author: |
|
- number: 1 |
|
orcid: "0000-0002-0786-7307" |
|
name: "Author One" |
|
correspond: true |
|
affiliation: "My City University" |
|
address: "Orenomachi, Orenoshi, Orenoken, Japan" |
|
email: "one@myuni.ac.jp" |
|
- number: 2 |
|
name: "Author Two" |
|
affiliation: "My Other City University" |
|
address: "Hokanomachi, Orenoshi, Orenoken, Japan" |
|
email: "two@myuni.ac.jp" |
|
collaborator: |
|
theme: "AAS Journal Data Editors" |
|
person: |
|
- number: 1 |
|
orcid: "0000-0002-0786-7307" |
|
name: "Author One" |
|
correspond: true |
|
affiliation: "My City University" |
|
address: "Orenomachi, Orenoshi, Orenoken, Japan" |
|
email: "one@myuni.ac.jp" |
|
- number: 2 |
|
name: "Author Two" |
|
affiliation: "My Other City University" |
|
address: "Hokanomachi, Orenoshi, Orenoken, Japan" |
|
email: "two@myuni.ac.jp" |
|
email: "xxx@myuni.ac.jp" |
|
titleshort: "Paperlighter Example" |
|
authorshort: "Author One et.al." |
|
#% Reintroduced the \received and \accepted commands from AASTeX v5.2 |
|
#\received{March 1, 2021} |
|
#\revised{April 1, 2021} |
|
#\accepted{\today} |
|
#\submitjournal{PSJ} |
|
#% \watermark{text} |
|
#% \setwatermarkfontsize{dimension} |
|
#\correspondingauthor{August Muench} |
|
#\email{greg.schwarz@aas.org, gus.muench@aas.org} |
|
#end of docs |
|
#\allauthors |
|
#\listofchanges |
|
processDate: |
|
received: "March 11, 2022" |
|
accepted: "April 11, 2022" |
|
linkDir: |
|
- Figure |
|
- Output |
|
appendix: |
|
- include/appendix1 |
|
- include/appendix2 |
|
- include/appendix3 |
|
- include/appendix4 |
|
- include/appendix5 |
|
graphicpaths: |
|
- Figure |
|
abstract: | |
|
This example manuscript is intended to serve as a tutorial and template for |
|
authors to use when writing their own AAS Journal articles. The manuscript |
|
includes a history of \aastex and documents the new features in the |
|
previous versions as well as the bug fixes in version 6.31. This |
|
manuscript includes many figure and table examples to illustrate these new |
|
features. Information on features not explicitly mentioned in the article |
|
can be viewed in the manuscript comments or more extensive online |
|
documentation. Authors are welcome replace the text, tables, figures, and |
|
bibliography with their own and submit the resulting manuscript to the AAS |
|
Journals peer review system. The first lesson in the tutorial is to remind |
|
authors that the AAS Journals, the Astrophysical Journal (ApJ), the |
|
Astrophysical Journal Letters (ApJL), the Astronomical Journal (AJ), and |
|
the Planetary Science Journal (PSJ) all have a 250 word limit for the |
|
abstract\footnote{Abstracts for Research Notes of the American Astronomical |
|
Society (RNAAS) are limited to 150 words}. If you exceed this length the |
|
Editorial office will ask you to shorten it. This abstract has 182 words. |
|
abstractTex: |
|
#\abstract{Context}{Aim}{Method}{Result}Conclusion} |
|
\abstract{To investigate the physical nature of the 'nuc\-leated instability' of |
|
proto giant planets, the stability of layers in static, radiative gas spheres is analysed on the basis of Baker's standard one-zone model.} |
|
{To investigate the physical nature of the 'nuc\-leated instability' of |
|
proto giant planets, the stability of layers in static, radiative gas spheres is analysed on the basis of Baker's standard one-zone model.} |
|
{It is shown that stability depends only upon the equations of state, the opacities and the local thermodynamic state in the layer. Stability and instability can therefore be expressed in the form of stability equations of state which are universal for a given composition.} |
|
{The stability equations of state are calculated for solar composition and are displayed in the domain $-14 \leq \lg \rho / \mathrm{[g\, cm^{-3}]} \leq 0 $, $ 8.8 \leq \lg e / \mathrm{[erg\, g^{-1}]} \leq 17.7$. These displays may be used to determine the one-zone stability of layers in stellar or planetary structure models by directly reading off the value of the stability equations for the thermodynamic state of these layers, specified by state quantities as density $\rho$, temperature $T$ or specific internal energy $e$. Regions of instability in the $(\rho,e)$-plane are described and related to the underlying microphysical processes.} |
|
{Vibrational instability is found to be a common phenomenon at temperatures lower than the second He ionisation zone. The $\kappa$-mechanism is widespread under 'cool' conditions.} |
|
keywords: |
|
# will use --- as separator |
|
- Classical Novae (251) |
|
- Ultraviolet astronomy(1736) |
|
- History of astronomy(1868) |
|
- Interdisciplinary astronomy(804) |
|
facilities: "HST(STIS), Swift(XRT and UVOT), AAVSO, CTIO:1.3m, CTIO:1.5m, CXO" |
|
acknowledgements: |
|
We thank all the people that have made this AASTeX what it is today. This |
|
includes but not limited to Bob Hanisch, Chris Biemesderfer, Lee Brotzman, |
|
Pierre Landau, Arthur Ogawa, Maxim Markevitch, Alexey Vikhlinin and Amy |
|
Hendrickson. Also special thanks to David Hogg and Daniel Foreman-Mackey |
|
for the new "modern" style design. Considerable help was provided via bug |
|
reports and hacks from numerous people including Patricio Cubillos, Alex |
|
Drlica-Wagner, Sean Lake, Michele Bannister, Peter Williams, and Jonathan |
|
Gagne. |
|
header-includes: | |
|
\usepackage{chemfig} |
|
\newcommand\mC[1]{\multicolumn{1}{c}{#1}} |
|
\newcommand{\vdag}{(v)^\dagger} |
|
\newcommand\aastex{AAS\TeX} |
|
\newcommand\latex{\LaTeX\xspace} |
|
|
|
--- |
|
|
|
# Introduction |
|
|
|
In the 'nucleated instability' (also called core |
|
instability) hypothesis of giant planet |
|
formation, a critical mass for static core envelope |
|
protoplanets has been found. \citet{langley00} determined |
|
the critical mass of the core to be about $12 \,M_\oplus$ |
|
($M_\oplus=5.975 \times 10^{27}\,\mathrm{g}$ is the Earth mass), which |
|
is independent of the outer boundary |
|
conditions and therefore independent of the location in the |
|
solar nebula. This critical value for the core mass corresponds |
|
closely to the cores of today's giant planets. |
|
|
|
Although no hydrodynamical study has been available many workers |
|
conjectured that a collapse or rapid contraction will ensue |
|
after accumulating the critical mass. The main motivation for |
|
this article |
|
is to investigate the stability of the static envelope at the |
|
critical mass. With this aim the local, linear stability of static |
|
radiative gas spheres is investigated on the basis of Baker's |
|
(\citeyear{mitchell80}) standard one-zone model. |
|
|
|
Phenomena similar to the ones described above for giant planet |
|
formation have been found in hydrodynamical models concerning |
|
star formation where protostellar cores explode |
|
(Tscharnuter \citeyear{kearns89}, Balluch \citeyear{MachineLearningI}), |
|
whereas earlier studies found quasi-steady collapse flows. The |
|
similarities in the (micro)physics, i.e., constitutive relations of |
|
protostellar cores and protogiant planets serve as a further |
|
motivation for this study. |
|
|
|
# Markdown |
|
|
|
pubsEngine use Markdown text-file as an input to be processed into \latex document. |
|
Markdown is a very simplified text markup language. |
|
This section would shows several common syntax of Markdown. |
|
More detailed syntax can be accessed in the Markdown cheatsheet. |
|
|
|
## Headings |
|
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). |
|
|
|
## Italic |
|
`*` Ex. `this text is *italic*` : this text is *italic* |
|
|
|
## Bold |
|
`**` Ex. `this text is **bold**` : this text is **bold** |
|
|
|
## Bold and Italic |
|
`***` Ex. `this text is ***bold and italic***` this text is ***bold and italic*** |
|
|
|
## Verbatim |
|
Verbatim should use backticks \v{`text`}, Ex. ``this is `the text` `` this is `the text`. |
|
To include backticks inside the text, use multiple bacticks. |
|
|
|
~~~ |
|
``this is `the text` multiple`` |
|
~~~ |
|
|
|
## CodeBlocks |
|
Multiple verbatim lines in Markdown can be expressed as a CodeBlock. |
|
This particular block is considered as special, due to its popular use in verbatim representation of source-code in the manuscript. |
|
Technically, a CodeBlock is a range of lines that surrounded by triple tilde `~~~`, for example: |
|
|
|
``` |
|
~~~ |
|
main :: IO () |
|
main = putStrLn "we are one" |
|
~~~ |
|
``` |
|
|
|
will produce: |
|
|
|
~~~ |
|
main :: IO () |
|
main = putStrLn "we are one" |
|
~~~ |
|
|
|
The abuse of CodeBlocks for another purpose will be discussed in another section (Enhancement by pubsEngine). |
|
|
|
## Mathematical Equations |
|
By default, we may use `$$` environment for mathematical formula. |
|
Nonetheless, actually, we can use any \latex scenario, such as: |
|
|
|
~~~ |
|
$$ $$ is equal with \begin{equation} |
|
\begin{eqnarray} |
|
\begin{array} |
|
\begin{displaymath} |
|
\begin{align} |
|
~~~ |
|
|
|
This is an example: |
|
|
|
~~~ |
|
\begin{align} |
|
\nabla \cdot \vec{E} &= \rho \nonumber \\ |
|
\nabla \cdot \vec{B} &= 0 \nonumber \\ |
|
\nabla \times \vec{E} &= -\frac{\vec{B}}{t} |
|
\end{align} |
|
~~~ |
|
|
|
\begin{align} |
|
\nabla \cdot \vec{E} &= \rho \nonumber \\ |
|
\nabla \cdot \vec{B} &= 0 \nonumber \\ |
|
\nabla \times \vec{E} &= -\frac{\vec{B}}{t} |
|
\end{align} |
|
|
|
Equations as independent paragraph equation is not numbered, as below. |
|
|
|
$$ |
|
\nabla \cdot \vec{W} = \sigma W \nonumber |
|
$$ |
|
|
|
And this is another example for inline equation, such as: $$y = 5\cdot x^2$$ |
|
You can see that inline equation have automatically numbered. |
|
|
|
## Tables |
|
