show specific minor tick labels in double logarithmic PGFPlots

Question

I use the following code to create the plot shown below.

\documentclass[a4paper]{article}
\usepackage{pgfplots}
\usepackage{pgfplotstable}%fitting functions
\usepackage{tikz}
\usetikzlibrary{tikzmark}
\usepackage{pgfplotstable}

\pgfplotsset{compat=1.15}
\pgfplotsset{label style={font=\Large},
            tick label style={font=\Large}}

\begin{document}

\begin{figure}
\centering
\begin{tikzpicture}
\begin{axis}[
    xmode=log,
    ymode=log,
    enable tick line clipping=false,
    width=9cm,
    height=7cm,
    axis line style=semithick,
    x tick style={black,semithick},
    xmin=1,xmax=100,
    xtick={1,10,100},
    xtick pos=bottom,
    minor x tick num=9,
    xtick align=outside,
    y tick style={black,semithick},
    ymin=0.1,ymax=10,
    ytick={0.1,1,10},
    ytick pos=left,
    minor y tick num=9,
    ytick align=outside,
]        
    \addplot [blue,mark=*,mark options={scale=1.5,blue}]
         table [x=x,y=y] {
         x      y
         2      0.5
         10     1
         50     3
    };

\end{axis}
\end{tikzpicture}
\end{figure}

\end{document}

When I want to show an additional minor tick label, let say 3, in y axis by simply adding 3 in the y axis range ytick={0.1,1,3,10}, it produces this graph

The tick 10^0.48 is a minor tick but its length somehow became equal to the major tick length. Also, why did the rest of the minor ticks disappeared? I used the command minor y tick num=9, in the code. How can I write 3 instead of 10^0.48 and add any minor tick label I want to, e.g. 0.5 or 7?

Answer 1

I guess that you are searching for something like the following, right?

When adding non-equidistant ticks the automatically computed minor ticks disappear. This is an intended behaviour (and usually what you want).

% used PGFPlots v1.16
\documentclass[border=5pt]{standalone}
\usepackage{pgfplots}
\begin{document}
\begin{tikzpicture}
    \begin{axis}[
        xmode=log,
        ymode=log,
        xmin=1,xmax=100,
        ymin=0.1,ymax=10,
        xtick={1,10,100},
        ytick={0.1,1,10},
        xtick pos=bottom,
        ytick pos=left,
        xtick align=outside,
        ytick align=outside,
        tick style={black,semithick},
        % these don't have any effect, because they are the default anyway
%        minor x tick num=9,
%        minor y tick num=9,
        % add an extra tick with the corresponding label
        extra y ticks={3.5},
        extra y tick labels={3.5},
        % and change the style of the tick to the ones of the minor ticks
        extra tick style={
            tickwidth=\pgfkeysvalueof{/pgfplots/minor tick length},
        },
    ]
        \addplot table [x=x,y=y] {
             x      y
             2      0.5
             10     1
             50     3
        };

    \end{axis}
\end{tikzpicture}
\end{document}