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shorttitle shortauthor title author collaborator titleshort authorshort processDate imageDir appendix graphicpaths abstract abstractTex keywords facilities acknowledgements header-includes
pubsEngine Author One, et al. pubsEngine: Manuscript Engine {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} [{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}] Paperlighter Example Author One et.al. [{received March 11, 2022} {accepted April 11, 2022}] [Figure Output] [include/appendix1 include/appendix2 include/appendix3 include/appendix4 include/appendix5] [Figure] 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. \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.} [Classical Novae (251) Ultraviolet astronomy(1736) History of astronomy(1868) Interdisciplinary astronomy(804)] HST(STIS), Swift(XRT and UVOT), AAVSO, CTIO:1.3m, CTIO:1.5m, CXO 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. \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

![the caption](Figure/icml_numpapers.eps)
{#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). Please be aware that size is considered as a multiplier of the \linewidth.

the caption{#fig:FigVibStab size=0.5}

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.

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.]
~~~

|              |          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` CodeBlock. 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.

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/addition1.md

Above paragraph was included from include/addition1.md.

Diagrams

We can include a diagram script, following an Embedded domain-specific Language from Haskell package diagrams. The implementation of following CodeBlock can be seen at Figure \ref{fig:dia1}. Please be aware that the size will be considered as a multiplier from \linewidth.

~~~{#fig:dia1 .diagram size=0.8 caption="dia"}
let x = circle 10
 in x
~~~

let t = circle 100
 in t

Running a subcommand

Currently, subcommand only valid for Python script. There are two possible class available for this subcommand.

To make this document can stands on its own and to remove repetitive codes, we can also include a python library inside _build/temp/lib directory. All script above, will include all files mentioned inside _build/temp/lib. Furthermore, the _build/temp/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 included inside every script, but there will never be any indication shown inside the pdf result. Please be aware that any code below description line will be neglected by the parser. We expect the description should be enough for single paragraph. This would remove the requirement for multiline description of a markdown code. More verbose treatment can be done by adding .show class indicator. With this indication, the script will be shown as a CodeBlock, and followed by the description. The following CodeBlock was produced using the headings of ~~~{.script .py .lib .show file="libPy1"}.

import subprocess

def sysrun(t,debug:bool=False):
    s = " ".join(t)
    res = subprocess.getoutput(s)
    if(debug):
        print(s)
        print(res)
    return res

description="This is the description of the additional `libPy1` library that will be inserted into the pdf output. Any **valid markdown syntax** can be used. The `import` statement to `libPy1` will be prepended by pubsEngine, thus removed the necessity of explicit import in any scripts below."

The class command .md will output a text document that 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"}
print("""
| as | dd |
|----|----|
| dd | dd |
Table: this is output of a python script
""")
~~~

The above snipplet would give us output:

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. This responsibility is purely on the shoulder of the author. 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}
#import subprocess
#subprocess.getoutput("wget 'https://upload.wikimedia.org/wikipedia/commons
/thumb/2/2c/Bismillah.svg/640px-Bismillah.svg.png' -O _build/auto/pyImage.png")

# we can call a function from included library above
sysrun(["wget 'https://upload.wikimedia.org/wikipedia/commons/thumb/2/2c
/Bismillah.svg/640px-Bismillah.svg.png' -O _build/auto/pyImage.png"])
~~~

sysrun(["wget 'https://upload.wikimedia.org/wikipedia/commons/thumb/2/2c/Bismillah.svg/640px-Bismillah.svg.png' -O _build/auto/pyImage.png"])

The same rules apply to .img .md .lib of SHELL (.sh). Under the hood, pubsEngine will run the script under zsh. The library will be saved in _build/temp/lib/sh. The picture at Figure \ref{fig:shImage} came from .sh script.

wget "https://upload.wikimedia.org/wikipedia/commons/thumb/f/fa/Bismillah_Calligraphy_37.svg/1200px-Bismillah_Calligraphy_37.svg.png" -O _build/auto/shImage.png

pubsEngine also implemented this mechanism on GNUplot scripts using .gnuplot class.

Subprocess delegation

|              |          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}
~~~

  \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

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

Inclusion of Mermaid diagrams at Figure \ref{fig:mermaid} can be done by the following syntax:

~~~{.mermaid #fig:mermaid caption="new mermaid"
file=mermaidExample size=0.8}
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 be sure that the size is a relative size compared with \linewidth. The size will always be in a constant aspect ratio of 800x600.


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!

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

\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.

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.

Vibrational stability equation of state $S_{\mathrm{vib}}(\lg e, \lg \rho)$. $>0$ means vibrational stability.{#fig:FigVibStab width=3.43in height=2.71in}

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 Bs 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}

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>\{}}. 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.

\software{astropy \citep{2013A&A...558A..33A,2018AJ....156..123A}, Cloudy \citep{2013RMxAA..49..137F}, Source Extractor \citep{1996A&AS..117..393B}}