why sometimes the figure is too close to the text?

Question

Here is the problem, you can see the figure is too close to the text, And it is even affecting the text.

the code I use is

\documentclass[ reprint,amsmath,amssymb,aps]{revtex4-1}
\usepackage{graphicx}% Include figure files
\usepackage{dcolumn}% Align table columns on decimal point
\usepackage{bm}% bold math
\usepackage{epstopdf}

\begin{document}
some text

\begin{figure}[htbp]
\includegraphics[width=\columnwidth]{FIG_3}
\end{figure}

some text
\end{document}

What is odd enough is that when I insert the same code between other paragraphs of my paper, the problem is not showing any more.

after add \fbox{} to show the bounding box as follows

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Edited

Here is the problematic tex file that I share on google drive problematic tex file

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here is the example show that two same figure code but different position have different space to the text.

Answer 1

See How to change the spacing between figures/tables and text?

An exaggerated example to play:

\documentclass[a4paper]{article}
\usepackage{geometry}
\usepackage{graphicx}
\usepackage{lipsum}

% for figure A between text
\setlength{\intextsep}{5em plus 1em minus .1em} 

% for the figure B on top (or bottom)
\setlength{\textfloatsep}{10em plus 5em minus .1em} % for figure B

\begin{document}
\lipsum[1]

\begin{figure}[h]
\includegraphics[width=\linewidth]{example-image-a}
\end{figure}
\lipsum[2]

\begin{figure}[t]
\includegraphics[width=\linewidth]{example-image-b}
\end{figure}

\lipsum[3-6]

\end{document}

Edit: the edited question now show a MWE with the problem in the revtex4-1 class. For some reason I obtained some wrongs compilations using this MWE but I cannot explain why. This code work fine:

\documentclass[reprint,amsmath,amssymb,aps]{revtex4-1}
\usepackage{graphicx}% Include figure files
\usepackage{dcolumn}% Align table columns on decimal point
\usepackage{bm}% bold math
\usepackage{epstopdf}
\usepackage{lipsum}

\setlength{\intextsep}{2cm} 
\setlength{\textfloatsep}{2cm} 

\begin{document}

\lipsum[2]

\begin{figure}[h]
\includegraphics[width=\columnwidth]{example-image-a}
\end{figure}

\lipsum[2]

\begin{figure}[t]
\includegraphics[width=\columnwidth]{example-image-b}
\end{figure}

\lipsum[2]

\begin{figure}[b]
\includegraphics[width=\columnwidth]{example-image-c}
\end{figure}

\lipsum[3-6]

\end{document}