Here I give a workable solution, but not a clever one. In whatever case, we have to make a third separate file for arXiv submission (say, with at least one line to include Supp.) unless they support supplementary directly.
Basically, the method is to append the supplementary material at the end of main text. Then add the commands to reset all counters and append the "S" for equations, figures, table and references. The resulting file would look like
The \pagebreak will put supplementary materials in the new page, but I don't know why it doesn't work here. The template codes are given below. Note the important codes is in the middle part. Also, please don't use same reference citation name, otherwise, there will be wrong numbering for citation.
\documentclass[twocolumn,superscriptaddress,floatfix,preprintnumbers]{revtex4}
\usepackage{graphics,amssymb,amsmath,epsfig,color}
\usepackage{graphicx}
\begin{document}
\title{Title for main text}
\author{You name here}
\affiliation{Somewhere}
\date{\today}
\begin{abstract}
Abstract...
\end{abstract}
\pacs{}
\maketitle
Paragraph 1. Main text here \cite{RefA}:
\begin{equation}
E=mc^2
\end{equation}
Paragraph 2.
Paragraph 3 \cite{RefB}:
\begin{equation}
S=k_B \ln(\Omega)
\end{equation}
\begin{thebibliography}{11}
\bibitem{RefA} A. Someone, C. Someone, D. Someone, Phys. Rev. Lett. {\bf 11}, 1111 (1911).
\bibitem{RefB} B. Someone, {\it et. al.}, Phys. Rev. Lett. {\bf 22}, 2222 (1922).
\end{thebibliography}
%%%%%%%%%% Merge with supplemental materials %%%%%%%%%%
\pagebreak
\widetext
\begin{center}
\textbf{\large Supplemental Materials: Title for main text}
\end{center}
%%%%%%%%%% Merge with supplemental materials %%%%%%%%%%
%%%%%%%%%% Prefix a "S" to all equations, figures, tables and reset the counter %%%%%%%%%%
\setcounter{equation}{0}
\setcounter{figure}{0}
\setcounter{table}{0}
\setcounter{page}{1}
\makeatletter
\renewcommand{\theequation}{S\arabic{equation}}
\renewcommand{\thefigure}{S\arabic{figure}}
\renewcommand{\bibnumfmt}[1]{[S#1]}
\renewcommand{\citenumfont}[1]{S#1}
%%%%%%%%%% Prefix a "S" to all equations, figures, tables and reset the counter %%%%%%%%%%
\section{Section 1}
Copy and paste your Supplemental Materials text here \cite{S_RefA}, blah, blah, blah, blah, blah, blah, ...
\begin{equation}
i\hbar\frac{\partial}{\partial t}\psi(x,t) = -\frac{\hbar^2}{2m}\frac{\partial^2}{\partial x^2}\psi(x,t) + V(x,t) \psi(x,t)
\end{equation}
\begin{thebibliography}{11}
\bibitem{S_RefA} A. Someone, C. Someone, D. Someone, Phys. Rev. Lett. {\bf 11}, 1111 (1911).
\end{thebibliography}
\end{document}
Start with an new directory. Copy your file mwe.tex and mwe.bib inside it.
File mwe.bib:
@Book{Goossens,
author = {Goossens, Michel and Mittelbach, Frank and
Samarin, Alexander},
title = {The LaTeX Companion},
edition = {1},
publisher = {Addison-Wesley},
location = {Reading, Mass.},
year = {1994},
}
@Book{adams,
title = {The Restaurant at the End of the Universe},
author = {Douglas Adams},
series = {The Hitchhiker's Guide to the Galaxy},
publisher = {Pan Macmillan},
year = {1980},
}
File mwe.tex:
\documentclass[10pt,a4paper]{article}
\usepackage{hyperref} % for better urls
\begin{document}
This is text with \cite{Goossens} and \cite{adams}.
\nocite{*} % to test all bib entrys
\bibliographystyle{unsrt}
\bibliography{mwe} % file mwe.bib
\end{document}
The trick is to run first pdflatex mwe.tex, suppose your tex code is mwe.tex. Then you will see more files in the directory, important is the new file mwe.auc, containing several informations, for example the used (cited) bib entrys.
Now run (second) bibtex mwe. Check the directory again. BiBTeX builds a new file, mwe.bbl and mwe.blg. In mwe.blg is the log file for the bibtex run, in mwe.bbl is that file you need for submitting.
Resulting file mwe.bbl:
\begin{thebibliography}{1}
\bibitem{Goossens}
Michel Goossens, Frank Mittelbach, and Alexander Samarin.
\newblock {\em The LaTeX Companion}.
\newblock Addison-Wesley, 1 edition, 1994.
\bibitem{adams}
Douglas Adams.
\newblock {\em The Restaurant at the End of the Universe}.
\newblock The Hitchhiker's Guide to the Galaxy. Pan Macmillan, 1980.
\end{thebibliography}
Now run (third) pdflatex mwe.tex twice to get a correct page numbering and ...
Now copy your file mwe.tex to mwe-arxiv.tex and delete the usage of bibtex to create the bibliography.
Insert instead the content of the mwe.bbl file.
New file mwe-arxiv.tex with included mwe.bbl:
\documentclass[10pt,a4paper]{article}
\usepackage{hyperref} % for better urls
\begin{document}
This is text with \cite{Goossens} and \cite{adams}.
\nocite{*} % to test all bib entrys
%\bibliographystyle{unsrt} % <======================== not longer needed!
%\bibliography{\jobname} % <========================== not longer needed!
\begin{thebibliography}{1} % <================================== mwe.bbl
\bibitem{Goossens}
Michel Goossens, Frank Mittelbach, and Alexander Samarin.
\newblock {\em The LaTeX Companion}.
\newblock Addison-Wesley, 1 edition, 1994.
\bibitem{adams}
Douglas Adams.
\newblock {\em The Restaurant at the End of the Universe}.
\newblock The Hitchhiker's Guide to the Galaxy. Pan Macmillan, 1980.
\end{thebibliography} % <======================================= mwe.bbl
\end{document}
Now you have only to submit this new file mwe-arxiv.tex ...
Or just use \input{mwe.bbl} (but please see I do not know if that is allowed by arxiv) but now see you have to submit two files (mwe-arxiv.tex and mwe.bbl).
New file mwe-arxiv-input.tex with \inputed mwe.bbl:
\documentclass[10pt,a4paper]{article}
\usepackage{hyperref} % for better urls
\begin{document}
This is text with \cite{Goossens} and \cite{adams}.
\nocite{*} % to test all bib entrys
%\bibliographystyle{unsrt} % <======================== not longer needed!
%\bibliography{\jobname} % <========================== not longer needed!
\input{mwe.bbl} % <============================================= mwe.bbl
\end{document}
Best Answer
Similar guidelines come from PRL journal
This is my solution to this problem:
\nocite{key}.\bibliography{bib_library}\input{modified_bibliography.bbl}