13 May 2014

576. Shortening the bash prompt in debian

This is yet another post in which I'm (almost) simply reposting a solution that someone else has already posted online.

Let's say that my contribution is to put it in context of debian.

Either way, here's the problem that needed solving: the debian prompt by default lists all directories, which sometimes means that the prompt itself breaks across two lines.

Luckily, it's not difficult to chop the prompt down to a more manageable, yet still informative, length. The solution is here (we do like a descriptive URL): http://superuser.com/questions/387673/how-can-i-limit-the-number-of-directories-in-my-prompt

That particular solution also allows you to change the permissible length of the path that will be shown -- change the 50 in the argument to droppath to set the number of chars.

Edit your ~/.bashrc and add the bits in red:
# drops first portion of a path $1 if length is greater than $2 function __droppath { if [[ ${#1} -gt $2 ]]; then p=$1 while [ ${#p} -gt $2 ]; do p="/"$(echo "$p"|cut -d"/" -f3-) done echo "..."$p else echo $1 fi } if [ "$color_prompt" = yes ]; then PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]$(_droppath "\w" 50)\[\033[00m\]\$ ' else PS1='${debian_chroot:+($debian_chroot)}\u@\h: $(__droppath "\w" 50)\$ ' fi

and here's an example using a length of 25 chars (which is a bit short).

Unmodified:
me@niobium: /usr/local/lib/python2.7/site-packages$\

Modified:
me@niobium: .../python2.7/site-packages$

You can always use pwd to figure out what the full path is if necessary:
me@niobium: .../python2.7/site-packages$ pwd
/usr/local/lib/python2.7/site-packages

12 May 2014

575. Gaussview: CConnetctionGFCHK::Parse_GFCHK() Missing or bad data: Alpha Orbital Energies Line Number XXXX

I've been getting a fair number of errors when trying to open .fchk files with gaussview 4.x that I've generated using g09. In particular, I've been getting this:



Thinking that it might have something to do with the version of gaussview being too old, I tried gaussview 5.x, which throws the same error. Gaussview (4.x), by the way, runs fine in wine 1.7.

Turns out it's a poorly written piece of software -- gaussview can't properly parse output generated by gaussian. Great...neither piece of software is cheap. Better yet, gabedit does not have any issue reading the unmodified fchk file.

If you do need to use gview though, the solution is outlined here: http://www.ccl.net/cgi-bin/ccl/message-new?2012+07+18+005

Briefly, edit your fchk file and change the "Number of basis functions" to the same number as is shown for the "Number of independent functions" i.e. change
1 alpha 2 FOpt RB3PW91 Gen 3 Number of atoms I 101 4 Info1-9 I N= 9 5 89 86 0 0 0 100 6 2 18 -602 7 Charge I 7 8 Multiplicity I 1 9 Number of electrons I 530 10 Number of alpha electrons I 265 11 Number of beta electrons I 265 12 Number of basis functions I 2015 13 Number of independent functions I 2005 14 Number of point charges in /Mol/ I 0 15 Number of translation vectors I 0
to
1 alpha 2 FOpt RB3PW91 Gen 3 Number of atoms I 101 4 Info1-9 I N= 9 5 89 86 0 0 0 100 6 2 18 -602 7 Charge I 7 8 Multiplicity I 1 9 Number of electrons I 530 10 Number of alpha electrons I 265 11 Number of beta electrons I 265 12 Number of basis functions I 2005 13 Number of independent functions I 2005 14 Number of point charges in /Mol/ I 0 15 Number of translation vectors I 0
And that's it.

09 May 2014

574. Texmaker and texlive on windows xp

There are two ways of dealing with latex on windows -- either using native packages or via cygwin. Here's the  native approach, which I tested in a virtual machine with Windows XP SP2

 
1. Install texlive

Go to http://www.tug.org/texlive/acquire-netinstall.html and download http://mirror.ctan.org/systems/texlive/tlnet/install-tl.exe

Run the file. You'll now be taken through the installation of texlive. Note that the full installation is ca 3.7 Gb and it will take a few hours to download and install. On the other hand, space is cheap and most people (in academia) don't pay for bandwidth, so it's not a bad idea to do the full install.

Anyway, here are a few screenshots of the installation process:



It's a good idea to change the mirror to speed up the download



Uncheck TexWorks since we'll be installing TexMaker


This step can take many hours


Finally done.


2. Install texmaker

Go to http://www.xm1math.net/texmaker/download.html and download http://www.xm1math.net/texmaker/texmakerwin32_install.exe

The same file will work on XP, Vista and 8 (and presumably 7, which is more or less a patched version of Vista) and it will work on both 32 and 64 bit systems.

Install texmaker.


3. Configure  texmaker
Start texmaker

Go to Options/Configure Texmaker.

Under Commands you can select to use an external pdf viewer. Note that you will need to make sure that the path is correct -- in my case it was pointing to adobe reader 11, whereas I had adobe reader 9 installed. Easy enough to change, but you need to do it manually. The embedded/internal pdf viewer works ok, but distorts the text and figures somewhat (everything got a bit squashed)
Choose internal or external pdf viewer. Make sure the path is correct
Under Quick Build you can tick Latex+Bib(la)tex+Latex(x2)+dvips+ps2pdf+View pdf. NOTE: if you do this you won't be able to compile any file which hasn't got a \cite command and a mathing .bib file.

Alternatively, pick latex + dvips + ps2pdf + View pdf.

Quick Build -- pick the one with bibtex in it
Under Editor you can disable code completion (which can get annoying at times):

You can now load a tex file and hit F1 to compile it:


Quick test example

0. Create a folder called e.g. testtex
 
1. Download UCSD.eps from here: http://vectorlogotypes.net/logo/68332_UCSD.htm

Put it in the testtex folder.


2. Create the following anothertest.bib file in either texmaker or notepad:
@Article{2014:example,
  AUTHOR = {Placeholder, A},
  TITLE = {Comprehensive title},
  YEAR = 2014,
  JOURNAL = {J. Comp. Chem.},
  VOLUME ={45},
  PAGES = {100-101}
}
Put it in the testtex folder.

3. Create a new tex file in texmaker:


Make sure to tick graphicx

Basic tex file
Save to your testtex folder.

4. Edit your tex file as shown below::
\documentclass[10pt,a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{graphicx}

\usepackage{url}
\title{This is a test}

\begin{document}

\section{The test}
This is a simple test which consists of inserting a figure and adding a reference via bibtex. You can download the logo from \url{http://vectorlogotypes.net/logo/68332_UCSD.htm}. Put the UCSD.eps file in the same directory as your .tex file.
\begin{figure}
 \includegraphics{UCSD.eps}
 \caption{UC San Diego logo.}
 \label{fig:test}
\end{figure}

Here's a citation.\cite{2014:example}

\bibliography{anothertest}
\bibliographystyle{ChemEurJ}
\end{document}
5. Compile.
If you set up your F1 as shown above (i.e. with bibtex support), then all you need to do is hit F1. Otherwise, if you used the alternative setup, do F2 (latex), F11 (bibtex), F2 (latex), F11 (bibtex), F1 (compile and view).