Table creation will be described in another section (Enhancement by pubsEngine). |
|
|
|
## Images |
|
~~~ |
|
 |
|
{#fig:FigVibStab width=3.43in height=2.71in} |
|
~~~ |
|
|
|
will produce Figure \ref{fig:FigVibStab}. |
|
Make sure that you calculated by yourself the appropriate width and height for the image to fit in a column. |
|
Full width image and automatic sized image for single-column will be described at another section (Enhancement by pubsEngine). |
|
|
|
{#fig:FigVibStab width=3.43in height=2.71in} |
|
|
|
## Lists |
|
We can have either ordered or unordered list |
|
|
|
### Ordered List |
|
For ordered list, we just use numbers. |
|
The block should be as an independent paragraph (blank line above and under the block). |
|
|
|
|
|
~~~ |
|
1. first in line |
|
2. second |
|
3. and the third |
|
~~~ |
|
will produce |
|
|
|
1. first in line |
|
2. second |
|
3. and the third |
|
|
|
## Unordered List |
|
For unordered list, use dash sign (`-`). |
|
We also can use asterisk and plus signs ( `* +`) |
|
|
|
~~~ |
|
- first in line |
|
- second |
|
should multiline |
|
- and the third |
|
~~~ |
|
|
|
will produce |
|
|
|
- first in line |
|
- second |
|
should multiline |
|
- and the third |
|
|
|
|
|
## Links |
|
|
|
~~~ |
|
We use [Duck Duck Go](https://duckduckgo.com). |
|
~~~ |
|
|
|
produces: We use [Duck Duck Go](https://duckduckgo.com). |
|
|
|
## Email link |
|
|
|
~~~ |
|
<myemail@myurl.org> |
|
~~~ |
|
|
|
produces email link: |
|
|
|
<myemail@myurl.org> |
|
|
|
# Enhancement by pubsEngine |
|
|
|
The enhancements provided by pubsEngine spans on various aspects. |
|
Most parts of this are expressed in terms of CodeBlocks. |
|
|
|
## Table |
|
|
|
pubsEngine provides its table capability outside the defaults available in Pandoc. |
|
Under the table, pubsEngine will use MultiMarkdown to process its table. |
|
We can create Table \ref{tbl:multi} using the following template: |
|
|
|
``` |
|
~~~{.multiTable #tbl:multi} |
|
| | Grouping || |
|
|First Header | Second Header | Third Header | |
|
| ------------ | :-----------: | -----------: | |
|
|Content | *Long Cell* || |
|
|Content | **Cell** | Cell | |
|
|New section | More | Data | |
|
|And more | With an escaped '\|' || |
|
[More complicated table caption.] |
|
~~~ |
|
``` |
|
|
|
~~~{.multiTable #tbl:multi} |
|
| | Grouping || |
|
|First Header | Second Header | Third Header | |
|
| ------------ | :-----------: | -----------: | |
|
|Content | *Long Cell* || |
|
|Content | **Cell** | Cell | |
|
|New section | More | Data | |
|
|And more | With an escaped '\|' || |
|
[More complicated table can be done using multimarkdown in .multiTable Code Block. You have to use this format for all table as default.] |
|
~~~ |
|
|
|
Currently, we cannot create full width two-columns table automatically using above default syntax. |
|
For the moment, we should use a complete \latex syntax to fulfill this. |
|
The detailed syntax for this purpose will be shown in the Appendix. |
|
|
|
<!-- |
|
We use `\begin{table*}` for full screen table as follows Table \ref{KapSou}. |
|
|
|
\begin{table*} |
|
\centering |
|
|
|
\caption[]{Opacity sources. Prototype for correct table. In full screen mode. \label{KapSou}} |
|
\begin{tabular}{@{}cc |
|
*{4}{S[table-format=6.3,output-decimal-marker={,}]} |
|
@{}} |
|
\toprule |
|
Lp. & Miejscowość |
|
& \multicolumn{2}{@{}c}{Zapotrzebowanie na wodę, \si{m^3/\day}} |
|
& \multicolumn{2}{c@{}}{Odpływ ścieków, \si{m^3/\day}} \\ |
|
& & \mC{$Q_{\text{śrd}}$} & \mC{$Q_{\text{maxd}}$} & |
|
\mC{$Q_{\text{rdś}}$} & \mC{$Q_{\text{maxd}}$} \\ |
|
\midrule |
|
1. & X1 & 57,2 & 74,4 & 54,3 & 70,7 \\ |
|
2. & X2 & 82,5 & 107,3 & 78,4 & 101,9 \\ |
|
3. & X3 & 47,3 & 61,5 & 44,9 & 58,4 \\ |
|
4. & X4 & 24,2 & 31,5 & 23,0 & 29,9 \\ |
|
5. & X5 & 211,2 & 274,7 & 200,6 & 260,9 \\ |
|
\bottomrule |
|
\end{tabular} |
|
\end{table*} |
|
--> |
|
|
|
|
|
## Include .md Files |
|
|
|
We can create a rather decent categorical separation of our documents by dividing the .md files and gather them using includes. |
|
|
|
``` |
|
~~~include |
|
include/addition1.md |
|
~~~ |
|
``` |
|
|
|
~~~include |
|
include/addition1.md |
|
~~~ |
|
|
|
Above paragraph was included from `include/addition1.md`. |
|
|
|
## Diagram |
|
|
|
We can include a diagram script, following an Embedded domain-specific Language from Haskell package [`diagrams`](https://hackage.haskell.org/package/diagrams). |
|
The implementation of following CodeBlock can be seen at Figure \ref{fig:dia1}. |
|
|
|
``` |
|
~~~{#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 |
|
~~~ |
|
--> |
|
|
|
## Running a subcommand |
|
|
|
Currently, subcommand only valid for Python script. |
|
There are two possible class available for this subcommand. |
|
`.md` would output a text document that would be translated to a markdown by pubsEngine. |
|
In this scenario, the script should output a valid markdown document to the stdout. |
|
We are expecting the usage of `.md` to produce some sort of table, or a dynamic paragraph. |
|
|
|
``` |
|
~~~{.script .py .md #tbl:py caption="this is a table script"} |
|
#!/usr/bin/env python3 |
|
|
|
print(""" |
|
| as | dd | |
|
|----|----| |
|
| dd | dd | |
|
Table: this is output of a python script |
|
""") |
|
~~~ |
|
``` |
|
|
|
The above snipplet would give us output: |
|
|
|
~~~{.script .py .md #tbl:py caption="this is a table script"} |
|
#!/usr/bin/env python3 |
|
|
|
print(""" |
|
| as | dd | |
|
|----|----| |
|
| dd | dd | |
|
Table: this is output of a python script |
|
""") |
|
~~~ |
|
|
|
On the otherhand, `.img` will produce an image in the document. |
|
This scenario expects the script will run an IO and must create an image file inside directory `_build/auto` by the filename designated by `file`. |
|
The image at Figure \ref{fig:py} can be produced using: |
|
|
|
``` |
|
~~~{.script .py .img #fig:py caption="this is a new image from script" width=400 height=300 file=pyImage} |
|
#!/usr/bin/env python3 |
|
|
|
print("image new image") |
|
~~~ |
|
``` |
|
|
|
~~~{.script .py .img #fig:py caption="this is a new image from script" width=400 height=300 file=pyImage} |
|
#!/usr/bin/env python3 |
|
|
|
print("image new image") |
|
~~~ |
|
|
|
To make this document can stands on its own and to remove repetitive codes, we can also include a python library inside `_build/lib` directory. |
|
All script above, will include all files mentioned inside `_build/lib`. |
|
Furthermore, the `_build/lib` will be populated by CodeBlock with `.lib` class. |
|
This is an example of the block: |
|
|
|
``` |
|
~~~{.script .py .lib #fig:py} |
|
#!/usr/bin/env python3 |
|
|
|
print("this is new block") |
|
~~~ |
|
``` |
|
|
|
We can choose the representation of this block inside the pdf output by providing `description` variable. |
|
When there is no `description`, then this `lib` CodeBlock will be considered as a *hidden library*, it will be still included inside every script, but it will be never mentioned inside the pdf result. |
|
|
|
|
|
~~~{.script .py .lib file="libPy1"} |
|
#!/usr/bin/env python3 |
|
|
|
def f(x): |
|
return x*x + 2*x + 3 |
|
|
|
description=""" |
|
This is the description of this library that will be inserted into the pdf output. |
|
We can use any valid markdown syntax. |
|
""" |
|
~~~ |
|
|
|
|
|
## Subprocess delegation |
|
|
|
~~~{.delegate .multimarkdown #tbl:delegate} |
|
| | Grouping || |
|
|First Header | Second Header | Third Header | |
|
| ------------ | :-----------: | -----------: | |
|
|Content | *Long Cell* || |
|
|Content | **Cell** | Cell | |
|
| |
|
|New section | More | Data | |
|
|And more | With an escaped '\|' || |
|
[Prototype table] |
|
~~~ |
|
|
|
We can delegate the compilation of our CodeBlock to other application. |
|
As an example, the creation of table \ref{tbl:delegate}, can be delegated to `multimarkdown` using following syntax. Please notice the use of `#tbl:delegate` for assignment of label that can be refered in the text using `\ref{tbl:delegate}`. |
|
|
|
``` |
|
~~~{.delegate .multimarkdown #tbl:delegate} |
|
| | Grouping || |
|
|First Header | Second Header | Third Header | |
|
| ------------ | :-----------: | -----------: | |
|
|Content | *Long Cell* || |
|
|Content | **Cell** | Cell | |
|
| |
|
|New section | More | Data | |
|
|And more | With an escaped '\|' || |
|
[Prototype table] |
|
~~~ |
|
``` |
|
|
|
## 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/hasanalrasyid/pandoc-mermaid) diagrams at Figure \ref{fig:mermaid} can be done by the following syntax: |
|
|
|
``` |
|
~~~{.mermaid #fig:mermaid caption="new mermaid" |
|
file="mermaidExample" |
|
width=320 height=240} |
|
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 <br/> |
|
prevail... |
|
John-->Alice: Great! |
|
John->Bob: How about you? |
|
Bob-->John: Jolly good! |
|
~~~ |
|
``` |
|
|
|
~~~{.mermaid #fig:mermaid caption="new mermaid" file="mermaidExample" width=320 height=240} |
|
|
|
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 <br/>prevail... |
|
John-->Alice: Great! |
|
John->Bob: How about you? |
|
Bob-->John: Jolly good! |
|
~~~ |
|
|
|
Please make sure that Mermaid executables have already installed in `$PATH`. |
|
pubsEngine need to call executable named `mermaid`. |
|
Common ways to install Mermaid is: |
|
|
|
~~~ |
|
npm install @mermaid-js/mermaid-cli |
|
ln -sf ~/node_modules/.bin/mmdc ~/.local/bin/mermaid |
|
~~~ |
|
|
|
## 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 |
|
|
|
<!-- we need figure* for make it full screen, so it must be in latex code as follows |
|
--> |
|
|
|
\begin{figure*} |
|
\centering |
|
\includegraphics{Figure/icml_numpapers.eps} |
|
\caption{Adiabatic exponent $\Gamma_1$. |
|
$\Gamma_1$ is plotted as a function of |
|
$\lg$ internal energy $\mathrm{[erg\,g^{-1}]}$ and $\lg$ |
|
density $\mathrm{[g\,cm^{-3}]}$.} |
|
\label{fig:FigGam}% |
|
\end{figure*} |
|
|
|
In this section the one-zone model of \citet{DudaHart2nd}, |
|
originally used to study the Cephe\text{\"{\i}}d pulsation mechanism, will |
|
be briefly reviewed. The resulting stability criteria will be |
|
rewritten in terms of local state variables, local timescales and |
|
constitutive relations. |
|
|
|
\citet{DudaHart2nd} investigates the stability of thin layers in |
|
self-gravitating, |
|
spherical gas clouds with the following properties: |
|
|
|
~~~ |
|
* hydrostatic equilibrium, |
|
* thermal equilibrium, |
|
* energy transport by grey radiation diffusion. |
|
~~~ |
|
|
|
non-numbered list can be written as above, and shown as: |
|
|
|
* hydrostatic equilibrium, |
|
* thermal equilibrium, |
|
* energy transport by grey radiation diffusion. |
|
|
|
For the one-zone-model Baker obtains necessary conditions |
|
for dynamical, secular and vibrational (or pulsational) |
|
stability (Eqs. (34a,b,c) in Baker \citeyear{DudaHart2nd}). Using Baker's |
|
notation: |
|
|
|
\noindent |
|
and with the definitions of the *local cooling time* |
|
(see == [@fig:FigGam] == Fig. \ref{fig:FigGam}) |
|
\begin{equation} |
|
\tau_{\mathrm{co}} = \frac{E_{\mathrm{th}}}{L_{r0}} \,, |
|
\end{equation} |
|
and the *local free-fall time* |
|
\begin{equation} |
|
\tau_{\mathrm{ff}} = |
|
\sqrt{ \frac{3 \pi}{32 G} \frac{4\pi r_0^3}{3 M_{\mathrm{r}}} |
|
}\,, |
|
\end{equation} |
|
Baker's $K$ and $\sigma_0$ have the following form: |
|
\begin{eqnarray} |
|
\sigma_0 & = & \frac{\pi}{\sqrt{8}} |
|
\frac{1}{ \tau_{\mathrm{ff}}} \\ |
|
K & = & \frac{\sqrt{32}}{\pi} \frac{1}{\delta} |
|
\frac{ \tau_{\mathrm{ff}} } |
|
{ \tau_{\mathrm{co}} }\,; |
|
\end{eqnarray} |
|
where $E_{\mathrm{th}} \approx m (P_0/{\rho_0})$ has been used and |
|
\begin{equation} |
|
\begin{array}{l} |
|
\delta = - \left( |
|
\frac{ \partial \ln \rho }{ \partial \ln T } |
|
\right)_P \\ |
|
e=mc^2 |
|
\end{array} |
|
\end{equation} |
|
is a thermodynamical quantity which is of order $1$ and equal to $1$ |
|
for nonreacting mixtures of classical perfect gases. The physical |
|
meaning of $\sigma_0$ and $K$ is clearly visible in the equations |
|
above. $\sigma_0$ represents a frequency of the order one per |
|
free-fall time. $K$ is proportional to the ratio of the free-fall |
|
time and the cooling time. Substituting into Baker's criteria, using |
|
thermodynamic identities and definitions of thermodynamic quantities, |
|
\begin{displaymath} |
|
\Gamma_1 = \left( \frac{ \partial \ln P}{ \partial\ln \rho} |
|
\right)_{S} \, , \; |
|
\chi^{}_\rho = \left( \frac{ \partial \ln P}{ \partial\ln \rho} |
|
\right)_{T} \, , \; |
|
\kappa^{}_{P} = \left( \frac{ \partial \ln \kappa}{ \partial\ln P} |
|
\right)_{T} |
|
\end{displaymath} |
|
\begin{displaymath} |
|
\nabla_{\mathrm{ad}} = \left( \frac{ \partial \ln T} |
|
{ \partial\ln P} \right)_{S} \, , \; |
|
\chi^{}_T = \left( \frac{ \partial \ln P} |
|
{ \partial\ln T} \right)_{\rho} \, , \; |
|
\kappa^{}_{T} = \left( \frac{ \partial \ln \kappa} |
|
{ \partial\ln T} \right)_{T} |
|
\end{displaymath} |
|
one obtains, after some pages of algebra, the conditions for |
|
*stability* given |
|
below: |
|
\begin{eqnarray} |
|
\frac{\pi^2}{8} \frac{1}{\tau_{\mathrm{ff}}^2} |
|
( 3 \Gamma_1 - 4 ) |
|
& > & 0 \label{ZSDynSta} \\ |
|
\frac{\pi^2}{\tau_{\mathrm{co}} |
|
\tau_{\mathrm{ff}}^2} |
|
\Gamma_1 \nabla_{\mathrm{ad}} |
|
\left[ \frac{ 1- 3/4 \chi^{}_\rho }{ \chi^{}_T } |
|
( \kappa^{}_T - 4 ) |
|
+ \kappa^{}_P + 1 |
|
\right] |
|
& > & 0 \label{ZSSecSta} \\ |
|
\frac{\pi^2}{4} \frac{3}{\tau_{ \mathrm{co} } |
|
\tau_{ \mathrm{ff} }^2 |
|
} |
|
\Gamma_1^2 \, \nabla_{\mathrm{ad}} \left[ |
|
4 \nabla_{\mathrm{ad}} |
|
- ( \nabla_{\mathrm{ad}} \kappa^{}_T |
|
+ \kappa^{}_P |
|
) |
|
- \frac{4}{3 \Gamma_1} |
|
\right] |
|
& > & 0 \label{ZSVibSta} |
|
\end{eqnarray} |
|
|
|
For a physical discussion of the stability criteria see \citet{DudaHart2nd} or \citet{anonymous}. |
|
|
|
We observe that these criteria for dynamical, secular and |
|
vibrational stability, respectively, can be factorized into |
|
|
|
1. a factor containing local timescales only, |
|
2. a factor containing only constitutive relations and |
|
their derivatives. |
|
3. To make a numered list, make sure that: |
|
1. it stands on its own paragraph (blank line above and below the list), |
|
2. the number starts at first column on each line. |
|
|
|
The first factors, depending on only timescales, are positive |
|
by definition. The signs of the left hand sides of the |
|
inequalities (\ref{ZSDynSta}), (\ref{ZSSecSta}) and (\ref{ZSVibSta}) |
|
therefore depend exclusively on the second factors containing |
|
the constitutive relations. Since they depend only |
|
on state variables, the stability criteria themselves are *functions of the thermodynamic state in the local zone*. The |
|
one-zone stability can therefore be determined |
|
from a simple equation of state, given for example, as a function |
|
of density and temperature. Once the microphysics, i.e. the thermodynamics |
|
and opacities (see Table \ref{KapSou}), are specified (in practice |
|
by specifying a chemical composition) the one-zone stability can |
|
be inferred if the thermodynamic state is specified. |
|
The zone -- or in other words the layer -- will be stable or unstable in |
|
whatever object it is imbedded as long as it satisfies the |
|
one-zone-model assumptions. Only the specific growth rates |
|
(depending upon the time scales) will be different for layers |
|
in different objects. |
|
|
|
|
|
<!-- |
|
| | Grouping || |
|
First Header | Second Header | Third Header | |
|
------------ | :-----------: | -----------: | |
|
Content | *Long Cell* || |
|
Content | **Cell** | Cell | |
|
New section | More | Data | |
|
And more | With an escaped '\|' || |
|
|
|
Table: Simple table using default markdown table. Currently not working in two-columns environment due to [this issue](https://github.com/jgm/pandoc/issues/1023) \label{simpleTable} |
|
--> |
|
|
|
We will now write down the sign (and therefore stability) |
|
determining parts of the left-hand sides of the inequalities |
|
(\ref{ZSDynSta}), (\ref{ZSSecSta}) and (\ref{ZSVibSta}) and thereby |
|
obtain *stability equations of state*. |
|
|
|
The sign determining part of inequality (\ref{ZSDynSta}) is |
|
$3\Gamma_1 - 4$ and it reduces to the criterion for dynamical stability |
|
\begin{equation} |
|
\Gamma_1 > \frac{4}{3}\,\cdot |
|
\end{equation} |
|
Stability of the thermodynamical equilibrium demands |
|
\begin{equation} |
|
\chi^{}_\rho > 0, \;\; c_v > 0\, , |
|
\end{equation} |
|
and |
|
\begin{equation} |
|
\chi^{}_T > 0 |
|
\end{equation} |
|
holds for a wide range of physical situations. |
|
With |
|
\begin{eqnarray} |
|
\Gamma_3 - 1 = \frac{P}{\rho T} \frac{\chi^{}_T}{c_v}&>&0\\ |
|
\Gamma_1 = \chi_\rho^{} + \chi_T^{} (\Gamma_3 -1)&>&0\\ |
|
\nabla_{\mathrm{ad}} = \frac{\Gamma_3 - 1}{\Gamma_1} &>&0 |
|
\end{eqnarray} |
|
we find the sign determining terms in inequalities (\ref{ZSSecSta}) |
|
and (\ref{ZSVibSta}) respectively and obtain the following form |
|
of the criteria for dynamical, secular and vibrational |
|
*stability*, respectively: |
|
\begin{eqnarray} |
|
3 \Gamma_1 - 4 =: S_{\mathrm{dyn}} > & 0 & \label{DynSta} \\ |
|
\frac{ 1- 3/4 \chi^{}_\rho }{ \chi^{}_T } ( \kappa^{}_T - 4 ) |
|
+ \kappa^{}_P + 1 =: S_{\mathrm{sec}} > & 0 & \label{SecSta} \\ |
|
4 \nabla_{\mathrm{ad}} - (\nabla_{\mathrm{ad}} \kappa^{}_T |
|
+ \kappa^{}_P) |
|
- \frac{4}{3 \Gamma_1} =: S_{\mathrm{vib}} |
|
> & 0\,.& \label{VibSta} |
|
\end{eqnarray} |
|
The constitutive relations are to be evaluated for the |
|
unperturbed thermodynamic state (say $(\rho_0, T_0)$) of the zone. |
|
We see that the one-zone stability of the layer depends only on |
|
the constitutive relations $\Gamma_1$, |
|
$\nabla_{\mathrm{ad}}$, $\chi_T^{},\,\chi_\rho^{}$, |
|
$\kappa_P^{},\,\kappa_T^{}$. |
|
These depend only on the unperturbed |
|
thermodynamical state of the layer. Therefore the above relations |
|
define the one-zone-stability equations of state |
|
$S_{\mathrm{dyn}},\,S_{\mathrm{sec}}$ |
|
and $S_{\mathrm{vib}}$. See == [@fig:FigVibStab] == Fig. \ref{fig:FigVibStab} for a picture of |
|
$S_{\mathrm{vib}}$. Regions of secular instability are |
|
listed in Table 1. |
|
|
|
<!-- calculate height and width of picture manually in inch, using evince -> Properties |
|
create label for \ref{FigVibStab} using #FigVibStab |
|
--> |
|
{#fig:FigVibStab width=3.43in height=2.71in} |
|
|
|
<!-- |
|
\begin{figure} |
|
\centering |
|
\caption{Vibrational stability equation of state |
|
$S_{\mathrm{vib}}(\lg e, \lg \rho)$. |
|
$>0$ means vibrational stability. |
|
} |
|
\label{FigVibStab} |
|
\end{figure} |
|
--> |
|
|
|
# Conclusions |
|
|
|
1. The conditions for the stability of static, radiative |
|
layers in gas spheres, as described by Baker's (\citeyear{DudaHart2nd}) |
|
standard one-zone model, can be expressed as stability |
|
equations of state. These stability equations of state depend |
|
only on the local thermodynamic state of the layer. |
|
2. If the constitutive relations -- equations of state and |
|
Rosseland mean opacities -- are specified, the stability |
|
equations of state can be evaluated without specifying |
|
properties of the layer. |
|
3. For solar composition gas the $\kappa$-mechanism is |
|
working in the regions of the ice and dust features |
|
in the opacities, the $\mathrm{H}_2$ dissociation and the |
|
combined H, first He ionization zone, as |
