537. Building ECCE 7.0 on CentOS 6.4

Following a report that there were issues building ECCE 7 on Centos 6.4 I decided to investigate.

1. Download 
Download the centos 6.4 iso: At ftp://mirror.stanford.edu/pub/mirrors/centos/6.4/isos/x86_64/ I downloaded ftp://mirror.stanford.edu/pub/mirrors/centos/6.4/isos/x86_64/CentOS-6.4-x86_64-minimal.iso

wget ftp://mirror.stanford.edu/pub/mirrors/centos/6.4/isos/x86_64/CentOS-6.4-x86_64-minimal.iso

2. Install centos in virtualbox
Not much to say other than that I gave the VM 12 gb disk and 1024 mb ram.
During installation I selected Install or Upgrade an existing system (option 1).  I went with all the defaults during installation.

3. Basic setup
Following the installation I rebooted.

First I activated eth by editing /etc/sysconfig/network-scripts/ifcfg-eth0 and changing onboot from no to yes. I rebooted and installed Gnome

Then install X and gnome.

yum groupinstall -y 'X Window System'
yum groupinstall -y 'Desktop'
useradd verahill
passwd verahill

Edit /etc/inittab and change

id:3:initdefault:

to

id:5:initdefault:

Reboot.

Install openGL libraries. The way to do that depends on what graphics chip your have, e.g. libgl1-nvidia-glx for nvidia. In my virtualbox example I didn't have to do anything.  

4. ECCE
Launch gnome-terminal
Become root and install packages, then exit:

su
yum install vim csh gcc gcc-c++ gcc-gfortran java-1.7.0-openjdk-devel python-devel ant gtk2-devel libjpeg-turbo-devel libtool ImageMagick libXt-devel xterm mesa-libGLU-devel kernel-devel perl-Digest-Perl-MD5 perl-Digest-MD5
yum install 
exit

mkdir ~/tmp
cd ~/tmp

Download ecce from http://ecce.pnl.gov/using/download.shtml into ~/tmp

tar xvf ecce-v7.0-src.tar.bz2
cd ecce-v7.0/
export ECCE_HOME=`pwd`
cd build/
./build_ecce
./build_ecce
./build_ecce
./build_ecce
./build_ecce
./build_ecce
./build_ecce

Everything builds just fine.

You can then install the ecce_install.v7.0.csh file created in the parent directory by following e.g. this post: http://verahill.blogspot.com.au/2013/08/487-version-70-of-ecce-out-now.html

536. Briefly: Getting ECCE to work with Gaussian 09 (G09) part 1: frequency calcs

I'm slowly looking at improving the support for G09 in ECCE. One of the things that haven't worked in the past is visualising frequency calcs.

Since I'm not using G03 I've been content with editing the g03 files so that they work with G09. My changes will be submitted upstreams at a later point.

Anyway, turns out this was a very simple one.

How ECCE works:
data is extracted from the output through the use of perl parser scripts. These are located in apps/scripts/parsers, and are fairly clearly named.

The script that deals with Gaussian vibrational analyses is called gaussian-03.vib

To use it manually with a gaussian 'log' file (here called g03.output), do

./gaussian-03.vib < g03.output

So far so easy. However, if you use it on a g09 output file you'll end up with a single message: 'Zero atoms'.

Turns out that the reason is that the script looks for instances of 'Atom AN', with a single white space between m and N. In G09, however, there are two white spaces: 'Atom AN'.

The fix:
So, edit line 277:

276     while ()  {
277       if (/Atom AN/) {
278         last;

and change it to

276     while ()  {
277       if (/Atom\s*AN/) {
278         last;

Do the same thing with line 315:

314     while ()  {
315       if (/Atom\s*AN/) {
316         last;

Done!

535. Briefly: ACS journal latex template -- achemso

There's no outright template for the preparation of tex files for ACS journals. However, there are two files provided: a bibtex styles file, achemso.bst, and a macro file, achemso.cls. Both are available in the texlive-latex-extra package on debian.

Luckily there's a lot of information online, including a demo file: ftp://ftp.dante.de/tex-archive/biblio/bibtex/contrib/achemso/

Anyway, here's a simple file that can act as a template. Have a look at the demo file at ftp.dante.de for a much more exhaustive example, including how to use schemes and insert references.

You can figure out the journal abbreviations from their URLs. Otherwise, page 4 in this pdf has a list: http://www.tug.org/texlive/Contents/live/texmf-dist/doc/latex/achemso/achemso.pdf

Anyway:

\documentclass[journal=inoraj, layout=twocolumn]{achemso}
\usepackage[latin1]{inputenc}
\usepackage[english]{babel}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{graphicx}
\author{Vera Hill}
\affiliation{Department of Chemistry, This University, This Country}
\email{my@email}
\author{I. Lindqvist}
\affiliation{Department of Chemistry, Another University, That Country}
\title{A quick, non-exhaustive tex template}

\begin{document}
\maketitle

%\begin{tocentry} %graphical TOC
%\includegraphics{example.eps}
%TOC text goes here
%\end{tocentry}

\begin{abstract}
The ACS should provide a simple template. They don't, so I do.
\end{abstract}

\section{Introduction}
\section{Results and Discussion}

%\begin{figure}
% \includegraphics{graphic}
% \caption{A figure}
% \label{fig:example}
%\end{figure}


\subsection{References}
\section{Experimental}
\begin{acknowledgement}
VH thanks the internet. IL thanks the electron.
\end{acknowledgement}

\begin{suppinfo}
See supporting information for additional experimental details.
\end{suppinfo}

\end{document}

---

Example: