I don't really get the question so I hope this is what you wanted. If you include a full document (such that we copy paste and see the problem on our systems) things are much more easier.
Here, you can change the default setting within a scope but your block
style had a node distance
which was resetting every time it is issued. I've made it 2mm such that we can see the difference easier.
\documentclass[tikz]{standalone}
\usetikzlibrary{arrows,shapes.geometric,positioning}
\begin{document}
\begin{tikzpicture}[decision/.style={diamond, draw, text width=4.5em, text badly centered, node distance=3.5cm, inner sep=0pt},
block/.style ={rectangle, draw, text width=6em, text centered, rounded corners, minimum height=4em, minimum height=2em},
cloud/.style ={draw, ellipse, minimum height=2em},
line/.style ={draw,-latex'},
node distance = 1cm,
auto]
\node [block] (1st) {1st};
\node [block, right= of 1st] (2nd1) {2nd1};
\begin{scope}[node distance=2mm and 10mm]%Here we change it for everything inside this scope
\node [block, above= of 2nd1] (2nd2) {2nd2};
\node [block, below= of 2nd1] (2nd3) {2nd3};
\node [block, right= of 2nd1] (3rd1) {3rd1};
\node [block, above= of 3rd1] (3rd2) {3rd2};
\node [block, above= of 3rd2] (3rd3) {3rd3};
\end{scope}
\node [block, below= of 3rd1] (3rd4) {3rd4};
\node [block, below= of 3rd4] (3rd5) {3rd5};
\path [line] (1st) -- (2nd1);
\path [line] (2nd1) -- (2nd2);
\path [line] (2nd1) -- (2nd3);
\path [line] (2nd2) -- (3rd3);
\path [line] (2nd1) -- (3rd1);
\path [line] (1st) -- (2nd1);
\end{tikzpicture}
\end{document}
(This answer assumes you want more than single spacing in your footnotes, which is not usually considered to look very nice, but is often required by university 'style'-setters.)
The thing is this: your class sets (on line 106)
\renewcommand \baselinestretch{1.5}
Now, if you are using the default 10pt, that means the footnote font size is 8pt with a baselineskip of 9.5pt. We're stretching that by 1.5. 9.5 x 1.5 = 14.25pt.
Test this by adding
\the\baselineskip
in a footnote. You should get 14.25pt.
Now setting (as I had suggested)
\setlength{\footnotesep}{\baselineskip}
makes the footnotesep
the equivalent of the baselineskip
for regular text (i.e., 12pt), but I think you want it to be 10pt. So you can set that directly:
\setlength{\footnotesep}{10pt}
EDIT:
One solution that mimics the settings of LaTeX2e would be to add this to your preamble (given the ratios suggested in my comment below):
\makeatletter
\ifcase \@ptsize
\setlength{\footnotesep}{0.83125\baselineskip}
\or
\setlength{\footnotesep}{0.85555\baselineskip}
\or
\setlength{\footnotesep}{0.84\baselineskip}
\fi
\makeatother
Or, if you prefer a more explicit setting (not quite identical):
\makeatletter
\ifcase \@ptsize
\setlength{\footnotesep}{10pt}
\or
\setlength{\footnotesep}{11pt}
\or
\setlength{\footnotesep}{12pt}
\fi
\makeatother
This will allow for automatic recalculation based on whether you are using the standard fontsize choices of 10, 11, or 12pt.
Here is an example based on the one you gave above:
\documentclass[10pt]{ucl_thesis}
\makeatletter
\ifcase \@ptsize
\setlength{\footnotesep}{0.83125\baselineskip}
\or
\setlength{\footnotesep}{0.85555\baselineskip}
\or
\setlength{\footnotesep}{0.84\baselineskip}
\fi
\makeatother
\makeatletter
\ifcase \@ptsize
\setlength{\footnotesep}{10pt}
\or
\setlength{\footnotesep}{11pt}
\or
\setlength{\footnotesep}{12pt}
\fi
\makeatother
\usepackage{xcolor}
\usepackage[grid, gridunit=pt,
gridcolor=red!20,
subgridcolor=blue!20]{eso-pic}
\usepackage{lipsum}
\begin{document}
\the\baselineskip
Some text.
\footnote{\the\baselineskip. The baselinestretch factor is: \baselinestretch. A short footnote on one line.}
Some more text.
\footnote{%
\the\footnotesep.
A longer footnote so that it spans multiple lines.
A longer footnote so that it spans multiple lines.
A longer footnote so that it spans multiple lines.
A longer footnote so that it spans multiple lines.
A longer footnote so that it spans multiple lines.
A longer footnote so that it spans multiple lines.
A longer footnote so that it spans multiple lines.}
\footnote{A short footnote on one line.}
\footnote{A short footnote on one line.}
\lipsum
\end{document}
Best Answer
You can define a
bprooftree
(boxed proof tree) that encloses the proof tree in a box as wide as the tree.