|
indicated by vibrational instability. These regions |
|
of instability are much larger in extent and degree of |
|
instability than the second He ionization zone |
|
that drives the Cephe\text{\"\i}d pulsations. |
|
|
|
|
|
|
|
# Introduction |
|
|
|
\latex \footnote{\url{http://www.latex-project.org/}} is a document markup |
|
language that is particularly well suited for the publication of |
|
mathematical and scientific articles \citep{lamport94}. \latex was written |
|
in 1985 by Leslie Lamport who based it on the \TeX typesetting language |
|
which itself was created by Donald E. Knuth in 1978. In 1988 a suite of |
|
\latex macros were developed to investigate electronic submission and |
|
publication of AAS Journal articles \citep{1989BAAS...21..780H}. Shortly |
|
afterwards, Chris Biemesdefer merged these macros and more into a \latex\ |
|
2.08 style file called \aastex. These early \aastex versions introduced |
|
many common commands and practices that authors take for granted today. |
|
Substantial revisions |
|
were made by Lee Brotzman and Pierre Landau when the package was updated to |
|
v4.0. AASTeX v5.0, written in 1995 by Arthur Ogawa, upgraded to \latex 2e |
|
which uses the document class in lieu of a style file. Other improvements |
|
to version 5 included hypertext support, landscape deluxetables and |
|
improved figure support to facilitate electronic submission. |
|
\aastex v5.2 was released in 2005 and introduced additional graphics |
|
support plus new mark up to identifier astronomical objects, datasets and |
|
facilities. |
|
|
|
In 1996 Maxim Markevitch modified the AAS preprint style file, aaspp4.sty, |
|
to closely emulate the very tight, two column style of a typeset |
|
Astrophysical Journal article. The result was emulateapj.sty. A year |
|
later Alexey Vikhlinin took over development and maintenance. In 2001 he |
|
converted emulateapj into a class file in \latex 2e and in 2003 Vikhlinin |
|
completely rewrote emulateapj based on the APS Journal's RevTEX class. |
|
|
|
During this time emulateapj gained growing acceptance in the astronomical |
|
community as it filled an author need to obtain an approximate number of |
|
manuscript pages prior to submission for cost and length estimates. The |
|
tighter typeset also had the added advantage of saving paper when printing |
|
out hard copies. |
|
|
|
Even though author publication charges are no longer based on print pages |
|
\footnote{see Section \ref{sec:pubcharge} in the Appendix for more details |
|
about how current article costs are calculated.} the emulateapj class file |
|
has proven to be extremely popular with AAS Journal authors. An |
|
analysis of submitted \latex manuscripts in 2015 revealed that sim65 |
|
either called emulateapj or have a commented emulateapj classfile call |
|
indicating it was used at some stage of the manuscript construction. |
|
Clearly authors want to have access to a tightly typeset version of the |
|
article when corresponding with co-authors and for preprint submissions. |
|
|
|
When planning the next \aastex release the popularity of emulateapj played |
|
an important roll in the decision to drop the old base code and adopt and |
|
modify emulateapj for \aastex v6.+ instead. The change brings \aastex\ |
|
inline with what the majority of authors are already using while still |
|
delivering new and improved features. \aastex v6.0 through v6.31 were |
|
written by Amy Hendrickson. The release dates were January 2016 (v6.0), |
|
October 2016 (v6.1), January 2018 (v6.2), June 2019 (v6.3), and March 2010 |
|
(v6.31) respectively. |
|
|
|
The new features in the recent releases includes: |
|
|
|
\begin{itemize} |
|
\item{v6.0} |
|
\begin{enumerate} |
|
\item line numbering and watermarking, |
|
\item improved citations for third party data repositories and software, |
|
\item easier construction of matrix figures consisting of multiple |
|
encapsulated postscript (EPS) or portable document format (PDF) files, |
|
\item figure set mark up for large collections of similar figures, |
|
\item color mark up to easily enable/disable revised text highlighting, |
|
\item improved url support, and |
|
\item numerous table options such as the ability to hide columns, column decimal alignment, automatic column math mode and numbering, plus splitting of wide tables (see Section \ref{subsec:tables} for details). |
|
\end{enumerate} |
|
\item{v6.1} |
|
\begin{enumerate} |
|
\item ORCID support for preprints, |
|
\item improved author, affiliation and collaboration mark up, |
|
\item reintroduced the old AASTeX v5.2 `\received`, `\revised`, `\accepted`, and `\published` commands plus added the new `\submitjournal` command to document which AAS Journal the manuscript was submitted to, plus |
|
\item new typeset style options including ` modern`. |
|
\end{enumerate} |
|
\item{v6.2} |
|
\begin{enumerate} |
|
\item A new RNAAS style option for Research Note manuscripts, |
|
\item Titles no longer put in all caps, |
|
\item No page skip between the title page and article body, |
|
\item re-introduce RevTeX's widetext environment for long lines in two column style formats, and |
|
\item upgrade to the `\doi` command. |
|
\end{enumerate} |
|
\item{v6.3} |
|
\begin{enumerate} |
|
\item New ` interactive` environment to highlight interactive figures (see Section \ref{animation}), |
|
\item Improved collaboration commands, |
|
\item New ` anonymous` style to keep the authors, affiliations and acknowledgments from showing in the compiled pdf for dual anonymous review, and |
|
\item Adoptions of IAU approved syntax for nominal units, see Section \ref{nominal}. |
|
\end{enumerate} |
|
\item{v6.31} |
|
\begin{enumerate} |
|
\item Fixes a bug in the ` anonymous` style for dual anonymous review. |
|
\item Improves line numbering with the ` linenumbers` style around equations due to the amsmath and lineno package compatibility issues. |
|
\item Depreciate the ` \\acknowledgment` command in favor of the ` acknowledgment` environment. |
|
\end{enumerate} |
|
\end{itemize} |
|
|
|
The rest of this article provides information and examples on how to create |
|
your own AAS Journal manuscript with v6.31. Special emphasis is placed on |
|
how to use the full potential of \aastex v6+. The next section describes |
|
the different manuscript styles available and how they differ from past |
|
releases. Section \ref{sec:floats} describes table and figure placement. |
|
Specific examples of tables, Section |
|
\ref{subsec:tables}, and figures, Section \ref{subsec:figures}, are also |
|
provided. A special emphasis is placed on interactive figures. |
|
Section \ref{sec:displaymath} discusses how to display math and |
|
incorporate equations in a manuscript while Section \ref{sec:highlight} |
|
discuss how to use different ways to highlight revisions. The last section, |
|
\ref{sec:cite}, shows how recognize software and external data as first |
|
class references in the manuscript bibliography. An appendix is included |
|
for additional information readers might find useful. |
|
More documentation is embedded in the comments of this \latex file and in the online documentation at |
|
\url{http://journals.aas.org/authors/aastex.html}. |
|
|
|
# Manuscript styles |
|
|
|
The default style in \aastex v6.31 is a tight single column style, e.g. 10 |
|
point font, single spaced. The single column style is very useful for |
|
article with wide equations. It is also the easiest to style to work with |
|
since figures and tables, see Section \ref{sec:floats}, will span the |
|
entire page, reducing the need for address float sizing. |
|
|
|
To invoke a two column style similar to the what is produced in |
|
the published PDF copy use |
|
|
|
~~~ |
|
\documentclass[twocolumn]{aastex631} |
|
~~~ |
|
|
|
Note that in the two column style figures and tables will only |
|
span one column unless specifically ordered across both with the ``*`` flag, |
|
e.g. |
|
|
|
~~~ |
|
\begin{figure*} ... \end{figure*}, |
|
\begin{table*} ... \end{table*}, |
|
\begin{deluxetable*} ... \end{deluxetable*}. |
|
~~~ |
|
|
|
This option is ignored in the onecolumn style. |
|
|
|
Some other style options are outlined in the commented sections of this |
|
article. Any combination of style options can be used. |
|
|
|
Two style options that are needed to fully use the new revision tracking |
|
feature, see Section \ref{sec:highlight}, are `linenumbers` which |
|
uses the lineno style file to number each article line in the left margin and |
|
`trackchanges` which controls the revision and commenting highlight |
|
output. |
|
|
|
There is also a new ` modern` option that uses a Daniel |
|
Foreman-Mackey and David Hogg design to produce stylish, single column |
|
output that has wider left and right margins. It is designed to have fewer |
|
words per line to improve reader retention. It also looks better on devices |
|
with smaller displays such as smart phones. |
|
|
|
The ` anonymous` option will prevent the author and affiliations |
|
from being shown in the compiled pdf copy. This option allows the author |
|
to keep this critical information in the latex file but prevent the reviewer |
|
from seeing it during peer review if dual anonymous review (DAR) is requested. |
|
Likewise, acknowledgments can also be hidden if placed in the new |
|
`\begin{acknowledgments} ... \end{acknowledgments` |
|
environment. The use of this option is highly recommended for PSJ submissions. |
|
Advice for anonymizing your manuscript for DAR is provided at |
|
\url{https://journals.aas.org/manuscript-preparation/#dar}. |
|
|
|
# Floats |
|
|
|
