538. Briefly: Sort folders before files in nautilus 3.8

I'm running debian jessie (current testing) on my laptop and after having held off upgrading for a while since I had to take it to a conference and didn't want to risk ending up with a broken system, I finally took the leap. I notice that there are a lot of references to systemd in dmesg, but haven't had a look at what it actually means -- are we past init and fully switched to systemd now? Or how do I go about modifying my network configuration if I can't use /etc/network/interfaces?

Anyway, one annoying little thing is that in Nautilus the folder content by default is arranged in alphabetical order, regardless of whether it's a file or a directory. The old behaviour was to arrange folders in alphabetical order, then files.

Here's how to get it back to 'normal' behaviour:

 

The new behaviour

Click on the 'Files' menu on the top desktop bar, select preferences:

Check 'Sort folders before files' to get back the normal behaviour

Check sort folders before files to make Nautilus behave well again

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!