Floats are non-text items that generally can not be split over a page. |
|
They also have captions and can be numbered for reference. Primarily these |
|
are figures and tables but authors can define their own. \latex tries to |
|
place a float where indicated in the manuscript but will move it later if |
|
there is not enough room at that location, hence the term ``float``. |
|
|
|
Authors are encouraged to embed their tables and figures within the text as |
|
they are mentioned. Please do not place the figures and text at the end of |
|
the article as was the old practice. Editors and the vast majority of |
|
referees find it much easier to read a manuscript with embedded figures and |
|
tables. |
|
|
|
Depending on the number of floats and the particular amount of text and |
|
equations present in a manuscript the ultimate location of any specific |
|
float can be hard to predict prior to compilation. It is recommended that |
|
authors textbf{not} spend significant time trying to get float placement |
|
perfect for peer review. The AAS Journal's publisher has sophisticated |
|
typesetting software that will produce the optimal layout during |
|
production. |
|
|
|
Note that authors of Research Notes are only allowed one float, either one |
|
table or one figure. |
|
|
|
For authors that do want to take the time to optimize the locations of |
|
their floats there are some techniques that can be used. The simplest |
|
solution is to placing a float earlier in the text to get the position |
|
right but this option will break down if the manuscript is altered. |
|
A better method is to force \latex to place a |
|
float in a general area with the use of the optional `[placement specifier]` |
|
parameter for figures and tables. This parameter goes after |
|
` \begin{figure}`, ` \begin{table}`, and |
|
` \begin{deluxetable}`. The main arguments the specifier takes |
|
are ``h``, ``t``, ``b``, and ``!``. These tell \latex to place the float |
|
\underline{h}ere (or as close as possible to this location as possible), at |
|
the \underline{t}op of the page, and at the \underline{b}ottom of the page. |
|
The last argument, `!`, tells \latex to override its internal method of |
|
calculating the float position. A sequence of rules can be created by |
|
using multiple arguments. For example, ` \begin{figure[htb!]}` |
|
tells \latex to try the current location first, then the top of the page |
|
and finally the bottom of the page without regard to what it thinks the |
|
proper position should be. Many of the tables and figures in this article |
|
use a placement specifier to set their positions. |
|
|
|
Note that the \latex ` tabular` environment is not a float. Only |
|
when a ` tabular` is surrounded by `\begin{table} ...\end{table}` is it a true float and the rules and suggestions |
|
above apply. |
|
|
|
In AASTeX v6.31 all deluxetables are float tables and thus if they are |
|
longer than a page will spill off the bottom. Long deluxetables should |
|
begin with the `\startlongtable` command. This initiates a |
|
longtable environment. Authors might have to use `\clearpage` to |
|
isolate a long table or optimally place it within the surrounding text. |
|
|
|
## Tables |
|
|
|
Tables can be constructed with \latex's standard table environment or the |
|
\aastex's deluxetable environment. The deluxetable construct handles long |
|
tables better but has a larger overhead due to the greater amount of |
|
defined mark up used set up and manipulate the table structure. The choice |
|
of which to use is up to the author. Examples of both environments are |
|
used in this manuscript. |
|
|
|
Tables longer than 200 data lines and complex tables should only have a |
|
short example table with the full data set available in the machine |
|
readable format. The machine readable table will be available in the HTML |
|
version of the article with just a short example in the PDF. Authors are |
|
required to indicate in the table comments that the data in machine |
|
readable format in the full article. |
|
Authors are encouraged to create their own machine |
|
readable tables using the online tool at |
|
\url{http://authortools.aas.org/MRT/upload.html}. |
|
|
|
\aastex v6 introduced five new table features that were designed to make |
|
table construction easier and the resulting display better for AAS Journal |
|
authors. The items are: |
|
|
|
1. Declaring math mode in specific columns, |
|
2. Column decimal alignment, |
|
3. Automatic column header numbering, |
|
4. Hiding columns, and |
|
5. Splitting wide tables into two or three parts. |
|
|
|
Full details on how to create each type are given in the following |
|
sections. Additional details are available in the AASTeX |
|
guidelines at \url{http://journals.aas.org/authors/aastex.html} |
|
|
|
### Column math mode |
|
|
|
Both the \latex tabular and \aastex deluxetable require an argument to |
|
define the alignment and number of columns. The most common values are |
|
``c``, ``l`` and ``r`` for \underline{c}enter, \underline{l}eft, and |
|
\underline{r}ight justification. If these values are capitalized, e.g. |
|
``C``, ``L``, or ``R``, then that specific column will automatically be in math |
|
mode meaning that \$s are not required. Note that having embedded dollar |
|
signs in the table does not affect the output. |
|
|
|
### Decimal alignment |
|
|
|
Aligning a column by the decimal point can be difficult with only center, |
|
left, and right justification options. It is possible to use phantom calls |
|
in the data, e.g. `\phn`, to align columns by hand but this can |
|
be tedious in long or complex tables. To address this \aastex introduces |
|
the `\decimals` command and a new column justification option, |
|
`D`, to align data in that column on the decimal. In deluxetable the |
|
`\decimals` command is invoked before the `\startdata` |
|
call but can be anywhere in \latex's tabular environment. |
|
|
|
Two other important thing to note when using decimal alignment is that each |
|
decimal column \textit{must end with a space before the ampersand}, e.g. |
|
``&&`` is not allowed. Empty decimal columns are indicated with a decimal, |
|
e.g. ``.``. Do not use deluxetable's `\nodata` command. |
|
|
|
The ``D`` alignment token works by splitting the column into two parts on the |
|
decimal. While this is invisible to the user one must be aware of how it |
|
works so that the headers are accounted for correctly. All decimal column |
|
headers need to span two columns to get the alignment correct. This can be |
|
done with a multicolumn call, e.g `\multicolumn2c{}` or |
|
`\multicolumn{2}{c}{}`, or use the new |
|
`\twocolhead{}` command in deluxetable. Since \latex is |
|
splitting these columns into two it is important to get the table width |
|
right so that they appear joined on the page. You may have to run the |
|
\latex compiler twice to get it right. |
|
|
|
### Automatic column header numbering |
|
|
|
The command `\colnumbers` can be included to automatically number |
|
each column as the last row in the header. Per the AAS Journal table format |
|
standards, each column index numbers will be surrounded by parentheses. In |
|
a \latex tabular environment the `\colnumbers` should be invoked |
|
at the location where the author wants the numbers to appear, e.g. after |
|
the last line of specified table header rows. In deluxetable this command |
|
has to come before `\startdata`. `\colnumbers` will |
|
not increment for columns hidden by the ``h`` command, see Section |
|
\ref{subsubsec:hide}. |
|
|
|
Note that when using decimal alignment in a table the command |
|
`\decimalcolnumbers` must be used instead of |
|
`\colnumbers` and `\decimals`. |
|
|
|
### Hiding columns |
|
|
|
Entire columns can be \underline{h}idden from display simply by changing |
|
the specified column identifier to ``h``. In the \latex tabular environment |
|
this column identifier conceals the entire column including the header |
|
columns. In \aastex's deluxetables the header row is specifically |
|
declared with the `\tablehead` call and each header column is |
|
marked with `\colhead` call. In order to make a specific header |
|
disappear with the ``h`` column identifier in deluxetable use |
|
`\nocolhead` instead to suppress that particular column header. |
|
|
|
Authors can use this option in many different ways. Since column data can |
|
be easily suppressed authors can include extra information and hid it |
|
based on the comments of co-authors or referees. For wide tables that will |
|
have a machine readable version, authors could put all the information in |
|
the \latex table but use this option to hid as many columns as needed until |
|
it fits on a page. This concealed column table would serve as the |
|
example table for the full machine readable version. Regardless of how |
|
columns are obscured, authors are responsible for removing any unneeded |
|
column data or alerting the editorial office about how to treat these |
|
columns during production for the final typeset article. |
|
|
|
Table \ref{tab:messier} provides some basic information about the first ten |
|
Messier Objects and illustrates how many of these new features can be used |
|
together. It has automatic column numbering, decimal alignment of the |
|
distances, and one concealed column. The Common name column |
|
is the third in the \latex deluxetable but does not appear when the article |
|
is compiled. This hidden column can be shown simply by changing the ``h`` in |
|
the column identifier preamble to another valid value. This table also |
|
uses `\tablenum` to renumber the table because a \latex tabular |
|
table was inserted before it. |
|
|
|
~~~ |
|
\begin{deluxetable*}{cchlDlc} |
|
\tablenum{1} |
|
\tablecaption{Fun facts about the first 10 messier objects\label{tab:messier}} |
|
\tablewidth{0pt} |
|
\tablehead{ |
|
\colhead{Messier} & \colhead{NGC/IC} & \nocolhead{Common} & \colhead{Object} & |
|
\multicolumn2c{Distance} & \colhead{} & \colhead{V} \\ |
|
\colhead{Number} & \colhead{Number} & \nocolhead{Name} & \colhead{Type} & |
|
\multicolumn2c{(kpc)} & \colhead{Constellation} & \colhead{(mag)} |
|
} |
|
\decimalcolnumbers |
|
\startdata |
|
M1 & NGC 1952 & Crab Nebula & Supernova remnant & 2 & Taurus & 8.4 \\ |
|
M2 & NGC 7089 & Messier 2 & Cluster, globular & 11.5 & Aquarius & 6.3 \\ |
|
M3 & NGC 5272 & Messier 3 & Cluster, globular & 10.4 & Canes Venatici & 6.2 \\ |
|
M4 & NGC 6121 & Messier 4 & Cluster, globular & 2.2 & Scorpius & 5.9 \\ |
|
M5 & NGC 5904 & Messier 5 & Cluster, globular & 24.5 & Serpens & 5.9 \\ |
|
M6 & NGC 6405 & Butterfly Cluster & Cluster, open & 0.31 & Scorpius & 4.2 \\ |
|
M7 & NGC 6475 & Ptolemy Cluster & Cluster, open & 0.3 & Scorpius & 3.3 \\ |
|
M8 & NGC 6523 & Lagoon Nebula & Nebula with cluster & 1.25 & Sagittarius & 6.0 \\ |
|
M9 & NGC 6333 & Messier 9 & Cluster, globular & 7.91 & Ophiuchus & 8.4 \\ |
|
M10 & NGC 6254 & Messier 10 & Cluster, globular & 4.42 & Ophiuchus & 6.4 \\ |
|
\enddata |
|
\tablecomments{This table ``hides`` the third column in the \latex when compiled. |
|
The Distance is also centered on the decimals. Note that when using decimal |
|
alignment you need to include the `\decimals` command before |
|
`startdata` and all of the values in that column have to have a |
|
space before the next ampersand.} |
|
end{deluxetable*} |
|
~~~ |
|
|
|
### Splitting a table into multiple horizontal components |
|
|
|
Since the AAS Journals are now all electronic with no print version there is |
|
no reason why tables can not be as wide as authors need them to be. |
|
However, there are some artificial limitations based on the width of a |
|
print page. The old way around this limitation was to rotate into |
|
landscape mode and use the smallest available table font |
|
sizes, e.g. `\tablewidth`, to get the table to fit. |
|
Unfortunately, this was not always enough but now along with the hide column |
|
option outlined in Section \ref{subsubsec:hide} there is a new way to break |
|
a table into two or three components so that it flows down a page by |
|
invoking a new table type, splittabular or splitdeluxetable. Within these |
|
tables a new ``B`` column separator is introduced. Much like the vertical |
|
bar option, ``$\vert$``, that produces a vertical table lines |
|
the new ``B`` separator indicates where to \underline{B}reak |
|
a table. Up to two ``B``s may be included. |
|
|
|
Table 2 % \ref{tab:deluxesplit} this freaks it out when it is used! |
|
shows how to split a wide deluxetable into three parts with |
|
the `\splitdeluxetable` command. The `\colnumbers` |
|
option is on to show how the automatic column numbering carries through the |
|
second table component, see Section \ref{subsubsec:autonumber}. |
|
|
|
\begin{splitdeluxetable*}{lccccBcccccBcccc} |
|
\tabletypesize{\scriptsize} |
|
\tablewidth{0pt} |
|
\tablenum{5} |
|
\tablecaption{Measurements of Emission Lines: two breaks \label{tab:deluxesplit}} |
|
\tablehead{ |
|
\colhead{Model} & \colhead{Component}& \colhead{Shift} & \colhead{FWHM} & |
|
\multicolumn{10}{c}{Flux} \\ |
|
\colhead{} & \colhead{} & \colhead{($\rm |
|
km~s^{-1}$)}& \colhead{($\rm km~s^{-1}$)} & \multicolumn{10}{c}{($\rm |
|
10^{-17}~erg~s^{-1}~cm^{-2}$)} \\ |
|
\cline{5-14} |
|
\colhead{} & \colhead{} & |
|
\colhead{} & \colhead{} & \colhead{Ly$\alpha$} & \colhead{N\,{\footnotesize |
|
V}} & \colhead{Si\,{\footnotesize IV}} & \colhead{C\,{\footnotesize IV}} & |
|
\colhead{Mg\,{\footnotesize II}} & \colhead{H$\gamma$} & \colhead{H$\beta$} |
|
& \colhead{H$\alpha$} & \colhead{He\,{\footnotesize I}} & |
|
\colhead{Pa$\gamma$} |
|
} |
|
\colnumbers |
|
\startdata |
|
{ }& BELs& -97.13 & 9117$\pm 38$& 1033$\pm 33$&$< 35$&$< 166$& 637$\pm 31$& 1951$\pm 26$& 991$\pm 30$& 3502$\pm 42$& 20285$\pm 80$& 2025$\pm 116$& 1289$\pm 107$\\ |
|
{Model 1}& IELs& -4049.123 & 1974$\pm 22$& 2495$\pm 30$&$< 42$&$< 109$& 995$\pm 186$& 83$\pm 30$& 75$\pm 23$& 130$\pm 25$& 357$\pm 94$& 194$\pm 64$& 36$\pm 23$\\ |
|
{ }& NELs& \nodata & 641$\pm 4$& 449$\pm 23$&$< 6$&$< 9$& -- & 275$\pm 18$& 150$\pm 11$& 313$\pm 12$& 958$\pm 43$& 318$\pm 34$& 151$\pm 17$\\ |
|
\hline |
|
{ }& BELs& -85 & 8991$\pm 41$& 988$\pm 29$&$< 24$&$< 173$& 623$\pm 28$& 1945$\pm 29$& 989$\pm 27$& 3498$\pm 37$& 20288$\pm 73$& 2047$\pm 143$& 1376$\pm 167$\\ |
|
{Model 2}& IELs& -51000 & 2025$\pm 26$& 2494$\pm 32$&$< 37$&$< 124$& 1005$\pm 190$& 72$\pm 28$& 72$\pm 21$& 113$\pm 18$& 271$\pm 85$& 205$\pm 72$& 34$\pm 21$\\ |
|
{ }& NELs& 52 & 637$\pm 10$& 477$\pm 17$&$< 4$&$< 8$& -- & 278$\pm 17$& 153$\pm 10$& 317$\pm 15$& 969$\pm 40$& 325$\pm 37$& |
|
147$\pm 22$\\ |
|
\enddata |
|
\tablecomments{This is an example of how to split a deluxetable. You can |
|
split any table with this command into two or three parts. The location of |
|
the split is given by the author based on the placement of the ``B`` |
|
indicators in the column identifier preamble. For more information please |
|
look at the new \aastex instructions.} |
|
\end{splitdeluxetable*} |
|
|
|
## Figures |
|
|
|
%% The "ht!" tells LaTeX to put the figure "here" first, at the "top" next |
|
%% and to override the normal way of calculating a float position |
|
\begin{figure}[ht!] |
|
\plotone{cost.pdf} |
|
\caption{The subscription (squares) and author publication (asterisks) |
|
costs from 1991 to 2013. Subscription cost are on the left Y axis while |
|
the author costs are on the right Y axis. All numbers in US dollars and |
|
adjusted for inflation. The author charges also account for the change |
|
from page charges to digital quanta in April 2011. \label{fig:general}} |
|
\end{figure} |
|
|
|
Authors can include a wide number of different graphics with their articles |
|
but encapsulated postscript (EPS) or portable document format (PDF) are |
|
encouraged. These range from general figures all authors are familiar with |
|
to new enhanced graphics that can only be fully experienced in HTML. The |
|
later include figure sets, animations and interactive figures. All |
|
enhanced graphics require a static two dimensional representation in the |
|
manuscript to serve as the example for the reader. All figures should |
|
include detailed and descriptive captions. These captions are absolutely |
|
critical for readers for whom the enhanced figure is inaccessible either |
|
due to a disability or offline access. This portion of the article |
|
provides examples for setting up all these types in with the latest version |
|
of \aastex. |
|
|
|
## General figures |
|
|
|
\aastex has a `\plotone` command to display a figure consisting |
|
of one EPS/PDF file. Figure \ref{fig:general} is an example which shows |
|
the approximate changes in the subscription costs and author publication |
|
charges from 1991 to 2013 in the AAS Journals. For a general figure |
|
consisting of two EPS/PDF files the `\plottwo` command can be |
|
used to position the two image files side by side. |
|
|
|
Both `\plotone` and `\plottwo` take a |
|
`\caption` and an optional `\figurenum` command to |
|
specify the figure number\footnote{It is better to not use |
|
`\figurenum` and let \latex auto-increment all the figures. If you |
|
do use this command you need to mark all of them accordingly.}. Each is |
|
based on the ` graphicx` package command, |
|
`\includegraphics`. Authors are welcome to use |
|
`\includegraphics` along with its optional arguments that control |
|
the height, width, scale, and position angle of a file within the figure. |
|
More information on the full usage of `\includegraphics` can be |
|
found at \break |
|
\url{https://en.wikibooks.org/wiki/LaTeX/Importing\_Graphics\#Including\_graphics}. |
|
|
|
## Grid figures |
|
|
|
Including more than two EPS/PDF files in a single figure call can be tricky to |
|
easily format. To make the process easier for authors \aastex v6 offers |
|
`\gridline` which allows any number of individual EPS/PDF file |
|
calls within a single figure. Each file cited in a `\gridline` |
|
will be displayed in a row. By adding more `\gridline` calls an |
|
author can easily construct a matrix X by Y individual files as a |
|
single general figure. |
|
|
|
For each `\gridline` command a EPS/PDF file is called by one of |
|
four different commands. These are `\fig`, |
|
`\rightfig`, `\leftfig`, and `\boxedfig`. |
|
The first file call specifies no image position justification while the |
|
next two will right and left justify the image, respectively. The |
|
`\boxedfig` is similar to `\fig` except that a box is |
|
drawn around the figure file when displayed. Each of these commands takes |
|
three arguments. The first is the file name. The second is the width that |
|
file should be displayed at. While any natural \latex unit is allowed, it |
|
is recommended that author use fractional units with the |
|
`\textwidth`. The last argument is text for a subcaption. |
|
|
|
Figure \ref{fig:pyramid} shows an inverted pyramid of individual |
|
figure constructed with six individual EPS files using the |
|
`\gridline` option. |
|
|
|
\begin{figure*} |
|
\gridline{\fig{V2491_Cyg.pdf}{0.3\textwidth}{(a)} |
|
\fig{HV_Cet.pdf}{0.3\textwidth}{(b)} |
|
\fig{LMC_2009.pdf}{0.3\textwidth}{(c)} |
|
} |
|
\gridline{\fig{RS_Oph.pdf}{0.3\textwidth}{(d)} |
|
\fig{U_Sco.pdf}{0.3\textwidth}{(e)} |
|
} |
|
\gridline{\fig{KT_Eri.pdf}{0.3\textwidth}{(f)}} |
|
\caption{Inverted pyramid figure of six individual files. The nova are |
|
(a) V2491 Cyg, (b) HV Cet, (c) LMC 2009, (d) RS Oph, (e) U Sco, and (f) |
|
KT Eri. These individual figures are taken from \citet{2011ApJS..197...31S}. |
|
\label{fig:pyramid}} |
|
\end{figure*} |
|
|
|
## Enhanced graphics |
|
|
|
Enhanced graphics have an example figure to serve as an example for the |
|
reader and the full graphical item available in the published HTML article. |
|
This includes Figure sets, animations, and interactive figures. The |
|
Astronomy Image Explorer (\url{http://www.astroexplorer.org/}) provides |
|
access to all the figures published in the AAS Journals since they offered |
|
an electronic version which was in the mid 1990s. You can filter image |
|
searches by specific terms, year, journal, or type. The type filter is |
|
particularly useful for finding all published enhanced graphics. As of |
|
March 2021 there are over 4000 videos, 1300 figure sets, and 100 interactive |
|
figures. The next sections describe how to include these types of graphics |
|
in your own manuscripts. |
|
|
|
### Figure sets |
|
|
|
The grid commands given above works great for a limited set of individual |
|
figure files but what do you do if you have many 10s or 100s or even 1000s of |
|
individual figure files? Figure sets represents a virtual flip book of a |
|
large group of similar style figures. The derived PDF article will only |
|
shows an example figure while the enhanced content is available in the |
|
figure set in the HTML edition. The advantage of a figure set gives the |
|
reader the ability to easily sort through a large collection to find |
|
individual component figures. The advantage to the author is that grouping |
|
similar figures into a figure set can result in significant cost savings in |
|
terms of reduced publication charges, see Appendix B. All of the figure set |
|
components, along with their html framework, are also available to the reader |
|
for download in a single .tar.gz package. |
|
|
|
Special \latex mark up is required to create a figure set. Prior to |
|
\aastex v6 the underlying mark up commands had to be inserted by hand |
|
but is now included. Note that when an article with figure set is compiled |
|
in \latex none of the component figures are shown and a floating Figure |
|
Set caption will appear in the resulting PDF. |
|
|
|
\figsetstart |
|
\figsetnum{4} |
|
\figsettitle{Swift X-ray light curves} |
|
|
|
\figsetgrpstart |
|
\figsetgrpnum{1.1} |
|
\figsetgrptitle{KT Eri} |
|
\figsetplot{KT_Eri.pdf} |
|
\figsetgrpnote{The Swift/XRT X-ray light curve for the first year after |
|
outburst of KT Eri.} |
|
\figsetgrpend |
|
|
|
\figsetgrpstart |
|
\figsetgrpnum{1.2} |
|
\figsetgrptitle{RS Oph} |
|
\figsetplot{RS_Oph.pdf} |
|
\figsetgrpnote{The Swift/XRT X-ray light curve for the first year after |
|
outburst of RS Oph.} |
|
\figsetgrpend |
|
|
|
\figsetgrpstart |
|
\figsetgrpnum{1.3} |
|
\figsetgrptitle{U Sco} |
|
\figsetplot{U_Sco.pdf} |
|
\figsetgrpnote{The Swift/XRT X-ray light curve for the first year after |
|
outburst of U Sco.} |
|
\figsetgrpend |
|
|
|
\figsetgrpstart |
|
\figsetgrpnum{1.4} |
|
\figsetgrptitle{V2491 Cyg} |
|
\figsetplot{V2491_Cyg.pdf} |
|
\figsetgrpnote{The Swift/XRT X-ray light curve for the first year after |
|
outburst of V2491 Cyg.} |
|
\figsetgrpend |
|
|
|
\figsetgrpstart |
|
\figsetgrpnum{1.5} |
|
\figsetgrptitle{Nova LMC 2009} |
|
\figsetplot{LMC_2009.pdf} |
|
\figsetgrpnote{The Swift/XRT X-ray light curve for the first year after |
|
outburst of nova LMC 2009.} |
|
\figsetgrpend |
|
|
|
\figsetgrpstart |
|
\figsetgrpnum{1.6} |
|
\figsetgrptitle{HV Cet} |
|
\figsetplot{HV_Cet.pdf} |
|
\figsetgrpnote{The Swift/XRT X-ray light curve for the first year after |
|
outburst of HV Cet.} |
|
\figsetgrpend |
|
|
|
\figsetend |
|
|
|
\begin{figure} |
|
\plotone{KT_Eri.pdf} |
|
\caption{The Swift/XRT X-ray light curve for the first year after |
|
outburst of the suspected recurrent nova KT Eri. At a maximum count rate of |
|
328 ct/s, KT Eri was the brightest nova in X-rays observed to date. All |
|
the component figures (6) are available in the Figure Set. Note that |
|
these components that are {\bf not} shown in the compiled pdf. The figure |
|
set consists of the same figures as shown in Figure \ref{fig:pyramid}. |
|
The example figure shown for figure sets can be one component or many. |
|
\label{fig:fig4}} |
|
\end{figure} |
|
|
|
Authors are encouraged to use an online tool at |
|
\url{http://authortools.aas.org/FIGSETS/make-figset.html} to generate their |
|
own specific figure set mark up to incorporate into their \latex articles. |
|
|
|
### Animations |
|
|
|
Authors may, and are in fact encouraged, to include animations in their |
|
manuscripts. The video will stream inline with the published article and |
|
also be available for download. When writing the manuscript, a stand alone |
|
figure is necessary to serve as an example for the reader. Ideally, this |
|
is a single still frame from the animation but in some case the animation |
|
may only represent a small portion of the example figure, say one many |
|
panels as shown in Figure \ref{fig:video}. Regardless, it is very |
|
important that the author provide descriptive text in the figure caption |
|
including start and stop times and the video duration. Authors should |
|
review the AAS animation guidelines in the graphics guide at |
|
\url{https://journals.aas.org/graphics-guide/#animations}. |
|
|
|
\begin{figure} |
|
\begin{interactive}{animation}{movie.mp4} |
|
\plotone{f4.pdf} |
|
\end{interactive} |
|
\caption{Figure 1 from \citet{2018ApJ...868L..33L}. AIA 171\AA (a,b), |
|
AIA 131\AA (c), and AIA 304\AA images are shown. The red rectangle |
|
in (a) shows the field of view of the other panels. An animation of |
|
panels (b-d) is available. It covers 8 hours of observing beginning |
|
at 01:00 UT on 2012 January 19. The video duration is 20 seconds. |
|
\label{fig:video}} |
|
\end{figure} |
|
|
|
Animations and interactive figures (Section \ref{sec:interactive}) should |
|
use the `\begin{interactive}` environment in the figure call. This |
|
environment |
|
places a blue border around the figure to indicate that the figure is |
|
enhanced in the published HTML article. The |
|
command also serves to alert the publisher what files are used to generate |
|
the dynamic HTML content. `\interactive` takes two arguments. The |
|
first details the type and currently only three are allowed. The types are |
|
` js` for generic javascript interactive figures, |
|
` animation` for inline videos, and |
|
` timeseries` for interactive light curves produced |
|
by astropy \citet{2013A&A...558A..33A}\footnote{To be release in the |
|
summer of 2019}. If these types are not provide the compiler will issue an |
|
error and quit. The second argument is the file that produces the enhanced |
|
feature in the HTML article. |
|
|
|
### Interactive figures |
|
|
|
Interactive figures give the reader the ability to manipulate the |
|
information contained in an image which can add clarity or help further the |
|
author's narrative. These figures consist of two parts, a static |
|
representative figure for the manuscript and the dynamic javascript plus |
|
HTML framework that allows for interactive control. |
|
|
|
An example of an interactive figure is a 3D model. |
|
The underlying figure is a X3D file while x3dom.js is the javascript driver |
|
that displays it. An author created interface is added via a html wrapper. |
|
The first 3D model published by the AAS Journals using this technique was |
|
\citet{2014ApJ...793..127V}. |
|
|
|
Figure \ref{fig:interactive} provides an interactive example which can be |
|
run locally to demonstrate how a simple javascript plus html interface |
|
allows a reader to switch between figures. The necessary files for this |
|
particular interactive figure are in the ` interactive.tar.gz` |
|
file included with this package. Unpack the file and point the browser to |
|
the local html file. In this case, the javascript that runs the interactive |
|
buttons is embedded in the html file but it could just as easily be calls |
|
to external javascript libraries. Ideally, the javascript should be |
|
included with the submitted package of interactive files to minimize |
|
external dependencies within the published article. |
|
|
|
\begin{figure} |
|
\begin{interactive}{js}{interactive.tar.gz} |
|
\plotone{f5.pdf} |
|
\end{interactive} |
|
\caption{Figure 4 from \citet{2018AJ....156...82C}. \emph{Upper panel}: the |
|
cumulative median observing time to measure the $3\sigma$ RV masses of TESS |
|
planets as a function of host star spectral type and up to $10^3$ hours. |
|
The \emph{dashed blue curves} represent the results from the optical |
|
spectrograph whereas the \emph{solid red curves} represent the near-IR |
|
spectrograph. \emph{Lower panel}: the time derivative of the cumulative |
|
observing time curves used to indicate the RV planet detection efficiency. |
|
The \emph{horizontal dashed line} highlights the value of the detection |
|
efficiency at 20 hours per detection. Note that unlike the lower panels, |
|
the upper panels do not share a common ordinate due to the differing number |
|
of planet detections around stars in each spectral type bin. The |
|
interactive version has two buttons that allows one to turn the optical and |
|
NIR layers. \label{fig:interactive}} |
|
\end{figure} |
|
|
|
Authors should consult the online tutorials at |
|
\url{https://journals.aas.org/graphics-guide/#interactive_figures} |
|
for more information on what is currently supported and links to |
|
tutorials and examples. |
|
|
|
# Displaying mathematics |
|
|
|
The most common mathematical symbols and formulas are in the amsmath |
|
package. \aastex requires this package so there is no need to |
|
specifically call for it in the document preamble. Most modern \latex\ |
|
distributions already contain this package. If you do not have this |
|
package or the other required packages, revtex4-1, latexsym, graphicx, |
|
amssymb, longtable, and epsf, they can be obtained from |
|
\url{http://www.ctan.org} |
|
|
|
Mathematics can be displayed either within the text, e.g. $E = mc^2$, or |
|
separate from in an equation. In order to be properly rendered, all inline |
|
math text has to be declared by surrounding the math by dollar signs (\$). |
|
|
|
A complex equation example with inline math as part of the explanation |
|
follows. |
|
|
|
\begin{equation} |
|
\bar v(p_2,\sigma_2)P_{-\tau}\hat a_1\hat a_2\cdots |
|
\hat a_nu(p_1,\sigma_1) , |
|
\end{equation} |
|
where $p$ and $\sigma$ label the initial $e^{\pm}$ four-momenta |
|
and helicities $(\sigma = \pm 1)$, $\hat a_i=a^\mu_i\gamma_\nu$ |
|
and $P_\tau=\frac{1}{2}(1+\tau\gamma_5)$ is a chirality projection |
|
operator $(\tau = \pm1)$. This produces a single line formula. \latex will |
|
auto-number this and any subsequent equations. If no number is desired then |
|
the ` equation` call should be replaced with ` displaymath`. |
|
|
|
\latex can also handle a a multi-line equation. Use ` eqnarray` |
|
for more than one line and end each line with a |
|
\textbackslash\textbackslash. Each line will be numbered unless the |
|
\textbackslash\textbackslash is preceded by a `\nonumber` |
|
command. Alignment points can be added with ampersands (\&). There should be |
|
two ampersands per line. In the examples they are centered on the equal |
|
symbol. |
|
\begin{eqnarray} |
|
\gamma^\mu & = & |
|
\left( |
|
\begin{array}{cc} |
|
0 & \sigma^\mu_+ \\ |
|
\sigma^\mu_- & 0 |
|
\end{array} \right) , |
|
\gamma^5= \left( |
|
\begin{array}{cc} |
|
-1 & 0\\ |
|
0 & 1 |
|
\end{array} \right) , \\ |
|
\sigma^\mu_{\pm} & = & ({\bf 1} ,\pm \sigma) , |
|
\end{eqnarray} |
|
|
|
\begin{eqnarray} |
|
\hat a & = & \left( |
|
\begin{array}{cc} |
|
0 & (\hat a)_+\\ |
|
(\hat a)_- & 0 |
|
\end{array}\right), \nonumber \\ |
|
(\hat a)_\pm & = & a_\mu\sigma^\mu_\pm |
|
\end{eqnarray} |
|
|
|
<!-- |
|
%% Putting eqnarrays or equations inside the mathletters environment groups |
|
%% the enclosed equations by letter. For instance, the eqnarray below, instead |
|
%% of being numbered, say, (4) and (5), would be numbered (4a) and (4b). |
|
%% LaTeX the paper and look at the output to see the results. |
|
--> |
|
|
|
# Revision tracking and color highlighting |
|
|
|
Authors sometimes use color to highlight changes to their manuscript in |
|
response to editor and referee comments. In \aastex new commands |
|
have been introduced to make this easier and formalize the process. |
|
|
|
The first method is through a new set of editing mark up commands that |
|
specifically identify what has been changed. These commands are |
|
`\added{<text>}`, `\deleted{<text>}`, and |
|
`\replaced{<old text>\`{<replaced text>\}}. To activate these |
|
commands the ` trackchanges` option must be used in the |
|
`\documentclass` call. When compiled this will produce the |
|
marked text in red. The `\explain{<text>}` can be used to add |
|
text to provide information to the reader describing the change. Its |
|
output is purple italic font. To see how `\added{<important added info>}`, `\deleted{<this can be deleted text>}`, |
|
`\replaced{<old data>}{<replaced data>}` and |
|
`\explain{<text explaining the change>}` commands will produce |
|
\added{important added information}\deleted{, deleted text, and } |
|
\replaced{old data}{and replaced data,} toggle between versions compiled with |
|
and without the ` \trackchanges` option.\explain{text explaining |
|
the change} |
|
|
|
A summary list of all these tracking commands can be produced at the end of |
|
the article by adding the `\listofchanges` just before the |
|
`\end{document}` call. The page number for each change will be |
|
provided. If the ` linenumbers` option is also included in the |
|
documentclass call then not only will all the lines in the article be |
|
numbered for handy reference but the summary list will also include the |
|
line number for each change. |
|
|
|
The second method does not have the ability to highlight the specific |
|
nature of the changes but does allow the author to document changes over |
|
multiple revisions. The commands are `\edit1{<text>}`, |
|
`\edit2{<text>}` and `\edit3{<text>}` and they |
|
produce `<text>` that is highlighted in bold, bold+italic and |
|
bold+underline, respectively. Authors should use the first command to |
|
\edit1{indicated which text has been changed from the first revision.} The |
|
second command is to highlight \edit2{new or modified text from a second |
|
revision}. If a third revision is needed then the last command should be used |
|
\edit3{to show this changed text}. Since over 90\% of all manuscripts are |
|
accepted after the 3rd revision these commands make it easy to identify |
|
what text has been added and when. Once the article is accepted all the |
|
highlight color can be turned off simply by adding the |
|
`\turnoffediting` command in the preamble. Likewise, the new commands |
|
`\turnoffeditone`, `\turnoffedittwo`, and |
|
`\turnoffeditthree` can be used to only turn off the |
|
`\edit1{<text>}`, `\edit2{<text>}` and |
|
`\edit3{<text>}`, respectively. |
|
|
|
Similar to marking editing changes with the `\edit` options there |
|
are also the `\authorcomments1{<text>}`, |
|
`\authorcomments2{<text>}` and |
|
`\authorcomments3{<text>}` commands. These produce the same |
|
bold red, italic blue and underlined purple text but when the |
|
`\turnoffediting` command is present the `<text>` |
|
material does not appear in the manuscript. Authors can use these commands |
|
to mark up text that they are not sure should appear in the final |
|
manuscript or as a way to communicate comments between co-authors when |
|
writing the article. |
|
|
|
# Software and third party data repository citations |
|
|
|
The AAS Journals would like to encourage authors to change software and |
|
third party data repository references from the current standard of a |
|
footnote to a first class citation in the bibliography. As a bibliographic |
|
citation these important references will be more easily captured and credit |
|
will be given to the appropriate people. |
|
|
|
The first step to making this happen is to have the data or software in |
|
a long term repository that has made these items available via a persistent |
|
identifier like a Digital Object Identifier (DOI). A list of repositories |
|
that satisfy this criteria plus each one's pros and cons are given at \break |
|
\url{https://github.com/AASJournals/Tutorials/tree/master/Repositories}. |
|
|
|
In the bibliography the format for data or code follows this format: |
|
|
|
\noindent author year, title, version, publisher, prefix:identifier |
|
|
|
\citet{2015ApJ...805...23C} provides a example of how the citation in the |
|
article references the external code at |
|
\doi{10.5281/zenodo.15991}. Unfortunately, bibtex does |
|
not have specific bibtex entries for these types of references so the |
|
``@misc`` type should be used. The Repository tutorial explains how to |
|
code the ``@misc`` type correctly. The most recent aasjournal.bst file, |
|
available with \aastex v6, will output bibtex ``@misc`` type properly. |
|
|
|
<!-- |
|
%% IMPORTANT! The old "\acknowledgment" command has be depreciated. It was |
|
%% not robust enough to handle our new dual anonymous review requirements and |
|
%% thus been replaced with the acknowledgment environment. If you try to |
|
%% compile with \acknowledgment you will get an error print to the screen |
|
%% and in the compiled pdf. |
|
--> |
|
|
|
<!-- |
|
%% To help institutions obtain information on the effectiveness of their |
|
%% telescopes the AAS Journals has created a group of keywords for telescope |
|
%% facilities. |
|
% |
|
%% Following the acknowledgments section, use the following syntax and the |
|
%% \facility{} or \facilities{} macros to list the keywords of facilities used |
|
%% in the research for the paper. Each keyword is check against the master |
|
%% list during copy editing. Individual instruments can be provided in |
|
%% parentheses, after the keyword, but they are not verified. |
|
--> |
|
|
|
<!-- |
|
%% Similar to \facility{}, there is the optional \software command to allow |
|
%% authors a place to specify which programs were used during the creation of |
|
%% the manuscript. Authors should list each code and include either a |
|
%% citation or url to the code inside ()s when available. |
|
--> |
|
\software{astropy \citep{2013A&A...558A..33A,2018AJ....156..123A}, Cloudy \citep{2013RMxAA..49..137F}, Source Extractor \citep{1996A&AS..117..393B}} |
|
|
|
<!-- |
|
%% Appendix material should be preceded with a single \appendix command. |
|
%% There should be a \section command for each appendix. Mark appendix |
|
%% subsections with the same markup you use in the main body of the paper. |
|
|
|
%% Each Appendix (indicated with \section) will be lettered A, B, C, etc. |
|
%% The equation counter will reset when it encounters the \appendix |
|
%% command and will number appendix equations (A1), (A2), etc. The |
|
%% Figure and Table counter will not reset. |
|
-->
|
|
|